5.0.0-dev.12

* MVS: Color map interpolation

* print validation errors to plugin log

* fixes

* background postprocessing

* fix resetCanvasProps

* fix link

* add example

CHANGELOG.md

@@ -13,6 +13,7 @@ Note that since we don't clearly distinguish between a public and private interf
   - 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
@@ -20,10 +21,10 @@ 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`
+  - `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
+  - `canvas` node: support custom property `molstar_postprocessing` with the ability to customize outline, depth of field, bloom, shadow, occlusion (SSAO), fog, and background
   - `clip` node support for structure and volume representations
   - `grid_slice` representation support for volumes
   - Support tethers and background for primitive labels
@@ -41,14 +42,19 @@ Note that since we don't clearly distinguish between a public and private interf
   - 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
+  - Print tree validation errors to plugin log
 - 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))
@@ -95,6 +101,7 @@ Note that since we don't clearly distinguish between a public and private interf
 - 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`
+- Fix renderer transparency check
 
 ## [v4.18.0] - 2025-06-08
 - MolViewSpec extension:

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

@@ -20,14 +20,19 @@ Generally, the command should be URL encoded, e.g., `a b` => `a%20b` (in JS, `en
 
 - `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%3Dresn%20HEM%26lang%3Dpymol%26action%3Dhighlight%2Cfocus)` highlights or focuses the HEM residue (the command must be URL encoded because it contains spaces and possibly other special characters)
+    - `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
 
@@ -36,11 +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 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
+    - `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-lock.json

@@ -1,12 +1,12 @@
 {
   "name": "molstar",
-  "version": "5.0.0-dev.7",
+  "version": "5.0.0-dev.12",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "molstar",
-      "version": "5.0.0-dev.7",
+      "version": "5.0.0-dev.12",
       "license": "MIT",
       "dependencies": {
         "@types/argparse": "^2.0.17",

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "5.0.0-dev.7",
+  "version": "5.0.0-dev.12",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -122,7 +122,8 @@
     "Lukáš Polák <admin@lukaspolak.cz>",
     "Chetan Mishra <chetan.s115@gmail.com>",
     "Zach Charlop-Powers <zach.charlop.powers@gmail.com>",
-    "Kim Juho <juho_kim@outlook.com>"
+    "Kim Juho <juho_kim@outlook.com>",
+    "Victoria Doshchenko <doshchenko.victoria@gmail.com>"
   ],
   "license": "MIT",
   "devDependencies": {

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/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/cli/mvs/mvs-print-schema.ts

@@ -11,7 +11,7 @@
  */
 
 import { ArgumentParser } from 'argparse';
-import { treeSchemaToMarkdown, treeSchemaToString } from '../../extensions/mvs/tree/generic/tree-schema';
+import { treeSchemaToMarkdown, treeSchemaToString } from '../../extensions/mvs/tree/generic/tree-validation';
 import { MVSTreeSchema } from '../../extensions/mvs/tree/mvs/mvs-tree';
 
 

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

@@ -22,7 +22,15 @@ const Steps = [
         header: 'Animation Demo',
         key: 'intro',
         description: `### Molecular Animation
-A story showcasing MolViewSpec animation capabilities.`,
+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 => {
@@ -41,7 +49,7 @@ A story showcasing MolViewSpec animation capabilities.`,
                 custom: {
                     molstar_trackball: {
                         name: 'rock',
-                        params: { speed: 1.5 },
+                        params: { speed: 0.5 },
                     }
                 }
             });
@@ -49,11 +57,23 @@ A story showcasing MolViewSpec animation capabilities.`,
                 kind: 'scalar',
                 ref: 'prims-opacity',
                 target_ref: 'prims',
-                duration_ms: 1000,
+                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
@@ -91,12 +111,28 @@ A story showcasing MolViewSpec animation capabilities.`,
             const builder = createMVSBuilder();
 
             const _1cbs = structure(builder, '1cbs');
-            const [poly,] = polymer(_1cbs, { color: Colors['1cbs'] });
+            const [poly, repr] = polymer(_1cbs, { color: Colors['1cbs'] });
+
+            repr.colorFromSource({
+                ref: 'residue_colors',
+                schema: 'residue',
+                category_name: 'atom_site',
+                field_name: 'label_comp_id',
+                palette: {
+                    kind: 'categorical',
+                    missing_color: 'white',
+                    colors: {
+                        ALA: 'red',
+                        ILE: 'white',
+                        LYS: 'white',
+                    }
+                }
+            });
 
             const surface = poly.representation({
                 type: 'surface',
                 surface_type: 'gaussian',
-            });
+            }).opacity({ opacity: 0.33 });
 
             _1cbs.component({ selector: 'ligand' })
                 .transform({
@@ -119,14 +155,32 @@ A story showcasing MolViewSpec animation capabilities.`,
 
             anim.interpolate({
                 kind: 'scalar',
-                ref: 'clip-transition',
                 target_ref: 'clip',
-                duration_ms: 2000,
+                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',
@@ -152,6 +206,20 @@ A story showcasing MolViewSpec animation capabilities.`,
                 end: Colors['ligand-docked'],
             });
 
+            anim.interpolate({
+                kind: 'color',
+                target_ref: 'residue_colors',
+                duration_ms: 2000,
+                property: ['palette', 'colors'],
+                start: {
+                    ALA: 'yellow',
+                },
+                end: {
+                    ILE: 'blue',
+                    LYS: 'purple',
+                },
+            });
+
             return builder;
         },
         camera: {
@@ -182,7 +250,7 @@ A story showcasing MolViewSpec animation capabilities.`,
                     ref: 'repr',
                     type: 'ball_and_stick',
                     custom: {
-                        molstar_reprepresentation_params: {
+                        molstar_representation_params: {
                             emissive: 0,
                         }
                     }
@@ -209,7 +277,7 @@ A story showcasing MolViewSpec animation capabilities.`,
                 kind: 'scalar',
                 target_ref: 'repr',
                 duration_ms: 1000,
-                property: ['custom', 'molstar_reprepresentation_params', 'emissive'],
+                property: ['custom', 'molstar_representation_params', 'emissive'],
                 end: 0.2,
             });
 
@@ -273,10 +341,12 @@ function structure(builder: Root, id: string): MVSStructure {
         .modelStructure();
 }
 
-function polymer(structure: MVSStructure, options: { color: ColorT }) {
+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 });
+    if (options?.color) {
+        reprensentation.color({ color: options.color });
+    }
     return [component, reprensentation] as const;
 }
 
@@ -294,6 +364,21 @@ export function buildStory(): MVSData_States {
                 molstar_postprocessing: {
                     enable_outline: true,
                     enable_ssao: true,
+                    background: {
+                        name: 'horizontalGradient',
+                        params: {
+                            topColor: 0x777777,
+                            bottomColor: 0xffffff,
+                        }
+                    },
+                    // Example with background image:
+                    // background: {
+                    //     name: 'image',
+                    //     params: {
+                    //         // URL can also be filename in MVSX archive
+                    //         source: { name: 'url', params: 'URL' }
+                    //     }
+                    // }
                 }
             }
         });

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

@@ -7,9 +7,13 @@
 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: 'animation', name: 'Molecular Animation', buildStory: animation },
+    { 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/README.md

@@ -1 +1 @@
-Find the MVS extension documentation [here](../../../docs/extensions/mvs/README.md).
+Please refer to the standalone documentation [here](https://molstar.org/mol-view-spec-docs/).

src/extensions/mvs/camera.ts

@@ -8,6 +8,7 @@
 import { Camera } from '../../mol-canvas3d/camera';
 import { CameraFogParams, Canvas3DParams, Canvas3DProps, DefaultCanvas3DParams } from '../../mol-canvas3d/canvas3d';
 import { TrackballControlsParams } from '../../mol-canvas3d/controls/trackball';
+import { BackgroundParams } from '../../mol-canvas3d/passes/background';
 import { BloomParams } from '../../mol-canvas3d/passes/bloom';
 import { DofParams } from '../../mol-canvas3d/passes/dof';
 import { OutlineParams } from '../../mol-canvas3d/passes/outline';
@@ -21,6 +22,7 @@ import { PluginState } from '../../mol-plugin/state';
 import { StateObjectSelector } from '../../mol-state';
 import { fovAdjustedPosition } from '../../mol-util/camera';
 import { ColorNames } from '../../mol-util/color/names';
+import { deepClone } from '../../mol-util/object';
 import { ParamDefinition } from '../../mol-util/param-definition';
 import { decodeColor } from './helpers/utils';
 import { MolstarLoadingContext } from './load';
@@ -132,6 +134,11 @@ function optionalParams(enable: boolean | undefined, values: any, params: ParamD
     return fallback;
 }
 
+function normalizeBackground(variant: any, prev: any): any {
+    if (!variant) return prev;
+    return ParamDefinition.normalizeParams(BackgroundParams, { variant }, 'children');
+}
+
 /** Create a deep copy of `oldCanvasProps` with values modified according to a canvas node params. */
 export function modifyCanvasProps(oldCanvasProps: Canvas3DProps, canvasNode: MolstarNode<'canvas'> | undefined, animationNode: MVSAnimationNode<'animation'> | undefined): Canvas3DProps {
     const params = canvasNode?.params;
@@ -157,6 +164,8 @@ export function modifyCanvasProps(oldCanvasProps: Canvas3DProps, canvasNode: Mol
     const bloom = molstar_postprocessing?.enable_bloom;
     const bloomParams = molstar_postprocessing?.bloom_params;
 
+    const background = molstar_postprocessing?.background;
+
     const trackballAnimation = animationNode?.custom?.molstar_trackball;
     const trackballAnimationName = trackballAnimation?.name;
     const trackballAnimationParams = trackballAnimation?.params ?? {};
@@ -170,6 +179,7 @@ export function modifyCanvasProps(oldCanvasProps: Canvas3DProps, canvasNode: Mol
             occlusion: optionalParams(occlusion, occlusionParams, SsaoParams, oldCanvasProps.postprocessing.occlusion),
             dof: optionalParams(dof, dofParams, DofParams, oldCanvasProps.postprocessing.dof),
             bloom: optionalParams(bloom, bloomParams, BloomParams, oldCanvasProps.postprocessing.bloom),
+            background: normalizeBackground(background, oldCanvasProps.postprocessing.background),
         },
         cameraFog: optionalParams(fog, fogParams, CameraFogParams, oldCanvasProps.cameraFog),
         renderer: {
@@ -200,13 +210,14 @@ export function resetCanvasProps(plugin: PluginContext) {
         ...old,
         postprocessing: {
             ...old,
-            outline: DefaultCanvas3DParams.postprocessing.outline,
-            shadow: DefaultCanvas3DParams.postprocessing.shadow,
-            occlusion: DefaultCanvas3DParams.postprocessing.occlusion,
-            dof: DefaultCanvas3DParams.postprocessing.dof,
-            bloom: DefaultCanvas3DParams.postprocessing.bloom,
+            outline: deepClone(DefaultCanvas3DParams.postprocessing.outline),
+            shadow: deepClone(DefaultCanvas3DParams.postprocessing.shadow),
+            occlusion: deepClone(DefaultCanvas3DParams.postprocessing.occlusion),
+            dof: deepClone(DefaultCanvas3DParams.postprocessing.dof),
+            bloom: deepClone(DefaultCanvas3DParams.postprocessing.bloom),
+            background: deepClone(DefaultCanvas3DParams.postprocessing.background),
         },
-        cameraFog: DefaultCanvas3DParams.cameraFog,
+        cameraFog: deepClone(DefaultCanvas3DParams.cameraFog),
         trackball: {
             ...old?.trackball,
             animate: { name: 'off', params: {} },

src/extensions/mvs/components/primitives.ts

@@ -149,6 +149,7 @@ 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') {
@@ -161,6 +162,7 @@ export const MVSBuildPrimitiveShape = MVSTransform({
                 params: {
                     ...PD.withDefaults(Mesh.Params, { alpha: a.data.options?.opacity ?? 1, ...customMeshParams }),
                     ...snapshotKey,
+                    ...markdownCommands,
                 },
                 getShape: (_, data, __, prev: any) => buildPrimitiveMesh(data, prev?.geometry),
                 geometryUtils: Mesh.Utils,
@@ -185,6 +187,7 @@ export const MVSBuildPrimitiveShape = MVSTransform({
                         ...customLabelParams,
                     }),
                     ...snapshotKey,
+                    ...markdownCommands,
                 },
                 getShape: (_, data, props, prev: any) => buildPrimitiveLabels(data, prev?.geometry, props),
                 geometryUtils: Text.Utils,
@@ -199,6 +202,7 @@ export const MVSBuildPrimitiveShape = MVSTransform({
                 params: {
                     ...PD.withDefaults(Lines.Params, { alpha: a.data.options?.opacity ?? 1, ...customLineParams }),
                     ...snapshotKey,
+                    ...markdownCommands,
                 },
                 getShape: (_, data, __, prev: any) => buildPrimitiveLines(data, prev?.geometry),
                 geometryUtils: Lines.Utils,
@@ -227,7 +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 });
             }
@@ -241,7 +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 });
             }
@@ -252,6 +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/helpers/animation.ts

@@ -5,20 +5,22 @@
  * @author Ludovic Autin <ludovic.autin@gmail.com>
  */
 
-import { create } from 'mutative';
-import { Snapshot } from '../mvs-data';
-import { Tree } from '../tree/generic/tree-schema';
-import { clamp, lerp } from '../../../mol-math/interpolate';
-import { MVSAnimationEasing, MVSAnimationNode, MVSAnimationSchema } from '../tree/animation/animation-tree';
-import { MVSTree } from '../tree/mvs/mvs-tree';
+import { SortedArray } from '../../../mol-data/int';
 import * as EasingFns from '../../../mol-math/easing';
-import { addDefaults } from '../tree/generic/tree-utils';
-import { RuntimeContext } from '../../../mol-task';
+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 { decodeColor } from '../../../mol-util/color/utils';
+import { produce } from '../../../mol-util/produce';
 import { makeContinuousPaletteCheckpoints, MVSContinuousPaletteProps, MVSDiscretePaletteProps } from '../components/annotation-color-theme';
 import { palettePropsFromMVSPalette } from '../load-helpers';
-import { SortedArray } from '../../../mol-data/int';
+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) {
@@ -33,17 +35,27 @@ export async function generateStateTransition(ctx: RuntimeContext, snapshot: Sna
         ...transitions.map(t => (t.params.start_ms ?? 0) + t.params.duration_ms)
     );
 
-    const frames: MVSTree[] = [];
+    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, transitions, t, cache, nodeMap);
-        frames.push(root);
+        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 });
@@ -77,74 +89,96 @@ const EasingFnMap: Record<MVSAnimationEasing, (t: number) => number> = {
 
 interface InterpolationCacheEntry {
     paletteFn?: (value: number) => Color,
+    startColor?: Color | Record<number | string, Color>,
+    endColor?: Color | Record<number | string, Color>,
     rotation?: { axis: Vec3, angle: number, start: Quat, end: Quat },
 }
 
-function createSnapshot(tree: MVSTree, transitions: MVSAnimationNode<'interpolate'>[], time: number, cache: Map<any, InterpolationCacheEntry>, nodeMap: Map<string, (string | number)[]>) {
-    return create(tree, (draft) => {
-        for (const transition of transitions) {
-            const nodePath = nodeMap.get(transition.params.target_ref);
+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 = transition.params.property[0] === 'custom' ? node?.custom : node?.params;
+            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 = transition.params.start_ms ?? 0;
-            let t = clamp((time - startTime) / transition.params.duration_ms, 0, 1);
-
-            if (transition.params.kind === 'transform_matrix') {
-                processTransformMatrix(transition, target, t, cacheEntry);
-                continue;
-            }
-
-            t = applyFrequency(t, transition.params.frequency ?? 1, !!transition.params.alternate_direction);
-
-            const offset = transition.params.property[0] === 'custom' ? 1 : 0;
-            const startBase = transition.params.start ?? 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 <= startTime) {
-                assign(target, transition.params.property, startValue, offset);
-                continue;
-            }
-
-            const easing = EasingFnMap[transition.params.easing ?? 'linear'] ?? EasingFnMap['linear'];
-            t = easing(t);
+            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 === 'scalar') {
-                next = interpolateScalars(startValue, endValue, t, transition.params.noise_magnitude ?? 0);
-            } else if (transition.params.kind === 'vec3') {
-                next = interpolateVectors(startValue, endValue, t, transition.params.noise_magnitude ?? 0, !!transition.params.spherical);
-            } else if (transition.params.kind === 'rotation_matrix') {
-                next = interpolateRotation(startValue, endValue, t, transition.params.noise_magnitude ?? 0, cacheEntry);
-            } else if (transition.params.kind === 'color') {
-                const color = paletteFn(t);
-                next = Color.toHexStyle(color);
+            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) {
@@ -163,6 +197,53 @@ function applyFrequency(t: number, frequency: number, alternate: boolean) {
     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 startValue = transition.params.start ?? getPreviousScalarEnd(previous) ?? select(target, transition.params.property, offset);
+    if (transition.params.kind === 'color' && !cacheEntry.paletteFn) {
+        cacheEntry.paletteFn = makePaletteFunction(transition);
+    }
+
+    const endValue: any = transition.params.end;
+
+    if (time <= 0) return startValue;
+    else if (time >= 1 - EPSILON && !transition.params.alternate_direction && transition.params.kind !== 'color') 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') {
+        if (cacheEntry.paletteFn) {
+            const color = cacheEntry.paletteFn(t);
+            return Color.toHexStyle(color);
+        }
+
+        const baseColors = typeof startValue === 'object' ? select(target, transition.params.property, offset) : undefined;
+        return interpolateColors(startValue, endValue, t, cacheEntry, baseColors);
+    }
+}
+
+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(),
@@ -172,31 +253,41 @@ const TransformState = {
     pivotNeg: Vec3(),
     temp: Mat4(),
 };
-function processTransformMatrix(transition: MVSAnimationNode<'interpolate'>, target: any, time: number, cache: InterpolationCacheEntry) {
+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 offset = transition.params.property[0] === 'custom' ? 1 : 0;
     const transform = select(target, transition.params.property, offset) ?? Mat4.identity();
 
-    const startRotation = transition.params.rotation_start ?? Mat3.fromMat4(Mat3(), transform);
-    const startTranslation = transition.params.translation_start ?? Mat4.getTranslation(Vec3(), transform);
-    const startScale = transition.params.scale_start ?? Mat4.getScaling(Vec3(), transform);
+    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 t = applyFrequency(time, transition.params.rotation_frequency ?? 1, !!transition.params.rotation_alternate_direction);
-    let easing = EasingFnMap[transition.params.rotation_easing ?? 'linear'] ?? EasingFnMap['linear'];
-    const rotation = interpolateRotation(startRotation as Mat3, endRotation as Mat3, easing(t), transition.params.rotation_noise_magnitude ?? 0, cache);
+    let rotation, translation, scale;
 
-    t = applyFrequency(time, transition.params.translation_frequency ?? 1, !!transition.params.translation_alternate_direction);
-    easing = EasingFnMap[transition.params.translation_easing ?? 'linear'] ?? EasingFnMap['linear'];
-    const translation = interpolateVec3(startTranslation as Vec3, endTranslation as Vec3 | undefined, easing(t), transition.params.translation_noise_magnitude ?? 0, false);
+    if (time <= 0) {
+        rotation = startRotation as Mat3;
+        translation = startTranslation as Vec3;
+        scale = startScale as Vec3;
+    } else {
+        const clampedTime = clamp(time, 0, 1);
 
-    t = applyFrequency(time, transition.params.scale_frequency ?? 1, !!transition.params.scale_alternate_direction);
-    easing = EasingFnMap[transition.params.scale_easing ?? 'linear'] ?? EasingFnMap['linear'];
-    const scale = interpolateVec3(startScale as Vec3, endScale as Vec3 | undefined, easing(t), transition.params.scale_noise_magnitude ?? 0, false);
+        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();
 
@@ -213,21 +304,21 @@ function processTransformMatrix(transition: MVSAnimationNode<'interpolate'>, tar
     Mat4.mul(result, TransformState.rotation, result);
     Mat4.mul(result, TransformState.translation, result);
 
-    assign(target, transition.params.property, result, offset);
+    return result;
 }
 
-function interpolateScalars(start: number | number[], end: number | number[] | undefined, t: number, noise: number) {
+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);
+                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);
+            ret[i] = interpolateScalar(start[i], end[i], t, noise, discrete);
         }
         return ret;
     }
@@ -235,19 +326,22 @@ function interpolateScalars(start: number | number[], end: number | number[] | u
     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);
+            ret[i] = interpolateScalar(start, end[i], t, noise, discrete);
         }
         return ret;
     }
 
-    return interpolateScalar(start, end, t, noise);
+    return interpolateScalar(start, end, t, noise, discrete);
 }
 
-function interpolateScalar(start: number, end: number | undefined, t: number, noise: number) {
+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;
 }
 
@@ -348,6 +442,76 @@ function interpolateRotation(start: Mat3, end: Mat3 | undefined, t: number, nois
     return Mat3.fromMat4(Mat3(), RotationState.temp);
 }
 
+function decodeColors(color: ColorT | Record<number | string, ColorT> | undefined, baseColors: Record<number | string, ColorT> | undefined) {
+    if (color === undefined || color === null) return undefined;
+
+    if (typeof color === 'object') {
+        const ret: Record<number | string, Color> = {};
+        if (baseColors) {
+            for (const key of Object.keys(baseColors)) {
+                const decoded = decodeColor(baseColors[key]);
+                if (decoded !== undefined) {
+                    ret[key] = decoded;
+                }
+            }
+        }
+        for (const key of Object.keys(color)) {
+            const decoded = decodeColor(color[key]);
+            if (decoded !== undefined) {
+                ret[key] = decoded;
+            }
+        }
+        return ret;
+    }
+
+    return decodeColor(color);
+}
+
+function interpolateColors(start: ColorT | Record<number, ColorT>, end: ColorT | Record<number, ColorT> | undefined, time: number, cacheEntry: InterpolationCacheEntry, baseColors: Record<number, ColorT> | undefined) {
+    const t = clamp(time, 0, 1);
+
+    if (cacheEntry.paletteFn) {
+        const c = cacheEntry.paletteFn(t);
+        return Color.toHexStyle(c);
+    }
+
+    if (cacheEntry.startColor === undefined) {
+        cacheEntry.startColor = decodeColors(start, baseColors);
+    }
+    if (cacheEntry.endColor === undefined) {
+        cacheEntry.endColor = decodeColors(end, undefined);
+    }
+
+    const { startColor, endColor } = cacheEntry;
+
+    if (typeof startColor === 'object') {
+        if (typeof baseColors !== 'object') {
+            throw new Error('Cannot interpolate from scalar color to color mapping');
+        }
+
+        const ret = { ...baseColors as any, ...startColor as any };
+        if (typeof endColor === 'object') {
+            for (const key of Object.keys(endColor)) {
+                ret[key] = Color.toHexStyle(Color.interpolate(startColor[key], endColor[key], t));
+            }
+        } else if (typeof endColor === 'number') {
+            for (const key of Object.keys(startColor)) {
+                ret[key] = Color.toHexStyle(Color.interpolate(startColor[key], endColor, t));
+            }
+        }
+        return ret;
+    }
+    if (typeof endColor === 'object') {
+        throw new Error('Cannot interpolate from scalar color to color mapping');
+    }
+
+    if (typeof endColor === 'number' && typeof startColor === 'number') {
+        return Color.toHexStyle(Color.interpolate(startColor, endColor, t));
+    }
+
+    return start;
+}
+
 function select(params: any, path: string | (string | number)[], offset: number) {
     if (typeof path === 'string') {
         return params?.[path];
@@ -400,12 +564,10 @@ function makeNodeMap(tree: Tree, map: Map<string, (string | number)[]>, currentP
     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;
+function makePaletteFunction(props: MVSAnimationNode<'interpolate'>): ((value: number) => Color) | undefined {
+    if (props.params.kind !== 'color' || !props.params.palette) return undefined;
 
-    const params = props.params.palette
-        ? palettePropsFromMVSPalette(props.params.palette)
-        : palettePropsFromMVSPalette({ kind: 'continuous', colors: [start ?? 'black', end ?? start ?? 'black'] });
+    const params = palettePropsFromMVSPalette(props.params.palette);
     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}`);

src/extensions/mvs/load-helpers.ts

@@ -412,8 +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;
 }

src/extensions/mvs/load.ts

@@ -33,8 +33,8 @@ import { NonCovalentInteractionsExtension } from './load-extensions/non-covalent
 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, Snapshot, SnapshotMetadata } from './mvs-data';
-import { MVSAnimationNode } from './tree/animation/animation-tree';
-import { validateTree } from './tree/generic/tree-schema';
+import { MVSAnimationNode, MVSAnimationSchema } from './tree/animation/animation-tree';
+import { validateTree } from './tree/generic/tree-validation';
 import { convertMvsToMolstar, mvsSanityCheck } from './tree/molstar/conversion';
 import { MolstarNode, MolstarNodeParams, MolstarSubtree, MolstarTree, MolstarTreeSchema } from './tree/molstar/molstar-tree';
 import { MVSTreeSchema } from './tree/mvs/mvs-tree';
@@ -51,6 +51,7 @@ export interface MVSLoadOptions {
     sanityChecks?: boolean,
     /** Base for resolving relative URLs/URIs. May itself be a relative URL (relative to the window URL). */
     sourceUrl?: string,
+
     doNotReportErrors?: boolean
 }
 
@@ -66,6 +67,9 @@ async function _loadMVS(ctx: RuntimeContext, plugin: PluginContext, data: MVSDat
         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);
 
@@ -75,10 +79,13 @@ async function _loadMVS(ctx: RuntimeContext, plugin: PluginContext, data: MVSDat
         for (let i = 0; i < multiData.snapshots.length; i++) {
             const snapshot = multiData.snapshots[i];
             const previousSnapshot = i > 0 ? multiData.snapshots[i - 1] : multiData.snapshots[multiData.snapshots.length - 1];
-            validateTree(MVSTreeSchema, snapshot.root, 'MVS');
+            validateTree(MVSTreeSchema, snapshot.root, 'MVS', plugin);
+            if (snapshot.animation) {
+                validateTree(MVSAnimationSchema, snapshot.animation, 'Animation', plugin);
+            }
             if (options.sanityChecks) mvsSanityCheck(snapshot.root);
             const molstarTree = convertMvsToMolstar(snapshot.root, options.sourceUrl);
-            validateTree(MolstarTreeSchema, molstarTree, 'Converted Molstar');
+            validateTree(MolstarTreeSchema, molstarTree, 'Converted Molstar', plugin);
             const entry = molstarTreeToEntry(
                 plugin,
                 molstarTree,
@@ -133,7 +140,7 @@ async function assignStateTransition(ctx: RuntimeContext, plugin: PluginContext,
 
     for (let i = 0; i < transitions.frames.length; i++) {
         const frame = transitions.frames[i];
-        const molstarTree = convertMvsToMolstar(frame, options.sourceUrl);
+        const molstarTree = convertMvsToMolstar(frame[0], options.sourceUrl);
         const entry = molstarTreeToEntry(
             plugin,
             molstarTree,
@@ -145,7 +152,7 @@ async function assignStateTransition(ctx: RuntimeContext, plugin: PluginContext,
         StateTree.reuseTransformParams(entry.snapshot.data!.tree, parentEntry.snapshot.data!.tree);
 
         animation.frames.push({
-            durationInMs: transitions.frametimeMs,
+            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,
@@ -176,6 +183,10 @@ function molstarTreeToEntry(
     }
     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,

src/extensions/mvs/mvs-data.ts

@@ -5,7 +5,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { treeValidationIssues } from './tree/generic/tree-schema';
+import { treeValidationIssues } from './tree/generic/tree-validation';
 import { treeToString } from './tree/generic/tree-utils';
 import { MVSAnimationSchema, MVSAnimationTree } from './tree/animation/animation-tree';
 import { Root, createMVSBuilder } from './tree/mvs/mvs-builder';

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

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { bool, float, int, list, OptionalField, RequiredField, str, union, nullable, literal, ValueFor } from '../generic/field-schema';
+import { bool, float, int, list, OptionalField, RequiredField, str, union, nullable, literal, ValueFor, dict } 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';
@@ -48,6 +48,7 @@ const ScalarInterpolation = {
     ..._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,
 };
 
@@ -74,8 +75,8 @@ 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.'),
+    start: OptionalField(union(nullable(ColorT), dict(union(int, str), ColorT)), null, 'Start value. If unset, parent state value is used.'),
+    end: OptionalField(union(nullable(ColorT), dict(union(int, str), ColorT)), null, 'End value.'),
     palette: OptionalField(nullable(union(DiscretePalette, ContinuousPalette)), null, 'Palette to sample colors from. Overrides start and end values.'),
 };
 

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

@@ -4,12 +4,8 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 
-import { onelinerJsonString } from '../../../../mol-util/json';
-import { isPlainObject, mapObjectMap } from '../../../../mol-util/object';
-import { Field } from './field-schema';
-import { AllRequired, ParamsSchema, SimpleParamsSchema, ValuesFor, paramsValidationIssues } from './params-schema';
-import { treeToString } from './tree-utils';
-
+import { mapObjectMap } from '../../../../mol-util/object';
+import { AllRequired, ParamsSchema, ValuesFor } from './params-schema';
 
 /** Type of "custom" of a tree node (key-value storage with arbitrary JSONable values) */
 export type CustomProps = Partial<Record<string, any>>
@@ -114,120 +110,3 @@ export type NodeFor<TTreeSchema extends TreeSchema, TKind extends keyof ParamsSc
 
 /** Type of tree which conforms to tree schema `TTreeSchema` */
 export type TreeFor<TTreeSchema extends TreeSchema> = Tree<NodeFor<TTreeSchema>, RootFor<TTreeSchema> & NodeFor<TTreeSchema>>
-
-
-/** Return `undefined` if a tree conforms to the given schema,
- * return validation issues (as a list of lines) if it does not conform.
- * If `options.requireAll`, all parameters (including optional) must have a value provided.
- * If `options.noExtra` is true, presence of any extra parameters is treated as an issue.
- * If `options.anyRoot` is true, the kind of the root node is not enforced.
- */
-export function treeValidationIssues(schema: TreeSchema, tree: Tree, options: { requireAll?: boolean, noExtra?: boolean, anyRoot?: boolean, parent?: string } = {}): string[] | undefined {
-    if (!isPlainObject(tree)) return [`Node must be an object, not ${tree}`];
-    if (!options.anyRoot && tree.kind !== schema.rootKind) return [`Invalid root node kind "${tree.kind}", root must be of kind "${schema.rootKind}"`];
-    const nodeSchema = schema.nodes[tree.kind];
-    if (!nodeSchema) return [`Unknown node kind "${tree.kind}"`];
-    if (nodeSchema.parent && (options.parent !== undefined) && !nodeSchema.parent.includes(options.parent)) {
-        return [`Node of kind "${tree.kind}" cannot appear as a child of "${options.parent}". Allowed parents for "${tree.kind}" are: ${nodeSchema.parent.map(s => `"${s}"`).join(', ')}`];
-    }
-    const issues = paramsValidationIssues(nodeSchema.params, getParams(tree), options);
-    if (issues) return [`Invalid parameters for node of kind "${tree.kind}":`, ...issues.map(s => '  ' + s)];
-    if (tree.custom !== undefined && (typeof tree.custom !== 'object' || tree.custom === null)) {
-        return [`Invalid "custom" for node of kind "${tree.kind}": must be an object, not ${tree.custom}.`];
-    }
-    for (const child of getChildren(tree)) {
-        const issues = treeValidationIssues(schema, child, { ...options, anyRoot: true, parent: tree.kind });
-        if (issues) return issues;
-    }
-    return undefined;
-}
-
-/** Validate a tree against the given schema.
- * Do nothing if OK; print validation issues on console and throw an error is the tree does not conform.
- * Include `label` in the printed output. */
-export function validateTree(schema: TreeSchema, tree: Tree, label: string): void {
-    const issues = treeValidationIssues(schema, tree, { noExtra: true });
-    if (issues) {
-        console.warn(`Invalid ${label} tree:\n${treeToString(tree)}`);
-        console.error(`${label} tree validation issues:`);
-        for (const line of issues) {
-            console.error(' ', line);
-        }
-        throw new Error('FormatError');
-    }
-}
-
-/** Return documentation for a tree schema as plain text */
-export function treeSchemaToString<S extends TreeSchema>(schema: S): string {
-    return treeSchemaToString_(schema, false);
-}
-/** Return documentation for a tree schema as markdown text */
-export function treeSchemaToMarkdown<S extends TreeSchema>(schema: S): string {
-    return treeSchemaToString_(schema, true);
-}
-function treeSchemaToString_<S extends TreeSchema>(schema: S, markdown: boolean = false): string {
-    const out: string[] = [];
-    const bold = (str: string) => markdown ? `**${str}**` : str;
-    const code = (str: string) => markdown ? `\`${str}\`` : str;
-    const h1 = markdown ? '## ' : '  - ';
-    const p1 = markdown ? '' : '    ';
-    const h2 = markdown ? '- ' : '      - ';
-    const p2 = markdown ? '  ' : '        ';
-    const h3 = markdown ? '  - ' : '          - ';
-    const p3 = markdown ? '    ' : '            ';
-    const newline = markdown ? '\n\n' : '\n';
-    out.push(`Tree schema:`);
-    for (const kind in schema.nodes) {
-        const { description, params, parent } = schema.nodes[kind];
-        out.push(`${h1}${code(kind)}`);
-        if (kind === schema.rootKind) {
-            out.push(`${p1}[Root of the tree must be of this kind]`);
-        }
-        if (description) {
-            out.push(`${p1}${description}`);
-        }
-        out.push(`${p1}Parent: ${!parent ? 'any' : parent.length === 0 ? 'none' : parent.map(code).join(' or ')}`);
-        out.push(`${p1}Params:${Object.keys(params).length > 0 ? '' : ' none'}`);
-        if (params.type === 'simple') {
-            formatSimpleParams(out, params, { h: h2, p: p2, code, bold });
-        } else {
-            const key = params.discriminator;
-            const casesStr = Object.keys(params.cases).join(' | ');
-            out.push(`${h2}${bold(code(key + ': '))}${code(casesStr)}`);
-            if (params.discriminatorDescription) {
-                out.push(`${p2}${params.discriminatorDescription}`);
-            }
-            out.push(`${p2}[This parameter determines the rest of parameters]`);
-            for (const case_ in params.cases) {
-                const caseStr = `${params.discriminator}: "${case_}"`;
-                out.push(`${p2}${bold(`Case ${code(caseStr)}:`)}`);
-                formatSimpleParams(out, params.cases[case_], { h: h3, p: p3, code, bold });
-            }
-        }
-    }
-    return out.join(newline);
-}
-
-function formatSimpleParams(out: string[], params: SimpleParamsSchema, formatting: { h: string, p: string, code: (str: string) => string, bold: (str: string) => string }): void {
-    const { h, p, code, bold } = formatting;
-    for (const key in params.fields) {
-        const field = params.fields[key];
-        out.push(`${h}${bold(code(key + (field.required ? ': ' : '?: ')))}${code(formatFieldType(field))}`);
-        const defaultValue = field.required ? undefined : field.default;
-        if (field.description) {
-            out.push(`${p}${field.description}`);
-        }
-        if (defaultValue !== undefined) {
-            out.push(`${p}Default: ${code(onelinerJsonString(defaultValue))}`);
-        }
-    }
-}
-
-function formatFieldType(field: Field): string {
-    const typeString = field.type.name;
-    if (typeString.startsWith('(') && typeString.endsWith(')')) {
-        return typeString.slice(1, -1);
-    } else {
-        return typeString;
-    }
-}

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

@@ -0,0 +1,125 @@
+import { PluginContext } from '../../../../mol-plugin/context';
+import { onelinerJsonString } from '../../../../mol-util/json';
+import { isPlainObject } from '../../../../mol-util/object';
+import { Field } from './field-schema';
+import { SimpleParamsSchema, paramsValidationIssues } from './params-schema';
+import { getChildren, getParams, Tree, TreeSchema } from './tree-schema';
+import { treeToString } from './tree-utils';
+
+/** Return `undefined` if a tree conforms to the given schema,
+ * return validation issues (as a list of lines) if it does not conform.
+ * If `options.requireAll`, all parameters (including optional) must have a value provided.
+ * If `options.noExtra` is true, presence of any extra parameters is treated as an issue.
+ * If `options.anyRoot` is true, the kind of the root node is not enforced.
+ */
+export function treeValidationIssues(schema: TreeSchema, tree: Tree, options: { requireAll?: boolean, noExtra?: boolean, anyRoot?: boolean, parent?: string } = {}): string[] | undefined {
+    if (!isPlainObject(tree)) return [`Node must be an object, not ${tree}`];
+    if (!options.anyRoot && tree.kind !== schema.rootKind) return [`Invalid root node kind "${tree.kind}", root must be of kind "${schema.rootKind}"`];
+    const nodeSchema = schema.nodes[tree.kind];
+    if (!nodeSchema) return [`Unknown node kind "${tree.kind}"`];
+    if (nodeSchema.parent && (options.parent !== undefined) && !nodeSchema.parent.includes(options.parent)) {
+        return [`Node of kind "${tree.kind}" cannot appear as a child of "${options.parent}". Allowed parents for "${tree.kind}" are: ${nodeSchema.parent.map(s => `"${s}"`).join(', ')}`];
+    }
+    const issues = paramsValidationIssues(nodeSchema.params, getParams(tree), options);
+    if (issues) return [`Invalid parameters for node of kind "${tree.kind}":`, ...issues.map(s => '  ' + s)];
+    if (tree.custom !== undefined && (typeof tree.custom !== 'object' || tree.custom === null)) {
+        return [`Invalid "custom" for node of kind "${tree.kind}": must be an object, not ${tree.custom}.`];
+    }
+    for (const child of getChildren(tree)) {
+        const issues = treeValidationIssues(schema, child, { ...options, anyRoot: true, parent: tree.kind });
+        if (issues) return issues;
+    }
+    return undefined;
+}
+
+/** Validate a tree against the given schema.
+ * Do nothing if OK; print validation issues on console and throw an error is the tree does not conform.
+ * Include `label` in the printed output. */
+export function validateTree(schema: TreeSchema, tree: Tree, label: string, plugin: PluginContext): void {
+    const issues = treeValidationIssues(schema, tree, { noExtra: true });
+    if (issues) {
+        console.warn(`Invalid ${label} tree:\n${treeToString(tree)}`);
+        console.error(`${label} tree validation issues:`);
+        plugin.log.error(`${label} tree validation issues:`);
+        for (const line of issues) {
+            console.error(' ', line);
+            plugin.log.error(line);
+        }
+        throw new Error('FormatError');
+    }
+}
+
+/** Return documentation for a tree schema as plain text */
+export function treeSchemaToString<S extends TreeSchema>(schema: S): string {
+    return treeSchemaToString_(schema, false);
+}
+/** Return documentation for a tree schema as markdown text */
+export function treeSchemaToMarkdown<S extends TreeSchema>(schema: S): string {
+    return treeSchemaToString_(schema, true);
+}
+function treeSchemaToString_<S extends TreeSchema>(schema: S, markdown: boolean = false): string {
+    const out: string[] = [];
+    const bold = (str: string) => markdown ? `**${str}**` : str;
+    const code = (str: string) => markdown ? `\`${str}\`` : str;
+    const h1 = markdown ? '## ' : '  - ';
+    const p1 = markdown ? '' : '    ';
+    const h2 = markdown ? '- ' : '      - ';
+    const p2 = markdown ? '  ' : '        ';
+    const h3 = markdown ? '  - ' : '          - ';
+    const p3 = markdown ? '    ' : '            ';
+    const newline = markdown ? '\n\n' : '\n';
+    out.push(`Tree schema:`);
+    for (const kind in schema.nodes) {
+        const { description, params, parent } = schema.nodes[kind];
+        out.push(`${h1}${code(kind)}`);
+        if (kind === schema.rootKind) {
+            out.push(`${p1}[Root of the tree must be of this kind]`);
+        }
+        if (description) {
+            out.push(`${p1}${description}`);
+        }
+        out.push(`${p1}Parent: ${!parent ? 'any' : parent.length === 0 ? 'none' : parent.map(code).join(' or ')}`);
+        out.push(`${p1}Params:${Object.keys(params).length > 0 ? '' : ' none'}`);
+        if (params.type === 'simple') {
+            formatSimpleParams(out, params, { h: h2, p: p2, code, bold });
+        } else {
+            const key = params.discriminator;
+            const casesStr = Object.keys(params.cases).join(' | ');
+            out.push(`${h2}${bold(code(key + ': '))}${code(casesStr)}`);
+            if (params.discriminatorDescription) {
+                out.push(`${p2}${params.discriminatorDescription}`);
+            }
+            out.push(`${p2}[This parameter determines the rest of parameters]`);
+            for (const case_ in params.cases) {
+                const caseStr = `${params.discriminator}: "${case_}"`;
+                out.push(`${p2}${bold(`Case ${code(caseStr)}:`)}`);
+                formatSimpleParams(out, params.cases[case_], { h: h3, p: p3, code, bold });
+            }
+        }
+    }
+    return out.join(newline);
+}
+
+function formatSimpleParams(out: string[], params: SimpleParamsSchema, formatting: { h: string, p: string, code: (str: string) => string, bold: (str: string) => string }): void {
+    const { h, p, code, bold } = formatting;
+    for (const key in params.fields) {
+        const field = params.fields[key];
+        out.push(`${h}${bold(code(key + (field.required ? ': ' : '?: ')))}${code(formatFieldType(field))}`);
+        const defaultValue = field.required ? undefined : field.default;
+        if (field.description) {
+            out.push(`${p}${field.description}`);
+        }
+        if (defaultValue !== undefined) {
+            out.push(`${p}Default: ${code(onelinerJsonString(defaultValue))}`);
+        }
+    }
+}
+
+function formatFieldType(field: Field): string {
+    const typeString = field.type.name;
+    if (typeString.startsWith('(') && typeString.endsWith(')')) {
+        return typeString.slice(1, -1);
+    } else {
+        return typeString;
+    }
+}

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

@@ -49,7 +49,7 @@ export const MolstarTreeSchema = TreeSchema({
         },
         /** Auxiliary node corresponding to Molstar's TrajectoryFrom*. */
         trajectory_with_coordinates: {
-            description: "Auxiliary node corresponding to assigning a separate coordinates to a trajectory.",
+            description: 'Auxiliary node corresponding to assigning a separate coordinates to a trajectory.',
             parent: ['model'],
             params: SimpleParamsSchema({
                 coordinates_ref: RequiredField(str, 'Coordinates reference'),

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

@@ -98,6 +98,12 @@ export class Root extends _Base<'root'> implements FocusMixin, PrimitivesMixin {
         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 {

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

@@ -53,7 +53,7 @@ const LinesParams = {
     vertices: RequiredField(FloatList, '3*n_vertices length array of floats with vertex position (x1, y1, z1, ...).'),
     /** 2*n_lines length array of indices into vertices that form lines (l1_1, l1_2, ...). */
     indices: RequiredField(IntList, '2*n_lines length array of indices into vertices that form lines (l1_1, l1_2, ...).'),
-    /** Assign a number to each triangle to group them. If not specified, each line is considered a separate group (line i = group i). */
+    /** Assign a number to each line to group them. If not specified, each line is considered a separate group (line i = group i). */
     line_groups: OptionalField(nullable(IntList), null, 'Assign a number to each triangle to group them. If not specified, each line is considered a separate group (line i = group i).'),
     /** Assign a color to each group. Where not assigned, uses `color`. */
     group_colors: OptionalField(dict(int, ColorT), {}, 'Assign a color to each group. Where not assigned, uses `color`.'),

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';
@@ -34,7 +34,6 @@ 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 { create as produce } from 'mutative';
 import { HandleHelperParams } from './helper/handle-helper';
 import { StereoCamera, StereoCameraParams } from './camera/stereo';
 import { Helper } from './helper/helper';
@@ -49,6 +48,7 @@ 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 }),
@@ -114,6 +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 */
@@ -360,6 +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']
@@ -379,9 +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>();
@@ -421,7 +428,7 @@ namespace Canvas3D {
         }, { 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);
 
@@ -1180,6 +1187,9 @@ namespace Canvas3D {
             get props() {
                 return getProps();
             },
+            get attribs() {
+                return a;
+            },
             get input() {
                 return input;
             },

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 }),
@@ -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);
 
@@ -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 { create as produce } from 'mutative';
+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 { create as produce } from 'mutative';
+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/passes/background.ts

@@ -445,8 +445,9 @@ function areImageTexturePropsEqual(sourceA: ImageProps['source'], sourceB: Image
 
 function getImageTexture(ctx: WebGLContext, assetManager: AssetManager, source: ImageProps['source'], onload?: (errored?: boolean) => void): { texture: Texture, asset: Asset } {
     const asset = source.name === 'url'
-        ? Asset.getUrlAsset(assetManager, source.params)
+        ? assetManager.tryFindFilename(source.params) ?? Asset.getUrlAsset(assetManager, source.params)
         : source.params!;
+
     if (typeof HTMLImageElement === 'undefined') {
         console.error(`Missing "HTMLImageElement" required for background image`);
         onload?.(true);

src/mol-gl/renderer.ts

@@ -483,13 +483,13 @@ namespace Renderer {
             const alpha = clamp(r.values.alpha.ref.value * r.state.alphaFactor, 0, 1);
             const xrayShaded = r.values.dXrayShaded?.ref.value === 'on' || r.values.dXrayShaded?.ref.value === 'inverted';
             return (
-                (alpha < 1 && alpha !== 0) ||
+                alpha !== 0 && (alpha < 1 ||
                 r.values.transparencyAverage.ref.value > 0 ||
                 r.values.dGeometryType.ref.value === 'directVolume' ||
                 r.values.dPointStyle?.ref.value === 'fuzzy' ||
                 r.values.dGeometryType.ref.value === 'text' ||
                 r.values.dGeometryType.ref.value === 'image' ||
-                xrayShaded
+                xrayShaded)
             );
         };
 

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

@@ -38,11 +38,11 @@ float getDepthOpaque(const in vec2 coords) {
     #endif
 }
 
-float getDepthTransparent(const in vec2 coords) {
+vec2 getDepthTransparentWithAlpha(const in vec2 coords) {
     #ifdef dTransparentOutline
-        return unpackRGBAToDepthWithAlpha(texture2D(tDepthTransparent, coords)).x;
+        return unpackRGBAToDepthWithAlpha(texture2D(tDepthTransparent, coords));
     #else
-        return 1.0;
+        return vec2(1.0, 1.0);
     #endif
 }
 
@@ -66,7 +66,7 @@ void main(void) {
     float selfViewZOpaque = isBackground(selfDepthOpaque) ? backgroundViewZ : getViewZ(selfDepthOpaque);
     float pixelSizeOpaque = getPixelSize(coords, selfDepthOpaque) * uOutlineThreshold;
 
-    float selfDepthTransparent = getDepthTransparent(coords);
+    float selfDepthTransparent = getDepthTransparentWithAlpha(coords).x;
     float selfViewZTransparent = isBackground(selfDepthTransparent) ? backgroundViewZ : getViewZ(selfDepthTransparent);
     float pixelSizeTransparent = getPixelSize(coords, selfDepthTransparent) * uOutlineThreshold;
 
@@ -79,12 +79,15 @@ void main(void) {
             vec2 sampleCoords = coords + vec2(float(x), float(y)) * invTexSize;
 
             float sampleDepthOpaque = getDepthOpaque(sampleCoords);
-            float sampleDepthTransparent = getDepthTransparent(sampleCoords);
+            vec2 sampleDepthTransparentWithAlpha = getDepthTransparentWithAlpha(sampleCoords);
+            float sampleDepthTransparent = sampleDepthTransparentWithAlpha.x;
+            float sampleAlphaTransparent = sampleDepthTransparentWithAlpha.y;
 
             float sampleViewZOpaque = isBackground(sampleDepthOpaque) ? backgroundViewZ : getViewZ(sampleDepthOpaque);
             if (abs(selfViewZOpaque - sampleViewZOpaque) > pixelSizeOpaque && selfDepthOpaque > sampleDepthOpaque && sampleDepthOpaque <= bestDepth) {
                 outline = 0.0;
                 bestDepth = sampleDepthOpaque;
+                transparentFlag = 0.0;
             }
 
             if (sampleDepthTransparent < sampleDepthOpaque) {
@@ -92,7 +95,7 @@ void main(void) {
                 if (abs(selfViewZTransparent - sampleViewZTransparent) > pixelSizeTransparent && selfDepthTransparent > sampleDepthTransparent && sampleDepthTransparent <= bestDepth) {
                     outline = 0.0;
                     bestDepth = sampleDepthTransparent;
-                    transparentFlag = 1.0;
+                    transparentFlag = sampleAlphaTransparent;
                 }
             }
         }

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

@@ -168,15 +168,25 @@ void main(void) {
         if (outline == 0.0) {
             float viewDist = abs(getViewZ(closestTexel));
             float fogFactor = smoothstep(uFogNear, uFogFar, viewDist);
-            if (!uTransparentBackground) {
-                    color.rgb = mix(uOutlineColor, uFogColor, fogFactor);
-            } else {
-                color.a = 1.0 - fogFactor;
-                color.rgb = mix(uOutlineColor, vec3(0.0), fogFactor);
-            }
             #ifdef dBlendTransparency
-                if (isTransparentOutline == 1.0 || transparentDepth > closestTexel) {
-                    blendTransparency = false;
+                if (isTransparentOutline > 0.0) {
+                    float outlineAlpha = clamp(isTransparentOutline * 2.0, 0.0, 1.0);        
+                    transparentColor.a = transparentColor.a + outlineAlpha * (1.0 - fogFactor) * (1.0 - transparentColor.a); 
+                    transparentColor.rgb = uOutlineColor;
+                } else {
+                    if (!uTransparentBackground) {
+                        color.rgb = mix(uOutlineColor, uFogColor, fogFactor);
+                    } else {
+                        color.a = 1.0 - fogFactor;
+                        color.rgb = mix(uOutlineColor, vec3(0.0), fogFactor);
+                    }
+                }
+            #else
+                if (!uTransparentBackground) {
+                    color.rgb = mix(uOutlineColor, uFogColor, fogFactor);
+                } else {
+                    color.a = 1.0 - fogFactor;
+                    color.rgb = mix(uOutlineColor, vec3(0.0), fogFactor);
                 }
             #endif
         }

src/mol-plugin-state/animation/built-in/state-snapshots.ts

@@ -13,9 +13,11 @@ async function setPartialSnapshot(plugin: PluginContext, entry: Partial<PluginSt
     if (entry.data) {
         await plugin.runTask(plugin.state.data.setSnapshot(entry.data));
         // update the canvas3d trackball with the snapshot
-        plugin.canvas3d?.setProps({
-            trackball: entry.canvas3d?.props?.trackball
-        });
+        if (entry.canvas3d?.props?.trackball) {
+            plugin.canvas3d?.setProps({
+                trackball: entry.canvas3d?.props?.trackball
+            });
+        }
 
     }
 
@@ -175,7 +177,7 @@ export const AnimateStateSnapshotTransition = PluginStateAnimation.create({
         if (t.current >= animState.totalDuration) {
             if (snapshot?.transition && animState.isInitial) {
                 const frameIndex = snapshot.transition.frames.length - 1;
-                ctx.plugin.managers.snapshot.setSnapshotAnimationFrame(frameIndex, false);
+                ctx.plugin.managers.snapshot.setSnapshotAnimationFrame(animState.totalDuration, false);
                 await setPartialSnapshot(ctx.plugin, snapshot.transition.frames[frameIndex]);
             }
             return { kind: 'finished' };
@@ -193,7 +195,7 @@ export const AnimateStateSnapshotTransition = PluginStateAnimation.create({
             return { kind: 'skip' };
         }
 
-        ctx.plugin.managers.snapshot.setSnapshotAnimationFrame(frameIndex, false);
+        ctx.plugin.managers.snapshot.setSnapshotAnimationFrame(t.current, false);
         if (frameIndex === 0) {
             await setPartialSnapshot(ctx.plugin, {
                 ...transition.frames[frameIndex],

src/mol-plugin-state/manager/focus-camera/focus-object.ts

@@ -13,7 +13,7 @@ import { Loci } from '../../../mol-model/loci';
 import { Structure } from '../../../mol-model/structure';
 import { PluginContext } from '../../../mol-plugin/context';
 import { PluginState } from '../../../mol-plugin/state';
-import { StateObject, StateTransform } from '../../../mol-state';
+import { StateObjectCell, StateSelection, StateTransform } from '../../../mol-state';
 import { PluginStateObject } from '../../objects';
 
 
@@ -65,7 +65,7 @@ export function getCellBoundingSphere(plugin: PluginContext, cellRef: StateTrans
 /** Push bounding spheres within cell `cellRef` to `out`. If a cell does not define bounding spheres, collect bounding spheres from subtree. */
 function collectCellBoundingSpheres(out: Sphere3D[], plugin: PluginContext, cellRef: StateTransform.Ref): Sphere3D[] {
     const cell = plugin.state.data.cells.get(cellRef);
-    const spheres = getStateObjectBoundingSpheres(cell?.obj);
+    const spheres = getStateObjectBoundingSpheres(plugin, cell);
     if (spheres) {
         out.push(...spheres);
     } else {
@@ -76,14 +76,17 @@ function collectCellBoundingSpheres(out: Sphere3D[], plugin: PluginContext, cell
 }
 
 /** Return a set of bounding spheres of a plugin state object. Return `undefined` if this plugin state object type does not define bounding spheres. */
-function getStateObjectBoundingSpheres(obj: StateObject | undefined): Sphere3D[] | undefined {
+function getStateObjectBoundingSpheres(plugin: PluginContext, cell: StateObjectCell | undefined): Sphere3D[] | undefined {
+    const obj = cell?.obj;
     if (!obj) return undefined;
     if (!obj.data) {
         console.warn('Focus: no data');
         return undefined;
     }
     if (obj.data instanceof Structure) {
-        const sphere = Loci.getBoundingSphere(Structure.Loci(obj.data));
+        const decorated = StateSelection.getDecorated<PluginStateObject.Molecule.Structure>(plugin.state.data, cell.transform.ref);
+        const data = decorated?.obj?.data ?? obj?.data;
+        const sphere = Loci.getBoundingSphere(Structure.Loci(data));
         return sphere ? [sphere] : [];
     } else if (PluginStateObject.isRepresentation3D(obj)) {
         const out: Sphere3D[] = [];

src/mol-plugin-state/manager/markdown-extensions.ts

@@ -6,10 +6,12 @@
 
 import { getCellBoundingSphere } from '../../mol-plugin-state/manager/focus-camera/focus-object';
 import { PluginStateObject } from '../../mol-plugin-state/objects';
-import { StateObjectCell } from '../../mol-state';
+import { StateObjectCell, StateSelection } from '../../mol-state';
 import { PluginContext } from '../../mol-plugin/context';
 import { Script } from '../../mol-script/script';
 import { QueryContext, QueryFn, StructureElement, StructureSelection } from '../../mol-model/structure';
+import { BehaviorSubject } from 'rxjs';
+import { AnimateStateSnapshotTransition } from '../animation/built-in/state-snapshots';
 
 export type MarkdownExtensionEvent = 'click' | 'mouse-enter' | 'mouse-leave';
 
@@ -45,6 +47,17 @@ export const BuiltInMarkdownExtension: MarkdownExtension[] = [
             manager.plugin.managers.snapshot.applyKey(key);
         }
     },
+    {
+        name: 'next-snapshot',
+        execute: ({ event, args, manager }) => {
+            if (event !== 'click' || !('next-snapshot' in args)) return;
+            let dir: -1 | 1 = (+args['next-snapshot'] || 1) as -1 | 1;
+            if (!dir) return;
+            if (dir < 0) dir = -1;
+            else dir = 1;
+            manager.plugin.managers.snapshot.applyNext(dir);
+        }
+    },
     {
         name: 'focus-refs',
         execute: ({ event, args, manager }) => {
@@ -135,7 +148,8 @@ export const BuiltInMarkdownExtension: MarkdownExtension[] = [
                 if (!action.includes('focus')) {
                     return;
                 }
-                const spheres = structures.map(s => {
+                const decorated = structures.map(s => StateSelection.getDecorated<PluginStateObject.Molecule.Structure>(manager.plugin.state.data, s.transform.ref));
+                const spheres = decorated.map(s => {
                     if (!s.obj?.data) return undefined;
                     const selection = query(new QueryContext(s.obj.data));
                     if (StructureSelection.isEmpty(selection)) return;
@@ -150,9 +164,74 @@ export const BuiltInMarkdownExtension: MarkdownExtension[] = [
             }
         },
     },
+    {
+        name: 'play-audio',
+        execute: ({ event, args, manager }) => {
+            if (event !== 'click') return;
+
+            const src = args['play-audio'];
+            if (!src?.length) return;
+            manager.audio.play(src);
+        }
+    },
+    {
+        name: 'toggle-audio',
+        execute: ({ event, args, manager }) => {
+            if (event !== 'click' || !('toggle-audio' in args)) return;
+
+            const src = args['toggle-audio'];
+            manager.audio.play(src, { toggle: true });
+        }
+    },
+    {
+        name: 'pause-audio',
+        execute: ({ event, args, manager }) => {
+            if (event !== 'click' || !('pause-audio' in args)) return;
+            manager.audio.pause();
+        }
+    },
+    {
+        name: 'stop-audio',
+        execute: ({ event, args, manager }) => {
+            if (event !== 'click' || !('stop-audio' in args)) return;
+            manager.audio.stop();
+        }
+    },
+    {
+        name: 'dispose-audio',
+        execute: ({ event, args, manager }) => {
+            if (event !== 'click' || !('dispose-audio' in args)) return;
+            manager.audio.dispose();
+        }
+    },
+    {
+        name: 'play-transition',
+        execute: ({ event, args, manager }) => {
+            if (event !== 'click' || !('play-transition' in args)) return;
+            manager.plugin.managers.animation.play(AnimateStateSnapshotTransition, {});
+        }
+    },
+    {
+        name: 'play-snapshots',
+        execute: ({ event, args, manager }) => {
+            if (event !== 'click' || !('play-snapshots' in args)) return;
+            manager.plugin.managers.snapshot.play({ restart: true });
+        }
+    },
+    {
+        name: 'stop-animation',
+        execute: ({ event, args, manager }) => {
+            if (event !== 'click' || !('stop-animation' in args)) return;
+            manager.plugin.managers.snapshot.stop();
+        }
+    },
 ];
 
 export class MarkdownExtensionManager {
+    state = {
+        audioPlayer: new BehaviorSubject<HTMLAudioElement | null>(null),
+    };
+
     private extension: MarkdownExtension[] = [];
     private refResolvers: Record<string, (plugin: PluginContext, refs: string[]) => StateObjectCell[]> = {
         default: (plugin: PluginContext, refs: string[]) => refs
@@ -286,6 +365,76 @@ export class MarkdownExtensionManager {
         return ret;
     }
 
+    private resolveAudioPlayer() {
+        if (this.state.audioPlayer.value) {
+            return this.state.audioPlayer.value;
+        }
+
+        const audio = document.createElement('audio');
+        audio.controls = true;
+        audio.preload = 'auto';
+        audio.style.width = '100%';
+        audio.style.height = '32px';
+        this.state.audioPlayer.next(audio);
+        return audio;
+    }
+
+    get audioPlayer() {
+        return this.state.audioPlayer.value;
+    }
+
+    audio = {
+        play: async (src: string, options?: { toggle?: boolean }) => {
+            try {
+                const audio = this.resolveAudioPlayer();
+
+                let newSource = false;
+                if (src?.trim()) {
+                    const resolved = this.tryResolveUri(src);
+                    let uri: string = src;
+                    if (typeof (resolved as Promise<string>)?.then === 'function') {
+                        uri = (await resolved) as string;
+                    } else if (resolved) {
+                        uri = resolved as string;
+                    }
+                    newSource = audio.src !== uri;
+                    if (newSource) {
+                        audio.src = uri;
+                        audio.load();
+                    }
+                }
+
+                if (!newSource && options?.toggle) {
+                    if (audio.paused) {
+                        await audio.play();
+                    } else {
+                        audio.pause();
+                    }
+                } else {
+                    audio.currentTime = 0;
+                    await audio.play();
+                }
+            } catch (e) {
+                console.error('Failed to play audio', e);
+            }
+        },
+        pause: () => {
+            this.audioPlayer?.pause();
+        },
+        stop: () => {
+            if (!this.audioPlayer) return;
+            this.audioPlayer.pause();
+            this.audioPlayer.currentTime = 0;
+        },
+        dispose: () => {
+            if (this.audioPlayer) {
+                this.audioPlayer.pause();
+                this.audioPlayer.currentTime = 0;
+                this.state.audioPlayer.next(null);
+            }
+        }
+    };
+
     constructor(public plugin: PluginContext) {
         for (const command of BuiltInMarkdownExtension) {
             this.registerExtension(command);

src/mol-plugin-state/manager/snapshots.ts

@@ -25,7 +25,7 @@ export { PluginStateSnapshotManager };
 
 interface StateManagerState {
     current?: UUID,
-    currentAnimationFrame?: number,
+    currentAnimationTimeMs?: number,
     entries: List<PluginStateSnapshotManager.Entry>,
     isPlaying: boolean,
     nextSnapshotDelayInMs: number
@@ -38,8 +38,8 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<StateManagerSta
     private defaultSnapshotId: UUID | undefined = undefined;
 
     protected updateState(state: Partial<StateManagerState>) {
-        if ('current' in state && !('curentAnimationFrame' in state)) {
-            return super.updateState({ ...state, currentAnimationFrame: 0 });
+        if ('current' in state && !('currentAnimationTimeMs' in state)) {
+            return super.updateState({ ...state, currentAnimationTimeMs: 0 });
         } else {
             return super.updateState(state);
         }
@@ -168,18 +168,23 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<StateManagerSta
     }
 
     private animationFrameQueue = new SingleTaskQueue();
-    setSnapshotAnimationFrame(frame: number, load = false) {
-        if (this.updateState({ currentAnimationFrame: frame })) {
+    setSnapshotAnimationFrame(currentAnimationTimeMs: number, load = false) {
+        const entry = this.getEntry(this.state.current);
+        if (!entry) return;
+
+        const frameIndex = PluginState.getStateTransitionFrameIndex(entry.snapshot, currentAnimationTimeMs) ?? 0;
+
+        if (this.updateState({ currentAnimationTimeMs })) {
             this.events.changed.next(void 0);
         }
 
         if (load) {
             this.animationFrameQueue.run(() => {
-                const entry = this.getEntry(this.state.current);
-                if (!entry) return Promise.resolve();
-                return this.plugin.state.setAnimationSnapshot(entry.snapshot, frame);
+                return this.plugin.state.setAnimationSnapshot(entry.snapshot, frameIndex ?? 0);
             });
         }
+
+        return frameIndex;
     }
 
     getNextId(id: string | undefined, dir: -1 | 1) {
@@ -233,7 +238,7 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<StateManagerSta
         const next = entry && entry.snapshot;
         if (!next) return;
         await this.plugin.state.setSnapshot(next);
-        if (snapshot.playback && snapshot.playback.isPlaying) this.play(true);
+        if (snapshot.playback?.isPlaying) this.play({ delayFirst: true });
         return next;
     }
 
@@ -380,10 +385,18 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<StateManagerSta
         }
     }
 
-    play(delayFirst: boolean = false) {
+    async play(options?: { delayFirst?: boolean, restart?: boolean }) {
+        if (this.state.isPlaying && !options?.delayFirst) {
+            if (options?.restart) {
+                await this.stop();
+            } else {
+                return;
+            }
+        }
+
         this.updateState({ isPlaying: true });
 
-        if (delayFirst) {
+        if (options?.delayFirst) {
             const e = this.getEntry(this.state.current);
             if (!e) {
                 this.next();
@@ -398,20 +411,20 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<StateManagerSta
         }
     }
 
-    stop() {
-        this.plugin.managers.animation.stop();
+    async stop() {
+        await this.plugin.managers.animation.stop();
         this.updateState({ isPlaying: false });
         if (typeof this.timeoutHandle !== 'undefined') clearTimeout(this.timeoutHandle);
         this.timeoutHandle = void 0;
         this.events.changed.next(void 0);
     }
 
-    togglePlay() {
+    async togglePlay() {
         if (this.state.isPlaying) {
-            this.stop();
-            this.plugin.managers.animation.stop();
+            await this.stop();
+            this.plugin.managers.markdownExtensions.audio.pause();
         } else {
-            this.play();
+            await this.play();
         }
     }
 

src/mol-plugin-ui/controls.tsx

@@ -29,6 +29,7 @@ import { StructureQuickStylesControls } from './structure/quick-styles';
 import { Markdown } from './controls/markdown';
 import { Slider } from './controls/slider';
 import { AnimateStateSnapshotTransition } from '../mol-plugin-state/animation/built-in/state-snapshots';
+import { PluginState } from '../mol-plugin/state';
 
 export class TrajectoryViewportControls extends PluginUIComponent<{}, { show: boolean, label: string }> {
     state = { show: false, label: '' };
@@ -61,7 +62,7 @@ export class TrajectoryViewportControls extends PluginUIComponent<{}, { show: bo
                 count++;
                 if (!label) {
                     const idx = (m.transform.params! as StateTransformer.Params<ModelFromTrajectory>).modelIndex;
-                    label = `Model ${idx + 1} / ${parent.data.frameCount}`;
+                    label = `Model ${Math.round(idx + 1)} / ${parent.data.frameCount}`;
                 }
             }
         }
@@ -111,37 +112,12 @@ export class StateSnapshotViewportControls extends PluginUIComponent<{}, { isBus
         this.subscribe(this.plugin.managers.snapshot.events.changed, () => this.forceUpdate());
         this.subscribe(this.plugin.behaviors.state.isBusy, isBusy => this.setState({ isBusy }));
         this.subscribe(this.plugin.behaviors.state.isAnimating, isBusy => this.setState({ isBusy }));
-
-        window.addEventListener('keyup', this.keyUp, false);
     }
 
     componentWillUnmount() {
         super.componentWillUnmount();
-        window.removeEventListener('keyup', this.keyUp, false);
     }
 
-    keyUp = (e: KeyboardEvent) => {
-        if (!e.ctrlKey || this.state.isBusy || e.target !== document.body) return;
-        const snapshots = this.plugin.managers.snapshot;
-        if (e.keyCode === 37 || e.key === 'ArrowLeft') {
-            if (snapshots.state.isPlaying) snapshots.stop();
-            this.prev();
-        } else if (e.keyCode === 38 || e.key === 'ArrowUp') {
-            if (snapshots.state.isPlaying) snapshots.stop();
-            if (snapshots.state.entries.size === 0) return;
-            const e = snapshots.state.entries.get(0)!;
-            this.update(e.snapshot.id);
-        } else if (e.keyCode === 39 || e.key === 'ArrowRight') {
-            if (snapshots.state.isPlaying) snapshots.stop();
-            this.next();
-        } else if (e.keyCode === 40 || e.key === 'ArrowDown') {
-            if (snapshots.state.isPlaying) snapshots.stop();
-            if (snapshots.state.entries.size === 0) return;
-            const e = snapshots.state.entries.get(snapshots.state.entries.size - 1)!;
-            this.update(e.snapshot.id);
-        }
-    };
-
     async update(id: string) {
         this.setState({ isBusy: true });
         await PluginCommands.State.Snapshots.Apply(this.plugin, { id });
@@ -176,6 +152,7 @@ export class StateSnapshotViewportControls extends PluginUIComponent<{}, { isBus
     toggleStateAnimation = () => {
         if (this.state.isBusy) {
             this.plugin.managers.animation.stop();
+            this.plugin.managers.markdownExtensions.audio.pause();
         } else {
             this.plugin.managers.animation.play(AnimateStateSnapshotTransition, {});
         }
@@ -210,19 +187,17 @@ export class StateSnapshotViewportControls extends PluginUIComponent<{}, { isBus
             {!isPlaying && <>
                 {count > 1 && <IconButton svg={NavigateBeforeSvg} title='Previous State' onClick={this.prev} disabled={disabled} />}
                 {count > 1 && <IconButton svg={NavigateNextSvg} title='Next State' onClick={this.next} disabled={disabled} />}
-                {hasAnimation && <IconButton svg={AnimationSvg} className='msp-state-snapshot-animation-button' title='Animation' onClick={this.toggleShowAnimation} disabled={!hasAnimation} toggleState={this.state.showAnimation} />}
+                {hasAnimation && <IconButton svg={AnimationSvg} className='msp-state-snapshot-animation-button' title='Snapshot Transition' onClick={this.toggleShowAnimation} disabled={!hasAnimation} toggleState={this.state.showAnimation} />}
             </>}
             {hasAnimation && this.state.showAnimation && !isPlaying && <>
                 <div className='msp-state-snapshot-animation-slider msp-form-control'>
                     <Slider
-                        value={snapshots.state.currentAnimationFrame ?? 0}
-                        min={1}
-                        step={1}
-                        max={(entry?.snapshot.transition?.frames.length ?? 1)}
+                        value={Math.round(100 * (snapshots.state.currentAnimationTimeMs ?? 0)) /100}
+                        min={0}
+                        step={PluginState.getMinFrameDuration(entry?.snapshot)}
+                        max={PluginState.getStateTransitionDuration(entry?.snapshot) ?? 1000}
                         onChange={() => { }}
-                        onChangeImmediate={v => {
-                            snapshots.setSnapshotAnimationFrame(v - 1, true);
-                        }}
+                        onChangeImmediate={v => snapshots.setSnapshotAnimationFrame(v, true)}
                         hideInput
                         disabled={this.state.isBusy}
                     />

src/mol-plugin-ui/controls/markdown.tsx

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { useContext, useEffect, useState } from 'react';
+import { useContext, useEffect, useRef, useState } from 'react';
 import ReactMarkdown, { Components } from 'react-markdown';
 import remarkGfm from 'remark-gfm';
 import { PluginReactContext } from '../base';
@@ -13,9 +13,11 @@ import { PluginContext } from '../../mol-plugin/context';
 import { MarkdownExtension } from '../../mol-plugin-state/manager/markdown-extensions';
 import { ColorLists } from '../../mol-util/color/lists';
 import { getColorGradient, getColorGradientBanded, parseColorList } from '../../mol-util/color/utils';
+import { useBehavior } from '../hooks/use-behavior';
 
 export function Markdown({ children, components }: { children?: string, components?: Components }) {
     return <div className='msp-markdown'>
+        <MarkdownAudioPlayer />
         <ReactMarkdown
             skipHtml
             components={{ a: MarkdownAnchor, img: MarkdownImg, ...components }}
@@ -26,6 +28,21 @@ export function Markdown({ children, components }: { children?: string, componen
     </div>;
 }
 
+export function MarkdownAudioPlayer() {
+    const parent = useRef<HTMLDivElement>(null);
+    const plugin: PluginUIContext | undefined = useContext(PluginReactContext);
+    const audio = useBehavior(plugin?.managers.markdownExtensions.state.audioPlayer);
+
+    useEffect(() => {
+        if (!parent.current) return;
+        parent.current.appendChild(audio!);
+        return () => { audio?.remove(); };
+    }, [audio]);
+    if (!audio) return null;
+
+    return <div className='msp-markdown-audio-player' ref={parent} />;
+}
+
 export function MarkdownImg({ src, element, alt }: { src?: string, element?: any, alt?: string }) {
     const plugin: PluginUIContext | undefined = useContext(PluginReactContext);
 

src/mol-plugin-ui/viewport/help.tsx

@@ -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 Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -97,7 +97,7 @@ export class ViewportHelpContent extends PluginUIComponent<{ selectOnly?: boolea
 
         return <>
             {(!this.props.selectOnly && this.plugin.canvas3d) && <HelpGroup key='trackball' header='Moving in 3D'>
-                <BindingsHelp bindings={this.plugin.canvas3d.props.trackball.bindings} />
+                <BindingsHelp bindings={this.plugin.canvas3d.attribs.trackball.bindings} />
             </HelpGroup>}
             {!!interactionBindings && <HelpGroup key='interactions' header='Mouse & Key Controls'>
                 <BindingsHelp bindings={interactionBindings} />

src/mol-plugin-ui/viewport/simple-settings.tsx

@@ -5,7 +5,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { create as produce } from 'mutative';
+import { produce } from '../../mol-util/produce';
 import { throttleTime } from 'rxjs';
 import { Canvas3DContext, Canvas3DParams, Canvas3DProps } from '../../mol-canvas3d/canvas3d';
 import { PluginCommands } from '../../mol-plugin/commands';

src/mol-plugin/behavior.ts

@@ -1,7 +1,8 @@
 /**
- * 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 David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 export * from './behavior/behavior';
@@ -13,6 +14,7 @@ import * as StaticMisc from './behavior/static/misc';
 
 import * as DynamicRepresentation from './behavior/dynamic/representation';
 import * as DynamicCamera from './behavior/dynamic/camera';
+import * as DynamicState from './behavior/dynamic/state';
 import * as DynamicCustomProps from './behavior/dynamic/custom-props';
 
 export const BuiltInPluginBehaviors = {
@@ -25,5 +27,6 @@ export const BuiltInPluginBehaviors = {
 export const PluginBehaviors = {
     Representation: DynamicRepresentation,
     Camera: DynamicCamera,
+    State: DynamicState,
     CustomProps: DynamicCustomProps
 };

src/mol-plugin/behavior/dynamic/camera.ts

@@ -79,6 +79,13 @@ export const FocusLoci = PluginBehavior.create<FocusLociProps>({
                     return;
                 }
 
+                // Prevent when interaction props are set
+                const snapshotKey = current.repr?.props?.snapshotKey?.trim() ?? '';
+                const markdownCommands = current.repr?.props?.markdownCommands;
+                if (snapshotKey || (typeof markdownCommands === 'object' && Object.keys(markdownCommands).length > 0)) {
+                    return;
+                }
+
                 if (Binding.match(binding, button, modifiers)) {
                     const loci = Loci.normalize(current.loci, this.ctx.managers.interactivity.props.granularity);
                     this.ctx.managers.camera.focusLoci(loci, this.params);

src/mol-plugin/behavior/dynamic/representation.ts

@@ -290,6 +290,15 @@ export const FocusLoci = PluginBehavior.create<FocusLociProps>({
                     return;
                 }
 
+                // Support executing markdown commands associated with a visual
+                const markdownCommands = current.repr?.props?.markdownCommands;
+                if (!this.ctx.selectionMode && matched && typeof markdownCommands === 'object') {
+                    if (Object.keys(markdownCommands).length > 0) {
+                        this.ctx.managers.markdownExtensions.tryExecute('click', markdownCommands);
+                        return;
+                    }
+                }
+
                 // only apply structure focus for appropriate granularity
                 const { granularity } = this.ctx.managers.interactivity.props;
                 if (granularity !== 'residue' && granularity !== 'element') return;

src/mol-plugin/behavior/dynamic/state.ts

@@ -0,0 +1,70 @@
+/**
+ * Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { PluginBehavior } from '../behavior';
+import { Binding } from '../../../mol-util/binding';
+import { ModifiersKeys } from '../../../mol-util/input/input-observer';
+
+const M = ModifiersKeys;
+const Key = Binding.TriggerKey;
+
+const DefaultSnapshotControlsBindings = {
+    next: Binding([
+        Key('ArrowRight', M.create({ control: true })),
+    ]),
+    previous: Binding([
+        Key('ArrowLeft', M.create({ control: true })),
+    ]),
+    first: Binding([
+        Key('ArrowUp', M.create({ control: true })),
+    ]),
+    last: Binding([
+        Key('ArrowDown', M.create({ control: true })),
+    ]),
+};
+const SnapshotControlsParams = {
+    bindings: PD.Value(DefaultSnapshotControlsBindings, { isHidden: true }),
+};
+type SnapshotControlsProps = PD.Values<typeof SnapshotControlsParams>
+
+export const SnapshotControls = PluginBehavior.create<SnapshotControlsProps>({
+    name: 'snapshot-controls',
+    category: 'interaction',
+    ctor: class extends PluginBehavior.Handler<SnapshotControlsProps> {
+        register(): void {
+            this.subscribeObservable(this.ctx.behaviors.interaction.keyReleased, ({ code, modifiers, key }) => {
+                if (!this.ctx.canvas3d || this.ctx.isBusy) return;
+
+                // include defaults for backwards state compatibility
+                const b = this.params.bindings;
+                const { snapshot } = this.ctx.managers;
+
+                if (Binding.matchKey(b.next, code, modifiers, key)) {
+                    snapshot.applyNext(1);
+                }
+
+                if (Binding.matchKey(b.previous, code, modifiers, key)) {
+                    snapshot.applyNext(-1);
+                }
+
+                if (Binding.matchKey(b.first, code, modifiers, key)) {
+                    const e = snapshot.state.entries.get(0)!;
+                    const s = snapshot.setCurrent(e.snapshot.id);
+                    if (s) return this.ctx.state.setSnapshot(s);
+                }
+
+                if (Binding.matchKey(b.last, code, modifiers, key)) {
+                    const e = snapshot.state.entries.get(snapshot.state.entries.size - 1)!;
+                    const s = snapshot.setCurrent(e.snapshot.id);
+                    if (s) return this.ctx.state.setSnapshot(s);
+                }
+            });
+        }
+    },
+    params: () => SnapshotControlsParams,
+    display: { name: 'Snapshot Controls' }
+});

src/mol-plugin/context.ts

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { create as produce } from 'mutative';
+import { produce } from '../mol-util/produce';
 import { List } from 'immutable';
 import { merge, Subscription } from 'rxjs';
 import { debounceTime, filter, take, throttleTime } from 'rxjs/operators';
@@ -382,6 +382,7 @@ export class PluginContext {
         }
         this.subs = [];
 
+        this.managers.markdownExtensions.audio.dispose();
         this.animationLoop.stop();
         this.commands.dispose();
         this.canvas3d?.dispose();

src/mol-plugin/spec.ts

@@ -124,6 +124,7 @@ export const DefaultPluginSpec = (): PluginSpec => ({
         PluginSpec.Behavior(PluginBehaviors.Camera.FocusLoci),
         PluginSpec.Behavior(PluginBehaviors.Camera.CameraAxisHelper),
         PluginSpec.Behavior(PluginBehaviors.Camera.CameraControls),
+        PluginSpec.Behavior(PluginBehaviors.State.SnapshotControls),
         PluginSpec.Behavior(StructureFocusRepresentation),
 
         PluginSpec.Behavior(PluginBehaviors.CustomProps.StructureInfo),

src/mol-plugin/state.ts

@@ -6,7 +6,7 @@
  * @author Adam Midlik <midlik@gmail.com>
  */
 
-import { create as produce } from 'mutative';
+import { produce } from '../mol-util/produce';
 import { merge } from 'rxjs';
 import { Camera } from '../mol-canvas3d/camera';
 import { Canvas3DContext, Canvas3DParams, Canvas3DProps } from '../mol-canvas3d/canvas3d';
@@ -27,6 +27,7 @@ import { PluginConfig } from './config';
 import { PluginContext } from './context';
 import { AnimateStateSnapshotTransition } from '../mol-plugin-state/animation/built-in/state-snapshots';
 import { Scheduler } from '../mol-task';
+import { memoizeLatest } from '../mol-util/memoize';
 
 export { PluginState };
 
@@ -118,6 +119,11 @@ class PluginState extends PluginComponent {
                 durationMs: snapshot.camera.transitionStyle === 'animate' ? snapshot.camera.transitionDurationInMs : undefined,
             });
         }
+
+        if (typeof snapshot?.onLoadMarkdownCommands === 'object' && Object.keys(snapshot.onLoadMarkdownCommands).length > 0) {
+            this.plugin.managers.markdownExtensions.tryExecute('click', snapshot.onLoadMarkdownCommands);
+        }
+
         if (snapshot.startAnimation) {
             this.animation.start();
             return;
@@ -147,6 +153,10 @@ class PluginState extends PluginComponent {
                 durationMs: frame.camera.transitionStyle === 'animate' ? frame.camera.transitionDurationInMs : undefined,
             });
         }
+
+        if (!frameIndex && typeof snapshot?.onLoadMarkdownCommands === 'object' && Object.keys(snapshot.onLoadMarkdownCommands).length > 0) {
+            this.plugin.managers.markdownExtensions.tryExecute('click', snapshot.onLoadMarkdownCommands);
+        }
     }
 
     updateTransform(state: State, a: StateTransform.Ref, params: any, canUndo?: string | boolean) {
@@ -241,6 +251,7 @@ namespace PluginState {
         },
         durationInMs?: number,
         transition?: StateTransition,
+        onLoadMarkdownCommands?: Record<string, any>
     }
 
     export interface StateTransition {
@@ -254,7 +265,23 @@ namespace PluginState {
         }[],
     }
 
-    export function getStateTransitionDuration(snapshot: Snapshot): number | undefined {
+    export const getMinFrameDuration = memoizeLatest((snapshot: Snapshot | undefined): number => {
+        if (!snapshot) return 1000 / 60;
+        const { transition } = snapshot;
+        if (!transition) return 1000 / 60;
+
+        let minDuration = Infinity;
+        for (const frame of transition.frames) {
+            if (frame.durationInMs > 0 && frame.durationInMs < minDuration) {
+                minDuration = frame.durationInMs;
+            }
+        }
+        if (!Number.isFinite(minDuration)) return 1000 / 60;
+        return minDuration;
+    });
+
+    export const getStateTransitionDuration = memoizeLatest((snapshot: Snapshot | undefined): number | undefined => {
+        if (!snapshot) return undefined;
         const { transition } = snapshot;
         if (!transition) return undefined;
         let totalDuration = 0;
@@ -263,7 +290,20 @@ namespace PluginState {
             totalDuration += frame.durationInMs;
         }
         return totalDuration;
-    }
+    });
+
+    export const getStateTransitionFrameTime = memoizeLatest((snapshot: Snapshot | undefined, frameIndex: number | undefined): number => {
+        if (!snapshot || frameIndex === undefined) return 0;
+        const { transition } = snapshot;
+        if (!transition) return 0;
+        let currentDuration = 0;
+        for (let i = 0; i < frameIndex; i++) {
+            if (transition.frames.length <= i) break;
+            const frame = transition.frames[i];
+            currentDuration += frame.durationInMs;
+        }
+        return currentDuration;
+    });
 
     export function getStateTransitionFrameIndex(snapshot: Snapshot, timestamp: number): number | undefined {
         const { transition } = snapshot;

src/mol-repr/representation.ts

@@ -507,7 +507,7 @@ namespace Representation {
 }
 
 let _EmptyRepresentation: Representation.Any | undefined = undefined;
-Object.defineProperty(Representation, "Empty", {
+Object.defineProperty(Representation, 'Empty', {
     get: () => {
         return _EmptyRepresentation ??= Representation.createEmpty();
     }

src/mol-script/language/symbol-table/structure-query.ts

@@ -276,7 +276,8 @@ const atomProperty = {
         instanceId: atomProp(Type.Str, 'Canonical name of the symmetry operator applied to this element.'),
         operatorKey: atomProp(Type.Num, 'Key of the symmetry operator applied to this element.'),
         modelIndex: atomProp(Type.Num, 'Index of the model in the input file.'),
-        modelLabel: atomProp(Type.Str, 'Label/header of the model in the input file.')
+        modelLabel: atomProp(Type.Str, 'Label/header of the model in the input file.'),
+        modelEntryId: atomProp(Type.Str, 'Entry ID of the model (e.g., PDB ID).')
     },
 
     topology: {

src/mol-script/runtime/query/table.ts

@@ -309,6 +309,7 @@ const symbols = [
     D(MolScript.structureQuery.atomProperty.core.operatorKey, atomProp(StructureProperties.unit.operator_key)),
     D(MolScript.structureQuery.atomProperty.core.modelIndex, atomProp(StructureProperties.unit.model_index)),
     D(MolScript.structureQuery.atomProperty.core.modelLabel, atomProp(StructureProperties.unit.model_label)),
+    D(MolScript.structureQuery.atomProperty.core.modelEntryId, atomProp(StructureProperties.unit.model_entry_id)),
     D(MolScript.structureQuery.atomProperty.core.atomKey, (ctx, xs) => {
         const e = (xs && xs[0] && xs[0](ctx) as any) || ctx.element;
         return cantorPairing(e.unit.id, e.element);

src/mol-script/script/mol-script/symbols.ts

@@ -215,6 +215,7 @@ export const SymbolTable = [
             Alias(MolScript.structureQuery.atomProperty.core.operatorKey, 'atom.op-key'),
             Alias(MolScript.structureQuery.atomProperty.core.modelIndex, 'atom.model-index'),
             Alias(MolScript.structureQuery.atomProperty.core.modelLabel, 'atom.model-label'),
+            Alias(MolScript.structureQuery.atomProperty.core.modelEntryId, 'atom.model-entry-id'),
             Alias(MolScript.structureQuery.atomProperty.core.atomKey, 'atom.key'),
             Alias(MolScript.structureQuery.atomProperty.core.bondCount, 'atom.bond-count'),
 

src/mol-state/state/builder.ts

@@ -11,7 +11,7 @@ import { StateObject, StateObjectCell, StateObjectSelector, StateObjectRef } fro
 import { StateTransform } from '../transform';
 import { StateTransformer } from '../transformer';
 import { State } from '../state';
-import { create as produce } from 'mutative';
+import { produce } from '../../mol-util/produce';
 
 export { StateBuilder };
 

src/mol-state/state/selection.ts

@@ -375,6 +375,14 @@ namespace StateSelection {
         const first = children.first();
         if (first && state.transforms.get(first).transformer.definition.isDecorator) return tryFindDecorator(state, first, transformer);
     }
+
+    export function getDecorated<T extends StateObject>(state: State, root: StateTransform.Ref): StateObjectCell<T> {
+        const children = state.tree.children.get(root);
+        if (children.size !== 1) return state.cells.get(root) as any;
+        const first = children.first();
+        if (first && state.transforms.get(first).transformer.definition.isDecorator) return getDecorated(state, first);
+        return state.cells.get(root) as any;
+    }
 }
 
 export { StateSelection };

src/mol-util/assets.ts

@@ -83,6 +83,15 @@ class AssetManager {
         }
     }
 
+    tryFindFilename(name: string): Asset | undefined {
+        const it = this._assets.values();
+        while (true) {
+            const { done, value } = it.next();
+            if (done) break;
+            if (value.file.name === name) return value.asset;
+        }
+    }
+
     set(asset: Asset, file: File, options?: { isStatic?: boolean, tag?: string }) {
         this._assets.set(asset.id, { asset, file, refCount: 0, tag: options?.tag, isStatic: options?.isStatic });
     }

src/mol-util/error-context.ts

@@ -5,13 +5,13 @@
  */
 
 export class ErrorContext {
-    private errors: { [tag: string]: any[] } = Object.create(null);
+    private errors: { [tag: string]: string[] } = Object.create(null);
 
-    get(tag: string): ReadonlyArray<any> {
+    get(tag: string): ReadonlyArray<string> {
         return this.errors[tag] ?? [];
     }
 
-    add(tag: string, error: any) {
+    add(tag: string, error: string) {
         if (tag in this.errors && Array.isArray(this.errors[tag])) {
             this.errors[tag].push(error);
         } else {

src/mol-util/file.ts

@@ -7,6 +7,7 @@
 export async function fileToDataUri(file: File): Promise<string> {
     const filename = file.name.toLowerCase() || 'file';
     const isImage = ['jpg', 'jpeg', 'png', 'gif', 'webp'].some(ext => filename.endsWith(`.${ext}`));
+    const isAudio = ['mp3', 'wav', 'ogg'].some(ext => filename.endsWith(`.${ext}`));
 
     let type = 'application/octet-stream';
     if (isImage) {
@@ -19,6 +20,16 @@ export async function fileToDataUri(file: File): Promise<string> {
                 type = `image/${ext}`;
                 break;
         }
+    } else if (isAudio) {
+        const ext = filename.split('.').pop()?.toLowerCase();
+        switch (ext) {
+            case 'mp3':
+                type = 'audio/mpeg';
+                break;
+            default:
+                type = `audio/${ext}`;
+                break;
+        }
     }
 
     const bytes = await file.arrayBuffer();

src/mol-util/param-definition.ts

@@ -534,7 +534,7 @@ export namespace ParamDefinition {
         if (a === undefined) return { ...b };
         if (b === undefined) return { ...a };
 
-        const o = Object.create(null);
+        const o = {} as any;
         for (const k of Object.keys(params)) {
             o[k] = mergeParam(params[k], a[k], b[k]);
         }
@@ -587,7 +587,7 @@ export namespace ParamDefinition {
         if (p.type === 'value') {
             return value;
         } else if (p.type === 'group') {
-            const ret = Object.create(null);
+            const ret = {} as any;
             for (const key of Object.keys(p.params)) {
                 const param = p.params[key];
                 if (value[key] === void 0) {
@@ -638,7 +638,7 @@ export namespace ParamDefinition {
             return defaultIfUndefined ? getDefaultValues(p) : value;
         }
 
-        const ret = Object.create(null);
+        const ret = {} as any;
         for (const key of Object.keys(p)) {
             const param = p[key];
             if (value[key] === void 0) {

src/mol-util/param-mapping.ts

@@ -5,7 +5,7 @@
  */
 
 import { ParamDefinition as PD } from './param-definition';
-import { create as produce } from 'mutative';
+import { produce } from './produce';
 import { Mutable } from './type-helpers';
 
 export interface ParamMapping<S, T, Ctx> {

src/mol-util/produce.ts

@@ -0,0 +1,23 @@
+/**
+ * Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { create, rawReturn } from 'mutative';
+
+let currentRecipe: any = undefined;
+function recipeWrapper(draft: any) {
+    const r = currentRecipe(draft);
+    if (r !== undefined && r !== draft) return rawReturn(r);
+    return r;
+}
+
+/** Apply changes to an immutable-like object */
+export function produce<T>(base: T, recipe: (draft: T) => T | void): T {
+    currentRecipe = recipe;
+    if (typeof base === 'object' && !('prototype' in (base as any))) {
+        return create({ ...base }, recipeWrapper) as T;
+    }
+    return create(base, recipeWrapper) as T;
+}