experimental sequence theme

* add intro scene

* fixes

* add author name

CHANGELOG.md

@@ -5,12 +5,15 @@ Note that since we don't clearly distinguish between a public and private interf
 
 ## [Unreleased]
 - [Breaking] Renamed some color schemes ('inferno' -> 'inferno-no-black', 'magma' -> 'magma-no-black', 'turbo' -> 'turbo-no-black', 'rainbow' -> 'simple-rainbow')
-- [Breaking] `Box3D.nearestIntersectionWithRay` -> `nearestIntersectionWithRay3D` (use `Ray3D`)
+- [Breaking] `Box3D.nearestIntersectionWithRay` -> `Ray3D.intersectBox3D`
 - [Breaking] `Plane3D.distanceToSpher3D` -> `distanceToSphere3D` (fix spelling)
 - [Breaking] fix typo `MarchinCubes` -> `MarchingCubes`
 - [Breaking] `PluginContext.initViewer/initContainer/mount` are now async and have been renamed to include `Async` postfix
 - [Breaking] Add `Volume.instances` support and a `VolumeInstances` transform to dynamically assign it
   - This change is breaking because all volume objects require the `instances` field now.
+- [Breaking] `Canvas3D.identify` now expects `Vec2` or `Ray3D`
+- [Breaking] `TrackballControlsParams.animate.spin.speed` now means "Number of rotations per second" instead of "radians per second"
+- [Breaking] `PluginStateSnapshotManager.play` now accepts an options object instead of a single boolean value
 - Update production build to use `esbuild`
 - Emit explicit paths in `import`s in `lib/`
 - Fix outlines on opaque elements using illumination mode
@@ -18,24 +21,39 @@ Note that since we don't clearly distinguish between a public and private interf
 - MolViewSpec extension:
   - Generic color schemes (`palette` parameter for color_from_* nodes)
   - Annotation field remapping (`field_remapping` parameter for color_from_* nodes)
-  - Representation node: support custom property `molstar_reprepresentation_params`,
-  - Canvas node: support custom properties `molstar_enable_outline`, `molstar_enable_shadow`, `molstar_enable_ssao`
+  - `representation` node: support custom property `molstar_representation_params`
+  - Add `backbone` and `line` representation types
+  - `primitives` node: support custom property `molstar_mesh/label/line_params`
+  - `canvas` node: support custom property `molstar_postprocessing` with the ability to customize outline, depth of field, bloom, shadow, occlusion (SSAO), and fog
   - `clip` node support for structure and volume representations
   - `grid_slice` representation support for volumes
   - Support tethers and background for primitive labels
   - Support `snapshot_key` parameter on primitives that enables transition between states via clicking on 3D objects
   - Inline selectors and MVS annotations support `instance_id`
   - Support `matrix` on transform params
+  - Support `surface_type` (`molecular` / `gaussian`) on for `surface` representation nodes
   - Add `instance` node type
+  - Add `transform.rotation_center` property that enables rotating an object around its centroid or a specific point
   - Support transforming and instancing of structures, components, and volumes
+  - Use params hash for node version for more performant tree diffs
+  - Add `Snapshot.animation` support that enables animating almost every property in a given tree
+  - Add `createMVSX` helper function
+  - Support Mol* trackball animation via `animation.custom.molstar_trackball`
+  - MVSX - use Murmur hash instead of FNV in archive URI
+  - Support additional file formats (pdbqt, gro, xyz, mol, sdf, mol2, xtc, lammpstrj)
+  - Support loading trajectory coordinates from separate nodes
+  - Trigger markdown commands from primitives using `molstar_markdown_commands` custom extensions
+  - Support `molstar_on_load_markdown_commands` custom state on the `root` node
 - Added new color schemes, synchronized with D3.js ('inferno', 'magma', 'turbo', 'rainbow', 'sinebow', 'warm', 'cool', 'cubehelix-default', 'category-10', 'observable-10', 'tableau-10')
 - Snapshot Markdown improvements
   - Add `MarkdownExtensionManager` (`PluginContext.managers.markdownExtensions`)
   - Support custom markdown commands to control the plugin via the `[link](!command)` pattern
   - Support rendering custom elements via the `![alt](!parameters)` pattern
   - Support tables
-  - Support loading images from MVSX files
+  - Support loading images and audio from MVSX files
   - Indicate external links with ⤴
+  - Audio support
+  - Add `PluginState.Snapshot.onLoadMarkdownCommands`
 - Avoid calculating rings for coarse-grained structures
 - Fix isosurface compute shader normals when transformation matrix is applied to volume
 - Symmetry operator naming for spacegroup symmetry - parenthesize multi-character indices (1_111-1 -> 1_(11)1(-1))
@@ -49,7 +67,39 @@ Note that since we don't clearly distinguish between a public and private interf
 - Add `Ray3D` object and helpers
 - Volume slice representation: add `relativeX/Y/Z` options for dimension
 - Add `StructureInstances` transform
-- Add `story-id` URL arg support to `mvs-stories` app
+- `mvs-stories` app
+  - Add `story-id` URL arg support
+  - Add `story-session-url` URL arg support
+  - Add "Download MVS State" link
+  - Add "Open in Mol*" link
+  - Add "Edit in MolViewStories" link for story states
+- Add ray-based picking
+    - Render narrow view of scene scene from ray origin & direction to a few pixel sized viewport
+    - Cast ray on every input as opposed to the standard "whole screen" picking
+    - Can be enabled with new `Canvas3dInteractionHelperParams.convertCoordsToRay` param
+    - Allows to have input methods that are 3D pointers in the scene
+    - Add `ray: Ray3D` property to `DragInput`, `ClickInput`, and `MoveInput`
+- Add async, non-blocking picking (only WebGL2)
+    - Refactor `Canvas3dInteractionHelper` internals to use async picking for move events
+- Add `enable` param for post-processing effects. If false, no effects are applied.
+- Dot volume representation improvements
+    - Add positional perturbation to avoid camera artifacts
+    - Fix handling of negative isoValues by considering only volume cells with values lower than isoValue (#1559)
+    - Fix volume-value size theme
+- Change the parsing of residue names in PDB files from 3-letter to 4-letter.
+- Support versioning transform using a hash function in `mol-state`
+- Support for "state snapshot transitions"
+    - Add `PluginState.Snapshot.transition` that enables associating a state snapshot with a list states that can be animated
+    - Add `AnimateStateSnapshotTransition` animation
+    - Update the snapshots UI to support this feature
+- Use "proper time" in the animation loop to prevent animation skips during blocking operations (e.g., shader complication)
+- Add `Hsl` and (normalized) `Rgb` color spaces
+- Add `Color.interpolateHsl`
+- Add `rotationCenter` property to `TransformParam`
+- Add Monolayer transparency (exploiting dpoit).
+- Add plugin config item ShowReset (shows/hides "Reset Zoom" button)
+- Fix transform params not being normalized when used together with param hash version
+- Replace `immer` with `mutative`
 
 ## [v4.18.0] - 2025-06-08
 - MolViewSpec extension:

docs/docs/plugin/managers/markdown-extensions.md

@@ -14,12 +14,25 @@ The main use case of this is enriching [MolViewSpec](`https://molstar.org/mol-vi
 
 Extends Markdown Hyperlink syntax to support expressions of the form `[title](!c1=v1&c2=v2&...)` into an executable command. The command can be executed either on click, mouse enter, or mouse leave.
 
+Generally, the command should be URL encoded, e.g., `a b` => `a%20b` (in JS, `encodeURIComponent`, in Python `urllib.parse.quote_plus/urlencode`).
+
 ### Built-in Commands
 
 - `center-camera` - Centers the camera
 - `apply-snapshot=key` - Loads snapshots with the provided key
+- `next-snapshot[=-1|1]` - Loads next/previous snapshot, the direction is optional and default to `1`
+- `play-snapshots` - Starts playback of state snapshots
+- `play-transition` - Plays an animation associated with the given snapshot
+- `stop-animation` - Stops currently playing animation
 - `focus-refs=ref1,ref2,...` - On click, focuses nodes with the provided refs
 - `highlight-refs=ref1,ref2,...` - On mouse over, highlights the provided refs
+- `query=...&lang=...&action=highlight,focus&focus-radius=...`
+    - `query` is an expression (e.g., `resn HEM` when using PyMol syntax)
+    - (optional) `lang` is one of `mol-script` (default), `pymol`, `vmd`, `jmol`
+    - (optional) `action` is an array of `highlight` (default), `focus` (multiple actions can be specified)
+    - (optional) `focus-radius` is extra distance applied when focusing the selection (default is `3`)
+    - Example: `[HEM](!query=resn%20HEM%26lang=pymol&action=highlight,focus)` highlights or focuses the HEM residue (the query must be URL encoded because it contains spaces and possibly other special characters)
+- `play-audio=src`, `toggle-audio[=src]`, `stop-audio`, `pause-audio`, `dispose-audio` - Audio playback support
 
 ## Custom Content
 
@@ -28,11 +41,11 @@ Extends Markdown Image syntax to support expressions of the form `![alt](!c1=v1&
 ### Built-in Custom Content
 - `color-swatch=color` - Renders a box with the provided color
 -  Color palettes:
-  - `color-palette-name=name` - Renders a gradient with the provivided named color palette (see `mol-util/color/lists.ts` for supported color schemes)
-  - `color-palette-colors=color1,color2` - Renders a gradient with the provided colors
-  - `color-palette-width=CCS-value` - Specifies the width of the element, defaults to `150px`
-  - `color-palette-height=CCS-value` - Specified the height of the element, defaults to `0.5em`
-  - `color-palette-discrete` - Renders discrete color list instead of interpolating
+    - `color-palette-name=name` - Renders a gradient with the provided named color palette (see `mol-util/color/lists.ts` for supported color schemes)
+    - `color-palette-colors=color1,color2` - Renders a gradient with the provided colors
+    - `color-palette-width=CCS-value` - Specifies the width of the element, defaults to `150px`
+    - `color-palette-height=CCS-value` - Specified the height of the element, defaults to `0.5em`
+    - `color-palette-discrete` - Renders discrete color list instead of interpolating
 
 
 ## Example

eslint.config.mjs

@@ -39,6 +39,7 @@ export default defineConfig([{
         "comma-spacing": "off",
         "space-infix-ops": "off",
         "comma-dangle": "off",
+        quotes: ["warn", "single", { "allowTemplateLiterals": true, "avoidEscape": true }],
         eqeqeq: ["error", "smart"],
         "import/order": "off",
         "no-eval": "warn",

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "5.0.0-dev.0",
+  "version": "5.0.0-dev.10",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -121,7 +121,9 @@
     "Andy Turner <agdturner@gmail.com>",
     "Lukáš Polák <admin@lukaspolak.cz>",
     "Chetan Mishra <chetan.s115@gmail.com>",
-    "Zach Charlop-Powers <zach.charlop.powers@gmail.com>"
+    "Zach Charlop-Powers <zach.charlop.powers@gmail.com>",
+    "Kim Juho <juho_kim@outlook.com>",
+    "Victoria Doshchenko <doshchenko.victoria@gmail.com>"
   ],
   "license": "MIT",
   "devDependencies": {
@@ -165,9 +167,9 @@
     "cors": "^2.8.5",
     "express": "^5.1.0",
     "h264-mp4-encoder": "^1.0.12",
-    "immer": "^10.1.1",
     "immutable": "^5.1.2",
     "io-ts": "^2.2.22",
+    "mutative": "^1.2.0",
     "node-fetch": "^2.7.0",
     "react-markdown": "^10.1.0",
     "remark-gfm": "^4.0.1",
@@ -202,4 +204,4 @@
       "optional": true
     }
   }
-}
+}

scripts/deploy.js

@@ -7,14 +7,14 @@
 
 const git = require('simple-git');
 const path = require('path');
-const fs = require("fs");
-const fse = require("fs-extra");
+const fs = require('fs');
+const fse = require('fs-extra');
 const argparse = require('argparse');
 
 const VERSION = require(path.resolve(__dirname, '../package.json')).version;
 const MVS_STORIES_VERSION = require(path.resolve(__dirname, '../src/apps/mvs-stories/version.ts')).VERSION;
 
-const remoteUrl = "https://github.com/molstar/molstar.github.io.git";
+const remoteUrl = 'https://github.com/molstar/molstar.github.io.git';
 const dataDir = path.resolve(__dirname, '../data/');
 const buildDir = path.resolve(__dirname, '../build/');
 const deployDir = path.resolve(__dirname, '../deploy/');

src/apps/mesoscale-explorer/app.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2022-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2022-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -147,6 +147,7 @@ export class MesoscaleExplorer {
             behaviors: [
                 PluginSpec.Behavior(PluginBehaviors.Camera.CameraAxisHelper),
                 PluginSpec.Behavior(PluginBehaviors.Camera.CameraControls),
+                PluginSpec.Behavior(PluginBehaviors.State.SnapshotControls),
 
                 PluginSpec.Behavior(MesoFocusLoci),
                 PluginSpec.Behavior(MesoSelectLoci),
@@ -261,7 +262,6 @@ export class MesoscaleExplorer {
             image: true,
             componentManager: false,
             structureSelection: true,
-            behavior: true,
         });
 
         plugin.managers.lociLabels.clearProviders();

src/apps/mvs-stories/context.ts

@@ -16,6 +16,7 @@ export class MVSStoriesContext {
     commands = new BehaviorSubject<MVSStoriesCommand | undefined>(undefined);
     state = {
         viewers: new BehaviorSubject<{ name?: string, model: MVSStoriesViewerModel }[]>([]),
+        currentStoryData: new BehaviorSubject<string | Uint8Array | undefined>(undefined),
         isLoading: new BehaviorSubject(false),
     };
 
@@ -27,7 +28,7 @@ export class MVSStoriesContext {
     }
 }
 
-export function getMVSStoriesContext(options?: { name?: string, container?: object }) {
+export function getMVSStoriesContext(options?: { name?: string, container?: object }): MVSStoriesContext {
     const container: any = options?.container ?? window;
     container.componentContexts ??= {};
     const name = options?.name ?? '<default>';

src/apps/mvs-stories/elements/viewer.tsx

@@ -6,6 +6,8 @@
 
 import { MolViewSpec } from '../../../extensions/mvs/behavior';
 import { loadMVSData } from '../../../extensions/mvs/components/formats';
+import { MVSData } from '../../../extensions/mvs/mvs-data';
+import { StringLike } from '../../../mol-io/common/string-like';
 import { PluginComponent } from '../../../mol-plugin-state/component';
 import { createPluginUI } from '../../../mol-plugin-ui';
 import { renderReact18 } from '../../../mol-plugin-ui/react18';
@@ -56,11 +58,17 @@ export class MVSStoriesViewerModel extends PluginComponent {
             try {
                 this.context.state.isLoading.next(true);
                 if (cmd.kind === 'load-mvs') {
+                    let loadedData: MVSData | StringLike | Uint8Array | undefined;
                     if (cmd.url) {
                         const data = await this.plugin.runTask(this.plugin.fetch({ url: cmd.url, type: cmd.format === 'mvsx' ? 'binary' : 'string' }));
-                        await loadMVSData(this.plugin, data, cmd.format ?? 'mvsj', { sourceUrl: cmd.url });
+                        loadedData = await loadMVSData(this.plugin, data, cmd.format ?? 'mvsj', { sourceUrl: cmd.url });
                     } else if (cmd.data) {
-                        await loadMVSData(this.plugin, cmd.data, cmd.format ?? 'mvsj');
+                        loadedData = await loadMVSData(this.plugin, cmd.data, cmd.format ?? 'mvsj');
+                    }
+                    if (StringLike.is(loadedData) || loadedData instanceof Uint8Array) {
+                        this.context.state.currentStoryData.next(loadedData as string | Uint8Array);
+                    } else if (loadedData) {
+                        this.context.state.currentStoryData.next(JSON.stringify(loadedData));
                     }
                 }
             } catch (e) {

src/apps/mvs-stories/index.html

@@ -38,6 +38,25 @@
             gap: 16px;
         }
 
+        #links {
+            position: absolute;
+            bottom: 4px;
+            right: 8px;
+            font-family: "Raleway", "HelveticaNeue", "Helvetica Neue", Helvetica, Arial, sans-serif;
+            font-size: 0.6rem;
+            z-index: -1;
+            color: #666;
+        }
+
+        #links a {
+            color: #666;
+            text-decoration: none;
+        }
+
+        #links .sep {
+            color: #aaa;
+        }
+
         @media (orientation:portrait) {
             #viewer {
                 position: absolute;
@@ -68,16 +87,23 @@
 <body>
     <!-- the context-name parameter is optional and useful when embedding multiple stories in a single page -->
     <div id="viewer">
-        <mvs-stories-viewer context-name="story1" />
+        <mvs-stories-viewer context-name="story1" ></mvs-stories-viewer>
     </div>
     <div id="controls">
-        <mvs-stories-snapshot-markdown context-name="story1" style="flex-grow: 1;" />
+        <mvs-stories-snapshot-markdown context-name="story1" style="flex-grow: 1;" ></mvs-stories-snapshot-markdown>
+    </div>
+
+    <div id="links">
+        <span id="open-in-stories"><a href="#" id="open-in-stories-link" target="_blank" rel="noopener noreferrer" title="Open and edit the story in the MolViewStories app">Edit in MolViewStories</a>&nbsp;<span class="sep">•</span></span>
+        <span id="open-in-molstar"><a href="#" id="open-in-molstar-link" target="_blank" rel="noopener noreferrer" title="Open the story in the Mol* Viewer app. Enables exporting an animation.">Open in Mol* Viewer</a>&nbsp;<span class="sep">•</span></span>
+        <a href="#" id="mvs-data" title="MolViewSpec State for this story. Can be opened in the Mol* app.">Download MVS</a> <span class="sep">•</span> <a href="https://github.com/molstar/molstar/tree/master/src/apps/mvs-stories" id="mvs-data" target="_blank" rel="noopener noreferrer">Source Code</a>
     </div>
 
     <script>
         var urlParams = new URLSearchParams(window.location.search);
         var storyId = urlParams.get('story-id');
         var storyUrl = urlParams.get('story-url');
+        var storySessionUrl = urlParams.get('story-session-url');
         var format = urlParams.get('data-format');
 
         // For testing purposes:
@@ -85,11 +111,36 @@
         //     storyUrl = 'https://raw.githubusercontent.com/molstar/molstar/master/examples/mvs/kinase-story.mvsj';
         // }
 
+        var molstarDataLink = storyUrl;
+        var editInStoriesUrl = undefined;
+
         if (storyId) {
-            mvsStories.loadFromID(storyId, { contextName: 'story1' });
+            mvsStories.loadFromID(storyId, { format: format || 'mvsj', contextName: 'story1' });
+            editInStoriesUrl = 'https://molstar.org/mol-view-stories/builder?published-session-id=' + storyId;
+            molstarDataLink = 'https://stories.molstar.org/api/story/' + storyId + '/data';
         } else if (storyUrl) {
             mvsStories.loadFromURL(storyUrl, { format: format || 'mvsj', contextName: 'story1' });
         }
+
+        if (!editInStoriesUrl && storySessionUrl) {
+            editInStoriesUrl = 'https://molstar.org/mol-view-stories/builder?session-url=' + encodeURIComponent(storySessionUrl);
+        }
+        
+        if (molstarDataLink) {
+            var molstarLink = 'https://molstar.org/viewer?mvs-url=' + encodeURIComponent(molstarDataLink) + '&mvs-format=' + encodeURIComponent(format || 'mvsj'); 
+            document.getElementById('open-in-molstar-link').setAttribute('href', molstarLink);
+            document.getElementById('open-in-molstar').style.display = 'inline';
+        }
+        
+        if (editInStoriesUrl) {
+            document.getElementById('open-in-stories-link').setAttribute('href', editInStoriesUrl);
+            document.getElementById('open-in-stories').style.display = 'inline';
+        }
+
+        document.getElementById('mvs-data').addEventListener('click', (e) => {
+            e.preventDefault();
+            mvsStories.downloadCurrentStory({ contextName: 'story1' });
+        });
     </script>
     <!-- __MOLSTAR_ANALYTICS__ -->
 </body>

src/apps/mvs-stories/index.tsx

@@ -7,6 +7,7 @@
 import { getMVSStoriesContext } from './context';
 import './elements';
 import { MVSData } from '../../extensions/mvs/mvs-data';
+import { download } from '../../mol-util/download';
 
 import './favicon.ico';
 import '../../mol-plugin-ui/skin/light.scss';
@@ -48,4 +49,16 @@ export function loadFromID(id: string, options?: { format?: 'mvsx' | 'mvsj', con
     );
 }
 
+export function downloadCurrentStory(options?: { contextName?: string, filename?: string }) {
+    const story = getContext(options?.contextName).state.currentStoryData.value;
+    if (!story) return;
+
+    const isMVSJ = typeof story === 'string';
+    const filename = `${options?.filename ?? 'story'}.${isMVSJ ? 'mvsj' : 'mvsx'}`;
+    download(
+        new Blob([typeof story === 'string' ? story : story.buffer], { type: isMVSJ ? 'application/json' : 'application/octet-stream' }),
+        filename
+    );
+};
+
 export { MVSData };

src/apps/mvs-stories/styles.scss

@@ -182,6 +182,15 @@
         max-width: 100%;
         height: auto;
     }
+
+    a {
+        text-decoration: none;
+        color: #1d4ed7;
+
+        &:hover {
+            text-decoration: underline;
+        }
+    }
 }
 
 @media (orientation:portrait) {

src/apps/viewer/app.ts

@@ -109,8 +109,10 @@ const DefaultViewerOptions = {
     resolutionMode: PluginConfig.General.ResolutionMode.defaultValue,
     illumination: false,
 
-    viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
+    viewportShowReset: PluginConfig.Viewport.ShowReset.defaultValue,
+    viewportShowScreenshotControls: PluginConfig.Viewport.ShowScreenshotControls.defaultValue,
     viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
+    viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
     viewportShowSettings: PluginConfig.Viewport.ShowSettings.defaultValue,
     viewportShowSelectionMode: PluginConfig.Viewport.ShowSelectionMode.defaultValue,
     viewportShowAnimation: PluginConfig.Viewport.ShowAnimation.defaultValue,
@@ -187,8 +189,10 @@ export class Viewer {
                 [PluginConfig.General.AllowMajorPerformanceCaveat, o.allowMajorPerformanceCaveat],
                 [PluginConfig.General.PowerPreference, o.powerPreference],
                 [PluginConfig.General.ResolutionMode, o.resolutionMode],
-                [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
+                [PluginConfig.Viewport.ShowReset, o.viewportShowReset],
+                [PluginConfig.Viewport.ShowScreenshotControls, o.viewportShowScreenshotControls],
                 [PluginConfig.Viewport.ShowControls, o.viewportShowControls],
+                [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
                 [PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
                 [PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode],
                 [PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation],

src/examples/ligand-editor/index.tsx

@@ -30,8 +30,8 @@ import { ExampleMol } from './example-data';
 import './index.html';
 import { jsonCifToMolfile } from './molfile';
 import { RGroupName } from './r-groups';
-import { SingleTaskQueue } from './utils';
 import { molfileToJSONCif } from '../../extensions/json-cif/utils';
+import { SingleTaskQueue } from '../../mol-util/single-task-queue';
 
 async function init(target: HTMLElement | string, molfile: string = ExampleMol) {
     const root = typeof target === 'string' ? document.getElementById(target)! : target;

src/examples/mvs-stories/index.html

@@ -98,14 +98,14 @@
 
 <body>
     <div id="viewer">
-        <mvs-stories-viewer />
+        <mvs-stories-viewer></mvs-stories-viewer>
     </div>
     <div id="controls">
         <div id="select-story" class="select-story"></div>
-        <mvs-stories-snapshot-markdown style="flex-grow: 1;" />
+        <mvs-stories-snapshot-markdown style="flex-grow: 1;"></mvs-stories-snapshot-markdown>
     </div>
     <div id="links">
-        <a href="#" id="mvs-data" filename="kinase-story.mvsj">Download MVS State</a> | <a href="https://github.com/molstar/molstar/tree/master/src/examples/mvs-stories" id="mvs-data" target="_blank" rel="noopener noreferrer">Source Code</a>
+        <a href="#" id="mvs-data">Download MVS State</a> | <a href="https://github.com/molstar/molstar/tree/master/src/examples/mvs-stories" id="mvs-data" target="_blank" rel="noopener noreferrer">Source Code</a>
     </div>
 
     <script>

src/examples/mvs-stories/stories/animation.ts

@@ -0,0 +1,360 @@
+/**
+ * Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { MVSData_States } from '../../../extensions/mvs/mvs-data';
+import { createMVSBuilder, Structure as MVSStructure, Root } from '../../../extensions/mvs/tree/mvs/mvs-builder';
+import { MVSNodeParams } from '../../../extensions/mvs/tree/mvs/mvs-tree';
+import { ColorT } from '../../../extensions/mvs/tree/mvs/param-types';
+import { Mat4 } from '../../../mol-math/linear-algebra';
+
+const Colors = {
+    '1cbs': '#4577B2' as ColorT,
+
+    'ligand-away': '#F3794C' as ColorT,
+    'ligand-docked': '#B9E3A0' as ColorT,
+};
+
+const Steps = [
+    {
+        header: 'Animation Demo',
+        key: 'intro',
+        description: `### Molecular Animation
+A story showcasing MolViewSpec animation capabilities.
+
+[\[**🔄 Replay Intro**\]](!play-transition)
+[\[**⏵ Play Snapshots**\]](!play-snapshots)
+[\[**⏹ Stop Animation**\]](!stop-animation)
+
+[\[**➡️ Next Snapshot**\]](!next-snapshot)
+
+`,
+        linger_duration_ms: 2000,
+        transition_duration_ms: 500,
+        state: (): Root => {
+            const builder = createMVSBuilder();
+
+            const _1cbs = structure(builder, '1cbs');
+            polymer(_1cbs, { color: Colors['1cbs'] });
+
+            const prims = _1cbs.primitives({
+                ref: 'prims',
+                label_opacity: 0,
+            });
+            prims.label({ text: 'Animation Demo', position: { label_asym_id: 'A' }, label_size: 10 });
+
+            const anim = builder.animation({
+                custom: {
+                    molstar_trackball: {
+                        name: 'rock',
+                        params: { speed: 0.5 },
+                    }
+                }
+            });
+            anim.interpolate({
+                kind: 'scalar',
+                ref: 'prims-opacity',
+                target_ref: 'prims',
+                start_ms: 500,
+                duration_ms: 500,
+                property: 'label_opacity',
+                end: 1,
+            });
+
+            anim.interpolate({
+                kind: 'scalar',
+                ref: 'prims-opacity',
+                target_ref: 'prims',
+                start_ms: 1500,
+                duration_ms: 500,
+                property: 'label_opacity',
+                start: 1,
+                end: 0.66,
+            });
+
+
+            // Uncomment this to make 2nd frame render much faster
+            // It will cause shader compilation to happen during the 1st snapshot
+
+            // const surface = poly.representation({
+            //     type: 'surface',
+            //     surface_type: 'gaussian',
+            // }).opacity({ opacity: 0 });
+
+            // _1cbs.component({ selector: 'ligand' })
+            //     .representation({ type: 'ball_and_stick' })
+            //     .opacity({ opacity: 0 });
+
+            // surface.clip({
+            //     ref: 'clip',
+            //     type: 'plane',
+            //     point: [22.0, 15, 0],
+            //     normal: [0, 0, 1],
+            // });
+
+            return builder;
+        },
+        camera: {
+            position: [-11.49, -37.05, 15.78],
+            target: [15.85, 17.26, 24.32],
+            up: [-0.88, 0.4, 0.26],
+        } satisfies MVSNodeParams<'camera'>,
+    },
+    {
+        header: 'Ligand Docking',
+        description: `Animate ligand moving to the binding site`,
+        linger_duration_ms: 2500,
+        transition_duration_ms: 500,
+        state: (): Root => {
+            const builder = createMVSBuilder();
+
+            const _1cbs = structure(builder, '1cbs');
+            const [poly,] = polymer(_1cbs, { color: Colors['1cbs'] });
+
+            const surface = poly.representation({
+                type: 'surface',
+                surface_type: 'gaussian',
+            });
+
+            _1cbs.component({ selector: 'ligand' })
+                .transform({
+                    ref: 'xform',
+                    translation: [5, 20, -20],
+                    rotation: [1, 0, 0, 0, 1, 0, 0, 0, 1],
+                    rotation_center: 'centroid',
+                })
+                .representation({ type: 'ball_and_stick' })
+                .color({ ref: 'ligand-color', color: 'red' });
+
+            surface.clip({
+                ref: 'clip',
+                type: 'plane',
+                point: [22.0, 15, 0],
+                normal: [0, 0, 1],
+            });
+
+            const anim = builder.animation();
+
+            anim.interpolate({
+                kind: 'scalar',
+                target_ref: 'clip',
+                duration_ms: 500,
+                property: ['point', 2],
+                end: 55,
+                easing: 'sin-in',
+            });
+
+            anim.interpolate({
+                kind: 'scalar',
+                target_ref: 'clip',
+                start_ms: 600,
+                duration_ms: 800,
+                property: ['point', 2],
+                end: 0,
+                easing: 'sin-out',
+            });
+
+            anim.interpolate({
+                kind: 'scalar',
+                target_ref: 'clip',
+                start_ms: 1500,
+                duration_ms: 500,
+                property: ['point', 2],
+                end: 55,
+            });
+
+            anim.interpolate({
+                kind: 'vec3',
+                target_ref: 'xform',
+                duration_ms: 2000,
+                property: 'translation',
+                end: [0, 0, 0],
+                noise_magnitude: 1,
+            });
+
+            anim.interpolate({
+                kind: 'rotation_matrix',
+                target_ref: 'xform',
+                duration_ms: 2000,
+                property: 'rotation',
+                noise_magnitude: 0.2,
+            });
+
+            anim.interpolate({
+                kind: 'color',
+                target_ref: 'ligand-color',
+                duration_ms: 2000,
+                property: 'color',
+                end: Colors['ligand-docked'],
+            });
+
+            return builder;
+        },
+        camera: {
+            position: [-30.63, 77.29, 2.28],
+            target: [19.16, 26.15, 22.82],
+            up: [0.69, 0.71, 0.09],
+        } satisfies MVSNodeParams<'camera'>,
+    },
+    {
+        header: 'Highlight & Opacity',
+        description: `Animate emissive, opacity and transform properties`,
+        linger_duration_ms: 2000,
+        transition_duration_ms: 0,
+        state: (): Root => {
+            const builder = createMVSBuilder();
+
+            const _1cbs = structure(builder, '1cbs');
+            const [poly,] = polymer(_1cbs, { color: Colors['1cbs'] });
+
+            poly.representation({
+                type: 'surface',
+                surface_type: 'gaussian'
+            }).opacity({ ref: 'opacity', opacity: 1 }).color({ ref: 'surface-color', color: 'white' });
+
+            _1cbs.component({ selector: 'ligand' })
+                .transform({ ref: 'xform', translation: [0, 0, 0] })
+                .representation({
+                    ref: 'repr',
+                    type: 'ball_and_stick',
+                    custom: {
+                        molstar_representation_params: {
+                            emissive: 0,
+                        }
+                    }
+                })
+                .color({ color: Colors['ligand-docked'] });
+
+            const primitives = builder.primitives({
+                ref: 'primitives',
+                instances: [
+                    Mat4.identity()
+                ],
+                opacity: 0,
+            });
+
+            primitives.ellipsoid({
+                center: [0, 0, 0],
+                radius: [2, 3, 2.5],
+                color: 'red'
+            });
+
+            const anim = builder.animation();
+
+            anim.interpolate({
+                kind: 'scalar',
+                target_ref: 'repr',
+                duration_ms: 1000,
+                property: ['custom', 'molstar_representation_params', 'emissive'],
+                end: 0.2,
+            });
+
+            anim.interpolate({
+                kind: 'scalar',
+                target_ref: 'opacity',
+                duration_ms: 1000,
+                frequency: 2,
+                alternate_direction: true,
+                property: 'opacity',
+                end: 0,
+            });
+
+            anim.interpolate({
+                kind: 'transform_matrix',
+                target_ref: 'primitives',
+                property: ['instances', 0],
+                translation_start: [20.24, 29.64, 14.85],
+                translation_end: [21.84, 21.71, 27.04],
+                translation_frequency: 4,
+                pivot: [0, 0, 0],
+                rotation_noise_magnitude: 0.2,
+                scale_end: [0.01, 0.01, 0.01],
+                duration_ms: 1000,
+            });
+
+            anim.interpolate({
+                kind: 'scalar',
+                target_ref: 'primitives',
+                duration_ms: 1000,
+                property: 'opacity',
+                end: 1,
+            });
+
+
+            anim.interpolate({
+                kind: 'color',
+                target_ref: 'surface-color',
+                duration_ms: 2000,
+                property: 'color',
+                palette: {
+                    kind: 'continuous',
+                    colors: ['white', Colors['1cbs'], 'white'],
+                }
+            });
+
+            return builder;
+        },
+        camera: {
+            position: [6.92, 47.17, 10.68],
+            target: [21.79, 22.2, 23.43],
+            up: [0.8, 0.57, 0.2],
+        } satisfies MVSNodeParams<'camera'>,
+    }
+];
+
+function structure(builder: Root, id: string): MVSStructure {
+    return builder
+        .download({ url: pdbUrl(id) })
+        .parse({ format: 'bcif' })
+        .modelStructure();
+}
+
+function polymer(structure: MVSStructure, options: { color: ColorT }) {
+    const component = structure.component({ selector: { label_asym_id: 'A' } });
+    const reprensentation = component.representation({ type: 'cartoon' });
+    reprensentation.color({ color: options.color });
+    return [component, reprensentation] as const;
+}
+
+function pdbUrl(id: string) {
+    return `https://www.ebi.ac.uk/pdbe/entry-files/download/${id.toLowerCase()}.bcif`;
+}
+
+export function buildStory(): MVSData_States {
+    const snapshots = Steps.map((s, i) => {
+        const builder = s.state();
+        if (s.camera) builder.camera(s.camera);
+
+        builder.canvas({
+            custom: {
+                molstar_postprocessing: {
+                    enable_outline: true,
+                    enable_ssao: true,
+                }
+            }
+        });
+
+        const description = i > 0 ? `${s.description}\n\n[Go to start](#intro)` : s.description;
+
+        return builder.getSnapshot({
+            title: s.header,
+            key: s.key,
+            description,
+            description_format: 'markdown',
+            linger_duration_ms: s.linger_duration_ms ?? 500,
+            transition_duration_ms: s.transition_duration_ms ?? 1000,
+        });
+    });
+
+    return {
+        kind: 'multiple',
+        snapshots,
+        metadata: {
+            title: 'Animation Showcase',
+            version: '1.0',
+            timestamp: new Date().toISOString(),
+        }
+    };
+}

src/examples/mvs-stories/stories/index.ts

@@ -6,8 +6,14 @@
 
 import { buildStory as kinase } from './kinase';
 import { buildStory as tbp } from './tbp';
+import { buildStory as animation } from './animation';
+import { buildStory as audio } from './audio';
+import { buildStory as motm1 } from './motm1';
 
 export const Stories = [
     { id: 'kinase', name: 'BCR-ABL: A Kinase Out of Control', buildStory: kinase },
     { id: 'tata', name: 'TATA-Binding Protein and its Role in Transcription Initiation ', buildStory: tbp },
+    { id: 'motm1', name: 'RCSB Molecule of the Month #1', buildStory: motm1 },
+    { id: 'animation-example', name: 'Molecular Animation Example', buildStory: animation },
+    { id: 'audio-example', name: 'Audio Playback Example', buildStory: audio },
 ] as const;

src/extensions/mvs/camera.ts

@@ -6,7 +6,10 @@
  */
 
 import { Camera } from '../../mol-canvas3d/camera';
-import { Canvas3DParams, Canvas3DProps } from '../../mol-canvas3d/canvas3d';
+import { CameraFogParams, Canvas3DParams, Canvas3DProps, DefaultCanvas3DParams } from '../../mol-canvas3d/canvas3d';
+import { TrackballControlsParams } from '../../mol-canvas3d/controls/trackball';
+import { BloomParams } from '../../mol-canvas3d/passes/bloom';
+import { DofParams } from '../../mol-canvas3d/passes/dof';
 import { OutlineParams } from '../../mol-canvas3d/passes/outline';
 import { ShadowParams } from '../../mol-canvas3d/passes/shadow';
 import { SsaoParams } from '../../mol-canvas3d/passes/ssao';
@@ -22,6 +25,7 @@ import { ParamDefinition } from '../../mol-util/param-definition';
 import { decodeColor } from './helpers/utils';
 import { MolstarLoadingContext } from './load';
 import { SnapshotMetadata } from './mvs-data';
+import { MVSAnimationNode } from './tree/animation/animation-tree';
 import { MolstarNode, MolstarNodeParams } from './tree/molstar/molstar-tree';
 import { MVSTreeSchema } from './tree/mvs/mvs-tree';
 
@@ -119,37 +123,93 @@ export function createPluginStateSnapshotCamera(plugin: PluginContext, context:
     return camera;
 }
 
-/** Set canvas properties based on a canvas node. */
-export function setCanvas(plugin: PluginContext, node: MolstarNode<'canvas'> | undefined) {
-    plugin.canvas3d?.setProps(old => modifyCanvasProps(old, node));
+function optionalParams(enable: boolean | undefined, values: any, params: ParamDefinition.Params, fallback: any) {
+    if (typeof enable === 'boolean') {
+        return enable
+            ? { name: 'on', params: { ...ParamDefinition.getDefaultValues(params), ...values } }
+            : { name: 'off', params: {} };
+    }
+    return fallback;
 }
 
 /** Create a deep copy of `oldCanvasProps` with values modified according to a canvas node params. */
-export function modifyCanvasProps(oldCanvasProps: Canvas3DProps, canvasNode: MolstarNode<'canvas'> | undefined, custom?: Record<string, any>): Canvas3DProps {
+export function modifyCanvasProps(oldCanvasProps: Canvas3DProps, canvasNode: MolstarNode<'canvas'> | undefined, animationNode: MVSAnimationNode<'animation'> | undefined): Canvas3DProps {
     const params = canvasNode?.params;
     const backgroundColor = decodeColor(params?.background_color) ?? DefaultCanvasBackgroundColor;
 
-    const outline = !!canvasNode?.custom?.molstar_enable_outline;
-    const shadow = !!canvasNode?.custom?.molstar_enable_shadow;
-    const occlusion = !!canvasNode?.custom?.molstar_enable_ssao;
+    const molstar_postprocessing = canvasNode?.custom?.molstar_postprocessing;
+
+    const outline = molstar_postprocessing?.enable_outline;
+    const outlineParams = molstar_postprocessing?.outline_params;
+
+    const shadow = molstar_postprocessing?.enable_shadow;
+    const shadowParams = molstar_postprocessing?.shadow_params;
+
+    const occlusion = molstar_postprocessing?.enable_ssao;
+    const occlusionParams = molstar_postprocessing?.ssao_params;
+
+    const fog = molstar_postprocessing?.enable_fog;
+    const fogParams = molstar_postprocessing?.fog_params;
+
+    const dof = molstar_postprocessing?.enable_depth_of_field;
+    const dofParams = molstar_postprocessing?.depth_of_field_params;
+
+    const bloom = molstar_postprocessing?.enable_bloom;
+    const bloomParams = molstar_postprocessing?.bloom_params;
+
+    const trackballAnimation = animationNode?.custom?.molstar_trackball;
+    const trackballAnimationName = trackballAnimation?.name;
+    const trackballAnimationParams = trackballAnimation?.params ?? {};
 
     return {
         ...oldCanvasProps,
         postprocessing: {
             ...oldCanvasProps.postprocessing,
-            outline: outline
-                ? { name: 'on', params: ParamDefinition.getDefaultValues(OutlineParams) }
-                : oldCanvasProps.postprocessing.outline,
-            shadow: shadow
-                ? { name: 'on', params: ParamDefinition.getDefaultValues(ShadowParams) }
-                : oldCanvasProps.postprocessing.shadow,
-            occlusion: occlusion
-                ? { name: 'on', params: ParamDefinition.getDefaultValues(SsaoParams) }
-                : oldCanvasProps.postprocessing.occlusion,
+            outline: optionalParams(outline, outlineParams, OutlineParams, oldCanvasProps.postprocessing.outline),
+            shadow: optionalParams(shadow, shadowParams, ShadowParams, oldCanvasProps.postprocessing.shadow),
+            occlusion: optionalParams(occlusion, occlusionParams, SsaoParams, oldCanvasProps.postprocessing.occlusion),
+            dof: optionalParams(dof, dofParams, DofParams, oldCanvasProps.postprocessing.dof),
+            bloom: optionalParams(bloom, bloomParams, BloomParams, oldCanvasProps.postprocessing.bloom),
         },
+        cameraFog: optionalParams(fog, fogParams, CameraFogParams, oldCanvasProps.cameraFog),
         renderer: {
             ...oldCanvasProps.renderer,
             backgroundColor: backgroundColor,
         },
+        trackball: {
+            ...oldCanvasProps?.trackball,
+            ...(trackballAnimationName
+                ? {
+                    animate: {
+                        name: trackballAnimationName,
+                        params: {
+                            ...TrackballControlsParams.animate.map(trackballAnimationName)?.defaultValue,
+                            ...trackballAnimationParams
+                        }
+                    }
+                }
+                : {}
+            ),
+        }
     };
 }
+
+export function resetCanvasProps(plugin: PluginContext) {
+    const old = plugin.canvas3d?.props;
+    plugin.canvas3d?.setProps({
+        ...old,
+        postprocessing: {
+            ...old,
+            outline: DefaultCanvas3DParams.postprocessing.outline,
+            shadow: DefaultCanvas3DParams.postprocessing.shadow,
+            occlusion: DefaultCanvas3DParams.postprocessing.occlusion,
+            dof: DefaultCanvas3DParams.postprocessing.dof,
+            bloom: DefaultCanvas3DParams.postprocessing.bloom,
+        },
+        cameraFog: DefaultCanvas3DParams.cameraFog,
+        trackball: {
+            ...old?.trackball,
+            animate: { name: 'off', params: {} },
+        }
+    });
+}

src/extensions/mvs/components/annotation-color-theme.ts

@@ -241,7 +241,7 @@ function makeNumericPaletteScale(props: MVSContinuousPaletteProps | MVSDiscreteP
     }
 }
 
-function makeContinuousPaletteCheckpoints(props: MVSContinuousPaletteProps) {
+export function makeContinuousPaletteCheckpoints(props: MVSContinuousPaletteProps) {
     if (props.colors.colors.every(x => Array.isArray(x))) {
         // Explicit checkpoints
         const sorted = props.colors.colors.sort((a, b) => a[1] - b[1]);

src/extensions/mvs/components/formats.ts

@@ -5,7 +5,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { hashFnv32a } from '../../../mol-data/util';
+import { murmurHash3_128_fromBytes } from '../../../mol-data/util';
 import { StringLike } from '../../../mol-io/common/string-like';
 import { DataFormatProvider } from '../../../mol-plugin-state/formats/provider';
 import { PluginStateObject as SO } from '../../../mol-plugin-state/objects';
@@ -118,7 +118,7 @@ export async function loadMVSX(plugin: PluginContext, runtimeCtx: RuntimeContext
     // states.
     clearMVSXFileAssets(plugin);
 
-    const archiveId = `ni,fnv1a;${hashFnv32a(data)}`;
+    const archiveId = `ni,MurmurHash3_128;${murmurHash3_128_fromBytes(data, 42)}`;
     let files: { [path: string]: Uint8Array };
     try {
         files = await unzip(runtimeCtx, data) as typeof files;
@@ -166,6 +166,8 @@ export async function loadMVSData(plugin: PluginContext, data: MVSData | StringL
     } else {
         throw new Error(`Unknown MolViewSpec format: ${format}`);
     }
+
+    return data;
 }
 
 function clearMVSXFileAssets(plugin: PluginContext) {
@@ -180,7 +182,7 @@ function tryGetDownloadUrl(pso: SO.Data.String, plugin: PluginContext): string |
 }
 
 /** Return a URI referencing a file within an archive, using ARCP scheme (https://arxiv.org/pdf/1809.06935.pdf).
- * `archiveId` corresponds to the `authority` part of URI (e.g. 'uuid,EYVwjDiZhM20PWbF1OWWvQ' or 'ni,fnv1a;938511930')
+ * `archiveId` corresponds to the `authority` part of URI (e.g. 'uuid,EYVwjDiZhM20PWbF1OWWvQ' or 'ni,MurmurHash3_128;e6494f6be71f34c556f3de73d306780c')
  * `path` corresponds to the path to a file within the archive */
 function arcpUri(archiveId: string, path: string): string {
     return new URL(path, `arcp://${archiveId}/`).href;

src/extensions/mvs/components/primitives.ts

@@ -39,8 +39,9 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { capitalize } from '../../../mol-util/string';
 import { rowsToExpression, rowToExpression } from '../helpers/selections';
 import { collectMVSReferences, decodeColor, isDefined } from '../helpers/utils';
-import { MolstarNode, MolstarSubtree } from '../tree/molstar/molstar-tree';
-import { MVSNode } from '../tree/mvs/mvs-tree';
+import { addParamDefaults } from '../tree/generic/params-schema';
+import { MolstarNode, MolstarNodeParams, MolstarSubtree } from '../tree/molstar/molstar-tree';
+import { MVSNode, MVSTreeSchema } from '../tree/mvs/mvs-tree';
 import { isComponentExpression, isPrimitiveComponentExpressions, isVector3, PrimitivePositionT } from '../tree/mvs/param-types';
 import { MVSTransform } from './annotation-structure-component';
 
@@ -97,6 +98,16 @@ export const MVSDownloadPrimitiveData = MVSTransform({
     },
 });
 
+/* Cannot use MolstarSubtree<'primitives'>> because information about type of children would be lost and cause TypeScript errors in dependent code */
+interface PrimitivesSubtree {
+    kind: 'primitives',
+    params: MolstarNodeParams<'primitives'>,
+    children?: {
+        kind: 'primitive',
+        params: MolstarNodeParams<'primitive'>,
+    }[],
+}
+
 export type MVSInlinePrimitiveData = typeof MVSInlinePrimitiveData
 export const MVSInlinePrimitiveData = MVSTransform({
     name: 'mvs-inline-primitive-data',
@@ -104,7 +115,10 @@ export const MVSInlinePrimitiveData = MVSTransform({
     from: [SO.Root, SO.Molecule.Structure],
     to: MVSPrimitivesData,
     params: {
-        node: PD.Value<MolstarSubtree<'primitives'>>(undefined as any, { isHidden: true }),
+        node: PD.Value<PrimitivesSubtree>({
+            kind: 'primitives',
+            params: addParamDefaults(MVSTreeSchema.nodes.primitives.params, {}),
+        }, { isHidden: true }),
     },
 })({
     apply({ a, params }) {
@@ -135,17 +149,20 @@ export const MVSBuildPrimitiveShape = MVSTransform({
         const context: PrimitiveBuilderContext = { ...a.data, structureRefs };
 
         const snapshotKey = { snapshotKey: { ...SnapshotKey, defaultValue: a.data.options?.snapshot_key ?? '' } };
+        const markdownCommands = { markdownCommands: { ...MarkdownCommands, defaultValue: a.data.node?.custom?.molstar_markdown_commands } };
 
         const label = capitalize(params.kind);
         if (params.kind === 'mesh') {
             if (!hasPrimitiveKind(a.data, 'mesh')) return StateObject.Null;
 
+            const customMeshParams = a.data.node.custom?.molstar_mesh_params;
             return new SO.Shape.Provider({
                 label,
                 data: context,
                 params: {
-                    ...PD.withDefaults(Mesh.Params, { alpha: a.data.options?.opacity ?? 1 }),
+                    ...PD.withDefaults(Mesh.Params, { alpha: a.data.options?.opacity ?? 1, ...customMeshParams }),
                     ...snapshotKey,
+                    ...markdownCommands,
                 },
                 getShape: (_, data, __, prev: any) => buildPrimitiveMesh(data, prev?.geometry),
                 geometryUtils: Mesh.Utils,
@@ -155,6 +172,7 @@ export const MVSBuildPrimitiveShape = MVSTransform({
 
             const options = a.data.options;
             const bgColor = options?.label_background_color;
+            const customLabelParams = a.data.node.custom?.molstar_label_params;
             return new SO.Shape.Provider({
                 label,
                 data: context,
@@ -166,8 +184,10 @@ export const MVSBuildPrimitiveShape = MVSTransform({
                         tetherLength: options?.label_tether_length ?? 1,
                         background: isDefined(bgColor),
                         backgroundColor: isDefined(bgColor) ? decodeColor(bgColor) : undefined,
+                        ...customLabelParams,
                     }),
                     ...snapshotKey,
+                    ...markdownCommands,
                 },
                 getShape: (_, data, props, prev: any) => buildPrimitiveLabels(data, prev?.geometry, props),
                 geometryUtils: Text.Utils,
@@ -175,12 +195,14 @@ export const MVSBuildPrimitiveShape = MVSTransform({
         } else if (params.kind === 'lines') {
             if (!hasPrimitiveKind(a.data, 'line')) return StateObject.Null;
 
+            const customLineParams = a.data.node.custom?.molstar_line_params;
             return new SO.Shape.Provider({
                 label,
                 data: context,
                 params: {
-                    ...PD.withDefaults(Lines.Params, { alpha: a.data.options?.opacity ?? 1 }),
+                    ...PD.withDefaults(Lines.Params, { alpha: a.data.options?.opacity ?? 1, ...customLineParams }),
                     ...snapshotKey,
+                    ...markdownCommands,
                 },
                 getShape: (_, data, __, prev: any) => buildPrimitiveLines(data, prev?.geometry),
                 geometryUtils: Lines.Utils,
@@ -209,7 +231,7 @@ export const MVSShapeRepresentation3D = MVSTransform({
             const repr = ShapeRepresentation(a.data.getShape, a.data.geometryUtils);
             await repr.createOrUpdate(props, a.data.data).runInContext(ctx);
 
-            const pickable = !!(params as any).snapshotKey?.trim();
+            const pickable = !!(params as any).snapshotKey?.trim() || !!(params as any).markdownCommands;
             if (pickable) {
                 repr.setState({ pickable, markerActions: MarkerActions.Highlighting });
             }
@@ -223,7 +245,7 @@ export const MVSShapeRepresentation3D = MVSTransform({
             await b.data.repr.createOrUpdate(props, a.data.data).runInContext(ctx);
             b.data.sourceData = a.data;
 
-            const pickable = !!(newParams as any).snapshotKey?.trim();
+            const pickable = !!(newParams as any).snapshotKey?.trim() || !!(newParams as any).markdownCommands;
             if (pickable) {
                 b.data.repr.setState({ pickable, markerActions: MarkerActions.Highlighting });
             }
@@ -234,6 +256,7 @@ export const MVSShapeRepresentation3D = MVSTransform({
 });
 
 const SnapshotKey = PD.Text('', { isEssential: true, disableInteractiveUpdates: true, description: 'Activate the snapshot with the provided key when clicking on the label' });
+const MarkdownCommands = PD.Value<any>(undefined, { isHidden: true });
 
 /* **************************************************** */
 

src/extensions/mvs/components/trajectory.ts

@@ -0,0 +1,36 @@
+/**
+ * Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { PluginStateObject } from '../../../mol-plugin-state/objects';
+import { getTrajectory } from '../../../mol-plugin-state/transforms/model';
+import { Task } from '../../../mol-task';
+import { ParamDefinition } from '../../../mol-util/param-definition';
+import { getMVSReferenceObject } from '../helpers/utils';
+import { MVSTransform } from './annotation-structure-component';
+
+export const MVSTrajectoryWithCoordinates = MVSTransform({
+    name: 'trajectory-with-coordinates',
+    display: { name: 'Trajectory with Coordinates', description: 'Create a trajectory from existing model and the provided coordinates.' },
+    from: PluginStateObject.Molecule.Model,
+    to: PluginStateObject.Molecule.Trajectory,
+    params: {
+        coordinatesRef: ParamDefinition.Text('', { isHidden: true }),
+    }
+})({
+    apply({ a, params, dependencies }) {
+        return Task.create('Create trajectory from model/topology and coordinates', async ctx => {
+            const coordinates = getMVSReferenceObject([PluginStateObject.Molecule.Coordinates], dependencies, params.coordinatesRef);
+
+            if (!coordinates) {
+                throw new Error('Coordinates not found.');
+            }
+
+            const trajectory = await getTrajectory(ctx, a, coordinates.data);
+            const props = { label: 'Trajectory', description: `${trajectory.frameCount} model${trajectory.frameCount === 1 ? '' : 's'}` };
+            return new PluginStateObject.Molecule.Trajectory(trajectory, props);
+        });
+    }
+});

src/extensions/mvs/export.ts

@@ -0,0 +1,26 @@
+/**
+ * Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Zip } from '../../mol-util/zip/zip';
+import { MVSData } from './mvs-data';
+
+/**
+ * Creates an MVSX zip file with from the provided data and assets
+ */
+export async function createMVSX(data: MVSData, assets: { name: string, content: string | Uint8Array }[]) {
+    const encoder = new TextEncoder();
+    const files: Record<string, Uint8Array> = {
+        'index.mvsj': encoder.encode(JSON.stringify(data)),
+    };
+    for (const asset of assets) {
+        files[asset.name] = typeof asset.content === 'string'
+            ? encoder.encode(asset.content)
+            : asset.content;
+    }
+
+    const zip = await Zip(files).run();
+    return new Uint8Array(zip);
+}

src/extensions/mvs/helpers/animation.ts

@@ -0,0 +1,605 @@
+/**
+ * Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Ludovic Autin <ludovic.autin@gmail.com>
+ */
+
+import { SortedArray } from '../../../mol-data/int';
+import * as EasingFns from '../../../mol-math/easing';
+import { clamp, lerp } from '../../../mol-math/interpolate';
+import { EPSILON, Mat3, Mat4, Quat, Vec3 } from '../../../mol-math/linear-algebra';
+import { RuntimeContext } from '../../../mol-task';
+import { deepEqual } from '../../../mol-util';
+import { Color } from '../../../mol-util/color';
+import { produce } from '../../../mol-util/produce';
+import { makeContinuousPaletteCheckpoints, MVSContinuousPaletteProps, MVSDiscretePaletteProps } from '../components/annotation-color-theme';
+import { palettePropsFromMVSPalette } from '../load-helpers';
+import { Snapshot } from '../mvs-data';
+import { MVSAnimationEasing, MVSAnimationNode, MVSAnimationSchema } from '../tree/animation/animation-tree';
+import { Tree } from '../tree/generic/tree-schema';
+import { addDefaults } from '../tree/generic/tree-utils';
+import { MVSTree } from '../tree/mvs/mvs-tree';
+import { ColorT } from '../tree/mvs/param-types';
+
+export async function generateStateTransition(ctx: RuntimeContext, snapshot: Snapshot, snapshotIndex: number, snapshotCount: number) {
+    if (!snapshot.animation) return undefined;
+
+    const tree = addDefaults(snapshot.animation, MVSAnimationSchema);
+    const transitions = tree.children?.filter(child => child.kind === 'interpolate');
+    if (!transitions?.length) return undefined;
+
+    const duration = Math.max(
+        snapshot.animation.params?.duration_ms ?? 0,
+        ...transitions.map(t => (t.params.start_ms ?? 0) + t.params.duration_ms)
+    );
+
+    const frames: [tree: MVSTree, time: number][] = [];
+    const dt = tree.params?.frame_time_ms ?? (1000 / 60);
+    const N = Math.ceil(duration / dt);
+
+    const nodeMap = makeNodeMap(snapshot.root, new Map(), []);
+    const cache = new Map<any, InterpolationCacheEntry>();
+
+    const transitionGroups = groupTranstions(transitions);
+
+    let prevRoot: MVSTree | undefined;
+    for (let i = 0; i <= N; i++) {
+        const t = i * dt;
+        const root = createSnapshot(snapshot.root, transitionGroups, t, cache, nodeMap);
+
+        if (root === prevRoot || (prevRoot && deepEqual(root, prevRoot))) {
+            frames[frames.length - 1][1] += dt;
+        } else {
+            frames.push([root, dt]);
+        }
+
+        prevRoot = root;
+
+        if (ctx.shouldUpdate) {
+            await ctx.update({ message: `Generating transition for snapshot ${snapshotIndex + 1}/${snapshotCount}`, current: i + 1, max: N });
+        }
+    }
+
+    return { tree, frametimeMs: dt, frames };
+}
+
+const EasingFnMap: Record<MVSAnimationEasing, (t: number) => number> = {
+    'linear': t => t,
+    'bounce-in': EasingFns.bounceIn,
+    'bounce-out': EasingFns.bounceOut,
+    'bounce-in-out': EasingFns.bounceInOut,
+    'circle-in': EasingFns.circleIn,
+    'circle-out': EasingFns.circleOut,
+    'circle-in-out': EasingFns.circleInOut,
+    'cubic-in': EasingFns.cubicIn,
+    'cubic-out': EasingFns.cubicOut,
+    'cubic-in-out': EasingFns.cubicInOut,
+    'exp-in': EasingFns.expIn,
+    'exp-out': EasingFns.expOut,
+    'exp-in-out': EasingFns.expInOut,
+    'quad-in': EasingFns.quadIn,
+    'quad-out': EasingFns.quadOut,
+    'quad-in-out': EasingFns.quadInOut,
+    'sin-in': EasingFns.sinIn,
+    'sin-out': EasingFns.sinOut,
+    'sin-in-out': EasingFns.sinInOut,
+};
+
+interface InterpolationCacheEntry {
+    paletteFn?: (value: number) => Color,
+    rotation?: { axis: Vec3, angle: number, start: Quat, end: Quat },
+}
+
+function getTransitionKey(transition: MVSAnimationNode<'interpolate'>) {
+    const prop = transition.params.property;
+    if (Array.isArray(prop)) {
+        return `${transition.params.target_ref}:${prop.join('.')}`;
+    }
+    return `${transition.params.target_ref}:${prop}`;
+}
+
+function groupTranstions(transitions: MVSAnimationNode<'interpolate'>[]) {
+    const map = new Map<string, MVSAnimationNode<'interpolate'>[]>();
+    const groups: MVSAnimationNode<'interpolate'>[][] = [];
+    for (const t of transitions) {
+        const key = getTransitionKey(t);
+        if (!map.has(key)) {
+            const group: MVSAnimationNode<'interpolate'>[] = [];
+            map.set(key, group);
+            groups.push(group);
+        }
+        map.get(key)!.push(t);
+    }
+    for (const group of groups) {
+        group.sort((a, b) => {
+            const s = (a.params.start_ms ?? 0) - (b.params.start_ms ?? 0);
+            if (s !== 0) return s;
+            return a.params.duration_ms - b.params.duration_ms;
+        });
+    }
+    return groups;
+}
+
+function createSnapshot(tree: MVSTree, transitionGroups: MVSAnimationNode<'interpolate'>[][], time: number, cache: Map<any, InterpolationCacheEntry>, nodeMap: Map<string, (string | number)[]>) {
+    let modified = false;
+    const ret = produce(tree, (draft) => {
+        for (const transitionGroup of transitionGroups) {
+
+            const pivot = transitionGroup[0];
+            const nodePath = nodeMap.get(pivot.params.target_ref);
+            if (!nodePath) continue;
+
+            const node = select(draft, nodePath, 0);
+            const target = pivot.params.property[0] === 'custom' ? node?.custom : node?.params;
+            if (!target) continue;
+
+
+            const offset = pivot.params.property[0] === 'custom' ? 1 : 0;
+
+            let transition: MVSAnimationNode<'interpolate'> = pivot;
+            let previous: MVSAnimationNode<'interpolate'> | undefined;
+
+            for (let i = transitionGroup.length - 1; i > 0; i--) {
+                const current = transitionGroup[i];
+                const currentStart = current.params.start_ms ?? 0;
+                if (time >= currentStart) {
+                    transition = current;
+                    previous = i > 0 ? transitionGroup[i - 1] : undefined;
+                    break;
+                }
+            }
+
+            if (!cache.has(transition)) {
+                cache.set(transition, {});
+            }
+
+            const cacheEntry: InterpolationCacheEntry = cache.get(transition)!;
+
+            const startTime: number = transition.params.start_ms ?? 0;
+            const durationMs: number = transition.params.duration_ms ?? 0;
+            const t = (time - startTime) / durationMs;
+
+            let next: any;
+            if (transition.params.kind === 'transform_matrix') {
+                next = processTransformMatrix(transition, target, clamp(t, 0, 1), cacheEntry, offset, previous);
+            } else {
+                next = processScalarLike(transition, target, t, cacheEntry, offset, previous);
+            }
+
+            if (next === undefined) {
+                continue;
+            }
+
+            modified = true;
+            assign(target, transition.params.property, next, offset);
+        }
+    });
+    return modified ? ret : tree;
+}
+
+function applyFrequency(t: number, frequency: number, alternate: boolean) {
+    let v = (t * (frequency || 1));
+    if (v < 1) return v;
+
+    if (!alternate) {
+        v = (v % 1);
+        if (v === 0) return 1;
+        return v;
+    }
+
+    if (Math.abs(v - 1) < EPSILON) return 1;
+    v = v % 2;
+    if (v > 1) return 2 - v;
+    return v;
+}
+
+function getPreviousScalarEnd(previous: MVSAnimationNode<'interpolate'> | undefined) {
+    if (!previous || previous.params.kind === 'transform_matrix') return undefined;
+    return previous.params.end;
+}
+
+function processScalarLike(transition: MVSAnimationNode<'interpolate'>, target: any, time: number, cacheEntry: InterpolationCacheEntry, offset: number, previous: MVSAnimationNode<'interpolate'> | undefined) {
+    if (transition.params.kind === 'transform_matrix') return;
+    if (previous && previous.params.kind === 'transform_matrix') return;
+
+    const startBase = transition.params.start ?? getPreviousScalarEnd(previous) ?? select(target, transition.params.property, offset);
+    if (transition.params.kind === 'color' && !cacheEntry.paletteFn) {
+        cacheEntry.paletteFn = makePaletteFunction(transition, startBase, transition.params.end as ColorT | undefined);
+    }
+
+    const paletteFn = cacheEntry.paletteFn!;
+
+    const startValue: any = transition.params.kind === 'color'
+        ? Color.toHexStyle(paletteFn(0))
+        : startBase;
+    const endValue: any = transition.params.kind === 'color'
+        ? Color.toHexStyle(paletteFn(1))
+        : transition.params.end;
+
+    if (time <= 0) return startValue;
+    else if (time >= 1 - EPSILON && !transition.params.alternate_direction) return endValue;
+
+    let t = clamp(time, 0, 1);
+    t = applyFrequency(t, transition.params.frequency ?? 1, !!transition.params.alternate_direction);
+
+    const easing = EasingFnMap[transition.params.easing ?? 'linear'] ?? EasingFnMap['linear'];
+    t = easing(t);
+
+    if (transition.params.kind === 'scalar') {
+        return interpolateScalars(startValue, endValue, t, transition.params.noise_magnitude ?? 0, !!transition.params.discrete);
+    } else if (transition.params.kind === 'vec3') {
+        return interpolateVectors(startValue, endValue, t, transition.params.noise_magnitude ?? 0, !!transition.params.spherical);
+    } else if (transition.params.kind === 'rotation_matrix') {
+        return interpolateRotation(startValue, endValue, t, transition.params.noise_magnitude ?? 0, cacheEntry);
+    } else if (transition.params.kind === 'color') {
+        const color = paletteFn(t);
+        return Color.toHexStyle(color);
+    }
+}
+
+function getPreviousMatrixEnd(previous: MVSAnimationNode<'interpolate'> | undefined, prop: 'rotation_start' | 'translation_start' | 'scale_start') {
+    if (!previous || previous.params.kind !== 'transform_matrix') return undefined;
+    return previous.params[prop];
+}
+
+const TransformState = {
+    pivotTranslation: Mat4(),
+    pivotTranslationInv: Mat4(),
+    rotation: Mat4(),
+    scale: Mat4(),
+    translation: Mat4(),
+    pivotNeg: Vec3(),
+    temp: Mat4(),
+};
+function processTransformMatrix(transition: MVSAnimationNode<'interpolate'>, target: any, time: number, cache: InterpolationCacheEntry, offset: number, previous: MVSAnimationNode<'interpolate'> | undefined) {
+    if (transition.params.kind !== 'transform_matrix') return;
+    if (previous && previous.params.kind !== 'transform_matrix') return;
+
+    const transform = select(target, transition.params.property, offset) ?? Mat4.identity();
+
+    const startRotation = transition.params.rotation_start ?? getPreviousMatrixEnd(previous, 'rotation_start') ?? Mat3.fromMat4(Mat3(), transform);
+    const startTranslation = transition.params.translation_start ?? getPreviousMatrixEnd(previous, 'translation_start') ?? Mat4.getTranslation(Vec3(), transform);
+    const startScale = transition.params.scale_start ?? getPreviousMatrixEnd(previous, 'scale_start') ?? Mat4.getScaling(Vec3(), transform);
+
+    const endRotation = transition.params.rotation_end;
+    const endTranslation = transition.params.translation_end;
+    const endScale = transition.params.scale_end;
+
+    let rotation, translation, scale;
+
+    if (time <= 0) {
+        rotation = startRotation as Mat3;
+        translation = startTranslation as Vec3;
+        scale = startScale as Vec3;
+    } else {
+        const clampedTime = clamp(time, 0, 1);
+
+        let t = applyFrequency(clampedTime, transition.params.rotation_frequency ?? 1, !!transition.params.rotation_alternate_direction);
+        let easing = EasingFnMap[transition.params.rotation_easing ?? 'linear'] ?? EasingFnMap['linear'];
+        rotation = interpolateRotation(startRotation as Mat3, endRotation as Mat3, easing(t), transition.params.rotation_noise_magnitude ?? 0, cache);
+
+        t = applyFrequency(clampedTime, transition.params.translation_frequency ?? 1, !!transition.params.translation_alternate_direction);
+        easing = EasingFnMap[transition.params.translation_easing ?? 'linear'] ?? EasingFnMap['linear'];
+        translation = interpolateVec3(startTranslation as Vec3, endTranslation as Vec3 | undefined, easing(t), transition.params.translation_noise_magnitude ?? 0, false);
+
+        t = applyFrequency(clampedTime, transition.params.scale_frequency ?? 1, !!transition.params.scale_alternate_direction);
+        easing = EasingFnMap[transition.params.scale_easing ?? 'linear'] ?? EasingFnMap['linear'];
+        scale = interpolateVec3(startScale as Vec3, endScale as Vec3 | undefined, easing(t), transition.params.scale_noise_magnitude ?? 0, false);
+    }
+
+    const pivot = transition.params.pivot ?? Vec3.zero();
+
+    Mat4.fromTranslation(TransformState.translation, translation);
+    Mat4.fromScaling(TransformState.scale, scale);
+    Mat4.setIdentity(TransformState.rotation);
+    Mat4.fromMat3(TransformState.rotation, rotation);
+    Mat4.fromTranslation(TransformState.pivotTranslation, pivot as Vec3);
+    Mat4.fromTranslation(TransformState.pivotTranslationInv, Vec3.negate(TransformState.pivotNeg, pivot as Vec3));
+
+    // translation . pivot . rotation . scale . pivotInv
+    const result = Mat4();
+    Mat4.mul(result, TransformState.scale, TransformState.pivotTranslationInv);
+    Mat4.mul(result, TransformState.rotation, result);
+    Mat4.mul(result, TransformState.translation, result);
+
+    return result;
+}
+
+function interpolateScalars(start: number | number[], end: number | number[] | undefined, t: number, noise: number, discrete: boolean) {
+    if (Array.isArray(start)) {
+        const ret = Array.from<number>({ length: start.length }).fill(0.1);
+        if (!end || !Array.isArray(end)) {
+            for (let i = 0; i < start.length; i++) {
+                ret[i] = interpolateScalar(start[i], end, t, noise, discrete);
+            }
+            return ret;
+        }
+
+        for (let i = 0; i < start.length; i++) {
+            ret[i] = interpolateScalar(start[i], end[i], t, noise, discrete);
+        }
+        return ret;
+    }
+
+    if (Array.isArray(end)) {
+        const ret = Array.from<number>({ length: end.length }).fill(0.1);
+        for (let i = 0; i < end.length; i++) {
+            ret[i] = interpolateScalar(start, end[i], t, noise, discrete);
+        }
+        return ret;
+    }
+
+    return interpolateScalar(start, end, t, noise, discrete);
+}
+
+function interpolateScalar(start: number, end: number | undefined, t: number, noise: number, discrete: boolean) {
+    let v = typeof end === 'number' ? lerp(start, end, t) : start;
+    if (noise) {
+        v += (Math.random() - 0.5) * noise;
+    }
+    if (discrete) {
+        v = Math.round(v);
+    }
+    return v;
+}
+
+const InterpolateVectorsState = {
+    start: Vec3(),
+    end: Vec3(),
+    v: Vec3(),
+};
+function interpolateVectors(start: number[], end: number[] | undefined, t: number, noise: number, isSpherical: boolean) {
+    if ((!end || start === end) && !noise) return start;
+
+    const ret: number[] = Array.from<number>({ length: start.length }).fill(0.1);
+
+    for (let i = 0; i < start.length; i += 3) {
+        const s = Vec3.fromArray(InterpolateVectorsState.start, start, i);
+
+        let v: Vec3;
+        if (end) {
+            const e = Vec3.fromArray(InterpolateVectorsState.end, end, i);
+            v = isSpherical
+                ? Vec3.slerp(InterpolateVectorsState.v, s, e, t)
+                : Vec3.lerp(InterpolateVectorsState.v, s, e, t);
+        } else {
+            v = Vec3.clone(s);
+        }
+
+        if (noise && t <= 1 - EPSILON) {
+            Vec3.random(Vec3Noise, noise);
+            Vec3.add(v, v, Vec3Noise);
+        }
+
+        Vec3.toArray(v, ret, i);
+    }
+
+    return ret;
+}
+
+const Vec3Noise = Vec3();
+function interpolateVec3(start: Vec3, end: Vec3 | undefined, t: number, noise: number, isSpherical: boolean) {
+    if ((!end || start === end) && !noise) return start;
+
+    let v: Vec3;
+
+    if (end) {
+        v = isSpherical
+            ? Vec3.slerp(Vec3(), start, end, t)
+            : Vec3.lerp(Vec3(), start, end, t);
+    } else {
+        v = Vec3.clone(start);
+    }
+
+    if (noise && t <= 1 - EPSILON) {
+        Vec3.random(Vec3Noise, noise);
+        Vec3.add(v, v, Vec3Noise);
+    }
+    return v;
+}
+
+const RotationState = {
+    start: Quat(),
+    end: Quat(),
+    v: Quat(),
+    noise: Quat(),
+    axis: Vec3(),
+    temp: Mat4(),
+};
+function interpolateRotation(start: Mat3, end: Mat3 | undefined, t: number, noise: number, cache: InterpolationCacheEntry) {
+    if ((!end || start === end) && !noise) return start;
+
+    if (end) {
+        if (!cache.rotation) {
+            cache.rotation = {
+                ...relativeAxisAngle(start, end),
+                start: Quat.fromMat3(Quat(), start),
+                end: Quat.fromMat3(Quat(), end),
+            };
+        }
+
+        const { axis, angle, start: startQ, end: endQ } = cache.rotation;
+
+        if (angle < 1e-6) {
+            // start ≈ end: make a clean spin about the detected (or default) axis
+            Quat.setAxisAngle(RotationState.v, axis, t * 2 * Math.PI); // Make a full turn
+        } else {
+            // Normal case: stick with your existing slerp between start/end
+            Quat.slerp(RotationState.v, startQ, endQ, t);
+        }
+    } else {
+        Quat.fromMat3(RotationState.v, start);
+    }
+
+    if (noise && t <= 1 - EPSILON) {
+        Vec3.random(RotationState.axis, 1);
+        Quat.setAxisAngle(RotationState.noise, RotationState.axis, 2 * Math.PI * noise * (Math.random() - 0.5));
+        Quat.multiply(RotationState.v, RotationState.noise, RotationState.v);
+    }
+    Mat4.fromQuat(RotationState.temp, RotationState.v);
+    return Mat3.fromMat4(Mat3(), RotationState.temp);
+}
+
+function select(params: any, path: string | (string | number)[], offset: number) {
+    if (typeof path === 'string') {
+        return params?.[path];
+    }
+
+    let f = params;
+    for (let i = offset; i < path.length; i++) {
+        if (!f) break;
+        f = f[path[i]];
+    }
+
+    return f;
+}
+
+function assign(params: any, path: string | (string | number)[], value: any, offset: number) {
+    if (!params) return;
+
+    if (typeof path === 'string') {
+        params[path] = value;
+        return;
+    }
+
+    let f = params;
+    for (let i = offset; i < path.length; i++) {
+        if (!f) break;
+        if (i === path.length - 1) {
+            f[path[i]] = value;
+        } else {
+            f = f[path[i]];
+        }
+    }
+}
+
+function makeNodeMap(tree: Tree, map: Map<string, (string | number)[]>, currentPath: (string | number)[]) {
+    if (tree.ref) {
+        map.set(tree.ref, [...currentPath]);
+    }
+
+    if (!tree.children) return map;
+
+    currentPath.push('children');
+    for (let i = 0; i < tree.children.length; i++) {
+        const child = tree.children[i];
+        currentPath.push(i);
+        makeNodeMap(child, map, currentPath);
+        currentPath.pop();
+    }
+    currentPath.pop();
+
+    return map;
+}
+
+function makePaletteFunction(props: MVSAnimationNode<'interpolate'>, start: ColorT | undefined | null, end: ColorT | undefined | null): ((value: number) => Color) | undefined {
+    if (props.params.kind !== 'color') return undefined;
+
+    const params = props.params.palette
+        ? palettePropsFromMVSPalette(props.params.palette)
+        : palettePropsFromMVSPalette({ kind: 'continuous', colors: [start ?? 'black', end ?? start ?? 'black'] });
+    if (params.name === 'discrete') return makePaletteFunctionDiscrete(params.params);
+    if (params.name === 'continuous') return makePaletteFunctionContinuous(params.params);
+    throw new Error(`NotImplementedError: makePaletteFunction for ${(props as any).name}`);
+}
+
+
+function makePaletteFunctionDiscrete(props: MVSDiscretePaletteProps): (value: number) => Color {
+    const defaultColor = Color(0x0);
+    if (props.colors.length === 0) return () => defaultColor;
+
+    return (value: number) => {
+        const x = clamp(value, 0, 1);
+        for (let i = props.colors.length - 1; i >= 0; i--) {
+            const { color, fromValue, toValue } = props.colors[i];
+            if (fromValue <= x && x <= toValue) return color;
+        }
+        return defaultColor;
+    };
+}
+
+function makePaletteFunctionContinuous(props: MVSContinuousPaletteProps): (value: number) => Color {
+    const defaultColor = Color(0x0);
+    const { colors, checkpoints } = makeContinuousPaletteCheckpoints(props);
+    if (colors.length === 0) return () => defaultColor;
+
+    const underflowColor = props.setUnderflowColor ? props.underflowColor : defaultColor;
+    const overflowColor = props.setOverflowColor ? props.overflowColor : defaultColor;
+
+    return (value: number) => {
+        const x = clamp(value, 0, 1);
+        const gteIdx = SortedArray.findPredecessorIndex(checkpoints, x); // Index of the first greater or equal checkpoint
+        if (gteIdx === 0) {
+            if (x === checkpoints[0]) return colors[0];
+            else return underflowColor;
+        }
+        if (gteIdx === checkpoints.length) {
+            return overflowColor;
+        }
+        const q = (x - checkpoints[gteIdx - 1]) / (checkpoints[gteIdx] - checkpoints[gteIdx - 1]);
+        return Color.interpolate(colors[gteIdx - 1], colors[gteIdx], q);
+    };
+}
+
+const RelativeAxisAngleState = {
+    Rt: Mat3(),
+    R: Mat3(),
+};
+function relativeAxisAngle(start: Mat3, end: Mat3): { axis: Vec3, angle: number } {
+    // R_rel = end * start^T
+    const R0 = start, R1 = end;
+    const Rt = Mat3.transpose(RelativeAxisAngleState.Rt, R0);
+    const R = Mat3.mul(RelativeAxisAngleState.R, R1, Rt);
+
+    const tr = R[0] + R[4] + R[8]; // trace
+    let angle = Math.acos(clamp((tr - 1) * 0.5, -1, 1)); // in [0, π]
+    const axis = Vec3();
+
+    const eps = 1e-6;
+    const sinA = Math.sin(angle);
+
+    if (angle < eps) {
+        // Near identity: axis undefined; return any unit axis (choose something stable)
+        Vec3.set(axis, 0, 0, 1);
+        angle = 0.0;
+        return { axis, angle };
+    }
+
+    if (Math.PI - angle > 1e-4) {
+        // General case
+        axis[0] = (R[5] - R[7]) / (2 * sinA); // (r32 - r23)
+        axis[1] = (R[6] - R[2]) / (2 * sinA); // (r13 - r31)
+        axis[2] = (R[1] - R[3]) / (2 * sinA); // (r21 - r12)
+        Vec3.normalize(axis, axis);
+        return { axis, angle };
+    }
+
+    // angle ~ π: use diagonal-based extraction for stability
+    // Compute squared components then pick the largest to avoid precision loss
+    const xx = Math.max(0, (R[0] + 1) * 0.5);
+    const yy = Math.max(0, (R[4] + 1) * 0.5);
+    const zz = Math.max(0, (R[8] + 1) * 0.5);
+
+    let x = Math.sqrt(xx), y = Math.sqrt(yy), z = Math.sqrt(zz);
+
+    if (x >= y && x >= z) {
+        x = Math.max(x, 1e-8);
+        y = (R[1] + R[3]) / (4 * x);
+        z = (R[2] + R[6]) / (4 * x);
+        Vec3.set(axis, x, y, z);
+    } else if (y >= x && y >= z) {
+        y = Math.max(y, 1e-8);
+        x = (R[1] + R[3]) / (4 * y);
+        z = (R[5] + R[7]) / (4 * y);
+        Vec3.set(axis, x, y, z);
+    } else {
+        z = Math.max(z, 1e-8);
+        x = (R[2] + R[6]) / (4 * z);
+        y = (R[5] + R[7]) / (4 * z);
+        Vec3.set(axis, x, y, z);
+    }
+
+    Vec3.normalize(axis, axis);
+    return { axis, angle: Math.PI };
+}

src/extensions/mvs/helpers/utils.ts

@@ -100,7 +100,10 @@ export type ElementOfSet<S> = S extends Set<infer T> ? T : never
 
 /** Convert `colorString` (either X11 color name like 'magenta' or hex code like '#ff00ff') to Color.
  * Return `undefined` if `colorString` cannot be converted. */
-export function decodeColor(colorString: string | undefined | null): Color | undefined {
+export function decodeColor(colorString: string | number | undefined | null): Color | undefined {
+    if (typeof colorString === 'number') {
+        return Color(colorString);
+    }
     return _decodeColor(colorString);
 }
 
@@ -149,4 +152,25 @@ export function collectMVSReferences<T extends StateObject.Ctor>(type: T[], depe
     }
 
     return ret;
+}
+
+export function getMVSReferenceObject<T extends StateObject.Ctor>(type: T[], dependencies: Record<string, StateObject> | undefined, ref: string): StateObject | undefined {
+    if (!dependencies) return undefined;
+
+    for (const key of Object.keys(dependencies)) {
+        const o = dependencies[key];
+        let okType = false;
+        for (const t of type) {
+            if (t.is(o)) {
+                okType = true;
+                break;
+            }
+        }
+        if (!okType || !o.tags) continue;
+        for (const tag of o.tags) {
+            if (tag.startsWith('mvs-ref:')) {
+                if (tag.substring(8) === ref) return o;
+            }
+        }
+    }
 }

src/extensions/mvs/load-generic.ts

@@ -46,7 +46,7 @@ export function loadTreeVirtual<TTree extends Tree, TContext>(
 ) {
     const updateRoot: UpdateTarget = UpdateTarget.create(plugin, options?.replaceExisting ?? false);
     loadTreeInUpdate(updateRoot, tree, loadingActions, context, options);
-    const stateTree: StateTree = updateRoot.update.getTree();
+    const stateTree: StateTree = updateRoot.update.getTree({ useHashVersion: true });
     const stateSnapshot: State.Snapshot = { tree: StateTree.toJSON(stateTree) };
     const pluginStateSnapshot: PluginState.Snapshot = { id: UUID.create22(), data: stateSnapshot };
     return pluginStateSnapshot;

src/extensions/mvs/load-helpers.ts

@@ -62,6 +62,19 @@ export function transformFromRotationTranslation(rotation: number[] | null | und
     return T;
 }
 
+export function decomposeRotationMatrix(rotation: number[] | null | undefined) {
+    if (rotation && rotation.length !== 9) throw new Error(`'rotation' param for 'transform' node must be array of 9 elements, found ${rotation}`);
+    if (rotation) {
+        const rotMatrix = Mat3.fromArray(Mat3(), rotation, 0);
+        ensureRotationMatrix(rotMatrix, rotMatrix);
+        const quat = Quat.fromMat3(Quat(), rotMatrix);
+        const axis = Vec3();
+        const angle = Quat.getAxisAngle(axis, quat) * 180 / Math.PI;
+        return { axis, angle };
+    }
+    return { axis: Vec3.create(1, 0, 0), angle: 0 };
+}
+
 /** Adjust values in a close-to-rotation matrix `a` to ensure it is a proper rotation matrix
  * (i.e. its columns and rows are orthonormal and determinant equal to 1, within available precission). */
 function ensureRotationMatrix(out: Mat3, a: Mat3) {
@@ -111,11 +124,32 @@ function transformProps(node: MolstarSubtree, kind: 'transform' | 'instance') {
     for (const transform of transforms) {
         let matrix: Mat4 | undefined = transform.params.matrix as Mat4 | undefined;
         if (!matrix) {
-            const { rotation, translation } = transform.params;
+            const { rotation, translation, rotation_center } = transform.params;
+            if (rotation_center) {
+                const axisAngle = decomposeRotationMatrix(rotation);
+                result.push({
+                    params: {
+                        transform: {
+                            name: 'components',
+                            params: {
+                                translation: translation ? Vec3.fromArray(Vec3(), translation, 0) : Vec3.create(0, 0, 0),
+                                angle: axisAngle.angle,
+                                axis: axisAngle.axis,
+                                rotationCenter: rotation_center === 'centroid'
+                                    ? { name: 'centroid', params: {} }
+                                    : { name: 'point', params: { point: Vec3.fromArray(Vec3(), rotation_center, 0) } }
+                            }
+                        }
+                    },
+                    ref: transform.ref
+                });
+                continue;
+            }
             matrix = transformFromRotationTranslation(rotation, translation);
         }
         result.push({ params: { transform: { name: 'matrix', params: { data: matrix, transpose: false } } }, ref: transform.ref });
     }
+
     return result;
 }
 
@@ -335,10 +369,20 @@ function representationPropsBase(node: MolstarSubtree<'representation'>): Partia
                 type: { name: 'cartoon', params: { alpha, tubularHelices: params.tubular_helices } },
                 sizeTheme: { name: 'uniform', params: { value: params.size_factor } },
             };
+        case 'backbone':
+            return {
+                type: { name: 'backbone', params: { alpha } },
+                sizeTheme: { name: 'uniform', params: { value: params.size_factor } },
+            };
         case 'ball_and_stick':
             return {
                 type: { name: 'ball-and-stick', params: { sizeFactor: (params.size_factor ?? 1) * 0.5, sizeAspectRatio: 0.5, alpha, ignoreHydrogens: params.ignore_hydrogens } },
             };
+        case 'line':
+            return {
+                type: { name: 'line', params: { alpha, ignoreHydrogens: params.ignore_hydrogens } },
+                sizeTheme: { name: 'uniform', params: { value: params.size_factor } },
+            };
         case 'spacefill':
             return {
                 type: { name: 'spacefill', params: { alpha, ignoreHydrogens: params.ignore_hydrogens } },
@@ -348,11 +392,15 @@ function representationPropsBase(node: MolstarSubtree<'representation'>): Partia
             return {
                 type: { name: 'carbohydrate', params: { alpha, sizeFactor: params.size_factor ?? 1 } },
             };
-        case 'surface':
+        case 'surface': {
             return {
-                type: { name: 'molecular-surface', params: { alpha, ignoreHydrogens: params.ignore_hydrogens } },
+                type: {
+                    name: params.surface_type === 'gaussian' ? 'gaussian-surface' : 'molecular-surface',
+                    params: { alpha, ignoreHydrogens: params.ignore_hydrogens }
+                },
                 sizeTheme: { name: 'physical', params: { scale: params.size_factor } },
             };
+        }
         default:
             throw new Error('NotImplementedError');
     }
@@ -364,8 +412,8 @@ export function representationProps(node: MolstarSubtree<'representation'>): Par
     if (clip) {
         base.type!.params = { ...base.type?.params, clip };
     }
-    if (node.custom?.molstar_reprepresentation_params) {
-        base.type!.params = { ...base.type!.params, ...node.custom.molstar_reprepresentation_params };
+    if (node.custom?.molstar_representation_params) {
+        base.type!.params = { ...base.type!.params, ...node.custom.molstar_representation_params };
     }
     return base;
 }
@@ -509,7 +557,7 @@ function appliesColorToWholeRepr(node: MolstarNode<'color' | 'color_from_uri' |
 
 const FALLBACK_COLOR = decodeColor(DefaultColor)!;
 
-function palettePropsFromMVSPalette(palette: MolstarNode<'color_from_uri' | 'color_from_source'>['params']['palette']): MVSAnnotationColorThemeProps['palette'] {
+export function palettePropsFromMVSPalette(palette: MolstarNode<'color_from_uri' | 'color_from_source'>['params']['palette']): MVSAnnotationColorThemeProps['palette'] {
     if (!palette) {
         return { name: 'direct', params: {} };
     }

src/extensions/mvs/load.ts

@@ -8,15 +8,17 @@
 
 import { PluginStateSnapshotManager } from '../../mol-plugin-state/manager/snapshots';
 import { PluginStateObject } from '../../mol-plugin-state/objects';
-import { Download, ParseCcp4, ParseCif } from '../../mol-plugin-state/transforms/data';
-import { CustomModelProperties, CustomStructureProperties, ModelFromTrajectory, StructureComponent, StructureFromModel, TrajectoryFromMmCif, TrajectoryFromPDB } from '../../mol-plugin-state/transforms/model';
+import { Download, ParseCif, ParseCcp4 } from '../../mol-plugin-state/transforms/data';
+import { CoordinatesFromLammpstraj, CoordinatesFromXtc, CustomModelProperties, CustomStructureProperties, ModelFromTrajectory, StructureComponent, StructureFromModel, TrajectoryFromGRO, TrajectoryFromLammpsTrajData, TrajectoryFromMmCif, TrajectoryFromMOL, TrajectoryFromMOL2, TrajectoryFromPDB, TrajectoryFromSDF, TrajectoryFromXYZ } from '../../mol-plugin-state/transforms/model';
 import { StructureRepresentation3D, VolumeRepresentation3D } from '../../mol-plugin-state/transforms/representation';
 import { VolumeFromCcp4, VolumeFromDensityServerCif } from '../../mol-plugin-state/transforms/volume';
 import { PluginCommands } from '../../mol-plugin/commands';
 import { PluginContext } from '../../mol-plugin/context';
-import { StateObjectSelector } from '../../mol-state';
+import { PluginState } from '../../mol-plugin/state';
+import { StateObjectSelector, StateTree } from '../../mol-state';
+import { RuntimeContext, Task } from '../../mol-task';
 import { MolViewSpec } from './behavior';
-import { createPluginStateSnapshotCamera, modifyCanvasProps } from './camera';
+import { createPluginStateSnapshotCamera, modifyCanvasProps, resetCanvasProps } from './camera';
 import { MVSAnnotationsProvider } from './components/annotation-prop';
 import { MVSAnnotationStructureComponent } from './components/annotation-structure-component';
 import { MVSAnnotationTooltipsProvider } from './components/annotation-tooltips-prop';
@@ -24,15 +26,18 @@ import { CustomLabelProps, CustomLabelRepresentationProvider } from './component
 import { CustomTooltipsProvider } from './components/custom-tooltips-prop';
 import { IsMVSModelProps, IsMVSModelProvider } from './components/is-mvs-model-prop';
 import { getPrimitiveStructureRefs, MVSBuildPrimitiveShape, MVSDownloadPrimitiveData, MVSInlinePrimitiveData, MVSShapeRepresentation3D } from './components/primitives';
+import { MVSTrajectoryWithCoordinates } from './components/trajectory';
+import { generateStateTransition } from './helpers/animation';
 import { IsHiddenCustomStateExtension } from './load-extensions/is-hidden-custom-state';
 import { NonCovalentInteractionsExtension } from './load-extensions/non-covalent-interactions';
 import { LoadingActions, LoadingExtension, loadTreeVirtual, UpdateTarget } from './load-generic';
 import { AnnotationFromSourceKind, AnnotationFromUriKind, collectAnnotationReferences, collectAnnotationTooltips, collectInlineLabels, collectInlineTooltips, colorThemeForNode, componentFromXProps, componentPropsFromSelector, isPhantomComponent, labelFromXProps, makeNearestReprMap, prettyNameFromSelector, representationProps, structureProps, transformAndInstantiateStructure, transformAndInstantiateVolume, volumeColorThemeForNode, volumeRepresentationProps } from './load-helpers';
-import { MVSData, MVSData_States, SnapshotMetadata } from './mvs-data';
+import { MVSData, MVSData_States, Snapshot, SnapshotMetadata } from './mvs-data';
+import { MVSAnimationNode } from './tree/animation/animation-tree';
 import { validateTree } from './tree/generic/tree-schema';
 import { convertMvsToMolstar, mvsSanityCheck } from './tree/molstar/conversion';
 import { MolstarNode, MolstarNodeParams, MolstarSubtree, MolstarTree, MolstarTreeSchema } from './tree/molstar/molstar-tree';
-import { type MVSTree, MVSTreeSchema } from './tree/mvs/mvs-tree';
+import { MVSTreeSchema } from './tree/mvs/mvs-tree';
 
 
 export interface MVSLoadOptions {
@@ -49,12 +54,24 @@ export interface MVSLoadOptions {
     doNotReportErrors?: boolean
 }
 
+export function loadMVS(plugin: PluginContext, data: MVSData, options: MVSLoadOptions = {}) {
+    const task = Task.create('Load MVS', ctx => _loadMVS(ctx, plugin, data, options));
+    return plugin.runTask(task);
+}
+
 /** Load a MolViewSpec (MVS) state(s) into the Mol* plugin as plugin state snapshots. */
-export async function loadMVS(plugin: PluginContext, data: MVSData, options: MVSLoadOptions = {}) {
+async function _loadMVS(ctx: RuntimeContext, plugin: PluginContext, data: MVSData, options: MVSLoadOptions = {}) {
     plugin.errorContext.clear('mvs');
     try {
         const mvsExtensionLoaded = plugin.state.hasBehavior(MolViewSpec);
         if (!mvsExtensionLoaded) throw new Error('MolViewSpec extension is not loaded.');
+
+        // Stop any currently running audio
+        plugin.managers.markdownExtensions.audio.dispose();
+
+        // Reset canvas props to default so that modifyCanvasProps works as expected
+        resetCanvasProps(plugin);
+
         // console.log(`MVS tree:\n${MVSData.toPrettyString(data)}`)
         const multiData: MVSData_States = data.kind === 'multiple' ? data : MVSData.stateToStates(data);
         const entries: PluginStateSnapshotManager.Entry[] = [];
@@ -68,11 +85,16 @@ export async function loadMVS(plugin: PluginContext, data: MVSData, options: MVS
             const entry = molstarTreeToEntry(
                 plugin,
                 molstarTree,
-                snapshot.root,
+                snapshot.animation,
                 { ...snapshot.metadata, previousTransitionDurationMs: previousSnapshot.metadata.transition_duration_ms },
                 options
             );
+            await assignStateTransition(ctx, plugin, entry, snapshot, options, i, multiData.snapshots.length);
             entries.push(entry);
+
+            if (ctx.shouldUpdate) {
+                await ctx.update({ message: 'Loading MVS...', current: i, max: multiData.snapshots.length });
+            }
         }
         if (!options.appendSnapshots) {
             plugin.managers.snapshot.clear();
@@ -80,6 +102,7 @@ export async function loadMVS(plugin: PluginContext, data: MVSData, options: MVS
         for (const entry of entries) {
             plugin.managers.snapshot.add(entry);
         }
+
         if (entries.length > 0) {
             await PluginCommands.State.Snapshots.Apply(plugin, { id: entries[0].snapshot.id });
         }
@@ -101,24 +124,65 @@ export async function loadMVS(plugin: PluginContext, data: MVSData, options: MVS
     }
 }
 
+async function assignStateTransition(ctx: RuntimeContext, plugin: PluginContext, parentEntry: PluginStateSnapshotManager.Entry, parent: Snapshot, options: MVSLoadOptions, snapshotIndex: number, snapshotCount: number) {
+    const transitions = await generateStateTransition(ctx, parent, snapshotIndex, snapshotCount);
+    if (!transitions?.frames.length) return;
+
+    const animation: PluginState.StateTransition = {
+        autoplay: !!transitions.tree.params?.autoplay,
+        loop: !!transitions.tree.params?.loop,
+        frames: [],
+    };
+
+    for (let i = 0; i < transitions.frames.length; i++) {
+        const frame = transitions.frames[i];
+        const molstarTree = convertMvsToMolstar(frame[0], options.sourceUrl);
+        const entry = molstarTreeToEntry(
+            plugin,
+            molstarTree,
+            parent.animation,
+            { ...parent.metadata, previousTransitionDurationMs: transitions.frametimeMs },
+            options
+        );
+
+        StateTree.reuseTransformParams(entry.snapshot.data!.tree, parentEntry.snapshot.data!.tree);
+
+        animation.frames.push({
+            durationInMs: frame[1],
+            data: entry.snapshot.data!,
+            camera: transitions.tree.params?.include_camera ? entry.snapshot.camera : undefined,
+            canvas3d: transitions.tree.params?.include_canvas ? entry.snapshot.canvas3d : undefined,
+        });
+
+        if (ctx.shouldUpdate) {
+            await ctx.update({ message: `Loading animation for snapshot ${snapshotIndex + 1}/${snapshotCount}...`, current: i + 1, max: transitions.frames.length });
+        }
+    }
+
+    parentEntry.snapshot.transition = animation;
+}
 
 function molstarTreeToEntry(
     plugin: PluginContext,
     tree: MolstarTree,
-    mvsTree: MVSTree,
+    animation: MVSAnimationNode<'animation'> | undefined,
     metadata: SnapshotMetadata & { previousTransitionDurationMs?: number },
     options: { keepCamera?: boolean, extensions?: MolstarLoadingExtension<any>[] }
 ) {
     const context = MolstarLoadingContext.create();
     const snapshot = loadTreeVirtual(plugin, tree, MolstarLoadingActions, context, { replaceExisting: true, extensions: options?.extensions ?? BuiltinLoadingExtensions });
     snapshot.canvas3d = {
-        props: plugin.canvas3d ? modifyCanvasProps(plugin.canvas3d.props, context.canvas, mvsTree.custom) : undefined,
+        props: plugin.canvas3d ? modifyCanvasProps(plugin.canvas3d.props, context.canvas, animation) : undefined,
     };
     if (!options?.keepCamera) {
         snapshot.camera = createPluginStateSnapshotCamera(plugin, context, metadata);
     }
     snapshot.durationInMs = metadata.linger_duration_ms + (metadata.previousTransitionDurationMs ?? 0);
 
+    if (tree.custom?.molstar_on_load_markdown_commands) {
+        snapshot.onLoadMarkdownCommands = tree.custom.molstar_on_load_markdown_commands;
+    }
+
     const entryParams: PluginStateSnapshotManager.EntryParams = {
         key: metadata.key,
         name: metadata.title,
@@ -165,31 +229,72 @@ const MolstarLoadingActions: LoadingActions<MolstarTree, MolstarLoadingContext>
     },
     parse(updateParent: UpdateTarget, node: MolstarNode<'parse'>): UpdateTarget | undefined {
         const format = node.params.format;
-        if (format === 'cif') {
-            return UpdateTarget.apply(updateParent, ParseCif, {});
-        } else if (format === 'pdb') {
-            return updateParent;
-        } else if (format === 'map') {
-            return UpdateTarget.apply(updateParent, ParseCcp4, {});
-        } else {
-            console.error(`Unknown format in "parse" node: "${format}"`);
-            return undefined;
+        switch (format) {
+            case 'cif':
+                return UpdateTarget.apply(updateParent, ParseCif, {});
+            case 'pdb':
+            case 'pdbqt':
+            case 'gro':
+            case 'xyz':
+            case 'mol':
+            case 'sdf':
+            case 'mol2':
+            case 'xtc':
+            case 'lammpstrj':
+                return updateParent;
+            case 'map':
+                return UpdateTarget.apply(updateParent, ParseCcp4, {});
+            default:
+                console.error(`Unknown format in "parse" node: "${format}"`);
+                return undefined;
+        }
+    },
+    coordinates(updateParent: UpdateTarget, node: MolstarNode<'coordinates'>): UpdateTarget | undefined {
+        const format = node.params.format;
+        switch (format) {
+            case 'xtc':
+                return UpdateTarget.apply(updateParent, CoordinatesFromXtc);
+            case 'lammpstrj':
+                return UpdateTarget.apply(updateParent, CoordinatesFromLammpstraj);
+            default:
+                console.error(`Unknown format in "coordinates" node: "${format}"`);
+                return undefined;
         }
     },
     trajectory(updateParent: UpdateTarget, node: MolstarNode<'trajectory'>): UpdateTarget | undefined {
         const format = node.params.format;
-        if (format === 'cif') {
-            return UpdateTarget.apply(updateParent, TrajectoryFromMmCif, {
-                blockHeader: node.params.block_header ?? '', // Must set to '' because just undefined would get overwritten by createDefaults
-                blockIndex: node.params.block_index ?? undefined,
-            });
-        } else if (format === 'pdb') {
-            return UpdateTarget.apply(updateParent, TrajectoryFromPDB, {});
-        } else {
-            console.error(`Unknown format in "trajectory" node: "${format}"`);
-            return undefined;
+        switch (format) {
+            case 'cif':
+                return UpdateTarget.apply(updateParent, TrajectoryFromMmCif, {
+                    blockHeader: node.params.block_header ?? '', // Must set to '' because just undefined would get overwritten by createDefaults
+                    blockIndex: node.params.block_index ?? undefined,
+                });
+            case 'pdb':
+            case 'pdbqt':
+                return UpdateTarget.apply(updateParent, TrajectoryFromPDB, { isPdbqt: format === 'pdbqt' });
+            case 'gro':
+                return UpdateTarget.apply(updateParent, TrajectoryFromGRO);
+            case 'xyz':
+                return UpdateTarget.apply(updateParent, TrajectoryFromXYZ);
+            case 'mol':
+                return UpdateTarget.apply(updateParent, TrajectoryFromMOL);
+            case 'sdf':
+                return UpdateTarget.apply(updateParent, TrajectoryFromSDF);
+            case 'mol2':
+                return UpdateTarget.apply(updateParent, TrajectoryFromMOL2);
+            case 'lammpstrj':
+                return UpdateTarget.apply(updateParent, TrajectoryFromLammpsTrajData);
+            default:
+                console.error(`Unknown format in "trajectory" node: "${format}"`);
+                return undefined;
         }
     },
+    trajectory_with_coordinates(updateParent: UpdateTarget, node: MolstarNode<'trajectory_with_coordinates'>): UpdateTarget | undefined {
+        const result = UpdateTarget.apply(updateParent, MVSTrajectoryWithCoordinates, {
+            coordinatesRef: node.params.coordinates_ref,
+        });
+        return UpdateTarget.setMvsDependencies(result, [node.params.coordinates_ref]);
+    },
     model(updateParent: UpdateTarget, node: MolstarSubtree<'model'>, context: MolstarLoadingContext): UpdateTarget {
         const annotations = collectAnnotationReferences(node, context);
         const model = UpdateTarget.apply(updateParent, ModelFromTrajectory, {
@@ -312,7 +417,7 @@ const MolstarLoadingActions: LoadingActions<MolstarTree, MolstarLoadingContext>
     },
     primitives(updateParent: UpdateTarget, tree: MolstarSubtree<'primitives'>, context: MolstarLoadingContext): UpdateTarget {
         const refs = getPrimitiveStructureRefs(tree);
-        const data = UpdateTarget.apply(updateParent, MVSInlinePrimitiveData, { node: tree });
+        const data = UpdateTarget.apply(updateParent, MVSInlinePrimitiveData, { node: tree as any });
         return applyPrimitiveVisuals(data, refs);
     },
     primitives_from_uri(updateParent: UpdateTarget, tree: MolstarNode<'primitives_from_uri'>, context: MolstarLoadingContext): UpdateTarget {

src/extensions/mvs/mvs-data.ts

@@ -1,11 +1,13 @@
 /**
- * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
+ * @author David Sehnal <david.sehnal@gmail.com>
  */
 
 import { treeValidationIssues } from './tree/generic/tree-schema';
 import { treeToString } from './tree/generic/tree-utils';
+import { MVSAnimationSchema, MVSAnimationTree } from './tree/animation/animation-tree';
 import { Root, createMVSBuilder } from './tree/mvs/mvs-builder';
 import { MVSTree, MVSTreeSchema } from './tree/mvs/mvs-tree';
 
@@ -53,6 +55,8 @@ export interface Snapshot {
     root: MVSTree,
     /** Associated metadata */
     metadata: SnapshotMetadata,
+    /** Optional animation */
+    animation?: MVSAnimationTree,
 }
 
 /** MVSData with a single state */
@@ -189,7 +193,14 @@ function majorVersion(semanticVersion: string | number): number | undefined {
 
 function snapshotValidationIssues(snapshot: MVSData_State | Snapshot, options: { noExtra?: boolean } = {}): string[] | undefined {
     if (snapshot.root === undefined) return [`"root" missing in snapshot`];
-    return treeValidationIssues(MVSTreeSchema, snapshot.root, options);
+    const state = treeValidationIssues(MVSTreeSchema, snapshot.root, options);
+    const animation = 'animation' in snapshot && snapshot.animation !== undefined
+        ? treeValidationIssues(MVSAnimationSchema, snapshot.animation, options)
+        : undefined;
+    if (state && animation) return [...state, ...animation];
+    if (state) return state;
+    if (animation) return animation;
+    return undefined;
 }
 
 /** Return the current universal time, in ISO format, e.g. '2023-11-24T10:45:49.873Z' */

src/extensions/mvs/tree/animation/animation-tree.ts

@@ -0,0 +1,143 @@
+/**
+ * Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { bool, float, int, list, OptionalField, RequiredField, str, union, nullable, literal, ValueFor } from '../generic/field-schema';
+import { SimpleParamsSchema, UnionParamsSchema } from '../generic/params-schema';
+import { NodeFor, ParamsOfKind, SubtreeOfKind, TreeFor, TreeSchema } from '../generic/tree-schema';
+import { ColorT, ContinuousPalette, DiscretePalette, Matrix, Vector3 } from '../mvs/param-types';
+
+const Easing = literal(
+    'linear',
+    'bounce-in', 'bounce-out', 'bounce-in-out',
+    'circle-in', 'circle-out', 'circle-in-out',
+    'cubic-in', 'cubic-out', 'cubic-in-out',
+    'exp-in', 'exp-out', 'exp-in-out',
+    'quad-in', 'quad-out', 'quad-in-out',
+    'sin-in', 'sin-out', 'sin-in-out',
+);
+
+export type MVSAnimationEasing = ValueFor<typeof Easing>;
+
+const _Noise = {
+    noise_magnitude: OptionalField(float, 0, 'Magnitude of the noise to apply to the interpolated value.')
+    // support cummulative noise?
+};
+
+const _Common = {
+    target_ref: RequiredField(str, 'Reference to the node.'),
+    property: RequiredField(union(str, list(union(str, int))), 'Value accessor.'),
+    start_ms: OptionalField(float, 0, 'Start time of the transition in milliseconds.'),
+    duration_ms: RequiredField(float, 'Duration of the transition in milliseconds.'),
+};
+
+const _Frequency = {
+    frequency: OptionalField(int, 1, 'Determines how many times the interpolation loops. Current T = frequency * t mod 1.'),
+    alternate_direction: OptionalField(bool, false, 'Whether to alternate the direction of the interpolation for frequency > 1.'),
+};
+
+const _Easing = {
+    easing: OptionalField(Easing, 'linear', 'Easing function to use for the transition.'),
+};
+
+const ScalarInterpolation = {
+    ..._Common,
+    ..._Frequency,
+    ..._Easing,
+    start: OptionalField(nullable(union(float, list(float))), null, 'Start value. If a list of values is provided, each element will be interpolated separately. If unset, parent state value is used.'),
+    end: OptionalField(nullable(union(float, list(float))), null, 'End value. If a list of values is provided, each element will be interpolated separately. If unset, only noise is applied.'),
+    discrete: OptionalField(bool, false, 'Whether to round the values to the closest integer. Useful for example for trajectory animation.'),
+    ..._Noise,
+};
+
+const Vec3Interpolation = {
+    ..._Common,
+    ..._Frequency,
+    ..._Easing,
+    start: OptionalField(nullable(list(float)), null, 'Start value. If unset, parent state value is used. Must be array of length 3N (x1, y1, z1, x2, y2, z2, ...).'),
+    end: OptionalField(nullable(list(float)), null, 'End value. Must be array of length 3N (x1, y1, z1, x2, y2, z2, ...). If unset, only noise is applied.'),
+    spherical: OptionalField(bool, false, 'Whether to use spherical interpolation.'),
+    ..._Noise,
+};
+
+const RotationMatrixInterpolation = {
+    ..._Common,
+    ..._Frequency,
+    ..._Easing,
+    start: OptionalField(nullable(Matrix), null, 'Start value. If unset, parent state value is used.'),
+    end: OptionalField(nullable(Matrix), null, 'End value. If unset, only noise is applied.'),
+    ..._Noise,
+};
+
+const ColorInterpolation = {
+    ..._Common,
+    ..._Frequency,
+    ..._Easing,
+    start: OptionalField(nullable(ColorT), null, 'Start value. If unset, parent state value is used.'),
+    end: OptionalField(nullable(ColorT), null, 'End value.'),
+    palette: OptionalField(nullable(union(DiscretePalette, ContinuousPalette)), null, 'Palette to sample colors from. Overrides start and end values.'),
+};
+
+const TransformationMatrixInterpolation = {
+    ..._Common,
+    pivot: OptionalField(nullable(Vector3), null, 'Pivot point for rotation and scale.'),
+    rotation_start: OptionalField(nullable(Matrix), null, 'Start rotation value. If unset, parent state value is used.'),
+    rotation_end: OptionalField(nullable(Matrix), null, 'End rotation value. If unset, only noise is applied.'),
+    rotation_noise_magnitude: OptionalField(float, 0, 'Magnitude of the noise to apply to the rotation.'),
+    rotation_easing: OptionalField(Easing, 'linear', 'Easing function to use for the rotation.'),
+    rotation_frequency: OptionalField(int, 1, 'Determines how many times the rotation interpolation loops. Current T = frequency * t mod 1.'),
+    rotation_alternate_direction: OptionalField(bool, false, 'Whether to alternate the direction of the interpolation for frequency > 1.'),
+    translation_start: OptionalField(nullable(Vector3), null, 'Start translation value. If unset, parent state value is used.'),
+    translation_end: OptionalField(nullable(Vector3), null, 'End translation value. If unset, only noise is applied.'),
+    translation_noise_magnitude: OptionalField(float, 0, 'Magnitude of the noise to apply to the translation.'),
+    translation_easing: OptionalField(Easing, 'linear', 'Easing function to use for the translation.'),
+    translation_frequency: OptionalField(int, 1, 'Determines how many times the translation interpolation loops. Current T = frequency * t mod 1.'),
+    translation_alternate_direction: OptionalField(bool, false, 'Whether to alternate the direction of the interpolation for frequency > 1.'),
+    scale_start: OptionalField(nullable(Vector3), null, 'Start scale value. If unset, parent state value is used.'),
+    scale_end: OptionalField(nullable(Vector3), null, 'End scale value. If unset, only noise is applied.'),
+    scale_noise_magnitude: OptionalField(float, 0, 'Magnitude of the noise to apply to the scale.'),
+    scale_easing: OptionalField(Easing, 'linear', 'Easing function to use for the scale.'),
+    scale_frequency: OptionalField(int, 1, 'Determines how many times the scale interpolation loops. Current T = frequency * t mod 1.'),
+    scale_alternate_direction: OptionalField(bool, false, 'Whether to alternate the direction of the interpolation for frequency > 1.'),
+};
+
+export const MVSAnimationSchema = TreeSchema({
+    rootKind: 'animation',
+    nodes: {
+        animation: {
+            description: 'Animation root node',
+            parent: [],
+            params: SimpleParamsSchema({
+                frame_time_ms: OptionalField(float, 1000 / 60, 'Frame time in milliseconds'),
+                duration_ms: OptionalField(nullable(float), null, 'Total duration of the animation. If not specified, computed as maximum of all transitions.'),
+                autoplay: OptionalField(bool, true, 'Determines whether the animation should autoplay when a snapshot is loaded'),
+                loop: OptionalField(bool, false, 'Determines whether the animation should loop when it reaches the end'),
+                include_camera: OptionalField(bool, false, 'Determines whether the camera state should be included in the animation'),
+                include_canvas: OptionalField(bool, false, 'Determines whether the canvas state should be included in the animation'),
+            }),
+        },
+        interpolate: {
+            description: 'This node enables interpolating between values',
+            parent: ['animation'],
+            params: UnionParamsSchema(
+                'kind',
+                'Interpolation kind',
+                {
+                    scalar: SimpleParamsSchema(ScalarInterpolation),
+                    vec3: SimpleParamsSchema(Vec3Interpolation),
+                    rotation_matrix: SimpleParamsSchema(RotationMatrixInterpolation),
+                    transform_matrix: SimpleParamsSchema(TransformationMatrixInterpolation),
+                    color: SimpleParamsSchema(ColorInterpolation),
+                },
+            )
+        }
+    }
+});
+
+export type MVSAnimationKind = keyof typeof MVSAnimationSchema.nodes
+export type MVSAnimationNode<TKind extends MVSAnimationKind = MVSAnimationKind> = NodeFor<typeof MVSAnimationSchema, TKind>
+export type MVSAnimationTree = TreeFor<typeof MVSAnimationSchema>
+export type MVSAnimationNodeParams<TKind extends MVSAnimationKind> = ParamsOfKind<MVSAnimationTree, TKind>
+export type MVSAnimationSubtree<TKind extends MVSAnimationKind = MVSAnimationKind> = SubtreeOfKind<MVSAnimationTree, TKind>

src/extensions/mvs/tree/generic/field-schema.ts

@@ -6,10 +6,8 @@
  */
 
 import * as iots from 'io-ts';
-import { PathReporter } from 'io-ts/PathReporter';
 import { onelinerJsonString } from '../../../../mol-util/json';
 
-
 /** All types that can be used in tree node params.
  * Can be extended, this is just to list them all in one place and possibly catch some typing errors */
 type AllowedValueTypes = string | number | boolean | null | [number, number, number] | string[] | number[] | {};
@@ -142,6 +140,41 @@ export function fieldValidationIssues<F extends Field>(field: F, value: any): st
     if (validation._tag === 'Right') {
         return undefined;
     } else {
-        return PathReporter.report(validation);
+        return reportErrors(validation.left);
     }
 }
+
+// Inlining `reportErrors` instead of `import { PathReporter } from 'io-ts/PathReporter'`;
+// because it breaks Deno usage.
+
+function reportErrors(errors: iots.Errors): string[] | undefined {
+    if (errors.length === 0) return undefined;
+    return errors.map(getMessage);
+}
+
+function getMessage(e: iots.ValidationError) {
+    return e.message !== undefined
+        ? e.message
+        : `Invalid value ${stringifyError(e.value)} supplied to ${getContextPath(e.context)}`;
+}
+
+function getContextPath(context: iots.ValidationError['context']) {
+    return context.map(a => `${a.key}: ${a.type.name}`).join('/');
+}
+
+function getFunctionName(f: Function & { displayName?: string }) {
+    return f.displayName || f.name || `<function ${f.length}>`;
+}
+
+function stringifyError(v: any) {
+    if (typeof v === 'function') {
+        return getFunctionName(v);
+    }
+    if (typeof v === 'number' && !isFinite(v)) {
+        if (isNaN(v)) {
+            return 'NaN';
+        }
+        return v > 0 ? 'Infinity' : '-Infinity';
+    }
+    return JSON.stringify(v);
+}

src/extensions/mvs/tree/generic/tree-utils.ts

@@ -86,7 +86,7 @@ export function copyTree<T extends Tree>(root: T): T {
  * nodes of kind `C` will be converted to `Y` with a child `Z` (original children moved to `Z`),
  * nodes of other kinds will just be copied. */
 export type ConversionRules<A extends Tree, B extends Tree> = {
-    [kind in Kind<Subtree<A>>]?: (node: SubtreeOfKind<A, kind>, parent?: Subtree<A>) => Subtree<B>[]
+    [kind in Kind<Subtree<A>>]?: (node: SubtreeOfKind<A, kind>, parent?: Subtree<A>) => { subtree: Subtree<B>[] }
 };
 
 /** Apply a set of conversion rules to a tree to change to a different schema. */
@@ -94,12 +94,12 @@ export function convertTree<A extends Tree, B extends Tree>(root: A, conversions
     const mapping = new Map<Subtree<A>, Subtree<B>>();
     let convertedRoot: Subtree<B>;
     dfs<A>(root, (node, parent) => {
-        const conversion = conversions[node.kind as (typeof node)['kind']] as ((n: typeof node, p?: Subtree<A>) => Subtree<B>[]) | undefined;
+        const conversion = conversions[node.kind as (typeof node)['kind']] as ((n: typeof node, p?: Subtree<A>) => { subtree: Subtree<B>[] }) | undefined;
         if (conversion) {
-            const convertidos = conversion(node, parent);
-            if (!parent && convertidos.length === 0) throw new Error('Cannot convert root to empty path');
+            const converted = conversion(node, parent);
+            if (!parent && converted?.subtree.length === 0) throw new Error('Cannot convert root to empty path');
             let convParent = parent ? mapping.get(parent) : undefined;
-            for (const conv of convertidos) {
+            for (const conv of converted.subtree) {
                 if (convParent) {
                     (convParent.children ??= []).push(conv);
                 } else {
@@ -153,12 +153,14 @@ export function addDefaults<S extends TreeSchema>(tree: TreeFor<S>, treeSchema:
     type TTree = TreeFor<S>;
     const rules: ConversionRules<TTree, TTree> = {};
     for (const kind in treeSchema.nodes) {
-        rules[kind as Kind<Subtree<TTree>>] = node => [{
-            kind: node.kind,
-            params: addParamDefaults(treeSchema.nodes[kind].params, node.params as any),
-            custom: node.custom,
-            ref: node.ref,
-        } as Node as any];
+        rules[kind as Kind<Subtree<TTree>>] = node => ({
+            subtree: [{
+                kind: node.kind,
+                params: addParamDefaults(treeSchema.nodes[kind].params, node.params as any),
+                custom: node.custom,
+                ref: node.ref,
+            } as Node as any]
+        });
     }
     return convertTree(tree, rules) as any;
 }

src/extensions/mvs/tree/molstar/conversion.ts

@@ -15,37 +15,76 @@ import { MolstarKind, MolstarNode, MolstarTree } from './molstar-tree';
 /** Convert `format` parameter of `parse` node in `MolstarTree`
  * into `format` and `is_binary` parameters in `MolstarTree` */
 export const ParseFormatMvsToMolstar = {
+    // trajectory
     mmcif: { format: 'cif', is_binary: false },
     bcif: { format: 'cif', is_binary: true },
     pdb: { format: 'pdb', is_binary: false },
+    pdbqt: { format: 'pdbqt', is_binary: false },
+    gro: { format: 'gro', is_binary: false },
+    xyz: { format: 'xyz', is_binary: false },
+    mol: { format: 'mol', is_binary: false },
+    sdf: { format: 'sdf', is_binary: false },
+    mol2: { format: 'mol2', is_binary: false },
+    lammpstrj: { format: 'lammpstrj', is_binary: false },
+    // coordinates
+    xtc: { format: 'xtc', is_binary: true },
+    // maps
     map: { format: 'map', is_binary: true },
 } satisfies { [p in ParseFormatT]: { format: MolstarParseFormatT, is_binary: boolean } };
 
-
 /** Conversion rules for conversion from `MVSTree` (with all parameter values) to `MolstarTree` */
 const mvsToMolstarConversionRules: ConversionRules<FullMVSTree, MolstarTree> = {
-    'download': node => [],
+    'download': node => ({ subtree: [] }),
     'parse': (node, parent) => {
         const { format, is_binary } = ParseFormatMvsToMolstar[node.params.format];
-        const convertedNode: MolstarNode<'parse'> = { kind: 'parse', params: { ...node.params, format }, custom: node.custom, ref: node.ref };
         if (parent?.kind === 'download') {
-            return [
-                { kind: 'download', params: { ...parent.params, is_binary }, custom: parent.custom, ref: parent.ref },
-                convertedNode,
-            ] satisfies MolstarNode[];
+            return {
+                subtree: [
+                    { kind: 'download', params: { ...parent.params, is_binary }, custom: parent.custom, ref: parent.ref },
+                    { kind: 'parse', params: { ...node.params, format }, custom: node.custom, ref: node.ref }
+                ] satisfies MolstarNode[]
+            };
         } else {
             console.warn('"parse" node is not being converted, this is suspicious');
-            return [convertedNode] satisfies MolstarNode[];
+            return {
+                subtree: [
+                    { kind: 'parse', params: { ...node.params, format }, custom: node.custom, ref: node.ref }
+                ] satisfies MolstarNode[]
+            };
         }
     },
+    'coordinates': (node, parent) => {
+        if (parent?.kind !== 'parse') throw new Error(`Parent of "coordinates" must be "parse", not "${parent?.kind}".`);
+        const { format } = ParseFormatMvsToMolstar[parent.params.format];
+        return {
+            subtree: [
+                { kind: 'coordinates', params: { format }, custom: node.custom, ref: node.ref }
+            ] satisfies MolstarNode[]
+        };
+    },
     'structure': (node, parent) => {
         if (parent?.kind !== 'parse') throw new Error(`Parent of "structure" must be "parse", not "${parent?.kind}".`);
         const { format } = ParseFormatMvsToMolstar[parent.params.format];
-        return [
-            { kind: 'trajectory', params: { format, ...pickObjectKeys(node.params, ['block_header', 'block_index']) } },
-            { kind: 'model', params: pickObjectKeys(node.params, ['model_index']) },
-            { kind: 'structure', params: omitObjectKeys(node.params, ['block_header', 'block_index', 'model_index']), custom: node.custom, ref: node.ref },
-        ] satisfies MolstarNode[];
+
+        if (node.params.coordinates_ref) {
+            return {
+                subtree: [
+                    { kind: 'trajectory', params: { format, ...pickObjectKeys(node.params, ['block_header', 'block_index']) } },
+                    { kind: 'model', params: { model_index: 0 } },
+                    { kind: 'trajectory_with_coordinates', params: { coordinates_ref: node.params.coordinates_ref } },
+                    { kind: 'model', params: pickObjectKeys(node.params, ['model_index']) },
+                    { kind: 'structure', params: omitObjectKeys(node.params, ['block_header', 'block_index', 'model_index', 'coordinates_ref']), custom: node.custom, ref: node.ref },
+                ] satisfies MolstarNode[]
+            };
+        } else {
+            return {
+                subtree: [
+                    { kind: 'trajectory', params: { format, ...pickObjectKeys(node.params, ['block_header', 'block_index']) } },
+                    { kind: 'model', params: pickObjectKeys(node.params, ['model_index']) },
+                    { kind: 'structure', params: omitObjectKeys(node.params, ['block_header', 'block_index', 'model_index', 'coordinates_ref']), custom: node.custom, ref: node.ref },
+                ] satisfies MolstarNode[]
+            };
+        }
     },
 };
 
@@ -70,9 +109,20 @@ function fileExtensionMatches(filename: string, extensions: (FileExtension | '*'
 }
 
 const StructureFormatExtensions: Record<ParseFormatT, (FileExtension | '*')[]> = {
+    // trajectory
     mmcif: ['.cif', '.mmif'],
     bcif: ['.bcif'],
     pdb: ['.pdb', '.ent'],
+    pdbqt: ['.pdbqt'],
+    gro: ['.gro'],
+    xyz: ['.xyz'],
+    mol: ['.mol'],
+    sdf: ['.sdf'],
+    mol2: ['.mol2'],
+    lammpstrj: ['.lammpstrj'],
+    // coordinates
+    xtc: ['.xtc'],
+    // volumes
     map: ['.map', '.ccp4', '.mrc', '.mrcs'],
 };
 

src/extensions/mvs/tree/molstar/molstar-tree.ts

@@ -5,7 +5,7 @@
  */
 
 import { omitObjectKeys, pickObjectKeys } from '../../../../mol-util/object';
-import { RequiredField, bool } from '../generic/field-schema';
+import { RequiredField, bool, str } from '../generic/field-schema';
 import { SimpleParamsSchema } from '../generic/params-schema';
 import { NodeFor, ParamsOfKind, SubtreeOfKind, TreeFor, TreeSchema } from '../generic/tree-schema';
 import { FullMVSTreeSchema } from '../mvs/mvs-tree';
@@ -30,6 +30,14 @@ export const MolstarTreeSchema = TreeSchema({
                 format: RequiredField(MolstarParseFormatT, 'File format'),
             }),
         },
+        /** Auxiliary node corresponding to Molstar's CoordinatesFrom*. */
+        coordinates: {
+            description: "Auxiliary node corresponding to Molstar's CoordinatesFrom*.",
+            parent: ['parse'],
+            params: SimpleParamsSchema({
+                format: RequiredField(MolstarParseFormatT, 'File format'),
+            }),
+        },
         /** Auxiliary node corresponding to Molstar's TrajectoryFrom*. */
         trajectory: {
             description: "Auxiliary node corresponding to Molstar's TrajectoryFrom*.",
@@ -39,10 +47,18 @@ export const MolstarTreeSchema = TreeSchema({
                 ...pickObjectKeys(FullMVSTreeSchema.nodes.structure.params.fields, ['block_header', 'block_index'] as const),
             }),
         },
+        /** Auxiliary node corresponding to Molstar's TrajectoryFrom*. */
+        trajectory_with_coordinates: {
+            description: 'Auxiliary node corresponding to assigning a separate coordinates to a trajectory.',
+            parent: ['model'],
+            params: SimpleParamsSchema({
+                coordinates_ref: RequiredField(str, 'Coordinates reference'),
+            }),
+        },
         /** Auxiliary node corresponding to Molstar's ModelFromTrajectory. */
         model: {
             description: "Auxiliary node corresponding to Molstar's ModelFromTrajectory.",
-            parent: ['trajectory'],
+            parent: ['trajectory', 'trajectory_with_coordinates'],
             params: SimpleParamsSchema(
                 pickObjectKeys(FullMVSTreeSchema.nodes.structure.params.fields, ['model_index'] as const)
             ),
@@ -52,7 +68,7 @@ export const MolstarTreeSchema = TreeSchema({
             ...FullMVSTreeSchema.nodes.structure,
             parent: ['model'],
             params: SimpleParamsSchema(
-                omitObjectKeys(FullMVSTreeSchema.nodes.structure.params.fields, ['block_header', 'block_index', 'model_index'] as const)
+                omitObjectKeys(FullMVSTreeSchema.nodes.structure.params.fields, ['block_header', 'block_index', 'model_index', 'coordinates_ref'] as const)
             ),
         },
     }

src/extensions/mvs/tree/mvs/mvs-builder.ts

@@ -8,6 +8,7 @@
 import { deepClone, pickObjectKeys } from '../../../../mol-util/object';
 import { GlobalMetadata, MVSData_State, Snapshot, SnapshotMetadata } from '../../mvs-data';
 import { CustomProps } from '../generic/tree-schema';
+import { MVSAnimationNodeParams, MVSAnimationSubtree } from '../animation/animation-tree';
 import { MVSKind, MVSNode, MVSNodeParams, MVSSubtree } from './mvs-tree';
 
 
@@ -50,6 +51,8 @@ class _Base<TKind extends MVSKind> {
 
 /** MVS builder pointing to the 'root' node */
 export class Root extends _Base<'root'> implements FocusMixin, PrimitivesMixin {
+    protected _animation: Animation | undefined = undefined;
+
     constructor(params_: CustomAndRef) {
         const { custom, ref } = params_;
         const node: MVSNode<'root'> = { kind: 'root', custom, ref };
@@ -69,6 +72,7 @@ export class Root extends _Base<'root'> implements FocusMixin, PrimitivesMixin {
         return {
             root: deepClone(this._node),
             metadata: { ...metadata },
+            animation: this?._animation ? deepClone(this._animation.node) : undefined,
         };
     }
 
@@ -89,6 +93,43 @@ export class Root extends _Base<'root'> implements FocusMixin, PrimitivesMixin {
     focus = bindMethod(this, FocusMixinImpl, 'focus');
     primitives = bindMethod(this, PrimitivesMixinImpl, 'primitives');
     primitives_from_uri = bindMethod(this, PrimitivesMixinImpl, 'primitives_from_uri');
+
+    animation(params: MVSAnimationNodeParams<'animation'> & CustomAndRef = {}): Animation {
+        this._animation ??= new Animation(params);
+        return this._animation;
+    }
+
+    /** Modifies custom state of the root */
+    extendRootCustomState(custom: Record<string, any>): this {
+        this._node.custom = { ...this._node.custom, ...custom };
+        return this;
+    }
+}
+
+export class Animation {
+    private _node: MVSAnimationSubtree<'animation'>;
+    constructor(
+        parameters: MVSAnimationNodeParams<'animation'> & CustomAndRef
+    ) {
+        this._node = {
+            kind: 'animation',
+            children: [],
+            ...splitParams<MVSAnimationNodeParams<'animation'>>(parameters),
+        };
+    }
+
+    get node(): MVSAnimationSubtree<'animation'> {
+        return this._node;
+    }
+
+    interpolate(params: MVSAnimationNodeParams<'interpolate'> & CustomAndRef): Animation {
+        const node = {
+            kind: 'interpolate',
+            ...splitParams<MVSAnimationNodeParams<'interpolate'>>(params)
+        } as MVSAnimationSubtree<'interpolate'>;
+        this._node.children!.push(node);
+        return this;
+    }
 }
 
 
@@ -103,10 +144,10 @@ export class Download extends _Base<'download'> {
 
 /** Subsets of 'structure' node params which will be passed to individual builder functions. */
 const StructureParamsSubsets = {
-    model: ['block_header', 'block_index', 'model_index'],
-    assembly: ['block_header', 'block_index', 'model_index', 'assembly_id'],
-    symmetry: ['block_header', 'block_index', 'model_index', 'ijk_min', 'ijk_max'],
-    symmetry_mates: ['block_header', 'block_index', 'model_index', 'radius'],
+    model: ['block_header', 'block_index', 'model_index', 'coordinates_ref'],
+    assembly: ['block_header', 'block_index', 'model_index', 'assembly_id', 'coordinates_ref'],
+    symmetry: ['block_header', 'block_index', 'model_index', 'ijk_min', 'ijk_max', 'coordinates_ref'],
+    symmetry_mates: ['block_header', 'block_index', 'model_index', 'radius', 'coordinates_ref'],
 } satisfies { [kind in MVSNodeParams<'structure'>['type']]: (keyof MVSNodeParams<'structure'>)[] };
 
 
@@ -156,6 +197,11 @@ export class Parse extends _Base<'parse'> {
     volume(params: MVSNodeParams<'volume'> & CustomAndRef = {}): Volume {
         return new Volume(this._root, this.addChild('volume', params));
     }
+    /** Add a 'coordinates' node indicating the parsed data type */
+    coordinates(params: MVSNodeParams<'coordinates'> & CustomAndRef = {}): Parse {
+        this.addChild('coordinates', params);
+        return this;
+    }
 }
 
 

src/extensions/mvs/tree/mvs/mvs-tree-representations.ts

@@ -15,6 +15,11 @@ const Cartoon = {
     tubular_helices: OptionalField(bool, false, 'Simplify corkscrew helices to tubes.'),
 };
 
+const Backbone = {
+    /** Scales the corresponding visuals */
+    size_factor: OptionalField(float, 1, 'Scales the corresponding visuals.'),
+};
+
 const BallAndStick = {
     /** Scales the corresponding visuals */
     size_factor: OptionalField(float, 1, 'Scales the corresponding visuals.'),
@@ -22,6 +27,13 @@ const BallAndStick = {
     ignore_hydrogens: OptionalField(bool, false, 'Controls whether hydrogen atoms are drawn.'),
 };
 
+const Line = {
+    /** Scales the corresponding visuals */
+    size_factor: OptionalField(float, 1, 'Scales the corresponding visuals.'),
+    /** Controls whether hydrogen atoms are drawn. */
+    ignore_hydrogens: OptionalField(bool, false, 'Controls whether hydrogen atoms are drawn.'),
+};
+
 const Spacefill = {
     /** Scales the corresponding visuals */
     size_factor: OptionalField(float, 1, 'Scales the corresponding visuals.'),
@@ -35,6 +47,8 @@ const Carbohydrate = {
 };
 
 const Surface = {
+    /** Type of surface representation. (Default is 'molecular') */
+    surface_type: OptionalField(literal('molecular', 'gaussian'), 'molecular', `Type of surface representation. (Default is 'molecular')`),
     /** Scales the corresponding visuals */
     size_factor: OptionalField(float, 1, 'Scales the corresponding visuals.'),
     /** Controls whether hydrogen atoms are drawn. */
@@ -46,7 +60,9 @@ export const MVSRepresentationParams = UnionParamsSchema(
     'Representation type',
     {
         cartoon: SimpleParamsSchema(Cartoon),
+        backbone: SimpleParamsSchema(Backbone),
         ball_and_stick: SimpleParamsSchema(BallAndStick),
+        line: SimpleParamsSchema(Line),
         spacefill: SimpleParamsSchema(Spacefill),
         carbohydrate: SimpleParamsSchema(Carbohydrate),
         surface: SimpleParamsSchema(Surface),

src/extensions/mvs/tree/mvs/mvs-tree.ts

@@ -57,6 +57,8 @@ const TransformParams = SimpleParamsSchema({
     rotation: OptionalField(Matrix, [1, 0, 0, 0, 1, 0, 0, 0, 1], 'Rotation matrix (3x3 matrix flattened in column major format (j*3+i indexing), this is equivalent to Fortran-order in numpy). This matrix will multiply the structure coordinates from the left. The default value is the identity matrix (corresponds to no rotation).'),
     /** Translation vector, applied to the structure coordinates after rotation. The default value is the zero vector (corresponds to no translation). */
     translation: OptionalField(Vector3, [0, 0, 0], 'Translation vector, applied to the structure coordinates after rotation. The default value is the zero vector (corresponds to no translation).'),
+    /** Point to rotate the object around. Can be either a 3D vector or dynamically computed object centroid. */
+    rotation_center: OptionalField(nullable(union(Vector3, literal('centroid'))), null, 'Point to rotate the object around. Can be either a 3D vector or dynamically computed object centroid.'),
     /** Transform matrix (4x4 matrix flattened in column major format (j*4+i indexing), this is equivalent to Fortran-order in numpy). This matrix will multiply the structure coordinates from the left. Takes precedence over `rotation` and `translation`. */
     matrix: OptionalField(nullable(Matrix), null, 'Transform matrix (4x4 matrix flattened in column major format (j*4+i indexing), this is equivalent to Fortran-order in numpy). This matrix will multiply the structure coordinates from the left. Takes precedence over `rotation` and `translation`.'),
 });
@@ -90,6 +92,12 @@ export const MVSTreeSchema = TreeSchema({
                 format: RequiredField(ParseFormatT, 'Format of the input data resource.'),
             }),
         },
+        /** This node instructs to retrieve molecular coordinates from a parsed data resource. */
+        coordinates: {
+            description: 'This node instructs to retrieve molecular coordinates from a parsed data resource.',
+            parent: ['parse'],
+            params: SimpleParamsSchema({}),
+        },
         /** This node instructs to create a structure from a parsed data resource. "Structure" refers to an internal representation of molecular coordinates without any visual representation. */
         structure: {
             description: 'This node instructs to create a structure from a parsed data resource. "Structure" refers to an internal representation of molecular coordinates without any visual representation.',
@@ -111,6 +119,8 @@ export const MVSTreeSchema = TreeSchema({
                 ijk_min: OptionalField(tuple([int, int, int]), [-1, -1, -1], 'Miller indices of the bottom-left unit cell to be included (only applies when `kind` is `"symmetry"`).'),
                 /** Miller indices of the top-right unit cell to be included (only applies when `kind` is `"symmetry"`). */
                 ijk_max: OptionalField(tuple([int, int, int]), [1, 1, 1], 'Miller indices of the top-right unit cell to be included (only applies when `kind` is `"symmetry"`).'),
+                /** Reference to a specific set of coordinates. */
+                coordinates_ref: OptionalField(nullable(str), null, 'Reference to a specific set of coordinates.')
             }),
         },
         /** This node instructs to rotate and/or translate structure coordinates. */
@@ -322,7 +332,7 @@ export const MVSTreeSchema = TreeSchema({
             parent: ['root'],
             params: SimpleParamsSchema({
                 /** Color of the canvas background. Can be either an X11 color name (e.g. `"red"`) or a hexadecimal code (e.g. `"#FF0011"`). */
-                background_color: RequiredField(ColorT, 'Color of the canvas background. Can be either an X11 color name (e.g. `"red"`) or a hexadecimal code (e.g. `"#FF0011"`).'),
+                background_color: OptionalField(ColorT, 'white', 'Color of the canvas background. Can be either an X11 color name (e.g. `"red"`) or a hexadecimal code (e.g. `"#FF0011"`). Defaults to white.'),
             }),
         },
         primitives: {

src/extensions/mvs/tree/mvs/param-types.ts

@@ -11,11 +11,42 @@ import { ValueFor, bool, dict, float, int, list, literal, nullable, object, part
 
 
 /** `format` parameter values for `parse` node in MVS tree */
-export const ParseFormatT = literal('mmcif', 'bcif', 'pdb', 'map');
+export const ParseFormatT = literal(
+    // trajectory
+    'mmcif',
+    'bcif', // +volumes
+    'pdb',
+    'pdbqt',
+    'gro',
+    'xyz',
+    'mol',
+    'sdf',
+    'mol2',
+    'lammpstrj', // + coordinates
+    // coordinates
+    'xtc',
+    // volumes
+    'map',
+);
 export type ParseFormatT = ValueFor<typeof ParseFormatT>
 
 /** `format` parameter values for `parse` node in Molstar tree */
-export const MolstarParseFormatT = literal('cif', 'pdb', 'map');
+export const MolstarParseFormatT = literal(
+    // trajectory
+    'cif', // +volumes
+    'pdb',
+    'pdbqt',
+    'gro',
+    'xyz',
+    'mol',
+    'sdf',
+    'mol2',
+    'lammpstrj',
+    // coordinates
+    'xtc',
+    // volumes
+    'map'
+);
 export type MolstarParseFormatT = ValueFor<typeof MolstarParseFormatT>
 
 /** `kind` parameter values for `structure` node in MVS tree */

src/mol-canvas3d/camera.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -11,6 +11,7 @@ import { CameraTransitionManager } from './camera/transition';
 import { BehaviorSubject } from 'rxjs';
 import { Scene } from '../mol-gl/scene';
 import { assertUnreachable } from '../mol-util/type-helpers';
+import { Ray3D } from '../mol-math/geometry/primitives/ray3d';
 
 export type { ICamera };
 
@@ -26,6 +27,7 @@ interface ICamera {
     readonly near: number,
     readonly fogFar: number,
     readonly fogNear: number,
+    readonly headRotation: Mat4,
 }
 
 const tmpClip = Vec4();
@@ -35,6 +37,7 @@ export class Camera implements ICamera {
     readonly projection: Mat4 = Mat4.identity();
     readonly projectionView: Mat4 = Mat4.identity();
     readonly inverseProjectionView: Mat4 = Mat4.identity();
+    readonly headRotation: Mat4 = Mat4.zero();
 
     readonly viewport: Viewport;
     readonly state: Readonly<Camera.Snapshot> = Camera.createDefaultSnapshot();
@@ -69,7 +72,7 @@ export class Camera implements ICamera {
             return false;
         }
 
-        const height = 2 * Math.tan(snapshot.fov / 2) * Vec3.distance(snapshot.position, snapshot.target);
+        const height = 2 * Math.tan(snapshot.fov / 2) * Vec3.distance(snapshot.position, snapshot.target) * this.state.scale;
         this.zoom = this.viewport.height / height;
 
         updateClip(this);
@@ -191,6 +194,22 @@ export class Camera implements ICamera {
         return (2 / w) / (rx * Math.abs(P00));
     }
 
+    getRay(out: Ray3D, x: number, y: number) {
+        if (this.state.mode === 'orthographic') {
+            Vec3.set(out.origin, x, y, 0);
+            this.unproject(out.origin, out.origin);
+            Vec3.normalize(out.direction, Vec3.sub(out.direction, this.target, this.position));
+            Vec3.scaleAndAdd(out.origin, out.origin, out.direction, -this.near);
+        } else {
+            Vec3.copy(out.origin, this.state.position);
+            Vec3.scale(out.origin, out.origin, this.state.scale);
+            Vec3.set(out.direction, x, y, 0.5);
+            this.unproject(out.direction, out.direction);
+            Vec3.normalize(out.direction, Vec3.sub(out.direction, out.direction, out.origin));
+        }
+        return out;
+    }
+
     constructor(state?: Partial<Camera.Snapshot>, viewport = Viewport.create(0, 0, 128, 128)) {
         this.viewport = viewport;
         Camera.copySnapshot(this.state, state);
@@ -270,6 +289,8 @@ export namespace Camera {
             clipFar: true,
             minNear: 5,
             minFar: 0,
+
+            scale: 1,
         };
     }
 
@@ -287,6 +308,8 @@ export namespace Camera {
         clipFar: boolean
         minNear: number
         minFar: number
+
+        scale: number
     }
 
     export function copySnapshot(out: Snapshot, source?: Partial<Snapshot>) {
@@ -306,6 +329,8 @@ export namespace Camera {
         if (typeof source.minNear !== 'undefined') out.minNear = source.minNear;
         if (typeof source.minFar !== 'undefined') out.minFar = source.minFar;
 
+        if (typeof source.scale !== 'undefined') out.scale = source.scale;
+
         return out;
     }
 
@@ -318,12 +343,26 @@ export namespace Camera {
             && a.clipFar === b.clipFar
             && a.minNear === b.minNear
             && a.minFar === b.minFar
+            && a.scale === b.scale
             && Vec3.exactEquals(a.position, b.position)
             && Vec3.exactEquals(a.up, b.up)
             && Vec3.exactEquals(a.target, b.target);
     }
 }
 
+const tmpPosition = Vec3();
+const tmpTarget = Vec3();
+
+function updateView(camera: Camera) {
+    if (camera.state.scale === 1) {
+        Mat4.lookAt(camera.view, camera.state.position, camera.state.target, camera.state.up);
+    } else {
+        Vec3.scale(tmpPosition, camera.state.position, camera.state.scale);
+        Vec3.scale(tmpTarget, camera.state.target, camera.state.scale);
+        Mat4.lookAt(camera.view, tmpPosition, tmpTarget, camera.state.up);
+    }
+}
+
 function updateOrtho(camera: Camera) {
     const { viewport, zoom, near, far, viewOffset } = camera;
 
@@ -357,7 +396,7 @@ function updateOrtho(camera: Camera) {
     Mat4.ortho(camera.projection, left, right, top, bottom, near, far);
 
     // build view matrix
-    Mat4.lookAt(camera.view, camera.position, camera.target, camera.up);
+    updateView(camera);
 }
 
 function updatePers(camera: Camera) {
@@ -381,15 +420,23 @@ function updatePers(camera: Camera) {
     Mat4.perspective(camera.projection, left, left + width, top, top - height, near, far);
 
     // build view matrix
-    Mat4.lookAt(camera.view, camera.position, camera.target, camera.up);
+    updateView(camera);
 }
 
 function updateClip(camera: Camera) {
-    let { radius, radiusMax, mode, fog, clipFar, minNear, minFar } = camera.state;
-    if (radius < 0.01) radius = 0.01;
+    let { radius, radiusMax, mode, fog, clipFar, minNear, minFar, scale } = camera.state;
+    radiusMax *= scale;
+    minFar *= scale;
+    minNear *= scale;
+    radius *= scale;
+
+    const minRadius = 0.01 * scale;
+    if (radius < minRadius) radius = minRadius;
 
     const normalizedFar = Math.max(clipFar ? radius : radiusMax, minFar);
-    const cameraDistance = Vec3.distance(camera.position, camera.target);
+    Vec3.scale(tmpTarget, camera.state.target, scale);
+    Vec3.scale(tmpPosition, camera.state.position, scale);
+    const cameraDistance = Vec3.distance(tmpPosition, tmpTarget);
     let near = cameraDistance - radius;
     let far = cameraDistance + normalizedFar;
 
@@ -405,7 +452,7 @@ function updateClip(camera: Camera) {
 
     if (near === far) {
         // make sure near and far are not identical to avoid Infinity in the projection matrix
-        far = near + 0.01;
+        far = near + 0.01 * scale;
     }
 
     const fogNearFactor = -(50 - fog) / 50;

src/mol-canvas3d/camera/stereo.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -61,6 +61,7 @@ class EyeCamera implements ICamera {
     projection = Mat4();
     projectionView = Mat4();
     inverseProjectionView = Mat4();
+    headRotation = Mat4();
     state: Readonly<Camera.Snapshot> = Camera.createDefaultSnapshot();
     viewOffset: Readonly<Camera.ViewOffset> = Camera.ViewOffset();
     far: number = 0;
@@ -69,30 +70,29 @@ class EyeCamera implements ICamera {
     fogNear: number = 0;
 }
 
-const eyeLeft = Mat4.identity(), eyeRight = Mat4.identity();
+const tmpEyeLeft = Mat4.identity();
+const tmpEyeRight = Mat4.identity();
+
+function copyStates(parent: Camera, eye: EyeCamera) {
+    Viewport.copy(eye.viewport, parent.viewport);
+    Mat4.copy(eye.view, parent.view);
+    Mat4.copy(eye.projection, parent.projection);
+    Mat4.copy(eye.headRotation, parent.headRotation);
+    Camera.copySnapshot(eye.state, parent.state);
+    Camera.copyViewOffset(eye.viewOffset, parent.viewOffset);
+    eye.far = parent.far;
+    eye.near = parent.near;
+    eye.fogFar = parent.fogFar;
+    eye.fogNear = parent.fogNear;
+}
+
+//
 
 function update(camera: Camera, props: StereoCameraProps, left: EyeCamera, right: EyeCamera) {
     // Copy the states
 
-    Viewport.copy(left.viewport, camera.viewport);
-    Mat4.copy(left.view, camera.view);
-    Mat4.copy(left.projection, camera.projection);
-    Camera.copySnapshot(left.state, camera.state);
-    Camera.copyViewOffset(left.viewOffset, camera.viewOffset);
-    left.far = camera.far;
-    left.near = camera.near;
-    left.fogFar = camera.fogFar;
-    left.fogNear = camera.fogNear;
-
-    Viewport.copy(right.viewport, camera.viewport);
-    Mat4.copy(right.view, camera.view);
-    Mat4.copy(right.projection, camera.projection);
-    Camera.copySnapshot(right.state, camera.state);
-    Camera.copyViewOffset(right.viewOffset, camera.viewOffset);
-    right.far = camera.far;
-    right.near = camera.near;
-    right.fogFar = camera.fogFar;
-    right.fogNear = camera.fogNear;
+    copyStates(camera, left);
+    copyStates(camera, right);
 
     // update the view offsets
 
@@ -112,8 +112,8 @@ function update(camera: Camera, props: StereoCameraProps, left: EyeCamera, right
 
     // translate xOffset
 
-    eyeLeft[12] = -eyeSepHalf;
-    eyeRight[12] = eyeSepHalf;
+    tmpEyeLeft[12] = -eyeSepHalf;
+    tmpEyeRight[12] = eyeSepHalf;
 
     // for left eye
 
@@ -123,7 +123,7 @@ function update(camera: Camera, props: StereoCameraProps, left: EyeCamera, right
     left.projection[0] = 2 * camera.near / (xmax - xmin);
     left.projection[8] = (xmax + xmin) / (xmax - xmin);
 
-    Mat4.mul(left.view, left.view, eyeLeft);
+    Mat4.mul(left.view, left.view, tmpEyeLeft);
     Mat4.mul(left.projectionView, left.projection, left.view);
     Mat4.invert(left.inverseProjectionView, left.projectionView);
 
@@ -135,7 +135,7 @@ function update(camera: Camera, props: StereoCameraProps, left: EyeCamera, right
     right.projection[0] = 2 * camera.near / (xmax - xmin);
     right.projection[8] = (xmax + xmin) / (xmax - xmin);
 
-    Mat4.mul(right.view, right.view, eyeRight);
+    Mat4.mul(right.view, right.view, tmpEyeRight);
     Mat4.mul(right.projectionView, right.projection, right.view);
     Mat4.invert(right.inverseProjectionView, right.projectionView);
 }

src/mol-canvas3d/canvas3d.ts

@@ -13,7 +13,7 @@ import { Vec3, Vec2 } from '../mol-math/linear-algebra';
 import { InputObserver, ModifiersKeys, ButtonsType } from '../mol-util/input/input-observer';
 import { Renderer, RendererStats, RendererParams } from '../mol-gl/renderer';
 import { GraphicsRenderObject } from '../mol-gl/render-object';
-import { TrackballControls, TrackballControlsParams } from './controls/trackball';
+import { DefaultTrackballControlsAttribs, TrackballControls, TrackballControlsParams } from './controls/trackball';
 import { Viewport } from './camera/util';
 import { createContext, WebGLContext, getGLContext } from '../mol-gl/webgl/context';
 import { Representation } from '../mol-repr/representation';
@@ -28,13 +28,12 @@ import { SetUtils } from '../mol-util/set';
 import { Canvas3dInteractionHelper, Canvas3dInteractionHelperParams } from './helper/interaction-events';
 import { PostprocessingParams } from './passes/postprocessing';
 import { MultiSampleHelper, MultiSampleParams, MultiSamplePass } from './passes/multi-sample';
-import { PickData } from './passes/pick';
-import { PickHelper } from './passes/pick';
+import { AsyncPickData, DefaultPickOptions, PickData } from './passes/pick';
+import { PickHelper } from './helper/pick-helper';
 import { ImagePass, ImageProps } from './passes/image';
 import { Sphere3D } from '../mol-math/geometry';
 import { addConsoleStatsProvider, isDebugMode, isTimingMode, removeConsoleStatsProvider } from '../mol-util/debug';
 import { CameraHelperParams } from './helper/camera-helper';
-import { produce } from 'immer';
 import { HandleHelperParams } from './helper/handle-helper';
 import { StereoCamera, StereoCameraParams } from './camera/stereo';
 import { Helper } from './helper/helper';
@@ -47,7 +46,13 @@ import { deepClone } from '../mol-util/object';
 import { HiZParams, HiZPass } from './passes/hi-z';
 import { IlluminationParams } from './passes/illumination';
 import { isMobileBrowser } from '../mol-util/browser';
+import { Ray3D } from '../mol-math/geometry/primitives/ray3d';
+import { RayHelper } from './helper/ray-helper';
+import { produce } from '../mol-util/produce';
 
+export const CameraFogParams = {
+    intensity: PD.Numeric(15, { min: 1, max: 100, step: 1 }),
+};
 export const Canvas3DParams = {
     camera: PD.Group({
         mode: PD.Select('perspective', PD.arrayToOptions(['perspective', 'orthographic'] as const), { label: 'Camera' }),
@@ -57,12 +62,11 @@ export const Canvas3DParams = {
             off: PD.Group({})
         }, { cycle: true, hideIf: p => p?.mode !== 'perspective' }),
         fov: PD.Numeric(45, { min: 10, max: 130, step: 1 }, { label: 'Field of View' }),
+        scale: PD.Numeric(1, { min: 0.001, max: 1, step: 0.001 }, { label: 'Scene scale' }),
         manualReset: PD.Boolean(false, { isHidden: true }),
     }, { pivot: 'mode' }),
     cameraFog: PD.MappedStatic('on', {
-        on: PD.Group({
-            intensity: PD.Numeric(15, { min: 1, max: 100, step: 1 }),
-        }),
+        on: PD.Group(CameraFogParams),
         off: PD.Group({})
     }, { cycle: true, description: 'Show fog in the distance' }),
     cameraClipping: PD.Group({
@@ -110,6 +114,11 @@ export type PartialCanvas3DProps = {
     [K in keyof Canvas3DProps]?: Canvas3DProps[K] extends { name: string, params: any } ? Canvas3DProps[K] : Partial<Canvas3DProps[K]>
 }
 
+export const DefaultCanvas3DAttribs = {
+    trackball: DefaultTrackballControlsAttribs,
+};
+export type Canvas3DAttribs = typeof DefaultCanvas3DAttribs
+
 export { Canvas3DContext };
 
 /** Can be used to create multiple Canvas3D objects */
@@ -330,7 +339,8 @@ interface Canvas3D {
     pause(noDraw?: boolean): void
     /** Sets drawPaused = false without starting the built in animation loop */
     resume(): void
-    identify(x: number, y: number): PickData | undefined
+    identify(target: Vec2 | Ray3D): PickData | undefined
+    asyncIdentify(target: Vec2 | Ray3D): AsyncPickData | undefined
     mark(loci: Representation.Loci, action: MarkerAction): void
     getLoci(pickingId: PickingId | undefined): Representation.Loci
 
@@ -355,6 +365,7 @@ interface Canvas3D {
 
     /** Returns a copy of the current Canvas3D instance props */
     readonly props: Readonly<Canvas3DProps>
+    readonly attribs: Readonly<Canvas3DAttribs>
     readonly input: InputObserver
     readonly stats: RendererStats
     readonly interaction: Canvas3dInteractionHelper['events']
@@ -374,9 +385,10 @@ namespace Canvas3D {
     export interface DragEvent { current: Representation.Loci, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys, pageStart: Vec2, pageEnd: Vec2 }
     export interface ClickEvent { current: Representation.Loci, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys, page?: Vec2, position?: Vec3 }
 
-    export function create(ctx: Canvas3DContext, props: Partial<Canvas3DProps> = {}): Canvas3D {
+    export function create(ctx: Canvas3DContext, props: Partial<Canvas3DProps> = {}, attribs: Partial<Canvas3DAttribs> = {}): Canvas3D {
         const { webgl, input, passes, assetManager, canvas, contextLost } = ctx;
         const p: Canvas3DProps = { ...deepClone(DefaultCanvas3DParams), ...deepClone(props) };
+        const a = { ...deepClone(DefaultCanvas3DAttribs), ...deepClone(attribs) };
 
         const reprRenderObjects = new Map<Representation.Any, Set<GraphicsRenderObject>>();
         const reprUpdatedSubscriptions = new Map<Representation.Any, Subscription>();
@@ -412,18 +424,24 @@ namespace Canvas3D {
             clipFar: p.cameraClipping.far,
             minNear: p.cameraClipping.minNear,
             fov: degToRad(p.camera.fov),
+            scale: p.camera.scale,
         }, { x, y, width, height });
         const stereoCamera = new StereoCamera(camera, p.camera.stereo.params);
 
-        const controls = TrackballControls.create(input, camera, scene, p.trackball);
+        const controls = TrackballControls.create(input, camera, scene, p.trackball, a.trackball);
         const helper = new Helper(webgl, scene, p);
         const hiZ = new HiZPass(webgl, passes.draw, canvas, p.hiZ);
 
         const renderer = Renderer.create(webgl, p.renderer);
         renderer.setOcclusionTest(hiZ.isOccluded);
 
-        const pickHelper = new PickHelper(webgl, renderer, scene, helper, passes.pick, { x, y, width, height }, p.pickPadding);
-        const interactionHelper = new Canvas3dInteractionHelper(identify, getLoci, input, camera, controls, p.interaction);
+        const pickOptions = {
+            pickPadding: p.pickPadding,
+            maxAsyncReadLag: DefaultPickOptions.maxAsyncReadLag,
+        };
+        const pickHelper = new PickHelper(webgl, renderer, scene, helper, passes.pick, { x, y, width, height }, pickOptions);
+        const rayHelper = new RayHelper(webgl, renderer, scene, helper, pickOptions);
+        const interactionHelper = new Canvas3dInteractionHelper(identify, asyncIdentify, getLoci, input, camera, controls, p.interaction);
         const multiSampleHelper = new MultiSampleHelper(passes.multiSample);
 
         passes.draw.postprocessing.background.update(camera, p.postprocessing.background, changed => {
@@ -649,9 +667,26 @@ namespace Canvas3D {
             animationFrameHandle = 0;
         }
 
-        function identify(x: number, y: number): PickData | undefined {
-            const cam = p.camera.stereo.name === 'on' ? stereoCamera : camera;
-            return webgl.isContextLost ? undefined : pickHelper.identify(x, y, cam);
+        function identify(target: Vec2 | Ray3D): PickData | undefined {
+            if (webgl.isContextLost) return undefined;
+
+            if ('origin' in target) {
+                return rayHelper.identify(target, camera);
+            } else {
+                const cam = (p.camera.stereo.name === 'on') ? stereoCamera : camera;
+                return pickHelper.identify(target[0], target[1], cam);
+            }
+        }
+
+        function asyncIdentify(target: Vec2 | Ray3D): AsyncPickData | undefined {
+            if (webgl.isContextLost) return undefined;
+
+            if ('origin' in target) {
+                return rayHelper.asyncIdentify(target, camera);
+            } else {
+                const cam = (p.camera.stereo.name === 'on') ? stereoCamera : camera;
+                return pickHelper.asyncIdentify(target[0], target[1], cam);
+            }
         }
 
         function commit(isSynchronous: boolean = false) {
@@ -841,6 +876,7 @@ namespace Canvas3D {
                     helper: { ...helper.camera.props },
                     stereo: { ...p.camera.stereo },
                     fov: Math.round(radToDeg(camera.state.fov)),
+                    scale: camera.state.scale,
                     manualReset: !!p.camera.manualReset
                 },
                 cameraFog: camera.state.fog > 0
@@ -875,6 +911,10 @@ namespace Canvas3D {
         });
 
         const contextRestoredSub = contextRestored.subscribe(() => {
+            pickHelper.reset();
+            rayHelper.reset();
+            hiZ.reset();
+
             scene.forEach(r => {
                 if (r.values.meta?.ref.value.reset) {
                     r.values.meta.ref.value.reset();
@@ -952,7 +992,7 @@ namespace Canvas3D {
             input.click.subscribe(e => {
                 if (!e.modifiers.control || e.button !== 2) return;
 
-                const p = identify(e.x, e.y);
+                const p = identify(Vec2.create(e.x, e.y));
                 if (!p) {
                     occlusionLoci = undefined;
                     printOcclusion(occlusionLoci);
@@ -1020,6 +1060,7 @@ namespace Canvas3D {
             pause,
             resume: () => { drawPaused = false; },
             identify,
+            asyncIdentify,
             mark,
             getLoci,
 
@@ -1060,6 +1101,9 @@ namespace Canvas3D {
                 if (props.camera && props.camera.fov !== undefined && props.camera.fov !== oldFov) {
                     cameraState.fov = degToRad(props.camera.fov);
                 }
+                if (props.camera && props.camera.scale !== undefined && props.camera.scale !== cameraState.scale) {
+                    cameraState.scale = props.camera.scale;
+                }
                 if (props.cameraFog !== undefined && props.cameraFog.params) {
                     const newFog = props.cameraFog.name === 'on' ? props.cameraFog.params.intensity : 0;
                     if (newFog !== camera.state.fog) cameraState.fog = newFog;
@@ -1143,6 +1187,9 @@ namespace Canvas3D {
             get props() {
                 return getProps();
             },
+            get attribs() {
+                return a;
+            },
             get input() {
                 return input;
             },
@@ -1170,6 +1217,9 @@ namespace Canvas3D {
                 renderer.dispose();
                 interactionHelper.dispose();
                 hiZ.dispose();
+                pickHelper.dispose();
+                rayHelper.dispose();
+
                 if (fenceSync !== null) {
                     webgl.deleteSync(fenceSync);
                     fenceSync = null;

src/mol-canvas3d/controls/trackball.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -56,8 +56,6 @@ export const DefaultTrackballBindings = {
 };
 
 export const TrackballControlsParams = {
-    noScroll: PD.Boolean(true, { isHidden: true }),
-
     rotateSpeed: PD.Numeric(5.0, { min: 1, max: 10, step: 1 }),
     zoomSpeed: PD.Numeric(7.0, { min: 1, max: 15, step: 1 }),
     panSpeed: PD.Numeric(1.0, { min: 0.1, max: 5, step: 0.1 }),
@@ -68,10 +66,10 @@ export const TrackballControlsParams = {
     animate: PD.MappedStatic('off', {
         off: PD.EmptyGroup(),
         spin: PD.Group({
-            speed: PD.Numeric(1, { min: -20, max: 20, step: 1 }, { description: 'Rotation speed in radians per second' }),
+            speed: PD.Numeric(0.3, { min: -5, max: 5, step: 0.1 }, { description: 'Number of rotations per second' }),
         }, { description: 'Spin the 3D scene around the x-axis in view space' }),
         rock: PD.Group({
-            speed: PD.Numeric(0.3, { min: -5, max: 5, step: 0.1 }),
+            speed: PD.Numeric(0.3, { min: -5, max: 5, step: 0.1 }, { description: 'Number of oscilations per second' }),
             angle: PD.Numeric(10, { min: 0, max: 90, step: 1 }, { description: 'How many degrees to rotate in each direction.' }),
         }, { description: 'Rock the 3D scene around the x-axis in view space' })
     }),
@@ -85,8 +83,6 @@ export const TrackballControlsParams = {
     gestureScaleFactor: PD.Numeric(1, {}, { isHidden: true }),
     maxWheelDelta: PD.Numeric(0.02, {}, { isHidden: true }),
 
-    bindings: PD.Value(DefaultTrackballBindings, { isHidden: true }),
-
     /**
      * minDistance = minDistanceFactor * boundingSphere.radius + minDistancePadding
      * maxDistance = max(maxDistanceFactor * boundingSphere.radius, maxDistanceMin)
@@ -103,6 +99,11 @@ export const TrackballControlsParams = {
 };
 export type TrackballControlsProps = PD.Values<typeof TrackballControlsParams>
 
+export const DefaultTrackballControlsAttribs = {
+    bindings: DefaultTrackballBindings,
+};
+export type TrackballControlsAttribs = typeof DefaultTrackballControlsAttribs
+
 export { TrackballControls };
 interface TrackballControls {
     readonly viewport: Viewport
@@ -112,20 +113,25 @@ interface TrackballControls {
     readonly props: Readonly<TrackballControlsProps>
     setProps: (props: Partial<TrackballControlsProps>) => void
 
+    readonly attribs: Readonly<TrackballControlsAttribs>
+    setAttribs: (attribs: Partial<TrackballControlsAttribs>) => void
+
     start: (t: number) => void
     update: (t: number) => void
     reset: () => void
     dispose: () => void
 }
 namespace TrackballControls {
-    export function create(input: InputObserver, camera: Camera, scene: Scene, props: Partial<TrackballControlsProps> = {}): TrackballControls {
+    export function create(input: InputObserver, camera: Camera, scene: Scene, props: Partial<TrackballControlsProps> = {}, attribs: Partial<TrackballControlsAttribs> = {}): TrackballControls {
         const p: TrackballControlsProps = {
             ...PD.getDefaultValues(TrackballControlsParams),
             ...props,
-            // include default bindings for backwards state compatibility
-            bindings: { ...DefaultTrackballBindings, ...props.bindings }
         };
-        const b = p.bindings;
+        const a: TrackballControlsAttribs = {
+            ...DefaultTrackballControlsAttribs,
+            ...attribs
+        };
+        const b = a.bindings;
 
         const viewport = Viewport.clone(camera.viewport);
 
@@ -825,7 +831,7 @@ namespace TrackballControls {
         function spin(deltaT: number) {
             if (p.animate.name !== 'spin' || p.animate.params.speed === 0 || _isInteracting) return;
 
-            const radPerMs = p.animate.params.speed / 1000;
+            const radPerMs = 2 * Math.PI * p.animate.params.speed / 1000;
             _spinSpeed[0] = deltaT * radPerMs / getRotateFactor();
             Vec2.add(_rotCurr, _rotPrev, _spinSpeed);
         }
@@ -885,7 +891,12 @@ namespace TrackballControls {
                     }
                 }
                 Object.assign(p, props);
-                Object.assign(b, props.bindings);
+            },
+
+            get attribs() { return a as Readonly<TrackballControlsAttribs>; },
+            setAttribs: (attribs: Partial<TrackballControlsAttribs>) => {
+                Object.assign(a, attribs);
+                Object.assign(b, a.bindings);
             },
 
             start,

src/mol-canvas3d/helper/camera-helper.ts

@@ -4,7 +4,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { produce } from 'immer';
+import { produce } from '../../mol-util/produce';
 import { Interval } from '../../mol-data/int/interval';
 import { addCylinder } from '../../mol-geo/geometry/mesh/builder/cylinder';
 import { addSphere } from '../../mol-geo/geometry/mesh/builder/sphere';

src/mol-canvas3d/helper/handle-helper.ts

@@ -16,7 +16,7 @@ import { addCylinder } from '../../mol-geo/geometry/mesh/builder/cylinder';
 import { ValueCell } from '../../mol-util';
 import { Sphere3D } from '../../mol-math/geometry';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { produce } from 'immer';
+import { produce } from '../../mol-util/produce';
 import { Shape } from '../../mol-model/shape';
 import { PickingId } from '../../mol-geo/geometry/picking';
 import { Camera } from '../camera';

src/mol-canvas3d/helper/interaction-events.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -14,14 +14,14 @@ import { Camera } from '../camera';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { Bond } from '../../mol-model/structure';
 import { TrackballControls } from '../controls/trackball';
+import { Ray3D } from '../../mol-math/geometry/primitives/ray3d';
+import { AsyncPickData } from '../passes/pick';
 
 type Canvas3D = import('../canvas3d').Canvas3D
 type HoverEvent = import('../canvas3d').Canvas3D.HoverEvent
 type DragEvent = import('../canvas3d').Canvas3D.DragEvent
 type ClickEvent = import('../canvas3d').Canvas3D.ClickEvent
 
-enum InputEvent { Move, Click, Drag }
-
 const tmpPosA = Vec3();
 const tmpPos = Vec3();
 const tmpNorm = Vec3();
@@ -29,6 +29,7 @@ const tmpNorm = Vec3();
 export const Canvas3dInteractionHelperParams = {
     maxFps: PD.Numeric(30, { min: 10, max: 60, step: 10 }),
     preferAtomPixelPadding: PD.Numeric(3, { min: 0, max: 20, step: 1 }, { description: 'Number of extra pixels at which to prefer atoms over bonds.' }),
+    convertCoordsToRay: PD.Boolean(false, { description: 'Convert screen coordinates to ray for picking.' }),
 };
 export type Canvas3dInteractionHelperParams = typeof Canvas3dInteractionHelperParams
 export type Canvas3dInteractionHelperProps = PD.Values<Canvas3dInteractionHelperParams>
@@ -47,10 +48,11 @@ export class Canvas3dInteractionHelper {
     private endX = -1;
     private endY = -1;
 
-    private id: PickingId | undefined = void 0;
+    private ray: Ray3D | undefined = void 0;
+
+    private pickData: AsyncPickData | undefined = void 0;
     private position: Vec3 | undefined = void 0;
 
-    private currentIdentifyT = 0;
     private isInteracting = false;
 
     private prevLoci: Representation.Loci = Representation.Loci.Empty;
@@ -68,46 +70,66 @@ export class Canvas3dInteractionHelper {
         Object.assign(this.props, props);
     }
 
-    private identify(e: InputEvent, t: number) {
-        const xyChanged = this.startX !== this.endX || this.startY !== this.endY || (this.input.pointerLock && !this.controls.isMoving);
-
-        if (e === InputEvent.Drag) {
-            if (xyChanged && !this.outsideViewport(this.startX, this.startY)) {
-                this.events.drag.next({ current: this.prevLoci, buttons: this.buttons, button: this.button, modifiers: this.modifiers, pageStart: Vec2.create(this.startX, this.startY), pageEnd: Vec2.create(this.endX, this.endY) });
-
-                this.startX = this.endX;
-                this.startY = this.endY;
-            }
-            return;
+    private getTarget(): Vec2 | Ray3D {
+        if (this.ray) {
+            return this.ray;
+        } else if (this.props.convertCoordsToRay) {
+            return this.camera.getRay(Ray3D(), this.endX, this.input.height - this.endY);
+        } else {
+            return Vec2.create(this.endX, this.endY);
         }
+    }
 
+    private handleMove() {
+        const xyChanged = this.startX !== this.endX || this.startY !== this.endY || (this.input.pointerLock && !this.controls.isMoving);
         if (xyChanged) {
-            const pickData = this.canvasIdentify(this.endX, this.endY);
-            this.id = pickData?.id;
-            this.position = pickData?.position;
+            this.pickData = this.canvasAsyncIdentify(this.getTarget());
             this.startX = this.endX;
             this.startY = this.endY;
         }
+    }
 
-        if (e === InputEvent.Click) {
-            const loci = this.getLoci(this.id, this.position);
-            this.events.click.next({ current: loci, buttons: this.buttons, button: this.button, modifiers: this.modifiers, page: Vec2.create(this.endX, this.endY), position: this.position });
-            this.prevLoci = loci;
-            return;
-        }
-
-        if (!this.inside || this.currentIdentifyT !== t || !xyChanged || this.outsideViewport(this.endX, this.endY)) return;
-
-        const loci = this.getLoci(this.id, this.position);
-        this.events.hover.next({ current: loci, buttons: this.buttons, button: this.button, modifiers: this.modifiers, page: Vec2.create(this.endX, this.endY), position: this.position });
+    private handleClick() {
+        const pickData = this.canvasIdentify(this.getTarget());
+        const loci = this.getLoci(pickData?.id, pickData?.position);
+        this.events.click.next({ current: loci, buttons: this.buttons, button: this.button, modifiers: this.modifiers, page: Vec2.create(this.endX, this.endY), position: pickData?.position });
         this.prevLoci = loci;
     }
 
+    private handleDrag() {
+        const xyChanged = this.startX !== this.endX || this.startY !== this.endY || (this.input.pointerLock && !this.controls.isMoving);
+
+        if (xyChanged && !this.outsideViewport(this.startX, this.startY, this.ray)) {
+            this.events.drag.next({ current: this.prevLoci, buttons: this.buttons, button: this.button, modifiers: this.modifiers, pageStart: Vec2.create(this.startX, this.startY), pageEnd: Vec2.create(this.endX, this.endY) });
+
+            this.startX = this.endX;
+            this.startY = this.endY;
+        }
+    }
+
     tick(t: number) {
-        if (this.inside && t - this.prevT > 1000 / this.props.maxFps) {
+        if (!this.inside) return;
+
+        if (this.pickData) {
+            const pickData = this.pickData.tryGet();
+            if (pickData !== 'pending') {
+                this.position = pickData?.position;
+                if (this.inside) {
+                    const loci = this.getLoci(pickData?.id, pickData?.position);
+                    this.events.hover.next({ current: loci, buttons: this.buttons, button: this.button, modifiers: this.modifiers, page: Vec2.create(this.endX, this.endY), position: pickData?.position });
+                    this.prevLoci = loci;
+                }
+                this.pickData = undefined;
+            }
+        }
+
+        if (t - this.prevT > 1000 / this.props.maxFps) {
             this.prevT = t;
-            this.currentIdentifyT = t;
-            this.identify(this.isInteracting ? InputEvent.Drag : InputEvent.Move, t);
+            if (this.isInteracting) {
+                this.handleDrag();
+            } else {
+                this.handleMove();
+            }
         }
     }
 
@@ -119,22 +141,24 @@ export class Canvas3dInteractionHelper {
         }
     }
 
-    private move(x: number, y: number, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys) {
+    private move(x: number, y: number, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys, ray?: Ray3D) {
         this.inside = true;
         this.buttons = buttons;
         this.button = button;
         this.modifiers = modifiers;
+        this.ray = ray;
         this.endX = x;
         this.endY = y;
     }
 
-    private click(x: number, y: number, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys) {
+    private click(x: number, y: number, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys, ray?: Ray3D) {
         this.endX = x;
         this.endY = y;
         this.buttons = buttons;
         this.button = button;
         this.modifiers = modifiers;
-        this.identify(InputEvent.Click, 0);
+        this.ray = ray;
+        this.handleClick();
     }
 
     private drag(x: number, y: number, buttons: ButtonsType, button: ButtonsType.Flag, modifiers: ModifiersKeys) {
@@ -143,7 +167,7 @@ export class Canvas3dInteractionHelper {
         this.buttons = buttons;
         this.button = button;
         this.modifiers = modifiers;
-        this.identify(InputEvent.Drag, 0);
+        this.handleDrag();
     }
 
     private modify(modifiers: ModifiersKeys) {
@@ -152,7 +176,9 @@ export class Canvas3dInteractionHelper {
         this.events.hover.next({ current: this.prevLoci, buttons: this.buttons, button: this.button, modifiers: this.modifiers, page: Vec2.create(this.endX, this.endY), position: this.position });
     }
 
-    private outsideViewport(x: number, y: number) {
+    private outsideViewport(x: number, y: number, ray?: Ray3D) {
+        if (ray) return false;
+
         const { input, camera: { viewport } } = this;
         x *= input.pixelRatio;
         y *= input.pixelRatio;
@@ -189,7 +215,7 @@ export class Canvas3dInteractionHelper {
         this.ev.dispose();
     }
 
-    constructor(private canvasIdentify: Canvas3D['identify'], private lociGetter: Canvas3D['getLoci'], private input: InputObserver, private camera: Camera, private controls: TrackballControls, props: Partial<Canvas3dInteractionHelperProps> = {}) {
+    constructor(private canvasIdentify: Canvas3D['identify'], private canvasAsyncIdentify: Canvas3D['asyncIdentify'], private lociGetter: Canvas3D['getLoci'], private input: InputObserver, private camera: Camera, private controls: TrackballControls, props: Partial<Canvas3dInteractionHelperProps> = {}) {
         this.props = { ...PD.getDefaultValues(Canvas3dInteractionHelperParams), ...props };
 
         input.drag.subscribe(({ x, y, buttons, button, modifiers }) => {
@@ -198,14 +224,14 @@ export class Canvas3dInteractionHelper {
             this.drag(x, y, buttons, button, modifiers);
         });
 
-        input.move.subscribe(({ x, y, inside, buttons, button, modifiers, onElement }) => {
+        input.move.subscribe(({ x, y, inside, buttons, button, modifiers, onElement, ray }) => {
             if (!inside || this.isInteracting) return;
             if (!onElement) {
                 this.leave();
                 return;
             }
             // console.log('move');
-            this.move(x, y, buttons, button, modifiers);
+            this.move(x, y, buttons, button, modifiers, ray);
         });
 
         input.leave.subscribe(() => {
@@ -213,10 +239,10 @@ export class Canvas3dInteractionHelper {
             this.leave();
         });
 
-        input.click.subscribe(({ x, y, buttons, button, modifiers }) => {
-            if (this.outsideViewport(x, y)) return;
+        input.click.subscribe(({ x, y, buttons, button, modifiers, ray }) => {
+            if (this.outsideViewport(x, y, ray)) return;
             // console.log('click');
-            this.click(x, y, buttons, button, modifiers);
+            this.click(x, y, buttons, button, modifiers, ray);
         });
 
         input.interactionEnd.subscribe(() => {

src/mol-canvas3d/helper/pick-helper.ts

@@ -0,0 +1,208 @@
+/**
+ * Copyright (c) 2019-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Renderer } from '../../mol-gl/renderer';
+import { Scene } from '../../mol-gl/scene';
+import { WebGLContext } from '../../mol-gl/webgl/context';
+import { Vec3 } from '../../mol-math/linear-algebra/3d/vec3';
+import { spiral2d } from '../../mol-math/misc';
+import { isTimingMode } from '../../mol-util/debug';
+import { Camera } from '../camera';
+import { StereoCamera } from '../camera/stereo';
+import { cameraUnproject, Viewport } from '../camera/util';
+import { Helper } from '../helper/helper';
+import { AsyncPickData, AsyncPickStatus, checkAsyncPickingSupport, PickBuffers, PickData, PickOptions, PickPass } from '../passes/pick';
+
+export class PickHelper {
+    dirty = true;
+
+    private pickPadding: number;
+    private buffers = new PickBuffers(this.webgl, this.pickPass);
+    private viewport = Viewport();
+
+    private pickRatio: number;
+    private pickX: number;
+    private pickY: number;
+    private pickWidth: number;
+    private pickHeight: number;
+    private halfPickWidth: number;
+
+    private spiral: [number, number][];
+
+    setViewport(x: number, y: number, width: number, height: number) {
+        Viewport.set(this.viewport, x, y, width, height);
+        this.update();
+    }
+
+    setPickPadding(pickPadding: number) {
+        if (this.pickPadding !== pickPadding) {
+            this.pickPadding = pickPadding;
+            this.update();
+        }
+    }
+
+    private update() {
+        const { x, y, width, height } = this.viewport;
+
+        this.pickRatio = this.pickPass.pickRatio;
+        this.pickX = Math.ceil(x * this.pickRatio);
+        this.pickY = Math.ceil(y * this.pickRatio);
+
+        const pickWidth = Math.floor(width * this.pickRatio);
+        const pickHeight = Math.floor(height * this.pickRatio);
+
+        if (pickWidth !== this.pickWidth || pickHeight !== this.pickHeight) {
+            this.pickWidth = pickWidth;
+            this.pickHeight = pickHeight;
+            this.halfPickWidth = Math.floor(this.pickWidth / 2);
+
+            this.buffers.setViewport(this.pickX, this.pickY, this.pickWidth, this.pickHeight);
+        }
+
+        this.spiral = spiral2d(Math.ceil(this.pickRatio * this.pickPadding));
+        this.dirty = true;
+    }
+
+    private render(camera: Camera | StereoCamera) {
+        if (isTimingMode) this.webgl.timer.mark('PickHelper.render', { captureStats: true });
+        const { pickX, pickY, pickWidth, pickHeight, halfPickWidth } = this;
+        const { renderer, scene, helper } = this;
+
+        renderer.setTransparentBackground(false);
+        renderer.setDrawingBufferSize(pickWidth, pickHeight);
+        renderer.setPixelRatio(this.pickRatio);
+
+        if (StereoCamera.is(camera)) {
+            renderer.setViewport(pickX, pickY, halfPickWidth, pickHeight);
+            this.pickPass.render(renderer, camera.left, scene, helper);
+
+            renderer.setViewport(pickX + halfPickWidth, pickY, pickWidth - halfPickWidth, pickHeight);
+            this.pickPass.render(renderer, camera.right, scene, helper);
+        } else {
+            renderer.setViewport(pickX, pickY, pickWidth, pickHeight);
+            this.pickPass.render(renderer, camera, scene, helper);
+        }
+
+        this.dirty = false;
+        if (isTimingMode) this.webgl.timer.markEnd('PickHelper.render');
+    }
+
+    private identifyInternal(x: number, y: number, camera: Camera | StereoCamera): PickData | undefined {
+        if (this.webgl.isContextLost) return;
+
+        const { webgl, pickRatio } = this;
+        if (webgl.isContextLost) return;
+
+        x *= webgl.pixelRatio;
+        y *= webgl.pixelRatio;
+        y = this.pickPass.drawingBufferHeight - y; // flip y
+
+        const { viewport } = this;
+
+        // check if within viewport
+        if (x < viewport.x ||
+            y < viewport.y ||
+            x > viewport.x + viewport.width ||
+            y > viewport.y + viewport.height
+        ) return;
+
+        const xv = x - viewport.x;
+        const yv = y - viewport.y;
+
+        const xp = Math.floor(xv * pickRatio);
+        const yp = Math.floor(yv * pickRatio);
+
+        const pickingId = this.buffers.getPickingId(xp, yp);
+        if (pickingId === undefined) return;
+
+        const z = this.buffers.getDepth(xp, yp);
+        const position = Vec3.create(x, y, z);
+        if (StereoCamera.is(camera)) {
+            const halfWidth = Math.floor(viewport.width / 2);
+            if (x > viewport.x + halfWidth) {
+                position[0] = viewport.x + (xv - halfWidth) * 2;
+                cameraUnproject(position, position, viewport, camera.right.inverseProjectionView);
+            } else {
+                position[0] = viewport.x + xv * 2;
+                cameraUnproject(position, position, viewport, camera.left.inverseProjectionView);
+            }
+        } else {
+            cameraUnproject(position, position, viewport, camera.inverseProjectionView);
+        }
+
+        return { id: pickingId, position };
+    }
+
+    private prepare() {
+        if (this.pickRatio !== this.pickPass.pickRatio) {
+            this.update();
+        }
+    }
+
+    private getPickData(x: number, y: number, camera: Camera | StereoCamera): PickData | undefined {
+        for (const d of this.spiral) {
+            const pickData = this.identifyInternal(x + d[0], y + d[1], camera);
+            if (pickData) return pickData;
+        }
+    }
+
+    identify(x: number, y: number, camera: Camera | StereoCamera): PickData | undefined {
+        this.prepare();
+
+        if (this.dirty) {
+            if (isTimingMode) this.webgl.timer.mark('PickHelper.identify');
+            this.render(camera);
+            this.buffers.read();
+            if (isTimingMode) this.webgl.timer.markEnd('PickHelper.identify');
+        }
+
+        return this.getPickData(x, y, camera);
+    }
+
+    asyncIdentify(x: number, y: number, camera: Camera | StereoCamera): AsyncPickData | undefined {
+        this.prepare();
+
+        if (this.dirty) {
+            if (isTimingMode) this.webgl.timer.mark('PickHelper.asyncIdentify');
+            this.render(camera);
+            this.buffers.asyncRead();
+            if (isTimingMode) this.webgl.timer.markEnd('PickHelper.asyncIdentify');
+        }
+
+        return {
+            tryGet: () => {
+                const status = this.buffers.check();
+                if (status === AsyncPickStatus.Resolved) {
+                    return this.getPickData(x, y, camera);
+                } else if (status === AsyncPickStatus.Pending) {
+                    return 'pending';
+                } else if (status === AsyncPickStatus.Failed) {
+                    this.dirty = true;
+                }
+            }
+        };
+    }
+
+    reset() {
+        this.buffers.reset();
+        this.dirty = true;
+    }
+
+    dispose() {
+        this.buffers.dispose();
+    }
+
+    constructor(private webgl: WebGLContext, private renderer: Renderer, private scene: Scene, private helper: Helper, private pickPass: PickPass, viewport: Viewport, options: PickOptions) {
+        this.setViewport(viewport.x, viewport.y, viewport.width, viewport.height);
+        this.pickPadding = options.pickPadding;
+
+        if (!checkAsyncPickingSupport(webgl)) {
+            this.asyncIdentify = (x, y, camera) => ({
+                tryGet: () => this.identify(x, y, camera)
+            });
+        }
+    }
+}

src/mol-canvas3d/helper/ray-helper.ts

@@ -0,0 +1,205 @@
+/**
+ * Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Renderer } from '../../mol-gl/renderer';
+import { Scene } from '../../mol-gl/scene';
+import { WebGLContext } from '../../mol-gl/webgl/context';
+import { Ray3D } from '../../mol-math/geometry/primitives/ray3d';
+import { Mat4, Quat, Vec3 } from '../../mol-math/linear-algebra';
+import { degToRad, spiral2d } from '../../mol-math/misc';
+import { isTimingMode } from '../../mol-util/debug';
+import { Camera } from '../camera';
+import { cameraUnproject } from '../camera/util';
+import { Viewport } from '../camera/util';
+import { Helper } from './helper';
+import { AsyncPickData, PickBuffers, PickData, PickPass, PickOptions, checkAsyncPickingSupport, AsyncPickStatus } from '../passes/pick';
+import { Sphere3D } from '../../mol-math/geometry/primitives/sphere3d';
+
+export class RayHelper {
+    private viewport = Viewport();
+    private size: number;
+    private spiral: [number, number][];
+
+    private pickPadding: number;
+    private camera: Camera;
+    private pickPass: PickPass;
+    private buffers: PickBuffers;
+
+    setPickPadding(pickPadding: number) {
+        if (this.pickPadding !== pickPadding) {
+            this.pickPadding = pickPadding;
+            this.update();
+        }
+    }
+
+    private update() {
+        const size = this.pickPadding * 2 + 1;
+        Viewport.set(this.viewport, 0, 0, size, size);
+        this.buffers.setViewport(0, 0, size, size);
+
+        this.spiral = spiral2d(this.pickPadding);
+        this.size = size;
+
+        this.pickPass.setSize(size, size);
+    }
+
+    private render(camera: Camera) {
+        if (isTimingMode) this.webgl.timer.mark('RayHelper.render', { captureStats: true });
+        const { renderer, scene, helper } = this;
+
+        renderer.setTransparentBackground(false);
+        renderer.setDrawingBufferSize(this.size, this.size);
+        renderer.setPixelRatio(1);
+
+        renderer.setViewport(0, 0, this.size, this.size);
+        this.pickPass.render(renderer, camera, scene, helper);
+
+        if (isTimingMode) this.webgl.timer.markEnd('RayHelper.render');
+    }
+
+    private identifyInternal(x: number, y: number): PickData | undefined {
+        if (this.webgl.isContextLost) return;
+
+        const { viewport } = this;
+
+        const pickingId = this.buffers.getPickingId(x, y);
+        if (pickingId === undefined) return;
+
+        const z = this.buffers.getDepth(x, y);
+        const position = Vec3.create(x, y, z);
+        cameraUnproject(position, position, viewport, this.camera.inverseProjectionView);
+
+        return { id: pickingId, position };
+    }
+
+    private prepare(ray: Ray3D, cam: Camera) {
+        this.camera.far = cam.far;
+        this.camera.near = cam.near;
+        this.camera.fogFar = cam.fogFar;
+        this.camera.fogNear = cam.fogNear;
+        Viewport.copy(this.camera.viewport, this.viewport);
+        Camera.copySnapshot(this.camera.state, { ...cam.state, mode: 'orthographic' });
+
+        updateOrthoRayCamera(this.camera, ray);
+        Mat4.mul(this.camera.projectionView, this.camera.projection, this.camera.view);
+        Mat4.tryInvert(this.camera.inverseProjectionView, this.camera.projectionView);
+    }
+
+    private getPickData(): PickData | undefined {
+        const c = this.pickPadding;
+        for (const d of this.spiral) {
+            const pickData = this.identifyInternal(c + d[0], c + d[1]);
+            if (pickData) return pickData;
+        }
+    }
+
+    sphere = Sphere3D();
+
+    private intersectsScene(ray: Ray3D, scale: number): boolean {
+        Sphere3D.scaleNX(this.sphere, this.scene.boundingSphereVisible, scale);
+        return Ray3D.isInsideSphere3D(ray, this.sphere) || Ray3D.isIntersectingSphere3D(ray, this.sphere);
+    }
+
+    identify(ray: Ray3D, cam: Camera): PickData | undefined {
+        if (!this.intersectsScene(ray, cam.state.scale)) return;
+
+        this.prepare(ray, cam);
+
+        if (isTimingMode) this.webgl.timer.mark('RayHelper.identify');
+        this.render(this.camera);
+        this.buffers.read();
+        if (isTimingMode) this.webgl.timer.markEnd('RayHelper.identify');
+
+        return this.getPickData();
+    }
+
+    asyncIdentify(ray: Ray3D, cam: Camera): AsyncPickData | undefined {
+        if (!this.intersectsScene(ray, cam.state.scale)) return;
+
+        this.prepare(ray, cam);
+
+        if (isTimingMode) this.webgl.timer.mark('RayHelper.asyncIdentify');
+        this.render(this.camera);
+        this.buffers.asyncRead();
+        if (isTimingMode) this.webgl.timer.markEnd('RayHelper.asyncIdentify');
+
+        return {
+            tryGet: () => {
+                const status = this.buffers.check();
+                if (status === AsyncPickStatus.Resolved) {
+                    return this.getPickData();
+                } else if (status === AsyncPickStatus.Pending) {
+                    return 'pending';
+                }
+            }
+        };
+    }
+
+    reset() {
+        this.buffers.reset();
+        this.pickPass.reset();
+    }
+
+    dispose() {
+        this.buffers.dispose();
+        this.pickPass.dispose();
+    }
+
+    constructor(private webgl: WebGLContext, private renderer: Renderer, private scene: Scene, private helper: Helper, options: PickOptions) {
+        const size = options.pickPadding * 2 + 1;
+
+        this.camera = new Camera();
+        this.pickPass = new PickPass(webgl, size, size, 1);
+        this.buffers = new PickBuffers(this.webgl, this.pickPass, options.maxAsyncReadLag);
+        this.pickPadding = options.pickPadding;
+
+        this.update();
+
+        if (!checkAsyncPickingSupport(webgl)) {
+            this.asyncIdentify = (ray, cam) => ({
+                tryGet: () => this.identify(ray, cam)
+            });
+        }
+    }
+}
+
+//
+
+function updateOrthoRayCamera(camera: Camera, ray: Ray3D) {
+    const { near, far, viewport } = camera;
+
+    const height = 2 * Math.tan(degToRad(0.1) / 2) * Vec3.distance(camera.position, camera.target) * camera.state.scale;
+    const zoom = viewport.height / height;
+
+    const fullLeft = -viewport.width / 2;
+    const fullRight = viewport.width / 2;
+    const fullTop = viewport.height / 2;
+    const fullBottom = -viewport.height / 2;
+
+    const dx = (fullRight - fullLeft) / (2 * zoom);
+    const dy = (fullTop - fullBottom) / (2 * zoom);
+    const cx = (fullRight + fullLeft) / 2;
+    const cy = (fullTop + fullBottom) / 2;
+
+    const left = cx - dx;
+    const right = cx + dx;
+    const top = cy + dy;
+    const bottom = cy - dy;
+
+    // build projection matrix
+    Mat4.ortho(camera.projection, left, right, top, bottom, near, far);
+
+    const direction = Vec3.normalize(Vec3(), ray.direction);
+    const r = Quat.fromUnitVec3(Quat(), direction, Vec3.negUnitZ);
+    Quat.invert(r, r);
+
+    const eye = Vec3.clone(ray.origin);
+    const up = Vec3.transformQuat(Vec3(), Vec3.unitY, r);
+    const target = Vec3.add(Vec3(), eye, direction);
+
+    // build view matrix
+    Mat4.lookAt(camera.view, eye, target, up);
+}

src/mol-canvas3d/passes/background.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2022-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2022-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -26,6 +26,7 @@ import { Vec4 } from '../../mol-math/linear-algebra/3d/vec4';
 import { degToRad, isPowerOfTwo } from '../../mol-math/misc';
 import { Mat3 } from '../../mol-math/linear-algebra/3d/mat3';
 import { Euler } from '../../mol-math/linear-algebra/3d/euler';
+import { PostprocessingProps } from './postprocessing';
 
 const SharedParams = {
     opacity: PD.Numeric(1, { min: 0.0, max: 1.0, step: 0.01 }),
@@ -172,10 +173,14 @@ export class BackgroundPass {
         }
 
         const m = this.renderable.values.uViewDirectionProjectionInverse.ref.value;
-        Vec3.sub(this.dir, cam.state.position, cam.state.target);
-        Vec3.setMagnitude(this.dir, this.dir, 0.1);
-        Vec3.copy(this.position, this.dir);
-        Mat4.lookAt(m, this.position, this.target, cam.state.up);
+        if (Mat4.isZero(camera.headRotation)) {
+            Vec3.sub(this.dir, cam.state.position, cam.state.target);
+            Vec3.setMagnitude(this.dir, this.dir, 0.1);
+            Vec3.copy(this.position, this.dir);
+            Mat4.lookAt(m, this.position, this.target, cam.state.up);
+        } else {
+            Mat4.invert(m, camera.headRotation);
+        }
         Mat4.mul(m, cam.projection, m);
         Mat4.invert(m, m);
         ValueCell.update(this.renderable.values.uViewDirectionProjectionInverse, m);
@@ -292,7 +297,7 @@ export class BackgroundPass {
         ValueCell.update(this.renderable.values.uViewport, Vec4.set(this.renderable.values.uViewport.ref.value, x, y, width, height));
     }
 
-    isEnabled(props: BackgroundProps) {
+    private _isEnabled(props: BackgroundProps) {
         return !!(
             (this.skybox && this.skybox.loaded) ||
             (this.image && this.image.loaded) ||
@@ -301,6 +306,10 @@ export class BackgroundPass {
         );
     }
 
+    isEnabled(props: PostprocessingProps) {
+        return props.enabled && this._isEnabled(props.background);
+    }
+
     private isReady() {
         return !!(
             (this.skybox && this.skybox.loaded) ||
@@ -315,7 +324,7 @@ export class BackgroundPass {
     clear(props: BackgroundProps, transparentBackground: boolean, backgroundColor: Color) {
         const { gl, state } = this.webgl;
 
-        if (this.isEnabled(props)) {
+        if (this._isEnabled(props)) {
             if (transparentBackground) {
                 state.clearColor(0, 0, 0, 0);
             } else {
@@ -332,7 +341,7 @@ export class BackgroundPass {
     }
 
     render(props: BackgroundProps) {
-        if (!this.isEnabled(props) || !this.isReady()) return;
+        if (!this._isEnabled(props) || !this.isReady()) return;
 
         if (this.renderable.values.dVariant.ref.value === 'image') {
             this.updateImageScaling();

src/mol-canvas3d/passes/bloom.ts

@@ -38,7 +38,7 @@ export type BloomProps = PD.Values<typeof BloomParams>
 
 export class BloomPass {
     static isEnabled(props: PostprocessingProps) {
-        return props.bloom.name === 'on';
+        return props.enabled && props.bloom.name === 'on';
     }
 
     readonly emissiveTarget: RenderTarget;

src/mol-canvas3d/passes/dof.ts

@@ -37,7 +37,7 @@ export type DofProps = PD.Values<typeof DofParams>
 
 export class DofPass {
     static isEnabled(props: PostprocessingProps) {
-        return props.dof.name !== 'off';
+        return props.enabled && props.dof.name !== 'off';
     }
 
     readonly target: RenderTarget;
@@ -119,18 +119,18 @@ export class DofPass {
             needsUpdate = true;
         }
 
-        const wolrdCenter = (props.center === 'scene-center' ? sphere.center : camera.state.target);
-        const distance = Vec3.distance(camera.state.position, wolrdCenter);
+        const worldCenter = (props.center === 'scene-center' ? sphere.center : camera.state.target);
+        const distance = Vec3.distance(camera.state.position, worldCenter);
         const inFocus = distance + props.inFocus;
-        ValueCell.updateIfChanged(this.renderable.values.uInFocus, inFocus);
+        ValueCell.updateIfChanged(this.renderable.values.uInFocus, inFocus * camera.state.scale);
 
         // transform center in view space
         const center = this.renderable.values.uCenter.ref.value;
-        Vec3.transformMat4(center, wolrdCenter, camera.view);
+        Vec3.transformMat4(center, worldCenter, camera.view);
         ValueCell.update(this.renderable.values.uCenter, center);
 
         ValueCell.updateIfChanged(this.renderable.values.uBlurSpread, props.blurSpread);
-        ValueCell.updateIfChanged(this.renderable.values.uPPM, props.PPM);
+        ValueCell.updateIfChanged(this.renderable.values.uPPM, props.PPM * camera.state.scale);
 
         if (needsUpdate) {
             this.renderable.update();

src/mol-canvas3d/passes/dpoit.ts

@@ -167,6 +167,7 @@ export class DpoitPass {
         if (isTimingMode) this.webgl.timer.mark('DpoitPass.render');
         const { state, gl } = this.webgl;
 
+        state.blendEquation(gl.FUNC_ADD);
         state.blendFunc(gl.ONE, gl.ONE_MINUS_SRC_ALPHA);
 
         ValueCell.update(this.renderable.values.tDpoitFrontColor, this.colorFrontTextures[this.writeId]);

src/mol-canvas3d/passes/draw.ts

@@ -198,8 +198,10 @@ export class DrawPass {
                 const dpoitTextures = this.dpoit.bindDualDepthPeeling();
                 renderer.renderDpoitTransparent(scene.primitives, camera, this.depthTextureOpaque, dpoitTextures);
 
-                target.bind();
-                this.dpoit.renderBlendBack();
+                if (iterations > 1) {
+                    target.bind();
+                    this.dpoit.renderBlendBack();
+                }
                 if (isTimingMode) this.webgl.timer.markEnd('DpoitPass.layer');
             }
 
@@ -377,6 +379,7 @@ export class DrawPass {
         const antialiasingEnabled = AntialiasingPass.isEnabled(props.postprocessing);
         const markingEnabled = MarkingPass.isEnabled(props.marking);
         const dofEnabled = DofPass.isEnabled(props.postprocessing);
+        const bloomEnabled = BloomPass.isEnabled(props.postprocessing);
 
         const { x, y, width, height } = camera.viewport;
         renderer.setViewport(x, y, width, height);
@@ -446,7 +449,7 @@ export class DrawPass {
             needsTargetCopy = true;
         }
 
-        if (props.postprocessing.dof.name === 'on') {
+        if (dofEnabled && props.postprocessing.dof.name === 'on') {
             const input = AntialiasingPass.isEnabled(props.postprocessing)
                 ? this.antialiasing.target.texture
                 : PostprocessingPass.isEnabled(props.postprocessing)
@@ -469,7 +472,7 @@ export class DrawPass {
             }
         }
 
-        if (props.postprocessing.bloom.name === 'on') {
+        if (bloomEnabled && props.postprocessing.bloom.name === 'on') {
             const emissiveBloom = props.postprocessing.bloom.params.mode === 'emissive';
 
             if (emissiveBloom && scene.emissiveAverage > 0) {
@@ -493,7 +496,7 @@ export class DrawPass {
         const { renderer, camera, scene, helper } = ctx;
 
         this.postprocessing.setTransparentBackground(props.transparentBackground);
-        const transparentBackground = props.transparentBackground || this.postprocessing.background.isEnabled(props.postprocessing.background);
+        const transparentBackground = props.transparentBackground || this.postprocessing.background.isEnabled(props.postprocessing);
 
         renderer.setTransparentBackground(transparentBackground);
         renderer.setDrawingBufferSize(this.colorTarget.getWidth(), this.colorTarget.getHeight());

src/mol-canvas3d/passes/hi-z.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -20,7 +20,7 @@ import { Camera } from '../camera';
 import { Viewport } from '../camera/util';
 import { DrawPass } from './draw';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { getBuffer } from '../../mol-gl/webgl/buffer';
+import { PixelPackBuffer } from '../../mol-gl/webgl/buffer';
 
 // avoiding namespace lookup improved performance in Chrome (Aug 2020)
 const v3transformMat4 = Vec3.transformMat4;
@@ -128,7 +128,7 @@ export class HiZPass {
 
     private readonly levelData: LevelData = [];
     private readonly fb: Framebuffer;
-    private readonly buf: WebGLBuffer;
+    private readonly buf: PixelPackBuffer;
     private readonly tex: Texture;
     private readonly renderable: HiZRenderable;
     private readonly supported: boolean;
@@ -221,10 +221,7 @@ export class HiZPass {
         const hw = this.tex.getWidth();
         const hh = this.tex.getHeight();
 
-        gl.bindBuffer(gl.PIXEL_PACK_BUFFER, this.buf);
-        gl.bufferData(gl.PIXEL_PACK_BUFFER, this.buffer.byteLength, gl.STREAM_READ);
-        gl.readPixels(0, 0, hw, hh, gl.RED, gl.FLOAT, 0);
-        gl.bindBuffer(gl.PIXEL_PACK_BUFFER, null);
+        this.buf.read(0, 0, hw, hh);
 
         this.sync = gl.fenceSync(gl.SYNC_GPU_COMMANDS_COMPLETE, 0);
         gl.flush();
@@ -249,9 +246,7 @@ export class HiZPass {
             this.frameLag += 1;
             // console.log(`waiting for buffer data for ${this.frameLag} frames`);
         } else {
-            gl.bindBuffer(gl.PIXEL_PACK_BUFFER, this.buf);
-            gl.getBufferSubData(gl.PIXEL_PACK_BUFFER, 0, this.buffer);
-            gl.bindBuffer(gl.PIXEL_PACK_BUFFER, null);
+            this.buf.getSubData(this.buffer);
             // console.log(`got buffer data after ${this.frameLag + 1} frames`);
             gl.deleteSync(this.sync);
             this.sync = null;
@@ -510,6 +505,16 @@ export class HiZPass {
 
     //
 
+    reset() {
+        this.sync = null;
+        this.ready = false;
+        this.frameLag = 0;
+        this.levelData.length = 0;
+
+        const { x, y, width, height } = this.viewport;
+        this.setViewport(x, y, width, height);
+    }
+
     dispose() {
         if (!this.supported) return;
 
@@ -517,7 +522,7 @@ export class HiZPass {
 
         this.fb.destroy();
         this.tex.destroy();
-        this.webgl.gl.deleteBuffer(this.buf);
+        this.buf.destroy();
         this.renderable.dispose();
 
         for (const td of this.levelData) {
@@ -527,6 +532,8 @@ export class HiZPass {
     }
 
     constructor(private webgl: WebGLContext, private drawPass: DrawPass, canvas: HTMLCanvasElement | undefined, props: Partial<HiZProps>) {
+        this.props = { ...PD.getDefaultValues(HiZParams), ...props };
+
         const { gl, extensions } = webgl;
         if (!isWebGL2(gl) || !extensions.colorBufferFloat) {
             if (isDebugMode) {
@@ -552,8 +559,7 @@ export class HiZPass {
         }
 
         this.supported = true;
-        this.props = { ...PD.getDefaultValues(HiZParams), ...props };
-        this.buf = getBuffer(gl);
+        this.buf = webgl.resources.pixelPack('alpha', 'float');
         this.renderable = createHiZRenderable(webgl, this.drawPass.depthTextureOpaque);
 
         if (isDebugMode && canvas) {

src/mol-canvas3d/passes/illumination.ts

@@ -33,6 +33,8 @@ import { JitterVectors, MultiSampleProps } from './multi-sample';
 import { compose_frag as multiSample_compose_frag } from '../../mol-gl/shader/compose.frag';
 import { clamp, lerp } from '../../mol-math/interpolate';
 import { SsaoProps } from './ssao';
+import { OutlinePass } from './outline';
+import { BloomPass } from './bloom';
 
 type Props = {
     transparentBackground: boolean;
@@ -169,13 +171,15 @@ export class IlluminationPass {
                 const dpoitTextures = this.drawPass.dpoit.bind();
                 renderer.renderDpoitTransparent(scene.primitives, camera, this.drawPass.depthTextureOpaque, dpoitTextures);
 
-                for (let i = 0, il = props.dpoitIterations; i < il; i++) {
+                for (let i = 0, iterations = props.dpoitIterations; i < iterations; i++) {
                     if (isTimingMode) this.webgl.timer.mark('DpoitPass.layer');
                     const dpoitTextures = this.drawPass.dpoit.bindDualDepthPeeling();
                     renderer.renderDpoitTransparent(scene.primitives, camera, this.drawPass.depthTextureOpaque, dpoitTextures);
 
-                    this.transparentTarget.bind();
-                    this.drawPass.dpoit.renderBlendBack();
+                    if (iterations > 1) {
+                        this.transparentTarget.bind();
+                        this.drawPass.dpoit.renderBlendBack();
+                    }
                     if (isTimingMode) this.webgl.timer.markEnd('DpoitPass.layer');
                 }
 
@@ -313,8 +317,11 @@ export class IlluminationPass {
 
         const orthographic = camera.state.mode === 'orthographic' ? 1 : 0;
 
-        const outlinesEnabled = props.postprocessing.outline.name === 'on' && !props.illumination.ignoreOutline;
+        const antialiasingEnabled = AntialiasingPass.isEnabled(props.postprocessing);
+        const outlinesEnabled = OutlinePass.isEnabled(props.postprocessing) && !props.illumination.ignoreOutline;
         const occlusionEnabled = PostprocessingPass.isTransparentSsaoEnabled(scene, props.postprocessing);
+        const bloomEnabled = BloomPass.isEnabled(props.postprocessing);
+        const dofEnabled = DofPass.isEnabled(props.postprocessing);
 
         const markingEnabled = MarkingPass.isEnabled(props.marking);
         const hasTransparent = scene.opacityAverage < 1;
@@ -327,7 +334,7 @@ export class IlluminationPass {
             ValueCell.update(this.composeRenderable.values.dOutlineEnable, outlinesEnabled);
         }
 
-        if (props.postprocessing.outline.name === 'on') {
+        if (outlinesEnabled && props.postprocessing.outline.name === 'on') {
             const { transparentOutline, outlineScale } = this.drawPass.postprocessing.outline.update(camera, props.postprocessing.outline.params, this.drawPass.depthTargetTransparent.texture, this.drawPass.depthTextureOpaque);
             this.drawPass.postprocessing.outline.render();
 
@@ -348,7 +355,7 @@ export class IlluminationPass {
             ValueCell.update(this.composeRenderable.values.dOcclusionEnable, occlusionEnabled);
         }
 
-        if (props.postprocessing.occlusion.name === 'on') {
+        if (occlusionEnabled && props.postprocessing.occlusion.name === 'on') {
             ValueCell.update(this.composeRenderable.values.uOcclusionColor, Color.toVec3Normalized(this.composeRenderable.values.uOcclusionColor.ref.value, props.postprocessing.occlusion.params.color));
         }
 
@@ -370,7 +377,7 @@ export class IlluminationPass {
 
         // background
 
-        const _toDrawingBuffer = toDrawingBuffer && !AntialiasingPass.isEnabled(props.postprocessing) && props.postprocessing.dof.name === 'off';
+        const _toDrawingBuffer = toDrawingBuffer && !antialiasingEnabled && !dofEnabled;
         if (_toDrawingBuffer) {
             this.webgl.bindDrawingBuffer();
         } else {
@@ -384,7 +391,7 @@ export class IlluminationPass {
 
         // compose
 
-        ValueCell.updateIfChanged(this.composeRenderable.values.uTransparentBackground, props.transparentBackground || this.drawPass.postprocessing.background.isEnabled(props.postprocessing.background));
+        ValueCell.updateIfChanged(this.composeRenderable.values.uTransparentBackground, props.transparentBackground || this.drawPass.postprocessing.background.isEnabled(props.postprocessing));
         if (this.composeRenderable.values.dDenoise.ref.value !== props.illumination.denoise) {
             ValueCell.update(this.composeRenderable.values.dDenoise, props.illumination.denoise);
             needsUpdateCompose = true;
@@ -421,8 +428,8 @@ export class IlluminationPass {
         let targetIsDrawingbuffer = false;
         let swapTarget = this.outputTarget;
 
-        if (AntialiasingPass.isEnabled(props.postprocessing)) {
-            const _toDrawingBuffer = toDrawingBuffer && props.postprocessing.dof.name === 'off';
+        if (antialiasingEnabled) {
+            const _toDrawingBuffer = toDrawingBuffer && !dofEnabled;
             this.drawPass.antialiasing.render(camera, this.tracing.composeTarget.texture, _toDrawingBuffer ? true : this.outputTarget, props.postprocessing);
 
             if (_toDrawingBuffer) {
@@ -433,13 +440,13 @@ export class IlluminationPass {
             }
         }
 
-        if (props.postprocessing.bloom.name === 'on') {
-            const _toDrawingBuffer = (toDrawingBuffer && props.postprocessing.dof.name === 'off') || targetIsDrawingbuffer;
+        if (bloomEnabled && props.postprocessing.bloom.name === 'on') {
+            const _toDrawingBuffer = (toDrawingBuffer && !dofEnabled) || targetIsDrawingbuffer;
             this.drawPass.bloom.update(this.tracing.colorTextureOpaque, this.tracing.normalTextureOpaque, this.drawPass.depthTextureOpaque, props.postprocessing.bloom.params);
             this.drawPass.bloom.render(camera.viewport, _toDrawingBuffer ? undefined : this._colorTarget);
         }
 
-        if (props.postprocessing.dof.name === 'on') {
+        if (dofEnabled && props.postprocessing.dof.name === 'on') {
             const _toDrawingBuffer = toDrawingBuffer || targetIsDrawingbuffer;
             this.drawPass.dof.update(camera, this._colorTarget.texture, this.drawPass.depthTextureOpaque, this.drawPass.depthTargetTransparent.texture, props.postprocessing.dof.params, scene.boundingSphereVisible);
             this.drawPass.dof.render(camera.viewport, _toDrawingBuffer ? undefined : swapTarget);

src/mol-canvas3d/passes/outline.ts

@@ -36,7 +36,7 @@ export type OutlineProps = PD.Values<typeof OutlineParams>
 
 export class OutlinePass {
     static isEnabled(props: PostprocessingProps) {
-        return props.outline.name !== 'off';
+        return props.enabled && props.outline.name !== 'off';
     }
 
     readonly target: RenderTarget;

src/mol-canvas3d/passes/passes.ts

@@ -20,7 +20,7 @@ export class Passes {
     constructor(private webgl: WebGLContext, assetManager: AssetManager, attribs: Partial<{ pickScale: number, transparency: 'wboit' | 'dpoit' | 'blended' }> = {}) {
         const drs = this.webgl.getDrawingBufferSize();
         this.draw = new DrawPass(webgl, assetManager, drs.width, drs.height, attribs.transparency || 'blended');
-        this.pick = new PickPass(webgl, this.draw, attribs.pickScale || 0.25);
+        this.pick = new PickPass(webgl, drs.width, drs.height, attribs.pickScale || 0.25);
         this.multiSample = new MultiSamplePass(webgl, this.draw);
         this.illumination = new IlluminationPass(webgl, this.draw);
     }
@@ -39,7 +39,7 @@ export class Passes {
         const width = Math.max(drs.width, 2);
         const height = Math.max(drs.height, 2);
         this.draw.setSize(width, height);
-        this.pick.syncSize();
+        this.pick.setSize(width, height);
         this.multiSample.syncSize();
         this.illumination.setSize(width, height);
     }

src/mol-canvas3d/passes/pick.ts

@@ -7,6 +7,7 @@
 import { PickingId } from '../../mol-geo/geometry/picking';
 import { PickType, Renderer } from '../../mol-gl/renderer';
 import { Scene } from '../../mol-gl/scene';
+import { PixelPackBuffer } from '../../mol-gl/webgl/buffer';
 import { isWebGL2 } from '../../mol-gl/webgl/compat';
 import { WebGLContext } from '../../mol-gl/webgl/context';
 import { Framebuffer } from '../../mol-gl/webgl/framebuffer';
@@ -14,20 +15,29 @@ import { RenderTarget } from '../../mol-gl/webgl/render-target';
 import { Renderbuffer } from '../../mol-gl/webgl/renderbuffer';
 import { Texture } from '../../mol-gl/webgl/texture';
 import { Vec3 } from '../../mol-math/linear-algebra';
-import { spiral2d } from '../../mol-math/misc';
-import { isTimingMode } from '../../mol-util/debug';
-import { unpackRGBToInt, unpackRGBAToDepth } from '../../mol-util/number-packing';
-import { Camera, ICamera } from '../camera';
-import { StereoCamera } from '../camera/stereo';
-import { cameraUnproject } from '../camera/util';
+import { isDebugMode, isTimingMode } from '../../mol-util/debug';
+import { now } from '../../mol-util/now';
+import { unpackRGBAToDepth, unpackRGBToInt } from '../../mol-util/number-packing';
+import { ICamera } from '../camera';
 import { Viewport } from '../camera/util';
 import { Helper } from '../helper/helper';
-import { DrawPass } from './draw';
 
 const NullId = Math.pow(2, 24) - 2;
 
 export type PickData = { id: PickingId, position: Vec3 }
 
+export type AsyncPickData = {
+    tryGet: () => 'pending' | PickData | undefined,
+}
+
+export const DefaultPickOptions = {
+    pickPadding: 1,
+    maxAsyncReadLag: 5,
+};
+export type PickOptions = typeof DefaultPickOptions
+
+//
+
 export class PickPass {
     private readonly objectPickTarget: RenderTarget;
     private readonly instancePickTarget: RenderTarget;
@@ -51,10 +61,10 @@ export class PickPass {
     private pickWidth: number;
     private pickHeight: number;
 
-    constructor(private webgl: WebGLContext, private drawPass: DrawPass, private pickScale: number) {
+    constructor(private webgl: WebGLContext, private width: number, private height: number, private pickScale: number) {
         const pickRatio = pickScale / webgl.pixelRatio;
-        this.pickWidth = Math.ceil(drawPass.colorTarget.getWidth() * pickRatio);
-        this.pickHeight = Math.ceil(drawPass.colorTarget.getHeight() * pickRatio);
+        this.pickWidth = Math.ceil(width * pickRatio);
+        this.pickHeight = Math.ceil(height * pickRatio);
 
         const { resources, extensions: { drawBuffers }, gl } = webgl;
 
@@ -109,13 +119,36 @@ export class PickPass {
         }
     }
 
+    dispose() {
+        if (this.webgl.extensions.drawBuffers) {
+            this.framebuffer.destroy();
+
+            this.objectPickTexture.destroy();
+            this.instancePickTexture.destroy();
+            this.groupPickTexture.destroy();
+            this.depthPickTexture.destroy();
+
+            this.objectPickFramebuffer.destroy();
+            this.instancePickFramebuffer.destroy();
+            this.groupPickFramebuffer.destroy();
+            this.depthPickFramebuffer.destroy();
+
+            this.depthRenderbuffer.destroy();
+        } else {
+            this.objectPickTarget.destroy();
+            this.instancePickTarget.destroy();
+            this.groupPickTarget.destroy();
+            this.depthPickTarget.destroy();
+        }
+    }
+
     get pickRatio() {
         return this.pickScale / this.webgl.pixelRatio;
     }
 
     setPickScale(pickScale: number) {
         this.pickScale = pickScale;
-        this.syncSize();
+        this.setSize(this.width, this.height);
     }
 
     bindObject() {
@@ -151,13 +184,16 @@ export class PickPass {
     }
 
     get drawingBufferHeight() {
-        return this.drawPass.colorTarget.getHeight();
+        return this.height;
     }
 
-    syncSize() {
+    setSize(width: number, height: number) {
+        this.width = width;
+        this.height = height;
+
         const pickRatio = this.pickScale / this.webgl.pixelRatio;
-        const pickWidth = Math.ceil(this.drawPass.colorTarget.getWidth() * pickRatio);
-        const pickHeight = Math.ceil(this.drawPass.colorTarget.getHeight() * pickRatio);
+        const pickWidth = Math.ceil(this.width * pickRatio);
+        const pickHeight = Math.ceil(this.height * pickRatio);
 
         if (pickWidth !== this.pickWidth || pickHeight !== this.pickHeight) {
             this.pickWidth = pickWidth;
@@ -225,6 +261,7 @@ export class PickPass {
         if (this.webgl.extensions.drawBuffers) {
             this.framebuffer.bind();
             this.renderVariant(renderer, camera, scene, helper, 'pick', PickType.None);
+            // printTextureImage(readTexture(this.webgl, this.groupPickTexture, new Uint8Array(this.pickWidth * this.pickHeight * 4)), { scale: 16, id: 'group', pixelated: true, useCanvas: true, flipY: true });
         } else {
             this.objectPickTarget.bind();
             this.renderVariant(renderer, camera, scene, helper, 'pick', PickType.Object);
@@ -234,7 +271,7 @@ export class PickPass {
 
             this.groupPickTarget.bind();
             this.renderVariant(renderer, camera, scene, helper, 'pick', PickType.Group);
-            // printTexture(this.webgl, this.groupPickTarget.texture, { id: 'group' })
+            // printTextureImage(readTexture(this.webgl, this.groupPickTarget.texture, new Uint8Array(this.pickWidth * this.pickHeight * 4)), { scale: 16, id: 'group', pixelated: true, useCanvas: true, flipY: true });
 
             this.depthPickTarget.bind();
             this.renderVariant(renderer, camera, scene, helper, 'depth', PickType.None);
@@ -242,200 +279,220 @@ export class PickPass {
     }
 }
 
-export class PickHelper {
-    dirty = true;
+let AsyncPickingWarningShown = false;
 
-    private objectBuffer: Uint8Array;
-    private instanceBuffer: Uint8Array;
-    private groupBuffer: Uint8Array;
-    private depthBuffer: Uint8Array;
+export function checkAsyncPickingSupport(webgl: WebGLContext): boolean {
+    if (webgl.isWebGL2) return true;
 
-    private viewport = Viewport();
+    if (isDebugMode && !AsyncPickingWarningShown) {
+        console.log('WebGL2 required for async picking. Falling back to synchronous picking.');
+        AsyncPickingWarningShown = true;
+    }
+    return false;
+}
 
-    private pickRatio: number;
-    private pickX: number;
-    private pickY: number;
-    private pickWidth: number;
-    private pickHeight: number;
-    private halfPickWidth: number;
+export enum AsyncPickStatus { Pending, Resolved, Failed };
 
-    private spiral: [number, number][];
+export class PickBuffers {
+    private object: Uint8Array;
+    private instance: Uint8Array;
+    private group: Uint8Array;
+    private depth: Uint8Array;
 
-    private setupBuffers() {
-        const bufferSize = this.pickWidth * this.pickHeight * 4;
-        if (!this.objectBuffer || this.objectBuffer.length !== bufferSize) {
-            this.objectBuffer = new Uint8Array(bufferSize);
-            this.instanceBuffer = new Uint8Array(bufferSize);
-            this.groupBuffer = new Uint8Array(bufferSize);
-            this.depthBuffer = new Uint8Array(bufferSize);
+    private objectBuffer: PixelPackBuffer;
+    private instanceBuffer: PixelPackBuffer;
+    private groupBuffer: PixelPackBuffer;
+    private depthBuffer: PixelPackBuffer;
+
+    private viewport = Viewport.create(0, 0, 0, 0);
+
+    private setup() {
+        const size = this.viewport.width * this.viewport.height * 4;
+        if (!this.object || this.object.length !== size) {
+            this.object = new Uint8Array(size);
+            this.instance = new Uint8Array(size);
+            this.group = new Uint8Array(size);
+            this.depth = new Uint8Array(size);
         }
     }
 
     setViewport(x: number, y: number, width: number, height: number) {
         Viewport.set(this.viewport, x, y, width, height);
-        this.update();
+        this.setup();
     }
 
-    setPickPadding(pickPadding: number) {
-        if (this.pickPadding !== pickPadding) {
-            this.pickPadding = pickPadding;
-            this.update();
-        }
-    }
-
-    private update() {
+    read() {
+        if (isTimingMode) this.webgl.timer.mark('PickBuffers.read');
         const { x, y, width, height } = this.viewport;
 
-        this.pickRatio = this.pickPass.pickRatio;
-        this.pickX = Math.ceil(x * this.pickRatio);
-        this.pickY = Math.ceil(y * this.pickRatio);
-
-        const pickWidth = Math.floor(width * this.pickRatio);
-        const pickHeight = Math.floor(height * this.pickRatio);
-
-        if (pickWidth !== this.pickWidth || pickHeight !== this.pickHeight) {
-            this.pickWidth = pickWidth;
-            this.pickHeight = pickHeight;
-            this.halfPickWidth = Math.floor(this.pickWidth / 2);
-
-            this.setupBuffers();
-        }
-
-        this.spiral = spiral2d(Math.ceil(this.pickRatio * this.pickPadding));
-        this.dirty = true;
-    }
-
-    private syncBuffers() {
-        if (isTimingMode) this.webgl.timer.mark('PickHelper.syncBuffers');
-        const { pickX, pickY, pickWidth, pickHeight } = this;
-
         this.pickPass.bindObject();
-        this.webgl.readPixels(pickX, pickY, pickWidth, pickHeight, this.objectBuffer);
+        this.webgl.readPixels(x, y, width, height, this.object);
 
         this.pickPass.bindInstance();
-        this.webgl.readPixels(pickX, pickY, pickWidth, pickHeight, this.instanceBuffer);
+        this.webgl.readPixels(x, y, width, height, this.instance);
 
         this.pickPass.bindGroup();
-        this.webgl.readPixels(pickX, pickY, pickWidth, pickHeight, this.groupBuffer);
+        this.webgl.readPixels(x, y, width, height, this.group);
 
         this.pickPass.bindDepth();
-        this.webgl.readPixels(pickX, pickY, pickWidth, pickHeight, this.depthBuffer);
-        if (isTimingMode) this.webgl.timer.markEnd('PickHelper.syncBuffers');
+        this.webgl.readPixels(x, y, width, height, this.depth);
+
+        this.ready = true;
+        if (isTimingMode) this.webgl.timer.markEnd('PickBuffers.read');
     }
 
-    private getBufferIdx(x: number, y: number): number {
-        return (y * this.pickWidth + x) * 4;
+    private fenceSync: WebGLSync | null = null;
+    private fenceTimestamp: number = 0;
+
+    private ready = false;
+    private lag = 0;
+
+    asyncRead() {
+        const { gl } = this.webgl;
+        if (!isWebGL2(gl)) return;
+
+        if (isTimingMode) this.webgl.timer.mark('PickBuffers.asyncRead');
+        if (this.fenceSync !== null) {
+            gl.deleteSync(this.fenceSync);
+        }
+        const { x, y, width, height } = this.viewport;
+
+        this.pickPass.bindObject();
+        this.objectBuffer.read(x, y, width, height);
+
+        this.pickPass.bindInstance();
+        this.instanceBuffer.read(x, y, width, height);
+
+        this.pickPass.bindGroup();
+        this.groupBuffer.read(x, y, width, height);
+
+        this.pickPass.bindDepth();
+        this.depthBuffer.read(x, y, width, height);
+
+        this.fenceTimestamp = now();
+        this.fenceSync = gl.fenceSync(gl.SYNC_GPU_COMMANDS_COMPLETE, 0);
+        // gl.flush();
+
+        this.ready = false;
+        if (isTimingMode) this.webgl.timer.markEnd('PickBuffers.asyncRead');
     }
 
-    private getDepth(x: number, y: number): number {
-        const idx = this.getBufferIdx(x, y);
-        const b = this.depthBuffer;
+    check(): AsyncPickStatus {
+        if (this.ready) return AsyncPickStatus.Resolved;
+        if (this.fenceSync === null) return AsyncPickStatus.Failed;
+
+        const { gl } = this.webgl;
+        if (!isWebGL2(gl)) return AsyncPickStatus.Failed;
+
+        const res = gl.clientWaitSync(this.fenceSync, 0, 0);
+        if (res === gl.WAIT_FAILED || this.lag >= this.maxAsyncReadLag) {
+            // console.log(`failed to get buffer data after ${this.lag + 1} checks`);
+            if (res !== gl.WAIT_FAILED && now() - this.fenceTimestamp < 1000 / 60) {
+                this.lag += 1;
+                return AsyncPickStatus.Pending;
+            }
+            gl.deleteSync(this.fenceSync);
+            this.fenceSync = null;
+            this.lag = 0;
+            this.ready = false;
+            return AsyncPickStatus.Failed;
+        } else if (res === gl.TIMEOUT_EXPIRED) {
+            this.lag += 1;
+            // console.log(`waiting for buffer data for ${this.lag} checks`);
+            return AsyncPickStatus.Pending;
+        } else {
+            this.objectBuffer.getSubData(this.object);
+            this.instanceBuffer.getSubData(this.instance);
+            this.groupBuffer.getSubData(this.group);
+            this.depthBuffer.getSubData(this.depth);
+
+            // console.log(`got buffer data after ${this.lag + 1} checks`);
+            gl.deleteSync(this.fenceSync);
+            this.fenceSync = null;
+            this.lag = 0;
+            this.ready = true;
+
+            return AsyncPickStatus.Resolved;
+        }
+    }
+
+    private getIdx(x: number, y: number): number {
+        return (y * this.viewport.width + x) * 4;
+    }
+
+    getDepth(x: number, y: number): number {
+        if (!this.ready) return -1;
+
+        const idx = this.getIdx(x, y);
+        const b = this.depth;
         return unpackRGBAToDepth(b[idx], b[idx + 1], b[idx + 2], b[idx + 3]);
     }
 
     private getId(x: number, y: number, buffer: Uint8Array) {
-        const idx = this.getBufferIdx(x, y);
+        if (!this.ready) return -1;
+
+        const idx = this.getIdx(x, y);
         return unpackRGBToInt(buffer[idx], buffer[idx + 1], buffer[idx + 2]);
     }
 
-    private render(camera: Camera | StereoCamera) {
-        if (isTimingMode) this.webgl.timer.mark('PickHelper.render', { captureStats: true });
-        const { pickX, pickY, pickWidth, pickHeight, halfPickWidth } = this;
-        const { renderer, scene, helper } = this;
-
-        renderer.setTransparentBackground(false);
-        renderer.setDrawingBufferSize(pickWidth, pickHeight);
-        renderer.setPixelRatio(this.pickRatio);
-
-        if (StereoCamera.is(camera)) {
-            renderer.setViewport(pickX, pickY, halfPickWidth, pickHeight);
-            this.pickPass.render(renderer, camera.left, scene, helper);
-
-            renderer.setViewport(pickX + halfPickWidth, pickY, pickWidth - halfPickWidth, pickHeight);
-            this.pickPass.render(renderer, camera.right, scene, helper);
-        } else {
-            renderer.setViewport(pickX, pickY, pickWidth, pickHeight);
-            this.pickPass.render(renderer, camera, scene, helper);
-        }
-
-        this.dirty = false;
-        if (isTimingMode) this.webgl.timer.markEnd('PickHelper.render');
+    getObjectId(x: number, y: number) {
+        return this.getId(x, y, this.object);
     }
 
-    private identifyInternal(x: number, y: number, camera: Camera | StereoCamera): PickData | undefined {
-        if (this.pickRatio !== this.pickPass.pickRatio) {
-            this.update();
-        }
+    getInstanceId(x: number, y: number) {
+        return this.getId(x, y, this.instance);
+    }
 
-        const { webgl, pickRatio } = this;
-        if (webgl.isContextLost) return;
+    getGroupId(x: number, y: number) {
+        return this.getId(x, y, this.group);
+    }
 
-        x *= webgl.pixelRatio;
-        y *= webgl.pixelRatio;
-        y = this.pickPass.drawingBufferHeight - y; // flip y
-
-        const { viewport } = this;
-
-        // check if within viewport
-        if (x < viewport.x ||
-            y < viewport.y ||
-            x > viewport.x + viewport.width ||
-            y > viewport.y + viewport.height
-        ) return;
-
-        if (this.dirty) {
-            if (isTimingMode) this.webgl.timer.mark('PickHelper.identify');
-            this.render(camera);
-            this.syncBuffers();
-            if (isTimingMode) this.webgl.timer.markEnd('PickHelper.identify');
-        }
-
-        const xv = x - viewport.x;
-        const yv = y - viewport.y;
-
-        const xp = Math.floor(xv * pickRatio);
-        const yp = Math.floor(yv * pickRatio);
-
-        const objectId = this.getId(xp, yp, this.objectBuffer);
+    getPickingId(x: number, y: number): PickingId | undefined {
+        const objectId = this.getObjectId(x, y);
         // console.log('objectId', objectId);
         if (objectId === -1 || objectId === NullId) return;
 
-        const instanceId = this.getId(xp, yp, this.instanceBuffer);
+        const instanceId = this.getInstanceId(x, y);
         // console.log('instanceId', instanceId);
         if (instanceId === -1 || instanceId === NullId) return;
 
-        const groupId = this.getId(xp, yp, this.groupBuffer);
+        const groupId = this.getGroupId(x, y);
         // console.log('groupId', groupId);
         if (groupId === -1 || groupId === NullId) return;
 
-        const z = this.getDepth(xp, yp);
-        // console.log('z', z);
-        const position = Vec3.create(x, y, z);
-        if (StereoCamera.is(camera)) {
-            const halfWidth = Math.floor(viewport.width / 2);
-            if (x > viewport.x + halfWidth) {
-                position[0] = viewport.x + (xv - halfWidth) * 2;
-                cameraUnproject(position, position, viewport, camera.right.inverseProjectionView);
-            } else {
-                position[0] = viewport.x + xv * 2;
-                cameraUnproject(position, position, viewport, camera.left.inverseProjectionView);
-            }
-        } else {
-            cameraUnproject(position, position, viewport, camera.inverseProjectionView);
-        }
-
-        // console.log({ id: { objectId, instanceId, groupId }, position });
-        return { id: { objectId, instanceId, groupId }, position };
+        return { objectId, instanceId, groupId };
     }
 
-    identify(x: number, y: number, camera: Camera | StereoCamera): PickData | undefined {
-        for (const d of this.spiral) {
-            const pickData = this.identifyInternal(x + d[0], y + d[1], camera);
-            if (pickData) return pickData;
+    reset() {
+        this.fenceSync = null;
+        this.ready = false;
+        this.lag = 0;
+        this.fenceTimestamp = 0;
+    }
+
+    dispose() {
+        const { gl } = this.webgl;
+        if (!isWebGL2(gl)) return;
+
+        this.objectBuffer.destroy();
+        this.instanceBuffer.destroy();
+        this.groupBuffer.destroy();
+        this.depthBuffer.destroy();
+
+        if (this.fenceSync !== null) {
+            gl.deleteSync(this.fenceSync);
+            this.fenceSync = null;
         }
     }
 
-    constructor(private webgl: WebGLContext, private renderer: Renderer, private scene: Scene, private helper: Helper, private pickPass: PickPass, viewport: Viewport, private pickPadding = 1) {
-        this.setViewport(viewport.x, viewport.y, viewport.width, viewport.height);
+    constructor(private webgl: WebGLContext, private pickPass: PickPass, public maxAsyncReadLag = 5) {
+        if (webgl.isWebGL2) {
+            this.objectBuffer = webgl.resources.pixelPack('rgba', 'ubyte');
+            this.instanceBuffer = webgl.resources.pixelPack('rgba', 'ubyte');
+            this.groupBuffer = webgl.resources.pixelPack('rgba', 'ubyte');
+            this.depthBuffer = webgl.resources.pixelPack('rgba', 'ubyte');
+        }
+
+        this.setup();
     }
-}
+}

src/mol-canvas3d/passes/postprocessing.ts

@@ -120,59 +120,60 @@ function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, t
 }
 
 export const PostprocessingParams = {
+    enabled: PD.Boolean(true),
     occlusion: PD.MappedStatic('on', {
         on: PD.Group(SsaoParams),
         off: PD.Group({})
-    }, { cycle: true, description: 'Darken occluded crevices with the ambient occlusion effect' }),
+    }, { cycle: true, description: 'Darken occluded crevices with the ambient occlusion effect', hideIf: p => p.enabled === false }),
     shadow: PD.MappedStatic('off', {
         on: PD.Group(ShadowParams),
         off: PD.Group({})
-    }, { cycle: true, description: 'Simplistic shadows' }),
+    }, { cycle: true, description: 'Simplistic shadows', hideIf: p => p.enabled === false }),
     outline: PD.MappedStatic('off', {
         on: PD.Group(OutlineParams),
         off: PD.Group({})
-    }, { cycle: true, description: 'Draw outline around 3D objects' }),
+    }, { cycle: true, description: 'Draw outline around 3D objects', hideIf: p => p.enabled === false }),
     dof: PD.MappedStatic('off', {
         on: PD.Group(DofParams),
         off: PD.Group({})
-    }, { cycle: true, description: 'DOF' }),
+    }, { cycle: true, description: 'DOF', hideIf: p => p.enabled === false }),
     antialiasing: PD.MappedStatic('smaa', {
         fxaa: PD.Group(FxaaParams),
         smaa: PD.Group(SmaaParams),
         off: PD.Group({})
-    }, { options: [['fxaa', 'FXAA'], ['smaa', 'SMAA'], ['off', 'Off']], description: 'Smooth pixel edges' }),
+    }, { options: [['fxaa', 'FXAA'], ['smaa', 'SMAA'], ['off', 'Off']], description: 'Smooth pixel edges', hideIf: p => p.enabled === false }),
     sharpening: PD.MappedStatic('off', {
         on: PD.Group(CasParams),
         off: PD.Group({})
-    }, { cycle: true, description: 'Contrast Adaptive Sharpening' }),
-    background: PD.Group(BackgroundParams, { isFlat: true }),
+    }, { cycle: true, description: 'Contrast Adaptive Sharpening', hideIf: p => p.enabled === false }),
+    background: PD.Group(BackgroundParams, { isFlat: true, hideIf: p => p.enabled === false }),
     bloom: PD.MappedStatic('on', {
         on: PD.Group(BloomParams),
         off: PD.Group({})
-    }, { cycle: true, description: 'Bloom' }),
+    }, { cycle: true, description: 'Bloom', hideIf: p => p.enabled === false }),
 };
 
 export type PostprocessingProps = PD.Values<typeof PostprocessingParams>
 
 export class PostprocessingPass {
     static isEnabled(props: PostprocessingProps) {
-        return SsaoPass.isEnabled(props) || ShadowPass.isEnabled(props) || OutlinePass.isEnabled(props) || props.background.variant.name !== 'off';
+        return props.enabled && (SsaoPass.isEnabled(props) || ShadowPass.isEnabled(props) || OutlinePass.isEnabled(props) || props.background.variant.name !== 'off');
     }
 
     static isTransparentDepthRequired(scene: Scene, props: PostprocessingProps) {
-        return DofPass.isEnabled(props) || OutlinePass.isEnabled(props) && PostprocessingPass.isTransparentOutlineEnabled(props) || SsaoPass.isEnabled(props) && PostprocessingPass.isTransparentSsaoEnabled(scene, props);
+        return props.enabled && (DofPass.isEnabled(props) || OutlinePass.isEnabled(props) && PostprocessingPass.isTransparentOutlineEnabled(props) || SsaoPass.isEnabled(props) && PostprocessingPass.isTransparentSsaoEnabled(scene, props));
     }
 
     static isTransparentOutlineEnabled(props: PostprocessingProps) {
-        return OutlinePass.isEnabled(props) && ((props.outline.params as OutlineProps).includeTransparent ?? true);
+        return props.enabled && OutlinePass.isEnabled(props) && ((props.outline.params as OutlineProps).includeTransparent ?? true);
     }
 
     static isTransparentSsaoEnabled(scene: Scene, props: PostprocessingProps) {
-        return SsaoPass.isEnabled(props) && SsaoPass.isTransparentEnabled(scene, props.occlusion.params as SsaoProps);
+        return props.enabled && SsaoPass.isEnabled(props) && SsaoPass.isTransparentEnabled(scene, props.occlusion.params as SsaoProps);
     }
 
     static isSsaoEnabled(props: PostprocessingProps) {
-        return SsaoPass.isEnabled(props);
+        return props.enabled && SsaoPass.isEnabled(props);
     }
 
     readonly target: RenderTarget;
@@ -354,7 +355,7 @@ export class PostprocessingPass {
 
 export class AntialiasingPass {
     static isEnabled(props: PostprocessingProps) {
-        return props.antialiasing.name !== 'off';
+        return props.enabled && (props.antialiasing.name !== 'off' || props.sharpening.name !== 'off');
     }
 
     readonly target: RenderTarget;

src/mol-canvas3d/passes/shadow.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Áron Samuel Kovács <aron.kovacs@mail.muni.cz>
@@ -35,7 +35,7 @@ export type ShadowProps = PD.Values<typeof ShadowParams>
 
 export class ShadowPass {
     static isEnabled(props: PostprocessingProps) {
-        return props.shadow.name !== 'off';
+        return props.enabled && props.shadow.name !== 'off';
     }
 
     readonly target: RenderTarget;
@@ -83,8 +83,8 @@ export class ShadowPass {
             needsUpdateShadows = true;
         }
 
-        ValueCell.updateIfChanged(this.renderable.values.uMaxDistance, props.maxDistance);
-        ValueCell.updateIfChanged(this.renderable.values.uTolerance, props.tolerance);
+        ValueCell.updateIfChanged(this.renderable.values.uMaxDistance, props.maxDistance * camera.state.scale);
+        ValueCell.updateIfChanged(this.renderable.values.uTolerance, props.tolerance * camera.state.scale);
         if (this.renderable.values.dSteps.ref.value !== props.steps) {
             ValueCell.update(this.renderable.values.dSteps, props.steps);
             needsUpdateShadows = true;

src/mol-canvas3d/passes/ssao.ts

@@ -63,7 +63,7 @@ type Levels = {
     bias: number[]
 }
 
-function getLevels(props: { radius: number, bias: number }[], levels?: Levels): Levels {
+function getLevels(props: { radius: number, bias: number }[], scale: number, levels?: Levels): Levels {
     const count = props.length;
     const { radius, bias } = levels || {
         radius: (new Array(count * 3)).fill(0),
@@ -72,7 +72,7 @@ function getLevels(props: { radius: number, bias: number }[], levels?: Levels):
     props = props.slice().sort((a, b) => a.radius - b.radius);
     for (let i = 0; i < count; ++i) {
         const p = props[i];
-        radius[i] = Math.pow(2, p.radius);
+        radius[i] = Math.pow(2, p.radius) * scale;
         bias[i] = p.bias;
     }
     return { count, radius, bias };
@@ -126,6 +126,7 @@ export class SsaoPass {
     private nSamples: number;
     private blurKernelSize: number;
     private texSize: [number, number];
+    private invProjection = Mat4.identity();
 
     private ssaoScale: number;
     private calcSsaoScale(resolutionScale: number) {
@@ -275,9 +276,7 @@ export class SsaoPass {
         let needsUpdateDepthHalf = false;
 
         const orthographic = camera.state.mode === 'orthographic' ? 1 : 0;
-
-        const invProjection = Mat4.identity();
-        Mat4.invert(invProjection, camera.projection);
+        const invProjection = Mat4.invert(this.invProjection, camera.projection);
 
         const [w, h] = this.texSize;
         const v = camera.viewport;
@@ -306,8 +305,8 @@ export class SsaoPass {
         ValueCell.update(this.blurFirstPassRenderable.values.uInvProjection, invProjection);
         ValueCell.update(this.blurSecondPassRenderable.values.uInvProjection, invProjection);
 
-        ValueCell.update(this.blurFirstPassRenderable.values.uBlurDepthBias, props.blurDepthBias);
-        ValueCell.update(this.blurSecondPassRenderable.values.uBlurDepthBias, props.blurDepthBias);
+        ValueCell.update(this.blurFirstPassRenderable.values.uBlurDepthBias, props.blurDepthBias * camera.state.scale);
+        ValueCell.update(this.blurSecondPassRenderable.values.uBlurDepthBias, props.blurDepthBias * camera.state.scale);
 
         if (this.blurFirstPassRenderable.values.dOrthographic.ref.value !== orthographic) {
             needsUpdateSsaoBlur = true;
@@ -349,7 +348,7 @@ export class SsaoPass {
                 needsUpdateSsao = true;
 
                 this.levels = mp.levels;
-                const levels = getLevels(mp.levels);
+                const levels = getLevels(mp.levels, camera.state.scale);
                 ValueCell.updateIfChanged(this.renderable.values.dLevels, levels.count);
 
                 ValueCell.update(this.renderable.values.uLevelRadius, levels.radius);
@@ -358,7 +357,7 @@ export class SsaoPass {
             ValueCell.updateIfChanged(this.renderable.values.uNearThreshold, mp.nearThreshold);
             ValueCell.updateIfChanged(this.renderable.values.uFarThreshold, mp.farThreshold);
         } else {
-            ValueCell.updateIfChanged(this.renderable.values.uRadius, Math.pow(2, props.radius));
+            ValueCell.updateIfChanged(this.renderable.values.uRadius, Math.pow(2, props.radius) * camera.state.scale);
         }
         ValueCell.updateIfChanged(this.renderable.values.uBias, props.bias);
 

src/mol-data/util/hash-functions.ts

@@ -1,8 +1,9 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Adam Midlik <midlik@gmail.com>
  */
 
 // from http://burtleburtle.net/bob/hash/integer.html
@@ -89,4 +90,456 @@ export function hashFnv32a(array: ArrayLike<number>) {
         hval += (hval << 1) + (hval << 4) + (hval << 7) + (hval << 8) + (hval << 24);
     }
     return hval >>> 0;
+}
+
+/**
+ * 256 bit FNV-1a hash, returns 8 32-bit words
+ * Based on the FNV-1a algorithm extended to 256 bits
+ */
+export function hashFnv256a(array: ArrayLike<number>, out: Uint32Array) {
+    out.set(Fnv256Base);
+
+    for (let i = 0, il = array.length; i < il; ++i) {
+        // XOR with input byte
+        out[0] ^= array[i] & 0xff;
+
+        // Multiply by FNV prime (256-bit multiplication)
+        multiplyBy256BitPrime(out);
+    }
+
+    return out;
+}
+
+/**
+ * 256-bit object hash function using FNV-1a
+ */
+export function hashFnv256o(obj: any): string {
+    return _Hasher256.hash(obj);
+}
+
+class ObjectHasher256 {
+    private hashTarget: Uint32Array = new Uint32Array(8);
+    private numberBytes = new Uint8Array(8);
+    private numberView = new DataView(this.numberBytes.buffer);
+
+    hash(obj: any): string {
+        this.hashTarget.set(Fnv256Base);
+        this.hashValue(obj, 0);
+        return hashFnv256aToHex(this.hashTarget);
+    }
+
+    private hashValue(value: any, depth: number): void {
+        if (depth > 50) return;
+
+        const type = typeof value;
+        this.addByte(type.charCodeAt(0));
+
+        switch (type) {
+            case 'string':
+                this.addString(value);
+                break;
+            case 'number':
+                this.addNumber(value);
+                break;
+            case 'boolean':
+                this.addByte(value ? 1 : 0);
+                break;
+            case 'object':
+                if (value === null) {
+                    this.addByte(0);
+                } else if (Array.isArray(value)) {
+                    this.addArray(value, depth);
+                } else {
+                    this.addObject(value, depth);
+                }
+                break;
+            case 'undefined':
+                this.addByte(255);
+                break;
+        }
+    }
+
+    private addByte(byte: number): void {
+        // XOR with input byte
+        this.hashTarget[0] ^= byte & 0xff;
+        // Multiply by FNV prime (256-bit multiplication)
+        multiplyBy256BitPrime(this.hashTarget);
+    }
+
+    private addString(str: string): void {
+        for (let i = 0; i < str.length; i++) {
+            const code = str.charCodeAt(i);
+            if (code < 128) {
+                this.addByte(code);
+            } else if (code < 2048) {
+                this.addByte(0xc0 | (code >> 6));
+                this.addByte(0x80 | (code & 0x3f));
+            } else {
+                this.addByte(0xe0 | (code >> 12));
+                this.addByte(0x80 | ((code >> 6) & 0x3f));
+                this.addByte(0x80 | (code & 0x3f));
+            }
+        }
+    }
+
+    private addNumber(num: number): void {
+        if (Number.isNaN(num)) {
+            this.addByte(0x7f); this.addByte(0xc0); this.addByte(0x00); this.addByte(0x00);
+            this.addByte(0x00); this.addByte(0x00); this.addByte(0x00); this.addByte(0x00);
+        } else if (!Number.isFinite(num)) {
+            if (num > 0) {
+                this.addByte(0x7f); this.addByte(0x80); this.addByte(0x00); this.addByte(0x00);
+            } else {
+                this.addByte(0xff); this.addByte(0x80); this.addByte(0x00); this.addByte(0x00);
+            }
+            this.addByte(0x00); this.addByte(0x00); this.addByte(0x00); this.addByte(0x00);
+        } else {
+            this.numberView.setFloat64(0, num, false);
+            for (let i = 0; i < 8; i++) {
+                this.addByte(this.numberBytes[i]);
+            }
+        }
+    }
+
+    private addArray(arr: any[], depth: number): void {
+        this.addNumber(arr.length);
+        for (let i = 0; i < arr.length; i++) {
+            this.addNumber(i);
+            this.hashValue(arr[i], depth + 1);
+        }
+    }
+
+    private addObject(obj: any, depth: number): void {
+        const keys = Object.keys(obj).sort();
+        this.addNumber(keys.length);
+
+        for (const key of keys) {
+            this.addString(key);
+            this.hashValue(obj[key], depth + 1);
+        }
+    }
+}
+
+const _Hasher256 = new ObjectHasher256();
+
+const Fnv256Base = new Uint32Array([
+    0x6c62272e, 0x07bb0142, 0x62b82175, 0x6295c58d,
+    0x16d67530, 0xdd7121e3, 0xb3174000, 0x00000100
+]);
+
+const MultTmp1 = new Uint32Array(8);
+const MultTmp2 = new Uint32Array(8);
+
+/**
+ * Helper function to multiply 256-bit number by FNV prime
+ */
+function multiplyBy256BitPrime(hash: Uint32Array): void {
+    // Since FNV 256-bit prime is 2^88 + 2^8 + 0x3b, we can optimize:
+    // hash * prime = hash * (2^88 + 2^8 + 0x3b) = (hash << 88) + (hash << 8) + hash * 0x3b
+
+    // hash << 88 (shift left by 88 bits = 2 full 32-bit words + 24 bits)
+    MultTmp1[0] = 0;
+    MultTmp1[1] = 0;
+    MultTmp1[2] = hash[0] << 24;
+    MultTmp1[3] = (hash[0] >>> 8) | (hash[1] << 24);
+    MultTmp1[4] = (hash[1] >>> 8) | (hash[2] << 24);
+    MultTmp1[5] = (hash[2] >>> 8) | (hash[3] << 24);
+    MultTmp1[6] = (hash[3] >>> 8) | (hash[4] << 24);
+    MultTmp1[7] = (hash[4] >>> 8) | (hash[5] << 24);
+
+    // hash << 8
+    MultTmp2[0] = hash[0] << 8;
+    MultTmp2[1] = (hash[0] >>> 24) | (hash[1] << 8);
+    MultTmp2[2] = (hash[1] >>> 24) | (hash[2] << 8);
+    MultTmp2[3] = (hash[2] >>> 24) | (hash[3] << 8);
+    MultTmp2[4] = (hash[3] >>> 24) | (hash[4] << 8);
+    MultTmp2[5] = (hash[4] >>> 24) | (hash[5] << 8);
+    MultTmp2[6] = (hash[5] >>> 24) | (hash[6] << 8);
+    MultTmp2[7] = (hash[6] >>> 24) | (hash[7] << 8);
+
+    // hash * 0x3b (simple multiplication by small constant)
+    let carry = 0;
+    for (let i = 0; i < 8; i++) {
+        const product = hash[i] * 0x3b + carry;
+        hash[i] = product >>> 0;
+        carry = Math.floor(product / 0x100000000);
+    }
+
+    // Add all three components: (hash << 88) + (hash << 8) + hash * 0x3b
+    carry = 0;
+    for (let i = 0; i < 8; i++) {
+        const sum = hash[i] + MultTmp1[i] + MultTmp2[i] + carry;
+        hash[i] = sum >>> 0;
+        carry = sum >= 0x100000000 ? 1 : 0;
+    }
+}
+
+const _8digit_padding = [
+    '00000000',
+    '0000000',
+    '000000',
+    '00000',
+    '0000',
+    '000',
+    '00',
+    '0'
+];
+
+
+function padHexNumber(num: number): string {
+    const base = num.toString(16);
+    if (base.length >= 8) return base; // No padding needed
+    return _8digit_padding[base.length] + base;
+}
+
+/**
+ * Convert 256-bit hash to hex string
+ */
+function hashFnv256aToHex(hash: Uint32Array): string {
+    let result = '';
+    for (let i = 7; i >= 0; i--) {
+        result += padHexNumber(hash[i]);
+    }
+    return result;
+}
+
+/**
+ * 32-bit Murmur hash
+ */
+export function hashMurmur32o(obj: any, seed: number = 42): number {
+    const jsonString = JSON.stringify(obj);
+    return murmurHash3_32(jsonString, seed);
+}
+
+/**
+ * 128-bit Murmur hash
+ */
+export function hashMurmur128o(obj: any, seed: number = 42): string {
+    const jsonString = JSON.stringify(obj);
+    return murmurHash3_128(jsonString, seed);
+}
+
+/**
+ * MurmurHash3 32-bit implementation
+ * @param key - The input string to hash
+ * @param seed - The seed value (default: 0)
+ * @returns The 32-bit hash as a number
+ */
+export function murmurHash3_32(key: string, seed: number): number {
+    let h = seed >>> 0;
+    const remainder = key.length % 4;
+    const bytes = key.length - remainder;
+
+    for (let i = 0; i < bytes; i += 4) {
+        let k = (key.charCodeAt(i) & 0xff) |
+            ((key.charCodeAt(i + 1) & 0xff) << 8) |
+            ((key.charCodeAt(i + 2) & 0xff) << 16) |
+            ((key.charCodeAt(i + 3) & 0xff) << 24);
+
+        k = Math.imul(k, 0xcc9e2d51);
+        k = (k << 15) | (k >>> 17);
+        k = Math.imul(k, 0x1b873593);
+
+        h ^= k;
+        h = (h << 13) | (h >>> 19);
+        h = Math.imul(h, 5) + 0xe6546b64;
+    }
+
+    let k = 0;
+    switch (remainder) {
+        case 3: k ^= (key.charCodeAt(bytes + 2) & 0xff) << 16;
+        case 2: k ^= (key.charCodeAt(bytes + 1) & 0xff) << 8;
+        case 1: k ^= (key.charCodeAt(bytes) & 0xff);
+            k = Math.imul(k, 0xcc9e2d51);
+            k = (k << 15) | (k >>> 17);
+            k = Math.imul(k, 0x1b873593);
+            h ^= k;
+    }
+
+    h ^= key.length;
+    h ^= h >>> 16;
+    h = Math.imul(h, 0x85ebca6b);
+    h ^= h >>> 13;
+    h = Math.imul(h, 0xc2b2ae35);
+    h ^= h >>> 16;
+
+    return h >>> 0;
+}
+
+/**
+ * MurmurHash3 128-bit implementation
+ * @param key - The input data to hash
+ * @param seed - The seed value (default: 0)
+ * @returns The 128-bit hash as a hexadecimal string
+ */
+export function murmurHash3_128_fromBytes(key: Uint8Array, seed: number): string {
+    // This fakeString approach is much faster than `new TextDecoder('ascii').decode(key)`
+    const fakeString = {
+        length: key.length,
+        charCodeAt(i: number) { return key[i]; },
+    };
+    return murmurHash3_128(fakeString as string, seed);
+}
+
+/**
+ * MurmurHash3 128-bit implementation
+ * @param key - The input string to hash
+ * @param seed - The seed value (default: 0)
+ * @returns The 128-bit hash as a hexadecimal string
+ */
+export function murmurHash3_128(key: string, seed: number): string {
+    let h1 = seed >>> 0;
+    let h2 = seed >>> 0;
+    let h3 = seed >>> 0;
+    let h4 = seed >>> 0;
+
+    const remainder = key.length % 16;
+    const bytes = key.length - remainder;
+
+    for (let i = 0; i < bytes; i += 16) {
+        let k1 = (key.charCodeAt(i) & 0xff) |
+            ((key.charCodeAt(i + 1) & 0xff) << 8) |
+            ((key.charCodeAt(i + 2) & 0xff) << 16) |
+            ((key.charCodeAt(i + 3) & 0xff) << 24);
+
+        let k2 = (key.charCodeAt(i + 4) & 0xff) |
+            ((key.charCodeAt(i + 5) & 0xff) << 8) |
+            ((key.charCodeAt(i + 6) & 0xff) << 16) |
+            ((key.charCodeAt(i + 7) & 0xff) << 24);
+
+        let k3 = (key.charCodeAt(i + 8) & 0xff) |
+            ((key.charCodeAt(i + 9) & 0xff) << 8) |
+            ((key.charCodeAt(i + 10) & 0xff) << 16) |
+            ((key.charCodeAt(i + 11) & 0xff) << 24);
+
+        let k4 = (key.charCodeAt(i + 12) & 0xff) |
+            ((key.charCodeAt(i + 13) & 0xff) << 8) |
+            ((key.charCodeAt(i + 14) & 0xff) << 16) |
+            ((key.charCodeAt(i + 15) & 0xff) << 24);
+
+        k1 = Math.imul(k1, 0x239b961b);
+        k1 = (k1 << 15) | (k1 >>> 17);
+        k1 = Math.imul(k1, 0xab0e9789);
+        h1 ^= k1;
+
+        h1 = (h1 << 19) | (h1 >>> 13);
+        h1 += h2;
+        h1 = Math.imul(h1, 5) + 0x561ccd1b;
+
+        k2 = Math.imul(k2, 0xab0e9789);
+        k2 = (k2 << 16) | (k2 >>> 16);
+        k2 = Math.imul(k2, 0x38b34ae5);
+        h2 ^= k2;
+
+        h2 = (h2 << 17) | (h2 >>> 15);
+        h2 += h3;
+        h2 = Math.imul(h2, 5) + 0x0bcaa747;
+
+        k3 = Math.imul(k3, 0x38b34ae5);
+        k3 = (k3 << 17) | (k3 >>> 15);
+        k3 = Math.imul(k3, 0xa1e38b93);
+        h3 ^= k3;
+
+        h3 = (h3 << 15) | (h3 >>> 17);
+        h3 += h4;
+        h3 = Math.imul(h3, 5) + 0x96cd1c35;
+
+        k4 = Math.imul(k4, 0xa1e38b93);
+        k4 = (k4 << 13) | (k4 >>> 19);
+        k4 = Math.imul(k4, 0x239b961b);
+        h4 ^= k4;
+
+        h4 = (h4 << 13) | (h4 >>> 19);
+        h4 += h1;
+        h4 = Math.imul(h4, 5) + 0x32ac3b17;
+    }
+
+    let k1 = 0, k2 = 0, k3 = 0, k4 = 0;
+
+    switch (remainder) {
+        case 15: k4 ^= key.charCodeAt(bytes + 14) << 16;
+        case 14: k4 ^= key.charCodeAt(bytes + 13) << 8;
+        case 13: k4 ^= key.charCodeAt(bytes + 12);
+            k4 = Math.imul(k4, 0xa1e38b93);
+            k4 = (k4 << 13) | (k4 >>> 19);
+            k4 = Math.imul(k4, 0x239b961b);
+            h4 ^= k4;
+
+        case 12: k3 ^= key.charCodeAt(bytes + 11) << 24;
+        case 11: k3 ^= key.charCodeAt(bytes + 10) << 16;
+        case 10: k3 ^= key.charCodeAt(bytes + 9) << 8;
+        case 9: k3 ^= key.charCodeAt(bytes + 8);
+            k3 = Math.imul(k3, 0x38b34ae5);
+            k3 = (k3 << 17) | (k3 >>> 15);
+            k3 = Math.imul(k3, 0xa1e38b93);
+            h3 ^= k3;
+
+        case 8: k2 ^= key.charCodeAt(bytes + 7) << 24;
+        case 7: k2 ^= key.charCodeAt(bytes + 6) << 16;
+        case 6: k2 ^= key.charCodeAt(bytes + 5) << 8;
+        case 5: k2 ^= key.charCodeAt(bytes + 4);
+            k2 = Math.imul(k2, 0xab0e9789);
+            k2 = (k2 << 16) | (k2 >>> 16);
+            k2 = Math.imul(k2, 0x38b34ae5);
+            h2 ^= k2;
+
+        case 4: k1 ^= key.charCodeAt(bytes + 3) << 24;
+        case 3: k1 ^= key.charCodeAt(bytes + 2) << 16;
+        case 2: k1 ^= key.charCodeAt(bytes + 1) << 8;
+        case 1: k1 ^= key.charCodeAt(bytes);
+            k1 = Math.imul(k1, 0x239b961b);
+            k1 = (k1 << 15) | (k1 >>> 17);
+            k1 = Math.imul(k1, 0xab0e9789);
+            h1 ^= k1;
+    }
+
+    h1 ^= key.length;
+    h2 ^= key.length;
+    h3 ^= key.length;
+    h4 ^= key.length;
+
+    h1 += h2;
+    h1 += h3;
+    h1 += h4;
+    h2 += h1;
+    h3 += h1;
+    h4 += h1;
+
+    h1 ^= h1 >>> 16;
+    h1 = Math.imul(h1, 0x85ebca6b);
+    h1 ^= h1 >>> 13;
+    h1 = Math.imul(h1, 0xc2b2ae35);
+    h1 ^= h1 >>> 16;
+
+    h2 ^= h2 >>> 16;
+    h2 = Math.imul(h2, 0x85ebca6b);
+    h2 ^= h2 >>> 13;
+    h2 = Math.imul(h2, 0xc2b2ae35);
+    h2 ^= h2 >>> 16;
+
+    h3 ^= h3 >>> 16;
+    h3 = Math.imul(h3, 0x85ebca6b);
+    h3 ^= h3 >>> 13;
+    h3 = Math.imul(h3, 0xc2b2ae35);
+    h3 ^= h3 >>> 16;
+
+    h4 ^= h4 >>> 16;
+    h4 = Math.imul(h4, 0x85ebca6b);
+    h4 ^= h4 >>> 13;
+    h4 = Math.imul(h4, 0xc2b2ae35);
+    h4 ^= h4 >>> 16;
+
+    h1 += h2;
+    h1 += h3;
+    h1 += h4;
+    h2 += h1;
+    h3 += h1;
+    h4 += h1;
+
+    return (
+        (h1 >>> 0).toString(16).padStart(8, '0') +
+        (h2 >>> 0).toString(16).padStart(8, '0') +
+        (h3 >>> 0).toString(16).padStart(8, '0') +
+        (h4 >>> 0).toString(16).padStart(8, '0')
+    );
 }

src/mol-geo/geometry/mesh/builder/cylinder.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Gianluca Tomasello <giagitom@gmail.com>
@@ -12,6 +12,7 @@ import { Cylinder, CylinderProps, DefaultCylinderProps } from '../../../primitiv
 import { Prism } from '../../../primitive/prism';
 import { polygon } from '../../../primitive/polygon';
 import { hashFnv32a } from '../../../../mol-data/util';
+import { Ray3D } from '../../../../mol-math/geometry/primitives/ray3d';
 
 const cylinderMap = new Map<number, Primitive>();
 const up = Vec3.create(0, 1, 0);
@@ -77,6 +78,11 @@ export function addSimpleCylinder(state: MeshBuilder.State, start: Vec3, end: Ve
     MeshBuilder.addPrimitive(state, tmpCylinderMat, getCylinder(props));
 }
 
+export function addCylinderFromRay3D(state: MeshBuilder.State, ray: Ray3D, length: number, props: BasicCylinderProps) {
+    setCylinderMat(tmpCylinderMat, ray.origin, ray.direction, length, false);
+    MeshBuilder.addPrimitive(state, tmpCylinderMat, getCylinder(props));
+}
+
 export function addCylinder(state: MeshBuilder.State, start: Vec3, end: Vec3, lengthScale: number, props: BasicCylinderProps) {
     const d = Vec3.distance(start, end) * lengthScale;
     Vec3.sub(tmpCylinderDir, end, start);

src/mol-gl/object3d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -22,10 +22,4 @@ export namespace Object3D {
             up: Vec3.create(0, 1, 0),
         };
     }
-
-    const center = Vec3.zero();
-    export function update(object3d: Object3D) {
-        Vec3.add(center, object3d.position, object3d.direction);
-        Mat4.lookAt(object3d.view, object3d.position, center, object3d.up);
-    }
 }

src/mol-gl/renderable/schema.ts

@@ -130,11 +130,14 @@ export const GlobalUniformSchema = {
     uInvProjection: UniformSpec('m4'),
     uModelViewProjection: UniformSpec('m4'),
     uInvModelViewProjection: UniformSpec('m4'),
+    uHasHeadRotation: UniformSpec('b'),
+    uInvHeadRotation: UniformSpec('m4'),
 
     uIsOrtho: UniformSpec('f'),
     uPixelRatio: UniformSpec('f'),
     uViewport: UniformSpec('v4'),
     uViewOffset: UniformSpec('v2'),
+    uModelScale: UniformSpec('f'),
     uDrawingBufferSize: UniformSpec('v2'),
 
     uCameraPosition: UniformSpec('v3'),

src/mol-gl/renderable/util.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -50,6 +50,7 @@ const DefaultPrintImageOptions = {
     id: 'molstar.debug.image',
     normalize: false,
     useCanvas: false,
+    flipY: false,
 };
 export type PrintImageOptions = typeof DefaultPrintImageOptions
 
@@ -101,6 +102,7 @@ export function printImageData(imageData: ImageData, options: Partial<PrintImage
         tmpContainer.style.right = '0px';
         tmpContainer.style.border = 'solid orange';
         tmpContainer.style.pointerEvents = 'none';
+        if (options.flipY) tmpContainer.style.transform = 'scaleY(-1)';
         document.body.appendChild(tmpContainer);
     }
 

src/mol-gl/renderer.ts

@@ -152,6 +152,16 @@ function getLight(props: RendererProps['light'], light?: Light): Light {
     return { count, direction, color };
 }
 
+export function getTransformedLightDirection(light: Light, t: Mat4): Light['direction'] {
+    const tld = new Array(light.count * 3);
+    for (let i = 0, il = light.count; i < il; ++i) {
+        Vec3.fromArray(tmpDir, light.direction, i * 3);
+        Vec3.transformDirection(tmpDir, tmpDir, t);
+        Vec3.toArray(tmpDir, tld, i * 3);
+    }
+    return tld;
+}
+
 namespace Renderer {
     const enum Flag {
         None = 0,
@@ -184,6 +194,7 @@ namespace Renderer {
             ['tDepth', emptyDepthTexture]
         ];
 
+        const model = Mat4();
         const view = Mat4();
         const invView = Mat4();
         const modelView = Mat4();
@@ -191,6 +202,7 @@ namespace Renderer {
         const invProjection = Mat4();
         const modelViewProjection = Mat4();
         const invModelViewProjection = Mat4();
+        const invHeadRotation = Mat4();
 
         const cameraDir = Vec3();
         const cameraPosition = Vec3();
@@ -198,6 +210,9 @@ namespace Renderer {
         const viewOffset = Vec2();
         const frustum = Frustum3D();
 
+        let modelScale = 1;
+        const boundingSphere = Sphere3D();
+
         const ambientColor = Vec3();
         Vec3.scale(ambientColor, Color.toArrayNormalized(p.ambientColor, ambientColor, 0), p.ambientIntensity);
 
@@ -213,9 +228,12 @@ namespace Renderer {
             uProjection: ValueCell.create(Mat4()),
             uModelViewProjection: ValueCell.create(modelViewProjection),
             uInvModelViewProjection: ValueCell.create(invModelViewProjection),
+            uHasHeadRotation: ValueCell.create(false),
+            uInvHeadRotation: ValueCell.create(invHeadRotation),
 
             uIsOrtho: ValueCell.create(1),
             uViewOffset: ValueCell.create(viewOffset),
+            uModelScale: ValueCell.create(1),
 
             uPixelRatio: ValueCell.create(ctx.pixelRatio),
             uViewport: ValueCell.create(Viewport.toVec4(Vec4(), viewport)),
@@ -274,28 +292,33 @@ namespace Renderer {
                 return;
             }
 
-            if (!Frustum3D.intersectsSphere3D(frustum, r.values.boundingSphere.ref.value)) {
+            Sphere3D.scaleNX(boundingSphere, r.values.boundingSphere.ref.value, modelScale);
+
+            if (!Frustum3D.intersectsSphere3D(frustum, boundingSphere)) {
                 return;
             }
 
             const [minDistance, maxDistance] = r.values.uLod.ref.value;
             if (minDistance !== 0 || maxDistance !== 0) {
-                const { center, radius } = r.values.boundingSphere.ref.value;
+                const { center, radius } = boundingSphere;
                 const d = Plane3D.distanceToPoint(cameraPlane, center);
-                if (d + radius < minDistance) return;
-                if (d - radius > maxDistance) return;
+                if (d + radius < minDistance * modelScale) return;
+                if (d - radius > maxDistance * modelScale) return;
             }
 
-            if (isOccluded !== null && isOccluded(r.values.boundingSphere.ref.value)) {
-                return;
-            }
+            const unscaled = modelScale === 1;
+            if (unscaled) {
+                if (isOccluded !== null && isOccluded(boundingSphere)) {
+                    return;
+                }
 
-            const hasInstanceGrid = r.values.instanceGrid.ref.value.cellSize > 0;
-            const hasMultipleInstances = r.values.uInstanceCount.ref.value > 1;
-            if (hasInstanceGrid && (hasMultipleInstances || r.values.lodLevels)) {
-                r.cull(cameraPlane, frustum, isOccluded, ctx.stats);
-            } else {
-                r.uncull();
+                const hasInstanceGrid = r.values.instanceGrid.ref.value.cellSize > 0;
+                const hasMultipleInstances = r.values.uInstanceCount.ref.value > 1;
+                if (hasInstanceGrid && (hasMultipleInstances || r.values.lodLevels)) {
+                    r.cull(cameraPlane, frustum, isOccluded, ctx.stats);
+                } else {
+                    r.uncull();
+                }
             }
 
             let needUpdate = false;
@@ -382,9 +405,12 @@ namespace Renderer {
 
             ValueCell.updateIfChanged(globalUniforms.uIsOrtho, camera.state.mode === 'orthographic' ? 1 : 0);
             ValueCell.update(globalUniforms.uViewOffset, camera.viewOffset.enabled ? Vec2.set(viewOffset, camera.viewOffset.offsetX * 16, camera.viewOffset.offsetY * 16) : Vec2.set(viewOffset, 0, 0));
+            ValueCell.updateIfChanged(globalUniforms.uModelScale, camera.state.scale);
 
-            ValueCell.update(globalUniforms.uCameraPosition, Vec3.copy(cameraPosition, camera.state.position));
-            ValueCell.update(globalUniforms.uCameraDir, Vec3.normalize(cameraDir, Vec3.sub(cameraDir, camera.state.target, camera.state.position)));
+            ValueCell.update(globalUniforms.uCameraPosition, Mat4.getTranslation(cameraPosition, invView));
+            const cameraTarget = Vec3.scale(Vec3(), camera.state.target, camera.state.scale);
+            Vec3.normalize(cameraDir, Vec3.sub(cameraDir, cameraTarget, cameraPosition));
+            ValueCell.update(globalUniforms.uCameraDir, cameraDir);
 
             ValueCell.updateIfChanged(globalUniforms.uFar, camera.far);
             ValueCell.updateIfChanged(globalUniforms.uNear, camera.near);
@@ -400,13 +426,26 @@ namespace Renderer {
             ValueCell.update(globalUniforms.uCameraPlane, Plane3D.toArray(cameraPlane, globalUniforms.uCameraPlane.ref.value, 0));
 
             ValueCell.updateIfChanged(globalUniforms.uMarkerAverage, scene.markerAverage);
+
+            const hasHeadRotation = !Mat4.isZero(camera.headRotation);
+            if (hasHeadRotation) {
+                ValueCell.updateIfChanged(globalUniforms.uHasHeadRotation, hasHeadRotation);
+                ValueCell.update(globalUniforms.uInvHeadRotation, Mat4.invert(invHeadRotation, camera.headRotation));
+                ValueCell.update(globalUniforms.uLightDirection, getTransformedLightDirection(light, invHeadRotation));
+            } else {
+                ValueCell.update(globalUniforms.uHasHeadRotation, false);
+                ValueCell.update(globalUniforms.uInvHeadRotation, Mat4.id);
+                ValueCell.update(globalUniforms.uLightDirection, light.direction);
+            }
         };
 
         const updateInternal = (group: Scene.Group, camera: ICamera, depthTexture: Texture | null, renderMask: Mask, markingDepthTest: boolean) => {
             arrayMapUpsert(sharedTexturesList, 'tDepth', depthTexture || emptyDepthTexture);
 
-            ValueCell.update(globalUniforms.uModel, group.view);
-            ValueCell.update(globalUniforms.uModelView, Mat4.mul(modelView, camera.view, group.view));
+            modelScale = camera.state.scale;
+
+            ValueCell.update(globalUniforms.uModel, Mat4.scaleUniformly(model, group.view, camera.state.scale));
+            ValueCell.update(globalUniforms.uModelView, Mat4.mul(modelView, camera.view, model));
             ValueCell.update(globalUniforms.uInvModelView, Mat4.invert(invModelView, modelView));
             ValueCell.update(globalUniforms.uModelViewProjection, Mat4.mul(modelViewProjection, modelView, camera.projection));
             ValueCell.update(globalUniforms.uInvModelViewProjection, Mat4.invert(invModelViewProjection, modelViewProjection));

src/mol-gl/scene.ts

@@ -312,7 +312,6 @@ namespace Scene {
                 }
             },
             update(objects, keepBoundingSphere) {
-                Object3D.update(object3d);
                 if (objects) {
                     for (let i = 0, il = objects.length; i < il; ++i) {
                         renderableMap.get(objects[i])?.update();

src/mol-gl/shader-code.ts

@@ -68,7 +68,6 @@ import { common } from './shader/chunks/common.glsl';
 import { fade_lod } from './shader/chunks/fade-lod.glsl';
 import { float_to_rgba } from './shader/chunks/float-to-rgba.glsl';
 import { light_frag_params } from './shader/chunks/light-frag-params.glsl';
-import { matrix_scale } from './shader/chunks/matrix-scale.glsl';
 import { normal_frag_params } from './shader/chunks/normal-frag-params.glsl';
 import { read_from_texture } from './shader/chunks/read-from-texture.glsl';
 import { rgba_to_float } from './shader/chunks/rgba-to-float.glsl';
@@ -104,7 +103,6 @@ const ShaderChunks: { [k: string]: string } = {
     fade_lod,
     float_to_rgba,
     light_frag_params,
-    matrix_scale,
     normal_frag_params,
     read_from_texture,
     rgba_to_float,

src/mol-gl/shader/chunks/assign-color-varying.glsl.ts

@@ -36,7 +36,7 @@ export const assign_color_varying = `
         vec3 cgridPos = (uColorGridTransform.w * (position - uColorGridTransform.xyz)) / uColorGridDim;
         vColor.rgb = texture3dFrom2dLinear(tColorGrid, cgridPos, uColorGridDim, uColorTexDim).rgb;
     #elif defined(dColorType_volumeInstance)
-        vec3 cgridPos = (uColorGridTransform.w * (vModelPosition - uColorGridTransform.xyz)) / uColorGridDim;
+        vec3 cgridPos = (uColorGridTransform.w * (vModelPosition / uModelScale - uColorGridTransform.xyz)) / uColorGridDim;
         vColor.rgb = texture3dFrom2dLinear(tColorGrid, cgridPos, uColorGridDim, uColorTexDim).rgb;
     #endif
 
@@ -52,7 +52,7 @@ export const assign_color_varying = `
         #elif defined(dOverpaintType_vertexInstance)
             vOverpaint = readFromTexture(tOverpaint, int(aInstance) * uVertexCount + vertexId, uOverpaintTexDim);
         #elif defined(dOverpaintType_volumeInstance)
-            vec3 ogridPos = (uOverpaintGridTransform.w * (vModelPosition - uOverpaintGridTransform.xyz)) / uOverpaintGridDim;
+            vec3 ogridPos = (uOverpaintGridTransform.w * (vModelPosition / uModelScale - uOverpaintGridTransform.xyz)) / uOverpaintGridDim;
             vOverpaint = texture3dFrom2dLinear(tOverpaintGrid, ogridPos, uOverpaintGridDim, uOverpaintTexDim);
         #endif
 
@@ -73,7 +73,7 @@ export const assign_color_varying = `
         #elif defined(dEmissiveType_vertexInstance)
             vEmissive = readFromTexture(tEmissive, int(aInstance) * uVertexCount + vertexId, uEmissiveTexDim).a;
         #elif defined(dEmissiveType_volumeInstance)
-            vec3 egridPos = (uEmissiveGridTransform.w * (vModelPosition - uEmissiveGridTransform.xyz)) / uEmissiveGridDim;
+            vec3 egridPos = (uEmissiveGridTransform.w * (vModelPosition / uModelScale - uEmissiveGridTransform.xyz)) / uEmissiveGridDim;
             vEmissive = texture3dFrom2dLinear(tEmissiveGrid, egridPos, uEmissiveGridDim, uEmissiveTexDim).a;
         #endif
         vEmissive *= uEmissiveStrength;
@@ -87,7 +87,7 @@ export const assign_color_varying = `
         #elif defined(dSubstanceType_vertexInstance)
             vSubstance = readFromTexture(tSubstance, int(aInstance) * uVertexCount + vertexId, uSubstanceTexDim);
         #elif defined(dSubstanceType_volumeInstance)
-            vec3 sgridPos = (uSubstanceGridTransform.w * (vModelPosition - uSubstanceGridTransform.xyz)) / uSubstanceGridDim;
+            vec3 sgridPos = (uSubstanceGridTransform.w * (vModelPosition / uModelScale - uSubstanceGridTransform.xyz)) / uSubstanceGridDim;
             vSubstance = texture3dFrom2dLinear(tSubstanceGrid, sgridPos, uSubstanceGridDim, uSubstanceTexDim);
         #endif
 
@@ -104,7 +104,7 @@ export const assign_color_varying = `
         #elif defined(dEmissiveType_vertexInstance)
             vEmissive = readFromTexture(tEmissive, int(aInstance) * uVertexCount + vertexId, uEmissiveTexDim).a;
         #elif defined(dEmissiveType_volumeInstance)
-            vec3 egridPos = (uEmissiveGridTransform.w * (vModelPosition - uEmissiveGridTransform.xyz)) / uEmissiveGridDim;
+            vec3 egridPos = (uEmissiveGridTransform.w * (vModelPosition / uModelScale - uEmissiveGridTransform.xyz)) / uEmissiveGridDim;
             vEmissive = texture3dFrom2dLinear(tEmissiveGrid, egridPos, uEmissiveGridDim, uEmissiveTexDim).a;
         #endif
         vEmissive *= uEmissiveStrength;
@@ -133,7 +133,7 @@ export const assign_color_varying = `
     #elif defined(dTransparencyType_vertexInstance)
         vTransparency = readFromTexture(tTransparency, int(aInstance) * uVertexCount + vertexId, uTransparencyTexDim).a;
     #elif defined(dTransparencyType_volumeInstance)
-        vec3 tgridPos = (uTransparencyGridTransform.w * (vModelPosition - uTransparencyGridTransform.xyz)) / uTransparencyGridDim;
+        vec3 tgridPos = (uTransparencyGridTransform.w * (vModelPosition / uModelScale - uTransparencyGridTransform.xyz)) / uTransparencyGridDim;
         vTransparency = texture3dFrom2dLinear(tTransparencyGrid, tgridPos, uTransparencyGridDim, uTransparencyTexDim).a;
     #endif
     vTransparency *= uTransparencyStrength;

src/mol-gl/shader/chunks/common-frag-params.glsl.ts

@@ -56,6 +56,7 @@ varying vec3 vModelPosition;
 varying vec3 vViewPosition;
 
 uniform vec2 uViewOffset;
+uniform float uModelScale;
 
 uniform float uNear;
 uniform float uFar;

src/mol-gl/shader/chunks/common-vert-params.glsl.ts

@@ -46,6 +46,8 @@ uniform int uPickType;
 varying vec3 vModelPosition;
 varying vec3 vViewPosition;
 
+uniform float uModelScale;
+
 #if defined(noNonInstancedActiveAttribs)
     // int() is needed for some Safari versions
     // see https://bugs.webkit.org/show_bug.cgi?id=244152

src/mol-gl/shader/chunks/matrix-scale.glsl.ts

@@ -1,12 +0,0 @@
-/**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-export const matrix_scale = `
-float matrixScale(in mat4 m){
-    vec4 r = m[0];
-    return sqrt(r[0] * r[0] + r[1] * r[1] + r[2] * r[2]);
-}
-`;

src/mol-gl/shader/cylinders.vert.ts

@@ -48,10 +48,10 @@ void main() {
 
     mat4 modelTransform = uModel * aTransform;
 
-    vTransform = aTransform;
+    vTransform = modelTransform;
     vStart = (modelTransform * vec4(aStart, 1.0)).xyz;
     vEnd = (modelTransform * vec4(aEnd, 1.0)).xyz;
-    vSize = size * aScale;
+    vSize = size * aScale * uModelScale;
     vCap = aCap;
 
     vModelPosition = (vStart + vEnd) * 0.5;

src/mol-gl/shader/direct-volume.frag.ts

@@ -29,11 +29,12 @@ precision highp int;
 
 uniform mat4 uProjection, uTransform, uModelView, uModel, uView;
 uniform vec3 uCameraDir;
+uniform float uModelScale;
 
 uniform sampler2D tDepth;
 uniform vec2 uDrawingBufferSize;
 
-varying vec3 vOrigPos;
+varying vec3 vModelPosition;
 varying float vInstance;
 varying vec4 vBoundingSphere;
 varying mat4 vTransform;
@@ -212,7 +213,7 @@ vec4 raymarch(vec3 startLoc, vec3 step, vec3 rayDir) {
         vec3 distVec = startLoc - pos;
         if (dot(distVec, distVec) > maxDistSq) break;
 
-        unitPos = v3m4(pos, cartnToUnit);
+        unitPos = v3m4(pos / uModelScale, cartnToUnit);
 
         // continue when outside of grid
         if (unitPos.x > posMax.x || unitPos.y > posMax.y || unitPos.z > posMax.z ||
@@ -228,7 +229,7 @@ vec4 raymarch(vec3 startLoc, vec3 step, vec3 rayDir) {
 
         if (uJumpLength > 0.0 && value < 0.01) {
             nextPos = pos + rayDir * uJumpLength;
-            nextValue = textureVal(v3m4(nextPos, cartnToUnit)).a;
+            nextValue = textureVal(v3m4(nextPos / uModelScale, cartnToUnit)).a;
             if (nextValue < 0.01) {
                 prevValue = nextValue;
                 pos = nextPos;
@@ -361,15 +362,15 @@ void main() {
         if (gl_FrontFacing)
             discard;
 
-        vec3 rayDir = mix(normalize(vOrigPos - uCameraPosition), uCameraDir, uIsOrtho);
-        vec3 step = rayDir * uStepScale;
+        vec3 rayDir = mix(normalize(vModelPosition - uCameraPosition), uCameraDir, uIsOrtho);
+        vec3 step = rayDir * uStepScale * uModelScale;
 
         float boundingSphereNear = distance(vBoundingSphere.xyz, uCameraPosition) - vBoundingSphere.w;
-        float d = max(uNear, boundingSphereNear) - mix(0.0, distance(vOrigPos, uCameraPosition), uIsOrtho);
-        vec3 start = mix(uCameraPosition, vOrigPos, uIsOrtho) + (d * rayDir);
+        float d = max(uNear, boundingSphereNear) - mix(0.0, distance(vModelPosition, uCameraPosition), uIsOrtho);
+        vec3 start = mix(uCameraPosition, vModelPosition, uIsOrtho) + (d * rayDir);
         gl_FragColor = raymarch(start, step, rayDir);
 
-        float fragmentDepth = calcDepth((uModelView * vec4(start, 1.0)).xyz);
+        float fragmentDepth = calcDepth((uView * vec4(start, 1.0)).xyz);
         float preFogAlpha = clamp(preFogAlphaBlended, 0.0, 1.0);
         #include wboit_write
     #endif

src/mol-gl/shader/direct-volume.vert.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Michael Krone <michael.krone@uni-tuebingen.de>
@@ -12,11 +12,13 @@ attribute vec3 aPosition;
 attribute mat4 aTransform;
 attribute float aInstance;
 
+uniform mat4 uModel;
 uniform mat4 uModelView;
 uniform mat4 uProjection;
 uniform vec4 uInvariantBoundingSphere;
+uniform float uModelScale;
 
-varying vec3 vOrigPos;
+varying vec3 vModelPosition;
 varying float vInstance;
 varying vec4 vBoundingSphere;
 varying mat4 vTransform;
@@ -33,11 +35,11 @@ void main() {
     vec4 unitCoord = vec4(aPosition + vec3(0.5), 1.0);
     vec4 mvPosition = uModelView * aTransform * uUnitToCartn * unitCoord;
 
-    vOrigPos = (aTransform * uUnitToCartn * unitCoord).xyz;
+    vModelPosition = (uModel * aTransform * uUnitToCartn * unitCoord).xyz;
     vInstance = aInstance;
     vBoundingSphere = vec4(
-        (aTransform * vec4(uInvariantBoundingSphere.xyz, 1.0)).xyz,
-        uInvariantBoundingSphere.w
+        (uModel * aTransform * vec4(uInvariantBoundingSphere.xyz, 1.0)).xyz,
+        uModelScale * uInvariantBoundingSphere.w
     );
     vTransform = aTransform;
 

src/mol-gl/shader/spheres.frag.ts

@@ -92,7 +92,7 @@ void main(void){
         vec3 vViewPosition = -vPointViewPosition;
         fragmentDepth = gl_FragCoord.z;
         #if !defined(dIgnoreLight) || defined(dXrayShaded) || defined(dRenderVariant_tracing)
-            pointDir.z -= cos(length(pointDir));
+            pointDir.z -= cos(length(pointDir)) * vRadius * 0.5;
             cameraNormal = -normalize(pointDir);
         #endif
         interior = false;

src/mol-gl/shader/spheres.vert.ts

@@ -18,6 +18,8 @@ precision highp int;
 uniform mat4 uModelView;
 uniform mat4 uInvProjection;
 uniform float uIsOrtho;
+uniform bool uHasHeadRotation;
+uniform mat4 uInvHeadRotation;
 
 uniform vec2 uTexDim;
 uniform sampler2D tPositionGroup;
@@ -29,8 +31,6 @@ varying float vRadius;
 varying vec3 vPoint;
 varying vec3 vPointViewPosition;
 
-#include matrix_scale
-
 /**
  * Bounding rectangle of a clipped, perspective-projected 3D Sphere.
  * Michael Mara, Morgan McGuire. 2013
@@ -81,7 +81,7 @@ void main(void){
     #include assign_clipping_varying
     #include assign_size
 
-    vRadius = size * matrixScale(uModelView);
+    vRadius = size * uModelScale;
 
     vec4 position4 = vec4(position, 1.0);
     vModelPosition = (uModel * aTransform * position4).xyz; // for clipping in frag shader
@@ -107,6 +107,10 @@ void main(void){
             vec4 mvCorner = vec4(mvPosition.xyz, 1.0);
             mvCorner.xy += mapping * vRadius;
             gl_Position = uProjection * mvCorner;
+        } else if (uHasHeadRotation) {
+            vec4 mvCorner = vec4(mvPosition.xyz, 1.0);
+            mvCorner.xy += mapping * vRadius * 1.4;
+            gl_Position = uProjection * mvCorner;
         } else {
             gl_Position = uProjection * vec4(mvPosition.xyz, 1.0);
             sphereProjection(mvPosition.xyz, vRadius, mapping);

src/mol-gl/shader/text.vert.ts

@@ -32,11 +32,11 @@ uniform float uOffsetZ;
 uniform float uIsOrtho;
 uniform float uPixelRatio;
 uniform vec4 uViewport;
+uniform mat4 uInvHeadRotation;
+uniform bool uHasHeadRotation;
 
 varying vec2 vTexCoord;
 
-#include matrix_scale
-
 void main(void){
     int vertexId = VertexID;
 
@@ -48,7 +48,7 @@ void main(void){
 
     vTexCoord = aTexCoord;
 
-    float scale = matrixScale(uModelView);
+    float scale = uModelScale;
 
     float offsetX = uOffsetX * scale;
     float offsetY = uOffsetY * scale;
@@ -75,9 +75,16 @@ void main(void){
         offsetZ -= 0.001 * distance(uCameraPosition, (uProjection * mvCorner).xyz);
     }
 
-    mvCorner.xy += aMapping * size * scale;
-    mvCorner.x += offsetX;
-    mvCorner.y += offsetY;
+    vec3 cornerOffset = vec3(0.0);
+    cornerOffset.xy += aMapping * size * scale;
+    cornerOffset.x += offsetX;
+    cornerOffset.y += offsetY;
+
+    if (uHasHeadRotation) {
+        mvCorner.xyz += (uInvHeadRotation * vec4(cornerOffset, 1.0)).xyz;
+    } else {
+        mvCorner.xyz += cornerOffset;
+    }
 
     if (uIsOrtho == 1.0) {
         mvCorner.z += offsetZ;

src/mol-gl/webgl/buffer.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -12,12 +12,13 @@ import { assertUnreachable, ValueOf } from '../../mol-util/type-helpers';
 import { GLRenderingContext, isWebGL2 } from './compat';
 import { WebGLExtensions } from './extensions';
 import { WebGLState } from './state';
+import { getBytesPerElement, getFormat, getType, TextureFormat, TextureType } from './texture';
 
 const getNextBufferId = idFactory();
 
 export type UsageHint = 'static' | 'dynamic' | 'stream'
 export type DataType = 'uint8' | 'int8' | 'uint16' | 'int16' | 'uint32' | 'int32' | 'float32'
-export type BufferType = 'attribute' | 'elements' | 'uniform'
+export type BufferType = 'attribute' | 'elements' | 'uniform' | 'pixel-pack'
 
 export type DataTypeArrayType = {
     'uint8': Uint8Array
@@ -36,6 +37,7 @@ export function getUsageHint(gl: GLRenderingContext, usageHint: UsageHint) {
         case 'static': return gl.STATIC_DRAW;
         case 'dynamic': return gl.DYNAMIC_DRAW;
         case 'stream': return gl.STREAM_DRAW;
+        default: assertUnreachable(usageHint);
     }
 }
 
@@ -81,6 +83,12 @@ export function getBufferType(gl: GLRenderingContext, bufferType: BufferType) {
             } else {
                 throw new Error('WebGL2 is required for uniform buffers');
             }
+        case 'pixel-pack':
+            if (isWebGL2(gl)) {
+                return gl.PIXEL_PACK_BUFFER;
+            } else {
+                throw new Error('WebGL2 is required for pixel-pack buffers');
+            }
     }
 }
 
@@ -258,4 +266,63 @@ export function createElementsBuffer(gl: GLRenderingContext, array: ElementsType
             gl.bindBuffer(gl.ELEMENT_ARRAY_BUFFER, buffer.getBuffer());
         }
     };
-}
+}
+
+//
+
+export interface PixelPackBuffer {
+    readonly id: number
+
+    readonly _type: number
+    readonly _format: number
+    readonly _bpe: number
+
+    read: (x: number, y: number, width: number, height: number) => void
+    getSubData: (array: ArrayType) => void
+
+    reset: () => void
+    destroy: () => void
+}
+
+export function createPixelPackBuffer(gl: WebGL2RenderingContext, extensions: WebGLExtensions, format: TextureFormat, type: TextureType): PixelPackBuffer {
+    let _buffer = getBuffer(gl);
+
+    const _type = getType(gl, extensions, type);
+    const _format = getFormat(gl, format, type);
+    const _bpe = getBytesPerElement(format, type);
+
+    function read(x: number, y: number, width: number, height: number) {
+        gl.bindBuffer(gl.PIXEL_PACK_BUFFER, _buffer);
+        gl.bufferData(gl.PIXEL_PACK_BUFFER, width * height * _bpe, gl.STREAM_READ);
+        gl.readPixels(x, y, width, height, _format, _type, 0);
+        gl.bindBuffer(gl.PIXEL_PACK_BUFFER, null);
+    }
+
+    function getSubData(array: ArrayType) {
+        gl.bindBuffer(gl.PIXEL_PACK_BUFFER, _buffer);
+        gl.getBufferSubData(gl.PIXEL_PACK_BUFFER, 0, array);
+        gl.bindBuffer(gl.PIXEL_PACK_BUFFER, null);
+    }
+
+    let destroyed = false;
+
+    return {
+        id: getNextBufferId(),
+
+        _type,
+        _format,
+        _bpe,
+
+        read,
+        getSubData,
+
+        reset: () => {
+            _buffer = getBuffer(gl);
+        },
+        destroy: () => {
+            if (destroyed) return;
+            gl.deleteBuffer(_buffer);
+            destroyed = true;
+        }
+    };
+}

src/mol-gl/webgl/context.ts

@@ -182,6 +182,7 @@ function createStats() {
         resourceCounts: {
             attribute: 0,
             elements: 0,
+            pixelPack: 0,
             framebuffer: 0,
             program: 0,
             renderbuffer: 0,
@@ -253,7 +254,6 @@ export interface WebGLContext {
     bindDrawingBuffer: () => void
     getDrawingBufferSize: () => { width: number, height: number }
     readPixels: (x: number, y: number, width: number, height: number, buffer: Uint8Array | Float32Array | Int32Array) => void
-    readPixelsAsync: (x: number, y: number, width: number, height: number, buffer: Uint8Array) => Promise<void>
     waitForGpuCommandsComplete: () => Promise<void>
     waitForGpuCommandsCompleteSync: () => void
     getFenceSync: () => WebGLSync | null
@@ -304,43 +304,6 @@ export function createContext(gl: GLRenderingContext, props: Partial<{ pixelScal
 
     let pixelScale = props.pixelScale || 1;
 
-    let readPixelsAsync: (x: number, y: number, width: number, height: number, buffer: Uint8Array) => Promise<void>;
-    if (isWebGL2(gl)) {
-        const pbo = gl.createBuffer();
-        let _buffer: Uint8Array | undefined = void 0;
-        let _resolve: (() => void) | undefined = void 0;
-        let _reading = false;
-
-        const bindPBO = () => {
-            gl.bindBuffer(gl.PIXEL_PACK_BUFFER, pbo);
-            gl.getBufferSubData(gl.PIXEL_PACK_BUFFER, 0, _buffer!);
-            gl.bindBuffer(gl.PIXEL_PACK_BUFFER, null);
-            _reading = false;
-            _resolve!();
-            _resolve = void 0;
-            _buffer = void 0;
-        };
-        readPixelsAsync = (x: number, y: number, width: number, height: number, buffer: Uint8Array): Promise<void> => new Promise<void>((resolve, reject) => {
-            if (_reading) {
-                reject('Can not call multiple readPixelsAsync at the same time');
-                return;
-            }
-            _reading = true;
-            gl.bindBuffer(gl.PIXEL_PACK_BUFFER, pbo);
-            gl.bufferData(gl.PIXEL_PACK_BUFFER, width * height * 4, gl.STREAM_READ);
-            gl.readPixels(x, y, width, height, gl.RGBA, gl.UNSIGNED_BYTE, 0);
-            gl.bindBuffer(gl.PIXEL_PACK_BUFFER, null);
-            // need to unbind/bind PBO before/after async awaiting the fence
-            _resolve = resolve;
-            _buffer = buffer;
-            fence(gl, bindPBO);
-        });
-    } else {
-        readPixelsAsync = async (x: number, y: number, width: number, height: number, buffer: Uint8Array) => {
-            readPixels(gl, x, y, width, height, buffer);
-        };
-    }
-
     const renderTargets = new Set<RenderTarget>();
 
     return {
@@ -429,7 +392,6 @@ export function createContext(gl: GLRenderingContext, props: Partial<{ pixelScal
         readPixels: (x: number, y: number, width: number, height: number, buffer: Uint8Array | Float32Array | Int32Array) => {
             readPixels(gl, x, y, width, height, buffer);
         },
-        readPixelsAsync,
         waitForGpuCommandsComplete: () => waitForGpuCommandsComplete(gl),
         waitForGpuCommandsCompleteSync: () => waitForGpuCommandsCompleteSync(gl),
         getFenceSync: () => {

src/mol-gl/webgl/resources.ts

@@ -6,11 +6,11 @@
 
 import { ProgramProps, createProgram, Program } from './program';
 import { ShaderType, createShader, Shader, ShaderProps } from './shader';
-import { GLRenderingContext } from './compat';
+import { GLRenderingContext, isWebGL2 } from './compat';
 import { Framebuffer, createFramebuffer } from './framebuffer';
 import { WebGLExtensions } from './extensions';
 import { WebGLState } from './state';
-import { AttributeBuffer, UsageHint, ArrayType, AttributeItemSize, createAttributeBuffer, ElementsBuffer, createElementsBuffer, ElementsType, AttributeBuffers } from './buffer';
+import { AttributeBuffer, UsageHint, ArrayType, AttributeItemSize, createAttributeBuffer, ElementsBuffer, createElementsBuffer, ElementsType, AttributeBuffers, PixelPackBuffer, createPixelPackBuffer } from './buffer';
 import { createReferenceCache, ReferenceItem } from '../../mol-util/reference-cache';
 import { WebGLStats } from './context';
 import { hashString, hashFnv32a } from '../../mol-data/util';
@@ -54,6 +54,7 @@ type ByteCounts = {
 export interface WebGLResources {
     attribute: (array: ArrayType, itemSize: AttributeItemSize, divisor: number, usageHint?: UsageHint) => AttributeBuffer
     elements: (array: ElementsType, usageHint?: UsageHint) => ElementsBuffer
+    pixelPack: (format: TextureFormat, type: TextureType) => PixelPackBuffer
     framebuffer: () => Framebuffer
     program: (defineValues: DefineValues, shaderCode: ShaderCode, schema: RenderableSchema) => Program
     renderbuffer: (format: RenderbufferFormat, attachment: RenderbufferAttachment, width: number, height: number) => Renderbuffer
@@ -72,6 +73,7 @@ export function createResources(gl: GLRenderingContext, state: WebGLState, stats
     const sets: { [k in ResourceName]: Set<Resource> } = {
         attribute: new Set<Resource>(),
         elements: new Set<Resource>(),
+        pixelPack: new Set<Resource>(),
         framebuffer: new Set<Resource>(),
         program: new Set<Resource>(),
         renderbuffer: new Set<Resource>(),
@@ -126,6 +128,12 @@ export function createResources(gl: GLRenderingContext, state: WebGLState, stats
         elements: (array: ElementsType, usageHint?: UsageHint) => {
             return wrap('elements', createElementsBuffer(gl, array, usageHint));
         },
+        pixelPack: (format: TextureFormat, type: TextureType) => {
+            if (!isWebGL2(gl)) {
+                throw new Error('WebGL2 is required for pixel-pack buffers');
+            }
+            return wrap('pixelPack', createPixelPackBuffer(gl, extensions, format, type));
+        },
         framebuffer: () => {
             return wrap('framebuffer', createFramebuffer(gl));
         },
@@ -171,6 +179,7 @@ export function createResources(gl: GLRenderingContext, state: WebGLState, stats
         reset: () => {
             sets.attribute.forEach(r => r.reset());
             sets.elements.forEach(r => r.reset());
+            sets.pixelPack.forEach(r => r.reset());
             sets.framebuffer.forEach(r => r.reset());
             sets.renderbuffer.forEach(r => r.reset());
             sets.shader.forEach(r => r.reset());
@@ -182,6 +191,7 @@ export function createResources(gl: GLRenderingContext, state: WebGLState, stats
         destroy: () => {
             sets.attribute.forEach(r => r.destroy());
             sets.elements.forEach(r => r.destroy());
+            sets.pixelPack.forEach(r => r.destroy());
             sets.framebuffer.forEach(r => r.destroy());
             sets.renderbuffer.forEach(r => r.destroy());
             sets.shader.forEach(r => r.destroy());

src/mol-gl/webgl/texture.ts

@@ -118,8 +118,11 @@ export function getInternalFormat(gl: GLRenderingContext, format: TextureFormat,
 }
 
 function getByteCount(format: TextureFormat, type: TextureType, width: number, height: number, depth: number): number {
-    const bpe = getFormatSize(format) * getTypeSize(type);
-    return bpe * width * height * (depth || 1);
+    return getBytesPerElement(format, type) * width * height * (depth || 1);
+}
+
+export function getBytesPerElement(format: TextureFormat, type: TextureType): number {
+    return getFormatSize(format) * getTypeSize(type);
 }
 
 function getFormatSize(format: TextureFormat) {

src/mol-io/reader/pdb/parser.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -11,11 +11,10 @@ import { ReaderResult } from '../result';
 import { Tokenizer } from '../common/text/tokenizer';
 import { StringLike } from '../../common/string-like';
 
-
 export function parsePDB(data: StringLike, id?: string, isPdbqt = false): Task<ReaderResult<PdbFile>> {
     return Task.create('Parse PDB', async ctx => ReaderResult.success({
         lines: await Tokenizer.readAllLinesAsync(data, ctx),
         id,
-        isPdbqt
+        isPdbqt,
     }));
 }

src/mol-io/reader/pdb/schema.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -10,5 +10,5 @@ import { Tokens } from '../common/text/tokenizer';
 export interface PdbFile {
     lines: Tokens
     id?: string,
-    isPdbqt?: boolean,
+    isPdbqt?: boolean
 }

src/mol-math/geometry/_spec/ray3d.spec.ts

@@ -0,0 +1,44 @@
+/**
+ * Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Gianluca Tomasello <giagitom@gmail.com>
+ */
+
+import { Vec3 } from '../../linear-algebra';
+import { Box3D } from '../primitives/box3d';
+import { Ray3D } from '../primitives/ray3d';
+
+describe('ray3d', () => {
+    it('intersectBox3D', () => {
+        const box = Box3D.create(Vec3.create(-1, -1, -1), Vec3.create(1, 1, 1));
+        const out = Vec3();
+
+        // 1. Ray starts outside and hits the box frontally
+        const ray1 = Ray3D.create(Vec3.create(-2, 0, 0), Vec3.create(1, 0, 0));
+        expect(Ray3D.intersectBox3D(out, ray1, box)).toBe(true);
+        expect(out).toEqual(Vec3.create(-1, 0, 0));
+
+        // 2. Ray grazes along the top edge (tangential)
+        const ray2 = Ray3D.create(Vec3.create(-2, 1, 0), Vec3.create(1, 0, 0));
+        expect(Ray3D.intersectBox3D(out, ray2, box)).toBe(true);
+        expect(out).toEqual(Vec3.create(-1, 1, 0));
+
+        // 3. Ray starts exactly on the surface and goes inward
+        const ray3 = Ray3D.create(Vec3.create(-1, 0, 0), Vec3.create(1, 0, 0));
+        expect(Ray3D.intersectBox3D(out, ray3, box)).toBe(true);
+        expect(out).toEqual(Vec3.create(-1, 0, 0));
+
+        // 4. Ray grazes a corner exactly
+        const ray4 = Ray3D.create(Vec3.create(-2, -2, -2), Vec3.create(1, 1, 1));
+        expect(Ray3D.intersectBox3D(out, ray4, box)).toBe(true);
+        expect(out).toEqual(Vec3.create(-1, -1, -1));
+
+        // 5. Ray starts inside the box and exits
+        const ray5 = Ray3D.create(Vec3.create(0, 0, 0), Vec3.create(1, 0, 0));
+        expect(Ray3D.intersectBox3D(out, ray5, box)).toBe(false);
+
+        // 6. Ray starts outside and points away (misses box completely)
+        const ray6 = Ray3D.create(Vec3.create(-2, 2, 0), Vec3.create(1, 0, 0));
+        expect(Ray3D.intersectBox3D(out, ray6, box)).toBe(false);
+    });
+});

src/mol-math/geometry/lookup3d/grid.ts

@@ -418,7 +418,7 @@ function queryNearest<T extends number = number>(ctx: QueryContext, result: Resu
     if (!Box3D.containsVec3(box, tmpRay.origin)) {
         // intersect ray pointing to box center
         Ray3D.targetTo(tmpRay, tmpRay, center);
-        Box3D.nearestIntersectionWithRay3D(tmpRay.origin, box, tmpRay);
+        Ray3D.intersectBox3D(tmpRay.origin, tmpRay, box);
         gX = Math.max(0, Math.min(sX - 1, Math.floor((tmpRay.origin[0] - min[0]) / delta[0])));
         gY = Math.max(0, Math.min(sY - 1, Math.floor((tmpRay.origin[1] - min[1]) / delta[1])));
         gZ = Math.max(0, Math.min(sZ - 1, Math.floor((tmpRay.origin[2] - min[2]) / delta[2])));

src/mol-math/geometry/primitives/box3d.ts

@@ -10,7 +10,6 @@ import { OrderedSet } from '../../../mol-data/int';
 import { Sphere3D } from './sphere3d';
 import { Vec3 } from '../../linear-algebra/3d/vec3';
 import { Mat4 } from '../../linear-algebra/3d/mat4';
-import { Ray3D } from './ray3d';
 
 interface Box3D { min: Vec3, max: Vec3 }
 
@@ -191,48 +190,6 @@ namespace Box3D {
         ) ? false : true;
     }
 
-    export function nearestIntersectionWithRay3D(out: Vec3, box: Box3D, ray: Ray3D): Vec3 {
-        const { origin, direction } = ray;
-        const [minX, minY, minZ] = box.min;
-        const [maxX, maxY, maxZ] = box.max;
-        const [x, y, z] = origin;
-        const invDirX = 1.0 / direction[0];
-        const invDirY = 1.0 / direction[1];
-        const invDirZ = 1.0 / direction[2];
-        let tmin, tmax, tymin, tymax, tzmin, tzmax;
-        if (invDirX >= 0) {
-            tmin = (minX - x) * invDirX;
-            tmax = (maxX - x) * invDirX;
-        } else {
-            tmin = (maxX - x) * invDirX;
-            tmax = (minX - x) * invDirX;
-        }
-        if (invDirY >= 0) {
-            tymin = (minY - y) * invDirY;
-            tymax = (maxY - y) * invDirY;
-        } else {
-            tymin = (maxY - y) * invDirY;
-            tymax = (minY - y) * invDirY;
-        }
-        if (invDirZ >= 0) {
-            tzmin = (minZ - z) * invDirZ;
-            tzmax = (maxZ - z) * invDirZ;
-        } else {
-            tzmin = (maxZ - z) * invDirZ;
-            tzmax = (minZ - z) * invDirZ;
-        }
-        if (tymin > tmin)
-            tmin = tymin;
-        if (tymax < tmax)
-            tmax = tymax;
-        if (tzmin > tmin)
-            tmin = tzmin;
-        if (tzmax < tmax)
-            tmax = tzmax;
-        Vec3.scale(out, direction, tmin);
-        return Vec3.set(out, out[0] + x, out[1] + y, out[2] + z);
-    }
-
     export function center(out: Vec3, box: Box3D): Vec3 {
         return Vec3.center(out, box.max, box.min);
     }

src/mol-math/geometry/primitives/ray3d.ts

@@ -2,10 +2,13 @@
  * Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Gianluca Tomasello <giagitom@gmail.com>
  */
 
 import { Mat4 } from '../../linear-algebra/3d/mat4';
 import { Vec3 } from '../../linear-algebra/3d/vec3';
+import { Box3D } from './box3d';
+import { Sphere3D } from './sphere3d';
 
 interface Ray3D { origin: Vec3, direction: Vec3 }
 
@@ -38,6 +41,96 @@ namespace Ray3D {
         Vec3.transformDirection(out.direction, ray.direction, m);
         return out;
     }
+
+    //
+
+    const tmpIR = Vec3();
+    function _intersectSphere3D(ray: Ray3D, sphere: Sphere3D): number {
+        const { center, radius } = sphere;
+        const { origin, direction } = ray;
+
+        const oc = Vec3.sub(tmpIR, origin, center);
+        const a = Vec3.dot(direction, direction);
+        const b = 2.0 * Vec3.dot(oc, direction);
+        const c = Vec3.dot(oc, oc) - radius * radius;
+        const discriminant = b * b - 4 * a * c;
+
+        if (discriminant < 0) return -1; // no intersection
+
+        const t = (-b - Math.sqrt(discriminant)) / (2.0 * a);
+        if (t < 0) return -1; // behind the ray
+
+        return t;
+    }
+
+    export function intersectSphere3D(out: Vec3, ray: Ray3D, sphere: Sphere3D): boolean {
+        const t = _intersectSphere3D(ray, sphere);
+        if (t < 0) return false;
+
+        Vec3.scaleAndAdd(out, ray.origin, ray.direction, t);
+        return true;
+    }
+
+    export function isIntersectingSphere3D(ray: Ray3D, sphere: Sphere3D): boolean {
+        return _intersectSphere3D(ray, sphere) >= 0;
+    }
+
+    export function isInsideSphere3D(ray: Ray3D, sphere: Sphere3D): boolean {
+        return Vec3.distance(ray.origin, sphere.center) < sphere.radius;
+    }
+
+    //
+
+    function _intersectBox3D(ray: Ray3D, box: Box3D): number {
+        const { origin, direction } = ray;
+        const [minX, minY, minZ] = box.min;
+        const [maxX, maxY, maxZ] = box.max;
+        const [x, y, z] = origin;
+        const invDirX = 1.0 / direction[0];
+        const invDirY = 1.0 / direction[1];
+        const invDirZ = 1.0 / direction[2];
+        let tmin, tmax, tymin, tymax, tzmin, tzmax;
+        if (invDirX >= 0) {
+            tmin = (minX - x) * invDirX;
+            tmax = (maxX - x) * invDirX;
+        } else {
+            tmin = (maxX - x) * invDirX;
+            tmax = (minX - x) * invDirX;
+        }
+        if (invDirY >= 0) {
+            tymin = (minY - y) * invDirY;
+            tymax = (maxY - y) * invDirY;
+        } else {
+            tymin = (maxY - y) * invDirY;
+            tymax = (minY - y) * invDirY;
+        }
+        if ((tmin > tymax) || (tymin > tmax)) return -1;
+        if (tymin > tmin) tmin = tymin;
+        if (tymax < tmax) tmax = tymax;
+        if (invDirZ >= 0) {
+            tzmin = (minZ - z) * invDirZ;
+            tzmax = (maxZ - z) * invDirZ;
+        } else {
+            tzmin = (maxZ - z) * invDirZ;
+            tzmax = (minZ - z) * invDirZ;
+        }
+        if ((tmin > tzmax) || (tzmin > tmax)) return -1;
+        if (tzmin > tmin) tmin = tzmin;
+        if (tzmax < tmax) tmax = tzmax;
+        return tmin >= 0 ? tmin : -1;
+    }
+
+    export function intersectBox3D(out: Vec3, ray: Ray3D, box: Box3D): boolean {
+        const t = _intersectBox3D(ray, box);
+        if (t < 0) return false;
+
+        Vec3.scaleAndAdd(out, ray.origin, ray.direction, t);
+        return true;
+    }
+
+    export function isIntersectingBox3D(ray: Ray3D, box: Box3D): boolean {
+        return _intersectBox3D(ray, box) >= 0;
+    }
 }
 
 export { Ray3D };

src/mol-math/geometry/primitives/sphere3d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -109,6 +109,23 @@ namespace Sphere3D {
         return out;
     }
 
+    /** Scale sphere by a number */
+    export function scale(out: Sphere3D, sphere: Sphere3D, s: number) {
+        Vec3.scale(out.center, sphere.center, s);
+        out.radius = sphere.radius * s;
+        if (hasExtrema(sphere)) {
+            setExtrema(out, sphere.extrema.map(e => Vec3.scale(Vec3(), e, s)));
+        }
+        return out;
+    }
+
+    /** Scale sphere by a number but without extrema */
+    export function scaleNX(out: Sphere3D, sphere: Sphere3D, s: number) {
+        Vec3.scale(out.center, sphere.center, s);
+        out.radius = sphere.radius * s;
+        return out;
+    }
+
     export function toArray<T extends NumberArray>(s: Sphere3D, out: T, offset: number) {
         Vec3.toArray(s.center, out, offset);
         out[offset + 3] = s.radius;

src/mol-math/linear-algebra/3d/mat3.ts

@@ -126,6 +126,11 @@ namespace Mat3 {
         return fromMat4(out, _m4);
     }
 
+    export function fromRotation(out: Mat3, rad: number, axis: Vec3) {
+        Mat4.fromRotation(_m4, rad, axis);
+        return fromMat4(out, _m4);
+    }
+
     export function create(a00: number, a01: number, a02: number, a10: number, a11: number, a12: number, a20: number, a21: number, a22: number): Mat3 {
         const out = zero();
         out[0] = a00;

src/mol-math/linear-algebra/3d/mat4.ts

@@ -84,6 +84,11 @@ namespace Mat4 {
         return mat;
     }
 
+    export function isZero(mat: Mat4): boolean {
+        for (let i = 0; i < 16; i++) if (mat[i] !== 0) return false;
+        return true;
+    }
+
     export function setZero(mat: Mat4): Mat4 {
         for (let i = 0; i < 16; i++) mat[i] = 0;
         return mat;
@@ -1265,6 +1270,14 @@ namespace Mat4 {
         return Math.sqrt(Math.max(scaleXSq, scaleYSq, scaleZSq));
     }
 
+    export function extractBasis(m: Mat4) {
+        return {
+            x: Vec3.create(m[0], m[1], m[2]),
+            y: Vec3.create(m[4], m[5], m[6]),
+            z: Vec3.create(m[8], m[9], m[10])
+        };
+    }
+
     const xAxis = [1, 0, 0] as unknown as Vec3;
     const yAxis = [0, 1, 0] as unknown as Vec3;
     const zAxis = [0, 0, 1] as unknown as Vec3;

src/mol-model-formats/structure/pdb/anisotropic.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Kim Juho <juho_kim@outlook.com>
  */
 
 import { CifField } from '../../../mol-io/reader/cif';
@@ -94,8 +95,10 @@ export function addAnisotropic(sites: AnisotropicTemplate, model: string, data:
         TokenBuilder.add(sites.pdbx_label_alt_id, s + 16, s + 17);
     }
 
-    // 18 - 20       Residue name  resName        Residue name.
-    TokenBuilder.addToken(sites.pdbx_auth_comp_id, Tokenizer.trim(data, s + 17, s + 20));
+    // 18 - 21       Residue name  resName        Residue name.
+    //                                            PDB spec defines 3-letter
+    //                                            but 4-letter are commonly used
+    TokenBuilder.addToken(sites.pdbx_auth_comp_id, Tokenizer.trim(data, s + 17, s + 21));
 
     // 22            Character     chainID        Chain identifier.
     TokenBuilder.add(sites.pdbx_auth_asym_id, s + 21, s + 22);

src/mol-model-formats/structure/pdb/atom-site.ts

@@ -1,8 +1,9 @@
 /**
-     * Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Kim Juho <juho_kim@outlook.com>
  */
 
 import { CifField } from '../../../mol-io/reader/cif';
@@ -237,8 +238,10 @@ export function addAtom(sites: AtomSiteTemplate, model: string, data: Tokenizer,
         TokenBuilder.add(sites.label_alt_id, s + 16, s + 17);
     }
 
-    // 18 - 20        Residue name    Residue name.
-    TokenBuilder.addToken(sites.auth_comp_id, Tokenizer.trim(data, s + 17, s + 20));
+    // 18 - 21        Residue name    Residue name.
+    //                                PDB spec defines 3-letter
+    //                                but 4-letter are commonly used
+    TokenBuilder.addToken(sites.auth_comp_id, Tokenizer.trim(data, s + 17, s + 21));
 
     // 22             Character       Chain identifier.
     TokenBuilder.add(sites.auth_asym_id, s + 21, s + 22);

src/mol-model-formats/structure/pdb/secondary-structure.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Kim Juho <juho_kim@outlook.com>
  */
 
 import { CifCategory, CifField } from '../../../mol-io/reader/cif';
@@ -62,18 +63,22 @@ export function parseHelix(lines: Tokens, lineStart: number, lineEnd: number): C
         const line = getLine(i);
         // COLUMNS        DATA  TYPE     FIELD         DEFINITION
         // -----------------------------------------------------------------------------------
-        // 1 -  6        Record name    "HELIX "
-        // 8 - 10        Integer        serNum        Serial number of the helix. This starts
+        //  1 -  6        Record name    "HELIX "
+        //  8 - 10        Integer        serNum        Serial number of the helix. This starts
         //                                             at 1  and increases incrementally.
         // 12 - 14        LString(3)     helixID       Helix  identifier. In addition to a serial
         //                                             number, each helix is given an
         //                                             alphanumeric character helix identifier.
-        // 16 - 18        Residue name   initResName   Name of the initial residue.
+        // 16 - 19        Residue name   initResName   Name of the initial residue.
+        //                                             PDB spec defines 3-letter for residue name,
+        //                                             but 4-letter are commonly used
         // 20             Character      initChainID   Chain identifier for the chain containing
         //                                             this  helix.
         // 22 - 25        Integer        initSeqNum    Sequence number of the initial residue.
         // 26             AChar          initICode     Insertion code of the initial residue.
-        // 28 - 30        Residue  name  endResName    Name of the terminal residue of the helix.
+        // 28 - 31        Residue name   endResName    Name of the terminal residue of the helix.
+        //                                             PDB spec defines 3-letter for residue name,
+        //                                             but 4-letter are commonly used
         // 32             Character      endChainID    Chain identifier for the chain containing
         //                                             this  helix.
         // 34 - 37        Integer        endSeqNum     Sequence number of the terminal residue.
@@ -82,19 +87,19 @@ export function parseHelix(lines: Tokens, lineStart: number, lineEnd: number): C
         // 41 - 70        String         comment       Comment about this helix.
         // 72 - 76        Integer        length        Length of this helix.
         helices.push({
-            serNum: line.substr(7, 3).trim(),
-            helixID: line.substr(11, 3).trim(),
-            initResName: line.substr(15, 3).trim(),
-            initChainID: line.substr(19, 1).trim(),
-            initSeqNum: line.substr(21, 4).trim(),
-            initICode: line.substr(25, 1).trim(),
-            endResName: line.substr(27, 3).trim(),
-            endChainID: line.substr(31, 3).trim(),
-            endSeqNum: line.substr(33, 4).trim(),
-            endICode: line.substr(37, 1).trim(),
-            helixClass: line.substr(38, 2).trim(),
-            comment: line.substr(40, 30).trim(),
-            length: line.substr(71, 5).trim()
+            serNum: line.substring(7, 10).trim(),
+            helixID: line.substring(11, 14).trim(),
+            initResName: line.substring(15, 19).trim(),
+            initChainID: line.substring(19, 20).trim(),
+            initSeqNum: line.substring(21, 25).trim(),
+            initICode: line.substring(25, 26).trim(),
+            endResName: line.substring(27, 31).trim(),
+            endChainID: line.substring(31, 34).trim(),
+            endSeqNum: line.substring(33, 37).trim(),
+            endICode: line.substring(37, 38).trim(),
+            helixClass: line.substring(38, 40).trim(),
+            comment: line.substring(40, 70).trim(),
+            length: line.substring(71, 76).trim()
         });
     }
 
@@ -167,19 +172,23 @@ export function parseSheet(lines: Tokens, lineStart: number, lineEnd: number): C
         const line = getLine(i);
         // COLUMNS       DATA  TYPE     FIELD          DEFINITION
         // -------------------------------------------------------------------------------------
-        // 1 -  6        Record name   "SHEET "
-        // 8 - 10        Integer       strand         Strand  number which starts at 1 for each
+        //  1 -  6        Record name   "SHEET "
+        //  8 - 10        Integer       strand         Strand  number which starts at 1 for each
         //                                             strand within a sheet and increases by one.
         // 12 - 14        LString(3)    sheetID        Sheet  identifier.
         // 15 - 16        Integer       numStrands     Number  of strands in sheet.
-        // 18 - 20        Residue name  initResName    Residue  name of initial residue.
+        // 18 - 21        Residue name  initResName    Residue  name of initial residue.
+        //                                             PDB spec defines 3-letter for residue name,
+        //                                             but 4-letter are commonly used
         // 22             Character     initChainID    Chain identifier of initial residue
         //                                             in strand.
         // 23 - 26        Integer       initSeqNum     Sequence number of initial residue
         //                                             in strand.
         // 27             AChar         initICode      Insertion code of initial residue
         //                                             in  strand.
-        // 29 - 31        Residue name  endResName     Residue name of terminal residue.
+        // 29 - 32        Residue name  endResName     Residue name of terminal residue.
+        //                                             PDB spec defines 3-letter for residue name,
+        //                                             but 4-letter are commonly used
         // 33             Character     endChainID     Chain identifier of terminal residue.
         // 34 - 37        Integer       endSeqNum      Sequence number of terminal residue.
         // 38             AChar         endICode       Insertion code of terminal residue.
@@ -187,7 +196,9 @@ export function parseSheet(lines: Tokens, lineStart: number, lineEnd: number): C
         //                                             strand in the sheet. 0 if first strand,
         //                                             1 if  parallel,and -1 if anti-parallel.
         // 42 - 45        Atom          curAtom        Registration.  Atom name in current strand.
-        // 46 - 48        Residue name  curResName     Registration.  Residue name in current strand
+        // 46 - 49        Residue name  curResName     Registration.  Residue name in current strand
+        //                                             PDB spec defines 3-letter for residue name,
+        //                                             but 4-letter are commonly used
         // 50             Character     curChainId     Registration. Chain identifier in
         //                                             current strand.
         // 51 - 54        Integer       curResSeq      Registration.  Residue sequence number
@@ -195,8 +206,10 @@ export function parseSheet(lines: Tokens, lineStart: number, lineEnd: number): C
         // 55             AChar         curICode       Registration. Insertion code in
         //                                             current strand.
         // 57 - 60        Atom          prevAtom       Registration.  Atom name in previous strand.
-        // 61 - 63        Residue name  prevResName    Registration.  Residue name in
+        // 61 - 64        Residue name  prevResName    Registration.  Residue name in
         //                                             previous strand.
+        //                                             PDB spec defines 3-letter for residue name,
+        //                                             but 4-letter are commonly used
         // 65             Character     prevChainId    Registration.  Chain identifier in
         //                                             previous  strand.
         // 66 - 69        Integer       prevResSeq     Registration. Residue sequence number
@@ -204,28 +217,28 @@ export function parseSheet(lines: Tokens, lineStart: number, lineEnd: number): C
         // 70             AChar         prevICode      Registration.  Insertion code in
         //                                             previous strand.
         sheets.push({
-            strand: line.substr(7, 3).trim(),
-            sheetID: line.substr(11, 3).trim(),
-            numStrands: line.substr(14, 2).trim(),
-            initResName: line.substr(17, 3).trim(),
-            initChainID: line.substr(21, 1).trim(),
-            initSeqNum: line.substr(22, 4).trim(),
-            initICode: line.substr(26, 1).trim(),
-            endResName: line.substr(28, 3).trim(),
-            endChainID: line.substr(32, 1).trim(),
-            endSeqNum: line.substr(33, 4).trim(),
-            endICode: line.substr(37, 1).trim(),
-            sense: line.substr(38, 2).trim(),
-            curAtom: line.substr(41, 4).trim(),
-            curResName: line.substr(45, 3).trim(),
-            curChainId: line.substr(49, 1).trim(),
-            curResSeq: line.substr(50, 4).trim(),
-            curICode: line.substr(54, 1).trim(),
-            prevAtom: line.substr(56, 4).trim(),
-            prevResName: line.substr(60, 3).trim(),
-            prevChainId: line.substr(64, 1).trim(),
-            prevResSeq: line.substr(65, 4).trim(),
-            prevICode: line.substr(69, 1).trim(),
+            strand: line.substring(7, 10).trim(),
+            sheetID: line.substring(11, 14).trim(),
+            numStrands: line.substring(14, 16).trim(),
+            initResName: line.substring(17, 21).trim(),
+            initChainID: line.substring(21, 22).trim(),
+            initSeqNum: line.substring(22, 26).trim(),
+            initICode: line.substring(26, 27).trim(),
+            endResName: line.substring(28, 32).trim(),
+            endChainID: line.substring(32, 33).trim(),
+            endSeqNum: line.substring(33, 37).trim(),
+            endICode: line.substring(37, 38).trim(),
+            sense: line.substring(38, 40).trim(),
+            curAtom: line.substring(41, 45).trim(),
+            curResName: line.substring(45, 49).trim(),
+            curChainId: line.substring(49, 50).trim(),
+            curResSeq: line.substring(50, 54).trim(),
+            curICode: line.substring(54, 55).trim(),
+            prevAtom: line.substring(56, 60).trim(),
+            prevResName: line.substring(60, 64).trim(),
+            prevChainId: line.substring(64, 65).trim(),
+            prevResSeq: line.substring(65, 69).trim(),
+            prevICode: line.substring(69, 70).trim(),
         });
     }