prototype parallel shader linking

* fix mutative use & assign NODE_ENV=production for prd builds

* fix type

CHANGELOG.md

@@ -12,6 +12,8 @@ Note that since we don't clearly distinguish between a public and private interf
 - [Breaking] Add `Volume.instances` support and a `VolumeInstances` transform to dynamically assign it
   - This change is breaking because all volume objects require the `instances` field now.
 - [Breaking] `Canvas3D.identify` now expects `Vec2` or `Ray3D`
+- [Breaking] `TrackballControlsParams.animate.spin.speed` now means "Number of rotations per second" instead of "radians per second"
+- [Breaking] `PluginStateSnapshotManager.play` now accepts an options object instead of a single boolean value
 - Update production build to use `esbuild`
 - Emit explicit paths in `import`s in `lib/`
 - Fix outlines on opaque elements using illumination mode
@@ -19,24 +21,40 @@ Note that since we don't clearly distinguish between a public and private interf
 - MolViewSpec extension:
   - Generic color schemes (`palette` parameter for color_from_* nodes)
   - Annotation field remapping (`field_remapping` parameter for color_from_* nodes)
-  - Representation node: support custom property `molstar_reprepresentation_params`,
-  - Canvas node: support custom properties `molstar_enable_outline`, `molstar_enable_shadow`, `molstar_enable_ssao`
+  - `representation` node: support custom property `molstar_representation_params`
+  - Add `backbone` and `line` representation types
+  - `primitives` node: support custom property `molstar_mesh/label/line_params`
+  - `canvas` node: support custom property `molstar_postprocessing` with the ability to customize outline, depth of field, bloom, shadow, occlusion (SSAO), fog, and background
   - `clip` node support for structure and volume representations
   - `grid_slice` representation support for volumes
   - Support tethers and background for primitive labels
   - Support `snapshot_key` parameter on primitives that enables transition between states via clicking on 3D objects
   - Inline selectors and MVS annotations support `instance_id`
   - Support `matrix` on transform params
+  - Support `surface_type` (`molecular` / `gaussian`) on for `surface` representation nodes
   - Add `instance` node type
+  - Add `transform.rotation_center` property that enables rotating an object around its centroid or a specific point
   - Support transforming and instancing of structures, components, and volumes
+  - Use params hash for node version for more performant tree diffs
+  - Add `Snapshot.animation` support that enables animating almost every property in a given tree
+  - Add `createMVSX` helper function
+  - Support Mol* trackball animation via `animation.custom.molstar_trackball`
+  - MVSX - use Murmur hash instead of FNV in archive URI
+  - Support additional file formats (pdbqt, gro, xyz, mol, sdf, mol2, xtc, lammpstrj)
+  - Support loading trajectory coordinates from separate nodes
+  - Trigger markdown commands from primitives using `molstar_markdown_commands` custom extensions
+  - Support `molstar_on_load_markdown_commands` custom state on the `root` node
+  - 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))
@@ -52,7 +70,10 @@ Note that since we don't clearly distinguish between a public and private interf
 - Add `StructureInstances` transform
 - `mvs-stories` app
   - Add `story-id` URL arg support
+  - Add `story-session-url` URL arg support
   - Add "Download MVS State" link
+  - Add "Open in Mol*" link
+  - Add "Edit in MolViewStories" link for story states
 - Add ray-based picking
     - Render narrow view of scene scene from ray origin & direction to a few pixel sized viewport
     - Cast ray on every input as opposed to the standard "whole screen" picking
@@ -62,6 +83,28 @@ Note that since we don't clearly distinguish between a public and private interf
 - Add async, non-blocking picking (only WebGL2)
     - Refactor `Canvas3dInteractionHelper` internals to use async picking for move events
 - Add `enable` param for post-processing effects. If false, no effects are applied.
+- Dot volume representation improvements
+    - Add positional perturbation to avoid camera artifacts
+    - Fix handling of negative isoValues by considering only volume cells with values lower than isoValue (#1559)
+    - Fix volume-value size theme
+- Change the parsing of residue names in PDB files from 3-letter to 4-letter.
+- Support versioning transform using a hash function in `mol-state`
+- Support for "state snapshot transitions"
+    - Add `PluginState.Snapshot.transition` that enables associating a state snapshot with a list states that can be animated
+    - Add `AnimateStateSnapshotTransition` animation
+    - Update the snapshots UI to support this feature
+- Use "proper time" in the animation loop to prevent animation skips during blocking operations (e.g., shader complication)
+- Add `Hsl` and (normalized) `Rgb` color spaces
+- Add `Color.interpolateHsl`
+- Add `rotationCenter` property to `TransformParam`
+- Add Monolayer transparency (exploiting dpoit).
+- Add plugin config item ShowReset (shows/hides "Reset Zoom" button)
+- Fix transform params not being normalized when used together with param hash version
+- Replace `immer` with `mutative`
+- Fix renderer transparency check
+- VolumeServer & "VolumeCIF": default to P 1 spacegroup
+- Fix `ColorScale` for continuous case without offsets (broke in v4.13.0)
+- Experimental: support for custom color themes in Sequence Panel
 
 ## [v4.18.0] - 2025-06-08
 - MolViewSpec extension:

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

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

eslint.config.mjs

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

package-lock.json

@@ -1,12 +1,12 @@
 {
   "name": "molstar",
-  "version": "5.0.0-dev.2",
+  "version": "5.0.0-dev.13",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "molstar",
-      "version": "5.0.0-dev.2",
+      "version": "5.0.0-dev.13",
       "license": "MIT",
       "dependencies": {
         "@types/argparse": "^2.0.17",
@@ -21,9 +21,9 @@
         "cors": "^2.8.5",
         "express": "^5.1.0",
         "h264-mp4-encoder": "^1.0.12",
-        "immer": "^10.1.1",
         "immutable": "^5.1.2",
         "io-ts": "^2.2.22",
+        "mutative": "^1.2.0",
         "node-fetch": "^2.7.0",
         "react-markdown": "^10.1.0",
         "remark-gfm": "^4.0.1",
@@ -1171,9 +1171,9 @@
       }
     },
     "node_modules/@eslint/plugin-kit": {
-      "version": "0.3.3",
-      "resolved": "https://registry.npmjs.org/@eslint/plugin-kit/-/plugin-kit-0.3.3.tgz",
-      "integrity": "sha512-1+WqvgNMhmlAambTvT3KPtCl/Ibr68VldY2XY40SL1CE0ZXiakFR/cbTspaF5HsnpDMvcYYoJHfl4980NBjGag==",
+      "version": "0.3.4",
+      "resolved": "https://registry.npmjs.org/@eslint/plugin-kit/-/plugin-kit-0.3.4.tgz",
+      "integrity": "sha512-Ul5l+lHEcw3L5+k8POx6r74mxEYKG5kOb6Xpy2gCRW6zweT6TEhAf8vhxGgjhqrd/VO/Dirhsb+1hNpD1ue9hw==",
       "dev": true,
       "license": "Apache-2.0",
       "dependencies": {
@@ -2763,7 +2763,7 @@
       "version": "5.0.1",
       "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-5.0.1.tgz",
       "integrity": "sha512-quJQXlTSUGL2LH9SUXo8VwsY4soanhgo6LNSm84E1LBcE8s3O0wpdiRzyR9z/ZZJMlMWv37qOOb9pdJlMUEKFQ==",
-      "devOptional": true,
+      "dev": true,
       "engines": {
         "node": ">=8"
       }
@@ -3021,7 +3021,7 @@
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/balanced-match/-/balanced-match-1.0.2.tgz",
       "integrity": "sha512-3oSeUO0TMV67hN1AmbXsK4yaqU7tjiHlbxRDZOpH0KW9+CeX4bRAaX0Anxt0tx2MrpRpWwQaPwIlISEJhYU5Pw==",
-      "devOptional": true
+      "dev": true
     },
     "node_modules/basic-auth": {
       "version": "2.0.1",
@@ -3081,7 +3081,7 @@
       "version": "2.0.2",
       "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-2.0.2.tgz",
       "integrity": "sha512-Jt0vHyM+jmUBqojB7E1NIYadt0vI0Qxjxd2TErW94wDz+E2LAm5vKMXXwg6ZZBTHPuUlDgQHKXvjGBdfcF1ZDQ==",
-      "devOptional": true,
+      "dev": true,
       "license": "MIT",
       "dependencies": {
         "balanced-match": "^1.0.0"
@@ -3494,7 +3494,7 @@
       "version": "0.0.1",
       "resolved": "https://registry.npmjs.org/concat-map/-/concat-map-0.0.1.tgz",
       "integrity": "sha512-/Srv4dswyQNBfohGpz9o6Yb3Gz3SrUDqBH5rTuhGR7ahtlbYKnVxw2bCFMRljaA7EXHaXZ8wsHdodFvbkhKmqg==",
-      "devOptional": true
+      "dev": true
     },
     "node_modules/concurrently": {
       "version": "9.1.2",
@@ -4127,7 +4127,7 @@
       "version": "8.0.0",
       "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-8.0.0.tgz",
       "integrity": "sha512-MSjYzcWNOA0ewAHpz0MxpYFvwg6yjy1NG3xteoqz644VCo/RPgnr1/GGt+ic3iJTzQ8Eu3TdM14SawnVUmGE6A==",
-      "devOptional": true
+      "dev": true
     },
     "node_modules/encodeurl": {
       "version": "2.0.0",
@@ -5012,7 +5012,7 @@
       "version": "1.0.0",
       "resolved": "https://registry.npmjs.org/fs.realpath/-/fs.realpath-1.0.0.tgz",
       "integrity": "sha512-OO0pH2lK6a0hZnAdau5ItzHPI6pUlvI7jMVnxUQRtw4owF2wk8lOSabtGDCTP4Ggrg2MbGnWO9X8K1t4+fGMDw==",
-      "devOptional": true
+      "dev": true
     },
     "node_modules/fsevents": {
       "version": "2.3.3",
@@ -5170,7 +5170,7 @@
       "version": "7.2.3",
       "resolved": "https://registry.npmjs.org/glob/-/glob-7.2.3.tgz",
       "integrity": "sha512-nFR0zLpU2YCaRxwoCJvL6UvCH2JFyFVIvwTLsIf21AuHlMskA1hhTdk+LlYJtOlYt9v6dvszD2BGRqBL+iQK9Q==",
-      "devOptional": true,
+      "dev": true,
       "dependencies": {
         "fs.realpath": "^1.0.0",
         "inflight": "^1.0.4",
@@ -5203,7 +5203,7 @@
       "version": "1.1.12",
       "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-1.1.12.tgz",
       "integrity": "sha512-9T9UjW3r0UW5c1Q7GTwllptXwhvYmEzFhzMfZ9H7FQWt+uZePjZPjBP/W1ZEyZ1twGWom5/56TF4lPcqjnDHcg==",
-      "devOptional": true,
+      "dev": true,
       "license": "MIT",
       "dependencies": {
         "balanced-match": "^1.0.0",
@@ -5214,7 +5214,7 @@
       "version": "3.1.2",
       "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-3.1.2.tgz",
       "integrity": "sha512-J7p63hRiAjw1NDEww1W7i37+ByIrOWO5XQQAzZ3VOcL0PNybwpfmV/N05zFAzwQ9USyEcX6t3UO+K5aqBQOIHw==",
-      "devOptional": true,
+      "dev": true,
       "dependencies": {
         "brace-expansion": "^1.1.7"
       },
@@ -5297,7 +5297,7 @@
       "version": "4.2.11",
       "resolved": "https://registry.npmjs.org/graceful-fs/-/graceful-fs-4.2.11.tgz",
       "integrity": "sha512-RbJ5/jmFcNNCcDV5o9eTnBLJ/HszWV0P73bc+Ff4nS/rJj+YaS6IGyiOL0VoBYX+l1Wrl3k63h/KrH+nhJ0XvQ==",
-      "devOptional": true
+      "dev": true
     },
     "node_modules/graphemer": {
       "version": "1.4.0",
@@ -5557,15 +5557,6 @@
         "node": ">= 4"
       }
     },
-    "node_modules/immer": {
-      "version": "10.1.1",
-      "resolved": "https://registry.npmjs.org/immer/-/immer-10.1.1.tgz",
-      "integrity": "sha512-s2MPrmjovJcoMaHtx6K11Ra7oD05NT97w1IC5zpMkT6Atjr7H8LjaDd81iIxUYpMKSRRNMJE703M1Fhr/TctHw==",
-      "funding": {
-        "type": "opencollective",
-        "url": "https://opencollective.com/immer"
-      }
-    },
     "node_modules/immutable": {
       "version": "5.1.2",
       "resolved": "https://registry.npmjs.org/immutable/-/immutable-5.1.2.tgz",
@@ -5621,7 +5612,7 @@
       "version": "0.1.4",
       "resolved": "https://registry.npmjs.org/imurmurhash/-/imurmurhash-0.1.4.tgz",
       "integrity": "sha512-JmXMZ6wuvDmLiHEml9ykzqO6lwFbof0GG4IkcGaENdCRDDmMVnny7s5HsIgHCbaq0w2MyPhDqkhTUgS2LU2PHA==",
-      "devOptional": true,
+      "dev": true,
       "engines": {
         "node": ">=0.8.19"
       }
@@ -5630,7 +5621,7 @@
       "version": "1.0.6",
       "resolved": "https://registry.npmjs.org/inflight/-/inflight-1.0.6.tgz",
       "integrity": "sha512-k92I/b08q4wvFscXCLvqfsHCrjrF7yiXsQuIVvVE7N82W3+aqpzuUdBbfhWcy/FZR3/4IgflMgKLOsvPDrGCJA==",
-      "devOptional": true,
+      "dev": true,
       "dependencies": {
         "once": "^1.3.0",
         "wrappy": "1"
@@ -5838,7 +5829,7 @@
       "version": "3.0.0",
       "resolved": "https://registry.npmjs.org/is-fullwidth-code-point/-/is-fullwidth-code-point-3.0.0.tgz",
       "integrity": "sha512-zymm5+u+sCsSWyD9qNaejV3DFvhCKclKdizYaJUuHA83RLjb7nSuGnddCHGv0hk+KY7BMAlsWeK4Ueg6EV6XQg==",
-      "devOptional": true,
+      "dev": true,
       "engines": {
         "node": ">=8"
       }
@@ -6080,7 +6071,7 @@
       "version": "2.0.0",
       "resolved": "https://registry.npmjs.org/isexe/-/isexe-2.0.0.tgz",
       "integrity": "sha512-RHxMLp9lnKHGHRng9QFhRCMbYAcVpn69smSGcq3f36xjgVVWThj4qqLbTLlq7Ssj8B+fIQ1EuCEGI2lKsyQeIw==",
-      "devOptional": true
+      "dev": true
     },
     "node_modules/istanbul-lib-coverage": {
       "version": "3.2.2",
@@ -7980,7 +7971,7 @@
       "version": "1.2.8",
       "resolved": "https://registry.npmjs.org/minimist/-/minimist-1.2.8.tgz",
       "integrity": "sha512-2yyAR8qBkN3YuheJanUpWC5U3bb5osDywNB8RzDVlDwDHbocAJveqqj1u8+SVD7jkWT4yvsHCpWqqWqAxb0zCA==",
-      "devOptional": true,
+      "dev": true,
       "funding": {
         "url": "https://github.com/sponsors/ljharb"
       }
@@ -7990,6 +7981,15 @@
       "resolved": "https://registry.npmjs.org/ms/-/ms-2.1.3.tgz",
       "integrity": "sha512-6FlzubTLZG3J2a/NVCAleEhjzq5oxgHyaCU9yYXvcLsvoVaHJq/s5xXI6/XXP6tz7R9xAOtHnSO/tXtF3WRTlA=="
     },
+    "node_modules/mutative": {
+      "version": "1.2.0",
+      "resolved": "https://registry.npmjs.org/mutative/-/mutative-1.2.0.tgz",
+      "integrity": "sha512-1muFw45Lwjso6TSBGiXfbjKS01fVSD/qaqBfTo/gXgp79e8KM4Sa1XP/S4iN2/DvSdIZgjFJI+JIhC7eKf3GTg==",
+      "license": "MIT",
+      "engines": {
+        "node": ">=14.0"
+      }
+    },
     "node_modules/mylas": {
       "version": "2.1.13",
       "resolved": "https://registry.npmjs.org/mylas/-/mylas-2.1.13.tgz",
@@ -8357,7 +8357,7 @@
       "version": "1.0.1",
       "resolved": "https://registry.npmjs.org/path-is-absolute/-/path-is-absolute-1.0.1.tgz",
       "integrity": "sha512-AVbw3UJ2e9bq64vSaS9Am0fje1Pa8pbGqTTsmXfaIiMpnr5DlDhfJOuLj9Sf95ZPVDAUerDfEk88MPmPe7UCQg==",
-      "devOptional": true,
+      "dev": true,
       "engines": {
         "node": ">=0.10.0"
       }
@@ -9162,7 +9162,7 @@
       "version": "5.1.2",
       "resolved": "https://registry.npmjs.org/safe-buffer/-/safe-buffer-5.1.2.tgz",
       "integrity": "sha512-Gd2UZBJDkXlY7GbJxfsE8/nvKkUEU1G38c1siN6QP6a9PT9MmHB8GnpscSmMJSoF8LOIrt8ud/wPtojys4G6+g==",
-      "devOptional": true
+      "dev": true
     },
     "node_modules/safe-identifier": {
       "version": "0.4.2",
@@ -9518,7 +9518,7 @@
       "version": "3.0.7",
       "resolved": "https://registry.npmjs.org/signal-exit/-/signal-exit-3.0.7.tgz",
       "integrity": "sha512-wnD2ZE+l+SPC/uoS0vXeE9L1+0wuaMqKlfz9AMUo38JsyLSBWSFcHR1Rri62LZc12vLr1gb3jl7iwQhgwpAbGQ==",
-      "devOptional": true
+      "dev": true
     },
     "node_modules/simple-git": {
       "version": "3.28.0",
@@ -9639,7 +9639,7 @@
       "version": "4.2.3",
       "resolved": "https://registry.npmjs.org/string-width/-/string-width-4.2.3.tgz",
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-      "devOptional": true,
+      "dev": true,
       "dependencies": {
         "emoji-regex": "^8.0.0",
         "is-fullwidth-code-point": "^3.0.0",
@@ -9721,7 +9721,7 @@
       "version": "6.0.1",
       "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz",
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-      "devOptional": true,
+      "dev": true,
       "dependencies": {
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       },
@@ -10454,7 +10454,7 @@
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/util-deprecate/-/util-deprecate-1.0.2.tgz",
       "integrity": "sha512-EPD5q1uXyFxJpCrLnCc1nHnq3gOa6DZBocAIiI2TaSCA7VCJ1UJDMagCzIkXNsUYfD1daK//LTEQ8xiIbrHtcw==",
-      "devOptional": true
+      "dev": true
     },
     "node_modules/util.promisify": {
       "version": "1.1.3",
@@ -10577,7 +10577,7 @@
       "version": "2.0.2",
       "resolved": "https://registry.npmjs.org/which/-/which-2.0.2.tgz",
       "integrity": "sha512-BLI3Tl1TW3Pvl70l3yq3Y64i+awpwXqsGBYWkkqMtnbXgrMD+yj7rhW0kuEDxzJaYXGjEW5ogapKNMEKNMjibA==",
-      "devOptional": true,
+      "dev": true,
       "dependencies": {
         "isexe": "^2.0.0"
       },

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "5.0.0-dev.2",
+  "version": "5.0.0-dev.13",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -121,7 +121,9 @@
     "Andy Turner <agdturner@gmail.com>",
     "Lukáš Polák <admin@lukaspolak.cz>",
     "Chetan Mishra <chetan.s115@gmail.com>",
-    "Zach Charlop-Powers <zach.charlop.powers@gmail.com>"
+    "Zach Charlop-Powers <zach.charlop.powers@gmail.com>",
+    "Kim Juho <juho_kim@outlook.com>",
+    "Victoria Doshchenko <doshchenko.victoria@gmail.com>"
   ],
   "license": "MIT",
   "devDependencies": {
@@ -165,9 +167,9 @@
     "cors": "^2.8.5",
     "express": "^5.1.0",
     "h264-mp4-encoder": "^1.0.12",
-    "immer": "^10.1.1",
     "immutable": "^5.1.2",
     "io-ts": "^2.2.22",
+    "mutative": "^1.2.0",
     "node-fetch": "^2.7.0",
     "react-markdown": "^10.1.0",
     "remark-gfm": "^4.0.1",

scripts/build.mjs

@@ -131,8 +131,8 @@ function getPaths(app) {
 
 async function createBundle(app) {
     const { name, kind } = app;
-
     const { prefix, entry, outfile } = getPaths(app);
+    const NODE_ENV_PRD = isProduction || process.env.NODE_ENV === 'production';
 
     const ctx = await esbuild.context({
         entryPoints: [entry],
@@ -161,6 +161,7 @@ async function createBundle(app) {
         color: true,
         logLevel: 'info',
         define: {
+            'process.env.NODE_ENV': JSON.stringify(NODE_ENV_PRD ? 'production' : 'development'),
             'process.env.DEBUG': JSON.stringify(process.env.DEBUG || false),
             __MOLSTAR_PLUGIN_VERSION__: JSON.stringify(VERSION),
             __MOLSTAR_BUILD_TIMESTAMP__: `${TIMESTAMP}`,

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/index.html

@@ -53,6 +53,10 @@
             text-decoration: none;
         }
 
+        #links .sep {
+            color: #aaa;
+        }
+
         @media (orientation:portrait) {
             #viewer {
                 position: absolute;
@@ -90,13 +94,16 @@
     </div>
 
     <div id="links">
-        <a href="#" id="mvs-data">Download MVS State</a> | <a href="https://github.com/molstar/molstar/tree/master/src/apps/mvs-stories" id="mvs-data" target="_blank" rel="noopener noreferrer">Source Code</a>
+        <span id="open-in-stories"><a href="#" id="open-in-stories-link" target="_blank" rel="noopener noreferrer" title="Open and edit the story in the MolViewStories app">Edit in MolViewStories</a>&nbsp;<span class="sep">•</span></span>
+        <span id="open-in-molstar"><a href="#" id="open-in-molstar-link" target="_blank" rel="noopener noreferrer" title="Open the story in the Mol* Viewer app. Enables exporting an animation.">Open in Mol* Viewer</a>&nbsp;<span class="sep">•</span></span>
+        <a href="#" id="mvs-data" title="MolViewSpec State for this story. Can be opened in the Mol* app.">Download MVS</a> <span class="sep">•</span> <a href="https://github.com/molstar/molstar/tree/master/src/apps/mvs-stories" id="mvs-data" target="_blank" rel="noopener noreferrer">Source Code</a>
     </div>
 
     <script>
         var urlParams = new URLSearchParams(window.location.search);
         var storyId = urlParams.get('story-id');
         var storyUrl = urlParams.get('story-url');
+        var storySessionUrl = urlParams.get('story-session-url');
         var format = urlParams.get('data-format');
 
         // For testing purposes:
@@ -104,12 +111,32 @@
         //     storyUrl = 'https://raw.githubusercontent.com/molstar/molstar/master/examples/mvs/kinase-story.mvsj';
         // }
 
+        var molstarDataLink = storyUrl;
+        var editInStoriesUrl = undefined;
+
         if (storyId) {
             mvsStories.loadFromID(storyId, { format: format || 'mvsj', contextName: 'story1' });
+            editInStoriesUrl = 'https://molstar.org/mol-view-stories/builder?published-session-id=' + storyId;
+            molstarDataLink = 'https://stories.molstar.org/api/story/' + storyId + '/data';
         } else if (storyUrl) {
             mvsStories.loadFromURL(storyUrl, { format: format || 'mvsj', contextName: 'story1' });
         }
 
+        if (!editInStoriesUrl && storySessionUrl) {
+            editInStoriesUrl = 'https://molstar.org/mol-view-stories/builder?session-url=' + encodeURIComponent(storySessionUrl);
+        }
+        
+        if (molstarDataLink) {
+            var molstarLink = 'https://molstar.org/viewer?mvs-url=' + encodeURIComponent(molstarDataLink) + '&mvs-format=' + encodeURIComponent(format || 'mvsj'); 
+            document.getElementById('open-in-molstar-link').setAttribute('href', molstarLink);
+            document.getElementById('open-in-molstar').style.display = 'inline';
+        }
+        
+        if (editInStoriesUrl) {
+            document.getElementById('open-in-stories-link').setAttribute('href', editInStoriesUrl);
+            document.getElementById('open-in-stories').style.display = 'inline';
+        }
+
         document.getElementById('mvs-data').addEventListener('click', (e) => {
             e.preventDefault();
             mvsStories.downloadCurrentStory({ contextName: 'story1' });

src/apps/mvs-stories/styles.scss

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

src/apps/viewer/app.ts

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

src/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/ligand-editor/index.tsx

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

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

@@ -0,0 +1,407 @@
+/**
+ * Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { MVSData_States } from '../../../extensions/mvs/mvs-data';
+import { createMVSBuilder, Structure as MVSStructure, Root } from '../../../extensions/mvs/tree/mvs/mvs-builder';
+import { MVSNodeParams } from '../../../extensions/mvs/tree/mvs/mvs-tree';
+import { ColorT } from '../../../extensions/mvs/tree/mvs/param-types';
+import { Mat4 } from '../../../mol-math/linear-algebra';
+
+const Colors = {
+    '1cbs': '#4577B2' as ColorT,
+
+    'ligand-away': '#F3794C' as ColorT,
+    'ligand-docked': '#B9E3A0' as ColorT,
+};
+
+const Steps = [
+    {
+        header: 'Animation Demo',
+        key: 'intro',
+        description: `### Molecular Animation
+A story showcasing MolViewSpec animation capabilities.
+
+[\[**🔄 Replay Intro**\]](!play-transition)
+[\[**⏵ Play Snapshots**\]](!play-snapshots)
+[\[**⏹ Stop Animation**\]](!stop-animation)
+
+[\[**➡️ Next Snapshot**\]](!next-snapshot)
+
+`,
+        linger_duration_ms: 2000,
+        transition_duration_ms: 500,
+        state: (): Root => {
+            const builder = createMVSBuilder();
+
+            const _1cbs = structure(builder, '1cbs');
+            polymer(_1cbs, { color: Colors['1cbs'] });
+
+            const prims = _1cbs.primitives({
+                ref: 'prims',
+                label_opacity: 0,
+            });
+            prims.label({ text: 'Animation Demo', position: { label_asym_id: 'A' }, label_size: 10 });
+
+            const anim = builder.animation({
+                custom: {
+                    molstar_trackball: {
+                        name: 'rock',
+                        params: { speed: 0.5 },
+                    }
+                }
+            });
+            anim.interpolate({
+                kind: 'scalar',
+                ref: 'prims-opacity',
+                target_ref: 'prims',
+                start_ms: 500,
+                duration_ms: 500,
+                property: 'label_opacity',
+                end: 1,
+            });
+
+            anim.interpolate({
+                kind: 'scalar',
+                ref: 'prims-opacity',
+                target_ref: 'prims',
+                start_ms: 1500,
+                duration_ms: 500,
+                property: 'label_opacity',
+                start: 1,
+                end: 0.66,
+            });
+
+
+            // Uncomment this to make 2nd frame render much faster
+            // It will cause shader compilation to happen during the 1st snapshot
+
+            // const surface = poly.representation({
+            //     type: 'surface',
+            //     surface_type: 'gaussian',
+            // }).opacity({ opacity: 0 });
+
+            // _1cbs.component({ selector: 'ligand' })
+            //     .representation({ type: 'ball_and_stick' })
+            //     .opacity({ opacity: 0 });
+
+            // surface.clip({
+            //     ref: 'clip',
+            //     type: 'plane',
+            //     point: [22.0, 15, 0],
+            //     normal: [0, 0, 1],
+            // });
+
+            return builder;
+        },
+        camera: {
+            position: [-11.49, -37.05, 15.78],
+            target: [15.85, 17.26, 24.32],
+            up: [-0.88, 0.4, 0.26],
+        } satisfies MVSNodeParams<'camera'>,
+    },
+    {
+        header: 'Ligand Docking',
+        description: `Animate ligand moving to the binding site`,
+        linger_duration_ms: 2500,
+        transition_duration_ms: 500,
+        state: (): Root => {
+            const builder = createMVSBuilder();
+
+            const _1cbs = structure(builder, '1cbs');
+            const [poly, 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({
+                    ref: 'xform',
+                    translation: [5, 20, -20],
+                    rotation: [1, 0, 0, 0, 1, 0, 0, 0, 1],
+                    rotation_center: 'centroid',
+                })
+                .representation({ type: 'ball_and_stick' })
+                .color({ ref: 'ligand-color', color: 'red' });
+
+            surface.clip({
+                ref: 'clip',
+                type: 'plane',
+                point: [22.0, 15, 0],
+                normal: [0, 0, 1],
+            });
+
+            const anim = builder.animation();
+
+            anim.interpolate({
+                kind: 'scalar',
+                target_ref: 'clip',
+                duration_ms: 500,
+                property: ['point', 2],
+                end: 55,
+                easing: 'sin-in',
+            });
+
+            anim.interpolate({
+                kind: 'scalar',
+                target_ref: 'clip',
+                start_ms: 600,
+                duration_ms: 800,
+                property: ['point', 2],
+                end: 0,
+                easing: 'sin-out',
+            });
+
+            anim.interpolate({
+                kind: 'scalar',
+                target_ref: 'clip',
+                start_ms: 1500,
+                duration_ms: 500,
+                property: ['point', 2],
+                end: 55,
+            });
+
+            anim.interpolate({
+                kind: 'vec3',
+                target_ref: 'xform',
+                duration_ms: 2000,
+                property: 'translation',
+                end: [0, 0, 0],
+                noise_magnitude: 1,
+            });
+
+            anim.interpolate({
+                kind: 'rotation_matrix',
+                target_ref: 'xform',
+                duration_ms: 2000,
+                property: 'rotation',
+                noise_magnitude: 0.2,
+            });
+
+            anim.interpolate({
+                kind: 'color',
+                target_ref: 'ligand-color',
+                duration_ms: 2000,
+                property: 'color',
+                end: Colors['ligand-docked'],
+            });
+
+            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: {
+            position: [-30.63, 77.29, 2.28],
+            target: [19.16, 26.15, 22.82],
+            up: [0.69, 0.71, 0.09],
+        } satisfies MVSNodeParams<'camera'>,
+    },
+    {
+        header: 'Highlight & Opacity',
+        description: `Animate emissive, opacity and transform properties`,
+        linger_duration_ms: 2000,
+        transition_duration_ms: 0,
+        state: (): Root => {
+            const builder = createMVSBuilder();
+
+            const _1cbs = structure(builder, '1cbs');
+            const [poly,] = polymer(_1cbs, { color: Colors['1cbs'] });
+
+            poly.representation({
+                type: 'surface',
+                surface_type: 'gaussian'
+            }).opacity({ ref: 'opacity', opacity: 1 }).color({ ref: 'surface-color', color: 'white' });
+
+            _1cbs.component({ selector: 'ligand' })
+                .transform({ ref: 'xform', translation: [0, 0, 0] })
+                .representation({
+                    ref: 'repr',
+                    type: 'ball_and_stick',
+                    custom: {
+                        molstar_representation_params: {
+                            emissive: 0,
+                        }
+                    }
+                })
+                .color({ color: Colors['ligand-docked'] });
+
+            const primitives = builder.primitives({
+                ref: 'primitives',
+                instances: [
+                    Mat4.identity()
+                ],
+                opacity: 0,
+            });
+
+            primitives.ellipsoid({
+                center: [0, 0, 0],
+                radius: [2, 3, 2.5],
+                color: 'red'
+            });
+
+            const anim = builder.animation();
+
+            anim.interpolate({
+                kind: 'scalar',
+                target_ref: 'repr',
+                duration_ms: 1000,
+                property: ['custom', 'molstar_representation_params', 'emissive'],
+                end: 0.2,
+            });
+
+            anim.interpolate({
+                kind: 'scalar',
+                target_ref: 'opacity',
+                duration_ms: 1000,
+                frequency: 2,
+                alternate_direction: true,
+                property: 'opacity',
+                end: 0,
+            });
+
+            anim.interpolate({
+                kind: 'transform_matrix',
+                target_ref: 'primitives',
+                property: ['instances', 0],
+                translation_start: [20.24, 29.64, 14.85],
+                translation_end: [21.84, 21.71, 27.04],
+                translation_frequency: 4,
+                pivot: [0, 0, 0],
+                rotation_noise_magnitude: 0.2,
+                scale_end: [0.01, 0.01, 0.01],
+                duration_ms: 1000,
+            });
+
+            anim.interpolate({
+                kind: 'scalar',
+                target_ref: 'primitives',
+                duration_ms: 1000,
+                property: 'opacity',
+                end: 1,
+            });
+
+
+            anim.interpolate({
+                kind: 'color',
+                target_ref: 'surface-color',
+                duration_ms: 2000,
+                property: 'color',
+                palette: {
+                    kind: 'continuous',
+                    colors: ['white', Colors['1cbs'], 'white'],
+                }
+            });
+
+            return builder;
+        },
+        camera: {
+            position: [6.92, 47.17, 10.68],
+            target: [21.79, 22.2, 23.43],
+            up: [0.8, 0.57, 0.2],
+        } satisfies MVSNodeParams<'camera'>,
+    }
+];
+
+function structure(builder: Root, id: string): MVSStructure {
+    return builder
+        .download({ url: pdbUrl(id) })
+        .parse({ format: 'bcif' })
+        .modelStructure();
+}
+
+function polymer(structure: MVSStructure, options?: { color?: ColorT }) {
+    const component = structure.component({ selector: { label_asym_id: 'A' } });
+    const reprensentation = component.representation({ type: 'cartoon' });
+    if (options?.color) {
+        reprensentation.color({ color: options.color });
+    }
+    return [component, reprensentation] as const;
+}
+
+function pdbUrl(id: string) {
+    return `https://www.ebi.ac.uk/pdbe/entry-files/download/${id.toLowerCase()}.bcif`;
+}
+
+export function buildStory(): MVSData_States {
+    const snapshots = Steps.map((s, i) => {
+        const builder = s.state();
+        if (s.camera) builder.camera(s.camera);
+
+        builder.canvas({
+            custom: {
+                molstar_postprocessing: {
+                    enable_outline: true,
+                    enable_ssao: true,
+                    background: {
+                        name: 'horizontalGradient',
+                        params: {
+                            topColor: 0x777777,
+                            bottomColor: 0xffffff,
+                        }
+                    },
+                    // Example with background image:
+                    // background: {
+                    //     name: 'image',
+                    //     params: {
+                    //         // URL can also be filename in MVSX archive
+                    //         source: { name: 'url', params: 'URL' }
+                    //     }
+                    // }
+                }
+            }
+        });
+
+        const description = i > 0 ? `${s.description}\n\n[Go to start](#intro)` : s.description;
+
+        return builder.getSnapshot({
+            title: s.header,
+            key: s.key,
+            description,
+            description_format: 'markdown',
+            linger_duration_ms: s.linger_duration_ms ?? 500,
+            transition_duration_ms: s.transition_duration_ms ?? 1000,
+        });
+    });
+
+    return {
+        kind: 'multiple',
+        snapshots,
+        metadata: {
+            title: 'Animation Showcase',
+            version: '1.0',
+            timestamp: new Date().toISOString(),
+        }
+    };
+}

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

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

src/extensions/mvs/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

@@ -6,7 +6,11 @@
  */
 
 import { Camera } from '../../mol-canvas3d/camera';
-import { Canvas3DParams, Canvas3DProps } from '../../mol-canvas3d/canvas3d';
+import { CameraFogParams, Canvas3DParams, Canvas3DProps, DefaultCanvas3DParams } from '../../mol-canvas3d/canvas3d';
+import { TrackballControlsParams } from '../../mol-canvas3d/controls/trackball';
+import { 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';
 import { ShadowParams } from '../../mol-canvas3d/passes/shadow';
 import { SsaoParams } from '../../mol-canvas3d/passes/ssao';
@@ -18,10 +22,12 @@ 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';
 import { SnapshotMetadata } from './mvs-data';
+import { MVSAnimationNode } from './tree/animation/animation-tree';
 import { MolstarNode, MolstarNodeParams } from './tree/molstar/molstar-tree';
 import { MVSTreeSchema } from './tree/mvs/mvs-tree';
 
@@ -119,37 +125,102 @@ export function createPluginStateSnapshotCamera(plugin: PluginContext, context:
     return camera;
 }
 
-/** Set canvas properties based on a canvas node. */
-export function setCanvas(plugin: PluginContext, node: MolstarNode<'canvas'> | undefined) {
-    plugin.canvas3d?.setProps(old => modifyCanvasProps(old, node));
+function optionalParams(enable: boolean | undefined, values: any, params: ParamDefinition.Params, fallback: any) {
+    if (typeof enable === 'boolean') {
+        return enable
+            ? { name: 'on', params: { ...ParamDefinition.getDefaultValues(params), ...values } }
+            : { name: 'off', params: {} };
+    }
+    return fallback;
+}
+
+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, custom?: Record<string, any>): Canvas3DProps {
+export function modifyCanvasProps(oldCanvasProps: Canvas3DProps, canvasNode: MolstarNode<'canvas'> | undefined, animationNode: MVSAnimationNode<'animation'> | undefined): Canvas3DProps {
     const params = canvasNode?.params;
     const backgroundColor = decodeColor(params?.background_color) ?? DefaultCanvasBackgroundColor;
 
-    const outline = !!canvasNode?.custom?.molstar_enable_outline;
-    const shadow = !!canvasNode?.custom?.molstar_enable_shadow;
-    const occlusion = !!canvasNode?.custom?.molstar_enable_ssao;
+    const molstar_postprocessing = canvasNode?.custom?.molstar_postprocessing;
+
+    const outline = molstar_postprocessing?.enable_outline;
+    const outlineParams = molstar_postprocessing?.outline_params;
+
+    const shadow = molstar_postprocessing?.enable_shadow;
+    const shadowParams = molstar_postprocessing?.shadow_params;
+
+    const occlusion = molstar_postprocessing?.enable_ssao;
+    const occlusionParams = molstar_postprocessing?.ssao_params;
+
+    const fog = molstar_postprocessing?.enable_fog;
+    const fogParams = molstar_postprocessing?.fog_params;
+
+    const dof = molstar_postprocessing?.enable_depth_of_field;
+    const dofParams = molstar_postprocessing?.depth_of_field_params;
+
+    const bloom = molstar_postprocessing?.enable_bloom;
+    const bloomParams = molstar_postprocessing?.bloom_params;
+
+    const background = molstar_postprocessing?.background;
+
+    const trackballAnimation = animationNode?.custom?.molstar_trackball;
+    const trackballAnimationName = trackballAnimation?.name;
+    const trackballAnimationParams = trackballAnimation?.params ?? {};
 
     return {
         ...oldCanvasProps,
         postprocessing: {
             ...oldCanvasProps.postprocessing,
-            outline: outline
-                ? { name: 'on', params: ParamDefinition.getDefaultValues(OutlineParams) }
-                : oldCanvasProps.postprocessing.outline,
-            shadow: shadow
-                ? { name: 'on', params: ParamDefinition.getDefaultValues(ShadowParams) }
-                : oldCanvasProps.postprocessing.shadow,
-            occlusion: occlusion
-                ? { name: 'on', params: ParamDefinition.getDefaultValues(SsaoParams) }
-                : oldCanvasProps.postprocessing.occlusion,
+            outline: optionalParams(outline, outlineParams, OutlineParams, oldCanvasProps.postprocessing.outline),
+            shadow: optionalParams(shadow, shadowParams, ShadowParams, oldCanvasProps.postprocessing.shadow),
+            occlusion: optionalParams(occlusion, occlusionParams, SsaoParams, oldCanvasProps.postprocessing.occlusion),
+            dof: optionalParams(dof, dofParams, DofParams, oldCanvasProps.postprocessing.dof),
+            bloom: optionalParams(bloom, bloomParams, BloomParams, oldCanvasProps.postprocessing.bloom),
+            background: normalizeBackground(background, oldCanvasProps.postprocessing.background),
         },
+        cameraFog: optionalParams(fog, fogParams, CameraFogParams, oldCanvasProps.cameraFog),
         renderer: {
             ...oldCanvasProps.renderer,
             backgroundColor: backgroundColor,
         },
+        trackball: {
+            ...oldCanvasProps?.trackball,
+            ...(trackballAnimationName
+                ? {
+                    animate: {
+                        name: trackballAnimationName,
+                        params: {
+                            ...TrackballControlsParams.animate.map(trackballAnimationName)?.defaultValue,
+                            ...trackballAnimationParams
+                        }
+                    }
+                }
+                : {}
+            ),
+        }
     };
 }
+
+export function resetCanvasProps(plugin: PluginContext) {
+    const old = plugin.canvas3d?.props;
+    plugin.canvas3d?.setProps({
+        ...old,
+        postprocessing: {
+            ...old,
+            outline: 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: deepClone(DefaultCanvas3DParams.cameraFog),
+        trackball: {
+            ...old?.trackball,
+            animate: { name: 'off', params: {} },
+        }
+    });
+}

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

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

src/extensions/mvs/components/formats.ts

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

src/extensions/mvs/components/primitives.ts

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

src/extensions/mvs/components/trajectory.ts

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

src/extensions/mvs/export.ts

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

src/extensions/mvs/helpers/animation.ts

@@ -0,0 +1,674 @@
+/**
+ * Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Ludovic Autin <ludovic.autin@gmail.com>
+ */
+
+import { SortedArray } from '../../../mol-data/int';
+import * as EasingFns from '../../../mol-math/easing';
+import { clamp, lerp } from '../../../mol-math/interpolate';
+import { EPSILON, Mat3, Mat4, Quat, Vec3 } from '../../../mol-math/linear-algebra';
+import { RuntimeContext } from '../../../mol-task';
+import { deepEqual } from '../../../mol-util';
+import { Color } from '../../../mol-util/color';
+import { 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 { Snapshot } from '../mvs-data';
+import { MVSAnimationEasing, MVSAnimationNode, MVSAnimationSchema } from '../tree/animation/animation-tree';
+import { Tree } from '../tree/generic/tree-schema';
+import { addDefaults } from '../tree/generic/tree-utils';
+import { MVSTree } from '../tree/mvs/mvs-tree';
+import { ColorT } from '../tree/mvs/param-types';
+
+export async function generateStateTransition(ctx: RuntimeContext, snapshot: Snapshot, snapshotIndex: number, snapshotCount: number) {
+    if (!snapshot.animation) return undefined;
+
+    const tree = addDefaults(snapshot.animation, MVSAnimationSchema);
+    const transitions = tree.children?.filter(child => child.kind === 'interpolate');
+    if (!transitions?.length) return undefined;
+
+    const duration = Math.max(
+        snapshot.animation.params?.duration_ms ?? 0,
+        ...transitions.map(t => (t.params.start_ms ?? 0) + t.params.duration_ms)
+    );
+
+    const frames: [tree: MVSTree, time: number][] = [];
+    const dt = tree.params?.frame_time_ms ?? (1000 / 60);
+    const N = Math.ceil(duration / dt);
+
+    const nodeMap = makeNodeMap(snapshot.root, new Map(), []);
+    const cache = new Map<any, InterpolationCacheEntry>();
+
+    const transitionGroups = groupTranstions(transitions);
+
+    let prevRoot: MVSTree | undefined;
+    for (let i = 0; i <= N; i++) {
+        const t = i * dt;
+        const root = createSnapshot(snapshot.root, transitionGroups, t, cache, nodeMap);
+
+        if (root === prevRoot || (prevRoot && deepEqual(root, prevRoot))) {
+            frames[frames.length - 1][1] += dt;
+        } else {
+            frames.push([root, dt]);
+        }
+
+        prevRoot = root;
+
+        if (ctx.shouldUpdate) {
+            await ctx.update({ message: `Generating transition for snapshot ${snapshotIndex + 1}/${snapshotCount}`, current: i + 1, max: N });
+        }
+    }
+
+    return { tree, frametimeMs: dt, frames };
+}
+
+const EasingFnMap: Record<MVSAnimationEasing, (t: number) => number> = {
+    'linear': t => t,
+    'bounce-in': EasingFns.bounceIn,
+    'bounce-out': EasingFns.bounceOut,
+    'bounce-in-out': EasingFns.bounceInOut,
+    'circle-in': EasingFns.circleIn,
+    'circle-out': EasingFns.circleOut,
+    'circle-in-out': EasingFns.circleInOut,
+    'cubic-in': EasingFns.cubicIn,
+    'cubic-out': EasingFns.cubicOut,
+    'cubic-in-out': EasingFns.cubicInOut,
+    'exp-in': EasingFns.expIn,
+    'exp-out': EasingFns.expOut,
+    'exp-in-out': EasingFns.expInOut,
+    'quad-in': EasingFns.quadIn,
+    'quad-out': EasingFns.quadOut,
+    'quad-in-out': EasingFns.quadInOut,
+    'sin-in': EasingFns.sinIn,
+    'sin-out': EasingFns.sinOut,
+    'sin-in-out': EasingFns.sinInOut,
+};
+
+interface InterpolationCacheEntry {
+    paletteFn?: (value: number) => Color,
+    startColor?: Color | Record<number | string, Color>,
+    endColor?: Color | Record<number | string, Color>,
+    rotation?: { axis: Vec3, angle: number, start: Quat, end: Quat },
+}
+
+function getTransitionKey(transition: MVSAnimationNode<'interpolate'>) {
+    const prop = transition.params.property;
+    if (Array.isArray(prop)) {
+        return `${transition.params.target_ref}:${prop.join('.')}`;
+    }
+    return `${transition.params.target_ref}:${prop}`;
+}
+
+function groupTranstions(transitions: MVSAnimationNode<'interpolate'>[]) {
+    const map = new Map<string, MVSAnimationNode<'interpolate'>[]>();
+    const groups: MVSAnimationNode<'interpolate'>[][] = [];
+    for (const t of transitions) {
+        const key = getTransitionKey(t);
+        if (!map.has(key)) {
+            const group: MVSAnimationNode<'interpolate'>[] = [];
+            map.set(key, group);
+            groups.push(group);
+        }
+        map.get(key)!.push(t);
+    }
+    for (const group of groups) {
+        group.sort((a, b) => {
+            const s = (a.params.start_ms ?? 0) - (b.params.start_ms ?? 0);
+            if (s !== 0) return s;
+            return a.params.duration_ms - b.params.duration_ms;
+        });
+    }
+    return groups;
+}
+
+function createSnapshot(tree: MVSTree, transitionGroups: MVSAnimationNode<'interpolate'>[][], time: number, cache: Map<any, InterpolationCacheEntry>, nodeMap: Map<string, (string | number)[]>) {
+    let modified = false;
+    const ret = produce(tree, (draft) => {
+        for (const transitionGroup of transitionGroups) {
+
+            const pivot = transitionGroup[0];
+            const nodePath = nodeMap.get(pivot.params.target_ref);
+            if (!nodePath) continue;
+
+            const node = select(draft, nodePath, 0);
+            const target = pivot.params.property[0] === 'custom' ? node?.custom : node?.params;
+            if (!target) continue;
+
+
+            const offset = pivot.params.property[0] === 'custom' ? 1 : 0;
+
+            let transition: MVSAnimationNode<'interpolate'> = pivot;
+            let previous: MVSAnimationNode<'interpolate'> | undefined;
+
+            for (let i = transitionGroup.length - 1; i > 0; i--) {
+                const current = transitionGroup[i];
+                const currentStart = current.params.start_ms ?? 0;
+                if (time >= currentStart) {
+                    transition = current;
+                    previous = i > 0 ? transitionGroup[i - 1] : undefined;
+                    break;
+                }
+            }
+
+            if (!cache.has(transition)) {
+                cache.set(transition, {});
+            }
+
+            const cacheEntry: InterpolationCacheEntry = cache.get(transition)!;
+
+            const startTime: number = transition.params.start_ms ?? 0;
+            const durationMs: number = transition.params.duration_ms ?? 0;
+            const t = (time - startTime) / durationMs;
+
+            let next: any;
+            if (transition.params.kind === 'transform_matrix') {
+                next = processTransformMatrix(transition, target, clamp(t, 0, 1), cacheEntry, offset, previous);
+            } else {
+                next = processScalarLike(transition, target, t, cacheEntry, offset, previous);
+            }
+
+            if (next === undefined) {
+                continue;
+            }
+
+            modified = true;
+            assign(target, transition.params.property, next, offset);
+        }
+    });
+    return modified ? ret : tree;
+}
+
+function applyFrequency(t: number, frequency: number, alternate: boolean) {
+    let v = (t * (frequency || 1));
+    if (v < 1) return v;
+
+    if (!alternate) {
+        v = (v % 1);
+        if (v === 0) return 1;
+        return v;
+    }
+
+    if (Math.abs(v - 1) < EPSILON) return 1;
+    v = v % 2;
+    if (v > 1) return 2 - v;
+    return v;
+}
+
+function getPreviousScalarEnd(previous: MVSAnimationNode<'interpolate'> | undefined) {
+    if (!previous || previous.params.kind === 'transform_matrix') return undefined;
+    return previous.params.end;
+}
+
+function processScalarLike(transition: MVSAnimationNode<'interpolate'>, target: any, time: number, cacheEntry: InterpolationCacheEntry, offset: number, previous: MVSAnimationNode<'interpolate'> | undefined) {
+    if (transition.params.kind === 'transform_matrix') return;
+    if (previous && previous.params.kind === 'transform_matrix') return;
+
+    const 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(),
+    rotation: Mat4(),
+    scale: Mat4(),
+    translation: Mat4(),
+    pivotNeg: Vec3(),
+    temp: Mat4(),
+};
+function processTransformMatrix(transition: MVSAnimationNode<'interpolate'>, target: any, time: number, cache: InterpolationCacheEntry, offset: number, previous: MVSAnimationNode<'interpolate'> | undefined) {
+    if (transition.params.kind !== 'transform_matrix') return;
+    if (previous && previous.params.kind !== 'transform_matrix') return;
+
+    const transform = select(target, transition.params.property, offset) ?? Mat4.identity();
+
+    const startRotation = transition.params.rotation_start ?? getPreviousMatrixEnd(previous, 'rotation_start') ?? Mat3.fromMat4(Mat3(), transform);
+    const startTranslation = transition.params.translation_start ?? getPreviousMatrixEnd(previous, 'translation_start') ?? Mat4.getTranslation(Vec3(), transform);
+    const startScale = transition.params.scale_start ?? getPreviousMatrixEnd(previous, 'scale_start') ?? Mat4.getScaling(Vec3(), transform);
+
+    const endRotation = transition.params.rotation_end;
+    const endTranslation = transition.params.translation_end;
+    const endScale = transition.params.scale_end;
+
+    let rotation, translation, scale;
+
+    if (time <= 0) {
+        rotation = startRotation as Mat3;
+        translation = startTranslation as Vec3;
+        scale = startScale as Vec3;
+    } else {
+        const clampedTime = clamp(time, 0, 1);
+
+        let t = applyFrequency(clampedTime, transition.params.rotation_frequency ?? 1, !!transition.params.rotation_alternate_direction);
+        let easing = EasingFnMap[transition.params.rotation_easing ?? 'linear'] ?? EasingFnMap['linear'];
+        rotation = interpolateRotation(startRotation as Mat3, endRotation as Mat3, easing(t), transition.params.rotation_noise_magnitude ?? 0, cache);
+
+        t = applyFrequency(clampedTime, transition.params.translation_frequency ?? 1, !!transition.params.translation_alternate_direction);
+        easing = EasingFnMap[transition.params.translation_easing ?? 'linear'] ?? EasingFnMap['linear'];
+        translation = interpolateVec3(startTranslation as Vec3, endTranslation as Vec3 | undefined, easing(t), transition.params.translation_noise_magnitude ?? 0, false);
+
+        t = applyFrequency(clampedTime, transition.params.scale_frequency ?? 1, !!transition.params.scale_alternate_direction);
+        easing = EasingFnMap[transition.params.scale_easing ?? 'linear'] ?? EasingFnMap['linear'];
+        scale = interpolateVec3(startScale as Vec3, endScale as Vec3 | undefined, easing(t), transition.params.scale_noise_magnitude ?? 0, false);
+    }
+
+    const pivot = transition.params.pivot ?? Vec3.zero();
+
+    Mat4.fromTranslation(TransformState.translation, translation);
+    Mat4.fromScaling(TransformState.scale, scale);
+    Mat4.setIdentity(TransformState.rotation);
+    Mat4.fromMat3(TransformState.rotation, rotation);
+    Mat4.fromTranslation(TransformState.pivotTranslation, pivot as Vec3);
+    Mat4.fromTranslation(TransformState.pivotTranslationInv, Vec3.negate(TransformState.pivotNeg, pivot as Vec3));
+
+    // translation . pivot . rotation . scale . pivotInv
+    const result = Mat4();
+    Mat4.mul(result, TransformState.scale, TransformState.pivotTranslationInv);
+    Mat4.mul(result, TransformState.rotation, result);
+    Mat4.mul(result, TransformState.translation, result);
+
+    return result;
+}
+
+function interpolateScalars(start: number | number[], end: number | number[] | undefined, t: number, noise: number, discrete: boolean) {
+    if (Array.isArray(start)) {
+        const ret = Array.from<number>({ length: start.length }).fill(0.1);
+        if (!end || !Array.isArray(end)) {
+            for (let i = 0; i < start.length; i++) {
+                ret[i] = interpolateScalar(start[i], end, t, noise, discrete);
+            }
+            return ret;
+        }
+
+        for (let i = 0; i < start.length; i++) {
+            ret[i] = interpolateScalar(start[i], end[i], t, noise, discrete);
+        }
+        return ret;
+    }
+
+    if (Array.isArray(end)) {
+        const ret = Array.from<number>({ length: end.length }).fill(0.1);
+        for (let i = 0; i < end.length; i++) {
+            ret[i] = interpolateScalar(start, end[i], t, noise, discrete);
+        }
+        return ret;
+    }
+
+    return interpolateScalar(start, end, t, noise, discrete);
+}
+
+function interpolateScalar(start: number, end: number | undefined, t: number, noise: number, discrete: boolean) {
+    let v = typeof end === 'number' ? lerp(start, end, t) : start;
+    if (noise) {
+        v += (Math.random() - 0.5) * noise;
+    }
+    if (discrete) {
+        v = Math.round(v);
+    }
+    return v;
+}
+
+const InterpolateVectorsState = {
+    start: Vec3(),
+    end: Vec3(),
+    v: Vec3(),
+};
+function interpolateVectors(start: number[], end: number[] | undefined, t: number, noise: number, isSpherical: boolean) {
+    if ((!end || start === end) && !noise) return start;
+
+    const ret: number[] = Array.from<number>({ length: start.length }).fill(0.1);
+
+    for (let i = 0; i < start.length; i += 3) {
+        const s = Vec3.fromArray(InterpolateVectorsState.start, start, i);
+
+        let v: Vec3;
+        if (end) {
+            const e = Vec3.fromArray(InterpolateVectorsState.end, end, i);
+            v = isSpherical
+                ? Vec3.slerp(InterpolateVectorsState.v, s, e, t)
+                : Vec3.lerp(InterpolateVectorsState.v, s, e, t);
+        } else {
+            v = Vec3.clone(s);
+        }
+
+        if (noise && t <= 1 - EPSILON) {
+            Vec3.random(Vec3Noise, noise);
+            Vec3.add(v, v, Vec3Noise);
+        }
+
+        Vec3.toArray(v, ret, i);
+    }
+
+    return ret;
+}
+
+const Vec3Noise = Vec3();
+function interpolateVec3(start: Vec3, end: Vec3 | undefined, t: number, noise: number, isSpherical: boolean) {
+    if ((!end || start === end) && !noise) return start;
+
+    let v: Vec3;
+
+    if (end) {
+        v = isSpherical
+            ? Vec3.slerp(Vec3(), start, end, t)
+            : Vec3.lerp(Vec3(), start, end, t);
+    } else {
+        v = Vec3.clone(start);
+    }
+
+    if (noise && t <= 1 - EPSILON) {
+        Vec3.random(Vec3Noise, noise);
+        Vec3.add(v, v, Vec3Noise);
+    }
+    return v;
+}
+
+const RotationState = {
+    start: Quat(),
+    end: Quat(),
+    v: Quat(),
+    noise: Quat(),
+    axis: Vec3(),
+    temp: Mat4(),
+};
+function interpolateRotation(start: Mat3, end: Mat3 | undefined, t: number, noise: number, cache: InterpolationCacheEntry) {
+    if ((!end || start === end) && !noise) return start;
+
+    if (end) {
+        if (!cache.rotation) {
+            cache.rotation = {
+                ...relativeAxisAngle(start, end),
+                start: Quat.fromMat3(Quat(), start),
+                end: Quat.fromMat3(Quat(), end),
+            };
+        }
+
+        const { axis, angle, start: startQ, end: endQ } = cache.rotation;
+
+        if (angle < 1e-6) {
+            // start ≈ end: make a clean spin about the detected (or default) axis
+            Quat.setAxisAngle(RotationState.v, axis, t * 2 * Math.PI); // Make a full turn
+        } else {
+            // Normal case: stick with your existing slerp between start/end
+            Quat.slerp(RotationState.v, startQ, endQ, t);
+        }
+    } else {
+        Quat.fromMat3(RotationState.v, start);
+    }
+
+    if (noise && t <= 1 - EPSILON) {
+        Vec3.random(RotationState.axis, 1);
+        Quat.setAxisAngle(RotationState.noise, RotationState.axis, 2 * Math.PI * noise * (Math.random() - 0.5));
+        Quat.multiply(RotationState.v, RotationState.noise, RotationState.v);
+    }
+    Mat4.fromQuat(RotationState.temp, RotationState.v);
+    return Mat3.fromMat4(Mat3(), RotationState.temp);
+}
+
+function 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];
+    }
+
+    let f = params;
+    for (let i = offset; i < path.length; i++) {
+        if (!f) break;
+        f = f[path[i]];
+    }
+
+    return f;
+}
+
+function assign(params: any, path: string | (string | number)[], value: any, offset: number) {
+    if (!params) return;
+
+    if (typeof path === 'string') {
+        params[path] = value;
+        return;
+    }
+
+    let f = params;
+    for (let i = offset; i < path.length; i++) {
+        if (!f) break;
+        if (i === path.length - 1) {
+            f[path[i]] = value;
+        } else {
+            f = f[path[i]];
+        }
+    }
+}
+
+function makeNodeMap(tree: Tree, map: Map<string, (string | number)[]>, currentPath: (string | number)[]) {
+    if (tree.ref) {
+        map.set(tree.ref, [...currentPath]);
+    }
+
+    if (!tree.children) return map;
+
+    currentPath.push('children');
+    for (let i = 0; i < tree.children.length; i++) {
+        const child = tree.children[i];
+        currentPath.push(i);
+        makeNodeMap(child, map, currentPath);
+        currentPath.pop();
+    }
+    currentPath.pop();
+
+    return map;
+}
+
+function makePaletteFunction(props: MVSAnimationNode<'interpolate'>): ((value: number) => Color) | undefined {
+    if (props.params.kind !== 'color' || !props.params.palette) return undefined;
+
+    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}`);
+}
+
+
+function makePaletteFunctionDiscrete(props: MVSDiscretePaletteProps): (value: number) => Color {
+    const defaultColor = Color(0x0);
+    if (props.colors.length === 0) return () => defaultColor;
+
+    return (value: number) => {
+        const x = clamp(value, 0, 1);
+        for (let i = props.colors.length - 1; i >= 0; i--) {
+            const { color, fromValue, toValue } = props.colors[i];
+            if (fromValue <= x && x <= toValue) return color;
+        }
+        return defaultColor;
+    };
+}
+
+function makePaletteFunctionContinuous(props: MVSContinuousPaletteProps): (value: number) => Color {
+    const defaultColor = Color(0x0);
+    const { colors, checkpoints } = makeContinuousPaletteCheckpoints(props);
+    if (colors.length === 0) return () => defaultColor;
+
+    const underflowColor = props.setUnderflowColor ? props.underflowColor : defaultColor;
+    const overflowColor = props.setOverflowColor ? props.overflowColor : defaultColor;
+
+    return (value: number) => {
+        const x = clamp(value, 0, 1);
+        const gteIdx = SortedArray.findPredecessorIndex(checkpoints, x); // Index of the first greater or equal checkpoint
+        if (gteIdx === 0) {
+            if (x === checkpoints[0]) return colors[0];
+            else return underflowColor;
+        }
+        if (gteIdx === checkpoints.length) {
+            return overflowColor;
+        }
+        const q = (x - checkpoints[gteIdx - 1]) / (checkpoints[gteIdx] - checkpoints[gteIdx - 1]);
+        return Color.interpolate(colors[gteIdx - 1], colors[gteIdx], q);
+    };
+}
+
+const RelativeAxisAngleState = {
+    Rt: Mat3(),
+    R: Mat3(),
+};
+function relativeAxisAngle(start: Mat3, end: Mat3): { axis: Vec3, angle: number } {
+    // R_rel = end * start^T
+    const R0 = start, R1 = end;
+    const Rt = Mat3.transpose(RelativeAxisAngleState.Rt, R0);
+    const R = Mat3.mul(RelativeAxisAngleState.R, R1, Rt);
+
+    const tr = R[0] + R[4] + R[8]; // trace
+    let angle = Math.acos(clamp((tr - 1) * 0.5, -1, 1)); // in [0, π]
+    const axis = Vec3();
+
+    const eps = 1e-6;
+    const sinA = Math.sin(angle);
+
+    if (angle < eps) {
+        // Near identity: axis undefined; return any unit axis (choose something stable)
+        Vec3.set(axis, 0, 0, 1);
+        angle = 0.0;
+        return { axis, angle };
+    }
+
+    if (Math.PI - angle > 1e-4) {
+        // General case
+        axis[0] = (R[5] - R[7]) / (2 * sinA); // (r32 - r23)
+        axis[1] = (R[6] - R[2]) / (2 * sinA); // (r13 - r31)
+        axis[2] = (R[1] - R[3]) / (2 * sinA); // (r21 - r12)
+        Vec3.normalize(axis, axis);
+        return { axis, angle };
+    }
+
+    // angle ~ π: use diagonal-based extraction for stability
+    // Compute squared components then pick the largest to avoid precision loss
+    const xx = Math.max(0, (R[0] + 1) * 0.5);
+    const yy = Math.max(0, (R[4] + 1) * 0.5);
+    const zz = Math.max(0, (R[8] + 1) * 0.5);
+
+    let x = Math.sqrt(xx), y = Math.sqrt(yy), z = Math.sqrt(zz);
+
+    if (x >= y && x >= z) {
+        x = Math.max(x, 1e-8);
+        y = (R[1] + R[3]) / (4 * x);
+        z = (R[2] + R[6]) / (4 * x);
+        Vec3.set(axis, x, y, z);
+    } else if (y >= x && y >= z) {
+        y = Math.max(y, 1e-8);
+        x = (R[1] + R[3]) / (4 * y);
+        z = (R[5] + R[7]) / (4 * y);
+        Vec3.set(axis, x, y, z);
+    } else {
+        z = Math.max(z, 1e-8);
+        x = (R[2] + R[6]) / (4 * z);
+        y = (R[5] + R[7]) / (4 * z);
+        Vec3.set(axis, x, y, z);
+    }
+
+    Vec3.normalize(axis, axis);
+    return { axis, angle: Math.PI };
+}

src/extensions/mvs/helpers/utils.ts

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

src/extensions/mvs/load-generic.ts

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

src/extensions/mvs/load-helpers.ts

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

src/extensions/mvs/load.ts

@@ -8,15 +8,17 @@
 
 import { PluginStateSnapshotManager } from '../../mol-plugin-state/manager/snapshots';
 import { PluginStateObject } from '../../mol-plugin-state/objects';
-import { Download, ParseCcp4, ParseCif } from '../../mol-plugin-state/transforms/data';
-import { CustomModelProperties, CustomStructureProperties, ModelFromTrajectory, StructureComponent, StructureFromModel, TrajectoryFromMmCif, TrajectoryFromPDB } from '../../mol-plugin-state/transforms/model';
+import { Download, ParseCif, ParseCcp4 } from '../../mol-plugin-state/transforms/data';
+import { CoordinatesFromLammpstraj, CoordinatesFromXtc, CustomModelProperties, CustomStructureProperties, ModelFromTrajectory, StructureComponent, StructureFromModel, TrajectoryFromGRO, TrajectoryFromLammpsTrajData, TrajectoryFromMmCif, TrajectoryFromMOL, TrajectoryFromMOL2, TrajectoryFromPDB, TrajectoryFromSDF, TrajectoryFromXYZ } from '../../mol-plugin-state/transforms/model';
 import { StructureRepresentation3D, VolumeRepresentation3D } from '../../mol-plugin-state/transforms/representation';
 import { VolumeFromCcp4, VolumeFromDensityServerCif } from '../../mol-plugin-state/transforms/volume';
 import { PluginCommands } from '../../mol-plugin/commands';
 import { PluginContext } from '../../mol-plugin/context';
-import { StateObjectSelector } from '../../mol-state';
+import { PluginState } from '../../mol-plugin/state';
+import { StateObjectSelector, StateTree } from '../../mol-state';
+import { RuntimeContext, Task } from '../../mol-task';
 import { MolViewSpec } from './behavior';
-import { createPluginStateSnapshotCamera, modifyCanvasProps } from './camera';
+import { createPluginStateSnapshotCamera, modifyCanvasProps, resetCanvasProps } from './camera';
 import { MVSAnnotationsProvider } from './components/annotation-prop';
 import { MVSAnnotationStructureComponent } from './components/annotation-structure-component';
 import { MVSAnnotationTooltipsProvider } from './components/annotation-tooltips-prop';
@@ -24,15 +26,18 @@ import { CustomLabelProps, CustomLabelRepresentationProvider } from './component
 import { CustomTooltipsProvider } from './components/custom-tooltips-prop';
 import { IsMVSModelProps, IsMVSModelProvider } from './components/is-mvs-model-prop';
 import { getPrimitiveStructureRefs, MVSBuildPrimitiveShape, MVSDownloadPrimitiveData, MVSInlinePrimitiveData, MVSShapeRepresentation3D } from './components/primitives';
+import { MVSTrajectoryWithCoordinates } from './components/trajectory';
+import { generateStateTransition } from './helpers/animation';
 import { IsHiddenCustomStateExtension } from './load-extensions/is-hidden-custom-state';
 import { NonCovalentInteractionsExtension } from './load-extensions/non-covalent-interactions';
 import { LoadingActions, LoadingExtension, loadTreeVirtual, UpdateTarget } from './load-generic';
 import { AnnotationFromSourceKind, AnnotationFromUriKind, collectAnnotationReferences, collectAnnotationTooltips, collectInlineLabels, collectInlineTooltips, colorThemeForNode, componentFromXProps, componentPropsFromSelector, isPhantomComponent, labelFromXProps, makeNearestReprMap, prettyNameFromSelector, representationProps, structureProps, transformAndInstantiateStructure, transformAndInstantiateVolume, volumeColorThemeForNode, volumeRepresentationProps } from './load-helpers';
-import { MVSData, MVSData_States, SnapshotMetadata } from './mvs-data';
-import { validateTree } from './tree/generic/tree-schema';
+import { MVSData, MVSData_States, Snapshot, SnapshotMetadata } from './mvs-data';
+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 { type MVSTree, MVSTreeSchema } from './tree/mvs/mvs-tree';
+import { MVSTreeSchema } from './tree/mvs/mvs-tree';
 
 
 export interface MVSLoadOptions {
@@ -46,33 +51,54 @@ 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
 }
 
+export function loadMVS(plugin: PluginContext, data: MVSData, options: MVSLoadOptions = {}) {
+    const task = Task.create('Load MVS', ctx => _loadMVS(ctx, plugin, data, options));
+    return plugin.runTask(task);
+}
+
 /** Load a MolViewSpec (MVS) state(s) into the Mol* plugin as plugin state snapshots. */
-export async function loadMVS(plugin: PluginContext, data: MVSData, options: MVSLoadOptions = {}) {
+async function _loadMVS(ctx: RuntimeContext, plugin: PluginContext, data: MVSData, options: MVSLoadOptions = {}) {
     plugin.errorContext.clear('mvs');
     try {
         const mvsExtensionLoaded = plugin.state.hasBehavior(MolViewSpec);
         if (!mvsExtensionLoaded) throw new Error('MolViewSpec extension is not loaded.');
+
+        // Stop any currently running audio
+        plugin.managers.markdownExtensions.audio.dispose();
+
+        // Reset canvas props to default so that modifyCanvasProps works as expected
+        resetCanvasProps(plugin);
+
         // console.log(`MVS tree:\n${MVSData.toPrettyString(data)}`)
         const multiData: MVSData_States = data.kind === 'multiple' ? data : MVSData.stateToStates(data);
         const entries: PluginStateSnapshotManager.Entry[] = [];
         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,
-                snapshot.root,
+                snapshot.animation,
                 { ...snapshot.metadata, previousTransitionDurationMs: previousSnapshot.metadata.transition_duration_ms },
                 options
             );
+            await assignStateTransition(ctx, plugin, entry, snapshot, options, i, multiData.snapshots.length);
             entries.push(entry);
+
+            if (ctx.shouldUpdate) {
+                await ctx.update({ message: 'Loading MVS...', current: i, max: multiData.snapshots.length });
+            }
         }
         if (!options.appendSnapshots) {
             plugin.managers.snapshot.clear();
@@ -80,6 +106,7 @@ export async function loadMVS(plugin: PluginContext, data: MVSData, options: MVS
         for (const entry of entries) {
             plugin.managers.snapshot.add(entry);
         }
+
         if (entries.length > 0) {
             await PluginCommands.State.Snapshots.Apply(plugin, { id: entries[0].snapshot.id });
         }
@@ -101,24 +128,65 @@ export async function loadMVS(plugin: PluginContext, data: MVSData, options: MVS
     }
 }
 
+async function assignStateTransition(ctx: RuntimeContext, plugin: PluginContext, parentEntry: PluginStateSnapshotManager.Entry, parent: Snapshot, options: MVSLoadOptions, snapshotIndex: number, snapshotCount: number) {
+    const transitions = await generateStateTransition(ctx, parent, snapshotIndex, snapshotCount);
+    if (!transitions?.frames.length) return;
+
+    const animation: PluginState.StateTransition = {
+        autoplay: !!transitions.tree.params?.autoplay,
+        loop: !!transitions.tree.params?.loop,
+        frames: [],
+    };
+
+    for (let i = 0; i < transitions.frames.length; i++) {
+        const frame = transitions.frames[i];
+        const molstarTree = convertMvsToMolstar(frame[0], options.sourceUrl);
+        const entry = molstarTreeToEntry(
+            plugin,
+            molstarTree,
+            parent.animation,
+            { ...parent.metadata, previousTransitionDurationMs: transitions.frametimeMs },
+            options
+        );
+
+        StateTree.reuseTransformParams(entry.snapshot.data!.tree, parentEntry.snapshot.data!.tree);
+
+        animation.frames.push({
+            durationInMs: frame[1],
+            data: entry.snapshot.data!,
+            camera: transitions.tree.params?.include_camera ? entry.snapshot.camera : undefined,
+            canvas3d: transitions.tree.params?.include_canvas ? entry.snapshot.canvas3d : undefined,
+        });
+
+        if (ctx.shouldUpdate) {
+            await ctx.update({ message: `Loading animation for snapshot ${snapshotIndex + 1}/${snapshotCount}...`, current: i + 1, max: transitions.frames.length });
+        }
+    }
+
+    parentEntry.snapshot.transition = animation;
+}
 
 function molstarTreeToEntry(
     plugin: PluginContext,
     tree: MolstarTree,
-    mvsTree: MVSTree,
+    animation: MVSAnimationNode<'animation'> | undefined,
     metadata: SnapshotMetadata & { previousTransitionDurationMs?: number },
     options: { keepCamera?: boolean, extensions?: MolstarLoadingExtension<any>[] }
 ) {
     const context = MolstarLoadingContext.create();
     const snapshot = loadTreeVirtual(plugin, tree, MolstarLoadingActions, context, { replaceExisting: true, extensions: options?.extensions ?? BuiltinLoadingExtensions });
     snapshot.canvas3d = {
-        props: plugin.canvas3d ? modifyCanvasProps(plugin.canvas3d.props, context.canvas, mvsTree.custom) : undefined,
+        props: plugin.canvas3d ? modifyCanvasProps(plugin.canvas3d.props, context.canvas, animation) : undefined,
     };
     if (!options?.keepCamera) {
         snapshot.camera = createPluginStateSnapshotCamera(plugin, context, metadata);
     }
     snapshot.durationInMs = metadata.linger_duration_ms + (metadata.previousTransitionDurationMs ?? 0);
 
+    if (tree.custom?.molstar_on_load_markdown_commands) {
+        snapshot.onLoadMarkdownCommands = tree.custom.molstar_on_load_markdown_commands;
+    }
+
     const entryParams: PluginStateSnapshotManager.EntryParams = {
         key: metadata.key,
         name: metadata.title,
@@ -165,31 +233,72 @@ const MolstarLoadingActions: LoadingActions<MolstarTree, MolstarLoadingContext>
     },
     parse(updateParent: UpdateTarget, node: MolstarNode<'parse'>): UpdateTarget | undefined {
         const format = node.params.format;
-        if (format === 'cif') {
-            return UpdateTarget.apply(updateParent, ParseCif, {});
-        } else if (format === 'pdb') {
-            return updateParent;
-        } else if (format === 'map') {
-            return UpdateTarget.apply(updateParent, ParseCcp4, {});
-        } else {
-            console.error(`Unknown format in "parse" node: "${format}"`);
-            return undefined;
+        switch (format) {
+            case 'cif':
+                return UpdateTarget.apply(updateParent, ParseCif, {});
+            case 'pdb':
+            case 'pdbqt':
+            case 'gro':
+            case 'xyz':
+            case 'mol':
+            case 'sdf':
+            case 'mol2':
+            case 'xtc':
+            case 'lammpstrj':
+                return updateParent;
+            case 'map':
+                return UpdateTarget.apply(updateParent, ParseCcp4, {});
+            default:
+                console.error(`Unknown format in "parse" node: "${format}"`);
+                return undefined;
+        }
+    },
+    coordinates(updateParent: UpdateTarget, node: MolstarNode<'coordinates'>): UpdateTarget | undefined {
+        const format = node.params.format;
+        switch (format) {
+            case 'xtc':
+                return UpdateTarget.apply(updateParent, CoordinatesFromXtc);
+            case 'lammpstrj':
+                return UpdateTarget.apply(updateParent, CoordinatesFromLammpstraj);
+            default:
+                console.error(`Unknown format in "coordinates" node: "${format}"`);
+                return undefined;
         }
     },
     trajectory(updateParent: UpdateTarget, node: MolstarNode<'trajectory'>): UpdateTarget | undefined {
         const format = node.params.format;
-        if (format === 'cif') {
-            return UpdateTarget.apply(updateParent, TrajectoryFromMmCif, {
-                blockHeader: node.params.block_header ?? '', // Must set to '' because just undefined would get overwritten by createDefaults
-                blockIndex: node.params.block_index ?? undefined,
-            });
-        } else if (format === 'pdb') {
-            return UpdateTarget.apply(updateParent, TrajectoryFromPDB, {});
-        } else {
-            console.error(`Unknown format in "trajectory" node: "${format}"`);
-            return undefined;
+        switch (format) {
+            case 'cif':
+                return UpdateTarget.apply(updateParent, TrajectoryFromMmCif, {
+                    blockHeader: node.params.block_header ?? '', // Must set to '' because just undefined would get overwritten by createDefaults
+                    blockIndex: node.params.block_index ?? undefined,
+                });
+            case 'pdb':
+            case 'pdbqt':
+                return UpdateTarget.apply(updateParent, TrajectoryFromPDB, { isPdbqt: format === 'pdbqt' });
+            case 'gro':
+                return UpdateTarget.apply(updateParent, TrajectoryFromGRO);
+            case 'xyz':
+                return UpdateTarget.apply(updateParent, TrajectoryFromXYZ);
+            case 'mol':
+                return UpdateTarget.apply(updateParent, TrajectoryFromMOL);
+            case 'sdf':
+                return UpdateTarget.apply(updateParent, TrajectoryFromSDF);
+            case 'mol2':
+                return UpdateTarget.apply(updateParent, TrajectoryFromMOL2);
+            case 'lammpstrj':
+                return UpdateTarget.apply(updateParent, TrajectoryFromLammpsTrajData);
+            default:
+                console.error(`Unknown format in "trajectory" node: "${format}"`);
+                return undefined;
         }
     },
+    trajectory_with_coordinates(updateParent: UpdateTarget, node: MolstarNode<'trajectory_with_coordinates'>): UpdateTarget | undefined {
+        const result = UpdateTarget.apply(updateParent, MVSTrajectoryWithCoordinates, {
+            coordinatesRef: node.params.coordinates_ref,
+        });
+        return UpdateTarget.setMvsDependencies(result, [node.params.coordinates_ref]);
+    },
     model(updateParent: UpdateTarget, node: MolstarSubtree<'model'>, context: MolstarLoadingContext): UpdateTarget {
         const annotations = collectAnnotationReferences(node, context);
         const model = UpdateTarget.apply(updateParent, ModelFromTrajectory, {
@@ -312,7 +421,7 @@ const MolstarLoadingActions: LoadingActions<MolstarTree, MolstarLoadingContext>
     },
     primitives(updateParent: UpdateTarget, tree: MolstarSubtree<'primitives'>, context: MolstarLoadingContext): UpdateTarget {
         const refs = getPrimitiveStructureRefs(tree);
-        const data = UpdateTarget.apply(updateParent, MVSInlinePrimitiveData, { node: tree });
+        const data = UpdateTarget.apply(updateParent, MVSInlinePrimitiveData, { node: tree as any });
         return applyPrimitiveVisuals(data, refs);
     },
     primitives_from_uri(updateParent: UpdateTarget, tree: MolstarNode<'primitives_from_uri'>, context: MolstarLoadingContext): UpdateTarget {

src/extensions/mvs/mvs-data.ts

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/mol-canvas3d/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 { produce } from 'immer';
 import { HandleHelperParams } from './helper/handle-helper';
 import { StereoCamera, StereoCameraParams } from './camera/stereo';
 import { Helper } from './helper/helper';
@@ -49,7 +48,11 @@ import { IlluminationParams } from './passes/illumination';
 import { isMobileBrowser } from '../mol-util/browser';
 import { Ray3D } from '../mol-math/geometry/primitives/ray3d';
 import { RayHelper } from './helper/ray-helper';
+import { produce } from '../mol-util/produce';
 
+export const CameraFogParams = {
+    intensity: PD.Numeric(15, { min: 1, max: 100, step: 1 }),
+};
 export const Canvas3DParams = {
     camera: PD.Group({
         mode: PD.Select('perspective', PD.arrayToOptions(['perspective', 'orthographic'] as const), { label: 'Camera' }),
@@ -63,9 +66,7 @@ export const Canvas3DParams = {
         manualReset: PD.Boolean(false, { isHidden: true }),
     }, { pivot: 'mode' }),
     cameraFog: PD.MappedStatic('on', {
-        on: PD.Group({
-            intensity: PD.Numeric(15, { min: 1, max: 100, step: 1 }),
-        }),
+        on: PD.Group(CameraFogParams),
         off: PD.Group({})
     }, { cycle: true, description: 'Show fog in the distance' }),
     cameraClipping: PD.Group({
@@ -113,6 +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 */
@@ -359,6 +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']
@@ -378,9 +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>();
@@ -420,7 +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);
 
@@ -1179,6 +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 }),
@@ -68,10 +66,10 @@ export const TrackballControlsParams = {
     animate: PD.MappedStatic('off', {
         off: PD.EmptyGroup(),
         spin: PD.Group({
-            speed: PD.Numeric(1, { min: -20, max: 20, step: 1 }, { description: 'Rotation speed in radians per second' }),
+            speed: PD.Numeric(0.3, { min: -5, max: 5, step: 0.1 }, { description: 'Number of rotations per second' }),
         }, { description: 'Spin the 3D scene around the x-axis in view space' }),
         rock: PD.Group({
-            speed: PD.Numeric(0.3, { min: -5, max: 5, step: 0.1 }),
+            speed: PD.Numeric(0.3, { min: -5, max: 5, step: 0.1 }, { description: 'Number of oscilations per second' }),
             angle: PD.Numeric(10, { min: 0, max: 90, step: 1 }, { description: 'How many degrees to rotate in each direction.' }),
         }, { description: 'Rock the 3D scene around the x-axis in view space' })
     }),
@@ -85,8 +83,6 @@ export const TrackballControlsParams = {
     gestureScaleFactor: PD.Numeric(1, {}, { isHidden: true }),
     maxWheelDelta: PD.Numeric(0.02, {}, { isHidden: true }),
 
-    bindings: PD.Value(DefaultTrackballBindings, { isHidden: true }),
-
     /**
      * minDistance = minDistanceFactor * boundingSphere.radius + minDistancePadding
      * maxDistance = max(maxDistanceFactor * boundingSphere.radius, maxDistanceMin)
@@ -103,6 +99,11 @@ export const TrackballControlsParams = {
 };
 export type TrackballControlsProps = PD.Values<typeof TrackballControlsParams>
 
+export const DefaultTrackballControlsAttribs = {
+    bindings: DefaultTrackballBindings,
+};
+export type TrackballControlsAttribs = typeof DefaultTrackballControlsAttribs
+
 export { TrackballControls };
 interface TrackballControls {
     readonly viewport: Viewport
@@ -112,20 +113,25 @@ interface TrackballControls {
     readonly props: Readonly<TrackballControlsProps>
     setProps: (props: Partial<TrackballControlsProps>) => void
 
+    readonly attribs: Readonly<TrackballControlsAttribs>
+    setAttribs: (attribs: Partial<TrackballControlsAttribs>) => void
+
     start: (t: number) => void
     update: (t: number) => void
     reset: () => void
     dispose: () => void
 }
 namespace TrackballControls {
-    export function create(input: InputObserver, camera: Camera, scene: Scene, props: Partial<TrackballControlsProps> = {}): TrackballControls {
+    export function create(input: InputObserver, camera: Camera, scene: Scene, props: Partial<TrackballControlsProps> = {}, attribs: Partial<TrackballControlsAttribs> = {}): TrackballControls {
         const p: TrackballControlsProps = {
             ...PD.getDefaultValues(TrackballControlsParams),
             ...props,
-            // include default bindings for backwards state compatibility
-            bindings: { ...DefaultTrackballBindings, ...props.bindings }
         };
-        const b = p.bindings;
+        const a: TrackballControlsAttribs = {
+            ...DefaultTrackballControlsAttribs,
+            ...attribs
+        };
+        const b = a.bindings;
 
         const viewport = Viewport.clone(camera.viewport);
 
@@ -825,7 +831,7 @@ namespace TrackballControls {
         function spin(deltaT: number) {
             if (p.animate.name !== 'spin' || p.animate.params.speed === 0 || _isInteracting) return;
 
-            const radPerMs = p.animate.params.speed / 1000;
+            const radPerMs = 2 * Math.PI * p.animate.params.speed / 1000;
             _spinSpeed[0] = deltaT * radPerMs / getRotateFactor();
             Vec2.add(_rotCurr, _rotPrev, _spinSpeed);
         }
@@ -885,7 +891,12 @@ namespace TrackballControls {
                     }
                 }
                 Object.assign(p, props);
-                Object.assign(b, props.bindings);
+            },
+
+            get attribs() { return a as Readonly<TrackballControlsAttribs>; },
+            setAttribs: (attribs: Partial<TrackballControlsAttribs>) => {
+                Object.assign(a, attribs);
+                Object.assign(b, a.bindings);
             },
 
             start,

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

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

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

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

src/mol-canvas3d/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-canvas3d/passes/dpoit.ts

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

src/mol-canvas3d/passes/draw.ts

@@ -106,6 +106,7 @@ export class DrawPass {
             this.depthTextureOpaque.define(width, height);
         }
 
+        // TODO: link programs in parallel
         this.wboit = new WboitPass(webgl, width, height);
         this.dpoit = new DpoitPass(webgl, width, height);
         this.marking = new MarkingPass(webgl, width, height);
@@ -198,8 +199,10 @@ export class DrawPass {
                 const dpoitTextures = this.dpoit.bindDualDepthPeeling();
                 renderer.renderDpoitTransparent(scene.primitives, camera, this.depthTextureOpaque, dpoitTextures);
 
-                target.bind();
-                this.dpoit.renderBlendBack();
+                if (iterations > 1) {
+                    target.bind();
+                    this.dpoit.renderBlendBack();
+                }
                 if (isTimingMode) this.webgl.timer.markEnd('DpoitPass.layer');
             }
 

src/mol-canvas3d/passes/illumination.ts

@@ -171,13 +171,15 @@ export class IlluminationPass {
                 const dpoitTextures = this.drawPass.dpoit.bind();
                 renderer.renderDpoitTransparent(scene.primitives, camera, this.drawPass.depthTextureOpaque, dpoitTextures);
 
-                for (let i = 0, il = props.dpoitIterations; i < il; i++) {
+                for (let i = 0, iterations = props.dpoitIterations; i < iterations; i++) {
                     if (isTimingMode) this.webgl.timer.mark('DpoitPass.layer');
                     const dpoitTextures = this.drawPass.dpoit.bindDualDepthPeeling();
                     renderer.renderDpoitTransparent(scene.primitives, camera, this.drawPass.depthTextureOpaque, dpoitTextures);
 
-                    this.transparentTarget.bind();
-                    this.drawPass.dpoit.renderBlendBack();
+                    if (iterations > 1) {
+                        this.transparentTarget.bind();
+                        this.drawPass.dpoit.renderBlendBack();
+                    }
                     if (isTimingMode) this.webgl.timer.markEnd('DpoitPass.layer');
                 }
 

src/mol-canvas3d/passes/ssao.ts

@@ -126,6 +126,7 @@ export class SsaoPass {
     private nSamples: number;
     private blurKernelSize: number;
     private texSize: [number, number];
+    private invProjection = Mat4.identity();
 
     private ssaoScale: number;
     private calcSsaoScale(resolutionScale: number) {
@@ -275,9 +276,7 @@ export class SsaoPass {
         let needsUpdateDepthHalf = false;
 
         const orthographic = camera.state.mode === 'orthographic' ? 1 : 0;
-
-        const invProjection = Mat4.identity();
-        Mat4.invert(invProjection, camera.projection);
+        const invProjection = Mat4.invert(this.invProjection, camera.projection);
 
         const [w, h] = this.texSize;
         const v = camera.viewport;

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

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

src/mol-gl/commit-queue.ts

@@ -23,6 +23,12 @@ export class CommitQueue {
         return this.removeMap.size + this.addMap.size;
     }
 
+    forEachAdd(cb: (o: GraphicsRenderObject) => void) {
+        for (let n = this.addList.first; n; n = n.next) {
+            cb(n.value);
+        }
+    }
+
     add(o: GraphicsRenderObject) {
         if (this.removeMap.has(o)) {
             const a = this.removeMap.get(o)!;

src/mol-gl/render-object.ts

@@ -8,14 +8,14 @@ import { RenderableState, Renderable } from './renderable';
 import { idFactory } from '../mol-util/id-factory';
 import { WebGLContext } from './webgl/context';
 import { DirectVolumeValues, DirectVolumeRenderable } from './renderable/direct-volume';
-import { MeshValues, MeshRenderable } from './renderable/mesh';
+import { MeshValues, MeshRenderable, linkMeshRenderableShader } from './renderable/mesh';
 import { PointsValues, PointsRenderable } from './renderable/points';
 import { LinesValues, LinesRenderable } from './renderable/lines';
-import { SpheresValues, SpheresRenderable } from './renderable/spheres';
+import { SpheresValues, SpheresRenderable, linkSpheresRenderableShader } from './renderable/spheres';
 import { TextValues, TextRenderable } from './renderable/text';
 import { TextureMeshValues, TextureMeshRenderable } from './renderable/texture-mesh';
 import { ImageValues, ImageRenderable } from './renderable/image';
-import { CylindersRenderable, CylindersValues } from './renderable/cylinders';
+import { CylindersRenderable, CylindersValues, linkCylindersRenderableShader } from './renderable/cylinders';
 import { Transparency } from './webgl/render-item';
 
 const getNextId = idFactory(0, 0x7FFFFFFF);
@@ -63,3 +63,13 @@ export function createRenderable<T extends RenderObjectType>(ctx: WebGLContext,
     }
     throw new Error('unsupported type');
 }
+
+export function linkRenderableShader<T extends RenderObjectType>(ctx: WebGLContext, o: GraphicsRenderObject<T>, transparency: Transparency) {
+    switch (o.type) {
+        case 'mesh': return linkMeshRenderableShader(ctx, o.id, o.values as MeshValues, o.state, o.materialId, transparency);
+        case 'spheres': return linkSpheresRenderableShader(ctx, o.id, o.values as SpheresValues, o.state, o.materialId, transparency);
+        case 'cylinders': return linkCylindersRenderableShader(ctx, o.id, o.values as CylindersValues, o.state, o.materialId, transparency);
+    }
+    console.log(o.type);
+    // throw new Error('unsupported type');
+}

src/mol-gl/renderable/cylinders.ts

@@ -6,7 +6,7 @@
 
 import { Renderable, RenderableState, createRenderable } from '../renderable';
 import { WebGLContext } from '../webgl/context';
-import { createGraphicsRenderItem, Transparency } from '../webgl/render-item';
+import { createGraphicsRenderItem, GraphicsRenderVariants, linkRenderItemProgram, Transparency } from '../webgl/render-item';
 import { GlobalUniformSchema, BaseSchema, AttributeSpec, Values, InternalSchema, SizeSchema, InternalValues, ElementsSpec, ValueSpec, DefineSpec, GlobalTextureSchema, UniformSpec } from './schema';
 import { CylindersShaderCode } from '../shader-code';
 import { ValueCell } from '../../mol-util';
@@ -45,4 +45,13 @@ export function CylindersRenderable(ctx: WebGLContext, id: number, values: Cylin
     const shaderCode = CylindersShaderCode;
     const renderItem = createGraphicsRenderItem(ctx, 'triangles', shaderCode, schema, { ...values, ...internalValues }, materialId, transparency);
     return createRenderable(renderItem, values, state);
+}
+
+export function linkCylindersRenderableShader(ctx: WebGLContext, id: number, values: CylindersValues, state: RenderableState, materialId: number, transparency: Transparency) {
+    const schema = { ...GlobalUniformSchema, ...GlobalTextureSchema, ...InternalSchema, ...CylindersSchema };
+    const internalValues: InternalValues = {
+        uObjectId: ValueCell.create(id),
+    };
+    const shaderCode = CylindersShaderCode;
+    linkRenderItemProgram(ctx, shaderCode, schema, { ...values, ...internalValues }, GraphicsRenderVariants, transparency);
 }

src/mol-gl/renderable/mesh.ts

@@ -6,7 +6,7 @@
 
 import { Renderable, RenderableState, createRenderable } from '../renderable';
 import { WebGLContext } from '../webgl/context';
-import { createGraphicsRenderItem, Transparency } from '../webgl/render-item';
+import { createGraphicsRenderItem, GraphicsRenderVariants, linkRenderItemProgram, Transparency } from '../webgl/render-item';
 import { GlobalUniformSchema, BaseSchema, AttributeSpec, ElementsSpec, DefineSpec, Values, InternalSchema, InternalValues, GlobalTextureSchema, ValueSpec, UniformSpec } from './schema';
 import { MeshShaderCode } from '../shader-code';
 import { ValueCell } from '../../mol-util';
@@ -41,4 +41,13 @@ export function MeshRenderable(ctx: WebGLContext, id: number, values: MeshValues
     const renderItem = createGraphicsRenderItem(ctx, 'triangles', shaderCode, schema, { ...values, ...internalValues }, materialId, transparency);
 
     return createRenderable(renderItem, values, state);
+}
+
+export function linkMeshRenderableShader(ctx: WebGLContext, id: number, values: MeshValues, state: RenderableState, materialId: number, transparency: Transparency) {
+    const schema = { ...GlobalUniformSchema, ...GlobalTextureSchema, ...InternalSchema, ...MeshSchema };
+    const internalValues: InternalValues = {
+        uObjectId: ValueCell.create(id),
+    };
+    const shaderCode = MeshShaderCode;
+    linkRenderItemProgram(ctx, shaderCode, schema, { ...values, ...internalValues }, GraphicsRenderVariants, transparency);
 }

src/mol-gl/renderable/spheres.ts

@@ -6,7 +6,7 @@
 
 import { Renderable, RenderableState, createRenderable } from '../renderable';
 import { WebGLContext } from '../webgl/context';
-import { createGraphicsRenderItem, Transparency } from '../webgl/render-item';
+import { createGraphicsRenderItem, GraphicsRenderVariants, linkRenderItemProgram, Transparency } from '../webgl/render-item';
 import { GlobalUniformSchema, BaseSchema, Values, InternalSchema, SizeSchema, InternalValues, ValueSpec, DefineSpec, GlobalTextureSchema, UniformSpec, TextureSpec } from './schema';
 import { SpheresShaderCode } from '../shader-code';
 import { ValueCell } from '../../mol-util';
@@ -46,4 +46,13 @@ export function SpheresRenderable(ctx: WebGLContext, id: number, values: Spheres
     const shaderCode = SpheresShaderCode;
     const renderItem = createGraphicsRenderItem(ctx, 'triangles', shaderCode, schema, { ...values, ...internalValues }, materialId, transparency);
     return createRenderable(renderItem, values, state);
+}
+
+export function linkSpheresRenderableShader(ctx: WebGLContext, id: number, values: SpheresValues, state: RenderableState, materialId: number, transparency: Transparency) {
+    const schema = { ...GlobalUniformSchema, ...GlobalTextureSchema, ...InternalSchema, ...SpheresSchema };
+    const internalValues: InternalValues = {
+        uObjectId: ValueCell.create(id),
+    };
+    const shaderCode = SpheresShaderCode;
+    linkRenderItemProgram(ctx, shaderCode, schema, { ...values, ...internalValues }, GraphicsRenderVariants, transparency);
 }

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/scene.ts

@@ -6,7 +6,7 @@
  */
 
 import { WebGLContext } from './webgl/context';
-import { GraphicsRenderObject, createRenderable } from './render-object';
+import { GraphicsRenderObject, createRenderable, linkRenderableShader as linkRenderableProgram } from './render-object';
 import { Object3D } from './object3d';
 import { Sphere3D } from '../mol-math/geometry/primitives/sphere3d';
 import { CommitQueue } from './commit-queue';
@@ -130,7 +130,9 @@ namespace Scene {
 
         function add(o: GraphicsRenderObject) {
             if (!renderableMap.has(o)) {
+                console.time(`create renderable ${o.type}`);
                 const renderable = createRenderable(ctx, o, transparency);
+                console.timeEnd(`create renderable ${o.type}`);
                 renderables.push(renderable);
                 if (o.type === 'direct-volume') {
                     volumes.push(renderable);
@@ -164,6 +166,10 @@ namespace Scene {
 
             let i = 0;
 
+            // TODO: have to destroy programs that were not added (=removed before added)
+            commitQueue.forEachAdd(o => linkRenderableProgram(ctx, o, transparency));
+            // there could also be a separate queue just for program linking that calls program.finalize()
+
             while (true) {
                 const o = commitQueue.tryGetRemove();
                 if (!o) break;

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-gl/webgl/program.ts

@@ -22,6 +22,7 @@ export interface Program {
     readonly id: number
 
     use: () => void
+    finalize: () => void
     setUniforms: (uniformValues: UniformsList) => void
     uniform: (k: string, v: UniformType) => void
     bindAttributes: (attribueBuffers: AttributeBuffers) => void
@@ -175,29 +176,38 @@ export function createProgram(gl: GLRenderingContext, state: WebGLState, extensi
     let locations: Locations;
     let uniformSetters: UniformSetters;
 
-    function init() {
+    function link() {
         vertShader.attach(program);
         fragShader.attach(program);
+        console.log('linking', programId)
         gl.linkProgram(program);
-        if (isDebugMode) {
-            checkProgram(gl, program);
-        }
 
-        locations = getLocations(gl, program, schema);
-        uniformSetters = getUniformSetters(schema);
+        // if (isDebugMode) {
+        //     checkProgram(gl, program);
+        // }
 
-        if (isDebugMode) {
-            checkActiveAttributes(gl, program, schema);
-            checkActiveUniforms(gl, program, schema);
-        }
+        // locations = getLocations(gl, program, schema);
+        // uniformSetters = getUniformSetters(schema);
+
+        // if (isDebugMode) {
+        //     checkActiveAttributes(gl, program, schema);
+        //     checkActiveUniforms(gl, program, schema);
+        // }
     }
-    init();
+    link();
 
     let destroyed = false;
 
     return {
         id: programId,
 
+        finalize: () => {
+            if (locations) return;
+            console.log('finalizing', programId)
+            locations = getLocations(gl, program, schema);
+            uniformSetters = getUniformSetters(schema);
+        },
+
         use: () => {
             // console.log('use', programId)
             state.currentProgramId = programId;
@@ -245,7 +255,7 @@ export function createProgram(gl: GLRenderingContext, state: WebGLState, extensi
 
         reset: () => {
             program = getProgram(gl);
-            init();
+            link();
         },
         destroy: () => {
             if (destroyed) return;

src/mol-gl/webgl/render-item.ts

@@ -128,6 +128,26 @@ export function createComputeRenderItem(ctx: WebGLContext, drawMode: DrawMode, s
     return createRenderItem(ctx, drawMode, shaderCode, schema, values, materialId, ComputeRenderVariants, undefined);
 }
 
+export function linkRenderItemProgram<T extends string>(ctx: WebGLContext, shaderCode: ShaderCode, schema: RenderableSchema, values: RenderableValues, renderVariants: T[], transparency: Transparency) {
+
+    // filter out unsupported variants
+    renderVariants = renderVariants.filter(v => {
+        if (v === 'tracing') return !!ctx.extensions.drawBuffers;
+        return true;
+    });
+
+    // TODO: optimize
+    const { defineValues } = splitValues(schema, values);
+
+    for (const rv of renderVariants) {
+        const defs = { ...defineValues, dRenderVariant: ValueCell.create(getRenderVariant(rv, transparency)) };
+        if (schema.dRenderVariant === undefined) {
+            Object.defineProperty(schema, 'dRenderVariant', { value: DefineSpec('string') });
+        }
+        ctx.resources.linkProgram(defs, shaderCode, schema);
+    }
+}
+
 /**
  * Creates a render item
  *

src/mol-gl/webgl/resources.ts

@@ -56,6 +56,7 @@ export interface WebGLResources {
     elements: (array: ElementsType, usageHint?: UsageHint) => ElementsBuffer
     pixelPack: (format: TextureFormat, type: TextureType) => PixelPackBuffer
     framebuffer: () => Framebuffer
+    linkProgram: (defineValues: DefineValues, shaderCode: ShaderCode, schema: RenderableSchema) => Program
     program: (defineValues: DefineValues, shaderCode: ShaderCode, schema: RenderableSchema) => Program
     renderbuffer: (format: RenderbufferFormat, attachment: RenderbufferAttachment, width: number, height: number) => Renderbuffer
     shader: (type: ShaderType, source: string) => Shader
@@ -137,9 +138,15 @@ export function createResources(gl: GLRenderingContext, state: WebGLState, stats
         framebuffer: () => {
             return wrap('framebuffer', createFramebuffer(gl));
         },
-        program: (defineValues: DefineValues, shaderCode: ShaderCode, schema: RenderableSchema) => {
+        linkProgram: (defineValues: DefineValues, shaderCode: ShaderCode, schema: RenderableSchema) => {
             return wrapCached(programCache.get({ defineValues, shaderCode, schema }));
         },
+        program: (defineValues: DefineValues, shaderCode: ShaderCode, schema: RenderableSchema) => {
+            // TODO: create function
+            const linked = wrapCached(programCache.get({ defineValues, shaderCode, schema }));
+            linked.finalize();
+            return linked;
+        },
         renderbuffer: (format: RenderbufferFormat, attachment: RenderbufferAttachment, width: number, height: number) => {
             return wrap('renderbuffer', createRenderbuffer(gl, format, attachment, width, height));
         },

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

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

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

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

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

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

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

@@ -1270,6 +1270,14 @@ namespace Mat4 {
         return Math.sqrt(Math.max(scaleXSq, scaleYSq, scaleZSq));
     }
 
+    export function extractBasis(m: Mat4) {
+        return {
+            x: Vec3.create(m[0], m[1], m[2]),
+            y: Vec3.create(m[4], m[5], m[6]),
+            z: Vec3.create(m[8], m[9], m[10])
+        };
+    }
+
     const xAxis = [1, 0, 0] as unknown as Vec3;
     const yAxis = [0, 1, 0] as unknown as Vec3;
     const zAxis = [0, 0, 1] as unknown as Vec3;

src/mol-math/linear-algebra/3d/minimize-rmsd.ts

@@ -15,7 +15,8 @@ export { MinimizeRmsd };
 namespace MinimizeRmsd {
     export interface Result {
         bTransform: Mat4,
-        rmsd: number
+        rmsd: number,
+        nAlignedElements: number,
     }
 
     export interface Positions { x: ArrayLike<number>, y: ArrayLike<number>, z: ArrayLike<number> }
@@ -33,7 +34,7 @@ namespace MinimizeRmsd {
     }
 
     export function compute(data: Input, result?: MinimizeRmsd.Result) {
-        if (typeof result === 'undefined') result = { bTransform: Mat4.zero(), rmsd: 0.0 };
+        result ??= { bTransform: Mat4.zero(), rmsd: 0.0, nAlignedElements: 0 };
         findMinimalRmsdTransformImpl(new RmsdTransformState(data, result));
         return result;
     }
@@ -170,4 +171,5 @@ function findMinimalRmsdTransformImpl(state: RmsdTransformState): void {
     rmsd = rmsd < 0.0 ? 0.0 : Math.sqrt(rmsd / state.a.x.length);
     makeTransformMatrix(state);
     state.result.rmsd = rmsd;
+    state.result.nAlignedElements = state.a.x.length;
 }

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

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

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

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

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

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

src/mol-model-formats/volume/density-server.ts

@@ -16,7 +16,7 @@ export function volumeFromDensityServerData(source: DensityServer_Data_Database,
     return Task.create<Volume>('Create Volume', async ctx => {
         const { volume_data_3d_info: info, volume_data_3d: values } = source;
         const cell = SpacegroupCell.create(
-            info.spacegroup_number.value(0),
+            info.spacegroup_number.value(0) || 'P 1',
             Vec3.ofArray(info.spacegroup_cell_size.value(0)),
             Vec3.scale(Vec3.zero(), Vec3.ofArray(info.spacegroup_cell_angles.value(0)), Math.PI / 180)
         );

src/mol-model-formats/volume/segmentation.ts

@@ -18,7 +18,7 @@ export function volumeFromSegmentationData(source: Segmentation_Data_Database, p
     return Task.create<Volume>('Create Segmentation Volume', async ctx => {
         const { volume_data_3d_info: info, segmentation_data_3d: values } = source;
         const cell = SpacegroupCell.create(
-            info.spacegroup_number.value(0),
+            info.spacegroup_number.value(0) || 'P 1',
             Vec3.ofArray(info.spacegroup_cell_size.value(0)),
             Vec3.scale(Vec3(), Vec3.ofArray(info.spacegroup_cell_angles.value(0)), Math.PI / 180)
         );

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

@@ -1,39 +1,48 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
 import { PluginContext } from '../../../mol-plugin/context';
+import { PluginState } from '../../../mol-plugin/state';
 import { PluginStateSnapshotManager } from '../../manager/snapshots';
 import { PluginStateAnimation } from '../model';
 
-async function setPartialSnapshot(plugin: PluginContext, entry: PluginStateSnapshotManager.Entry, first = false) {
-    if (entry.snapshot.data) {
-        await plugin.runTask(plugin.state.data.setSnapshot(entry.snapshot.data));
+async function setPartialSnapshot(plugin: PluginContext, entry: Partial<PluginStateSnapshotManager.Entry['snapshot']>, first = false) {
+    if (entry.data) {
+        await plugin.runTask(plugin.state.data.setSnapshot(entry.data));
         // update the canvas3d trackball with the snapshot
-        plugin.canvas3d?.setProps({
-            trackball: entry.snapshot.canvas3d?.props?.trackball
-        });
+        if (entry.canvas3d?.props?.trackball) {
+            plugin.canvas3d?.setProps({
+                trackball: entry.canvas3d?.props?.trackball
+            });
+        }
 
     }
 
-    if (entry.snapshot.camera?.current) {
+    if (entry.camera?.current) {
         plugin.canvas3d?.requestCameraReset({
-            snapshot: entry.snapshot.camera.current,
-            durationMs: first || entry.snapshot.camera.transitionStyle === 'instant'
-                ? 0 : entry.snapshot.camera.transitionDurationInMs,
+            snapshot: entry.camera.current,
+            durationMs: first || entry.camera.transitionStyle === 'instant'
+                ? 0 : entry.camera.transitionDurationInMs,
         });
-    } else if (entry.snapshot.camera?.focus) {
+    } else if (entry.camera?.focus) {
         plugin.managers.camera.focusObject({
-            ...entry.snapshot.camera.focus,
-            durationMs: first || entry.snapshot.camera.transitionStyle === 'instant'
-                ? 0 : entry.snapshot.camera.transitionDurationInMs,
+            ...entry.camera.focus,
+            durationMs: first || entry.camera.transitionStyle === 'instant'
+                ? 0 : entry.camera.transitionDurationInMs,
         });
     }
 }
 
-type State = { totalDuration: number, snapshots: PluginStateSnapshotManager.Entry[], currentIndex: 0 };
+type State = {
+    totalDuration: number,
+    snapshots: PluginStateSnapshotManager.Entry[],
+    currentIndex: number,
+    currentTransitionFrame?: number,
+    isInitial?: boolean,
+};
 
 export const AnimateStateSnapshots = PluginStateAnimation.create({
     name: 'built-in.animate-state-snapshots',
@@ -42,17 +51,17 @@ export const AnimateStateSnapshots = PluginStateAnimation.create({
     params: () => ({}),
     canApply(plugin) {
         const entries = plugin.managers.snapshot.state.entries;
-        if (entries.size < 2) {
-            return { canApply: false, reason: 'At least 2 states required.' };
+        if (entries.size < 1) {
+            return { canApply: false, reason: 'At least 1 state required.' };
         }
         if (entries.some(e => !!e?.snapshot.startAnimation)) {
             return { canApply: false, reason: 'Nested animations not supported.' };
         }
-        return { canApply: plugin.managers.snapshot.state.entries.size > 1 };
+        return { canApply: plugin.managers.snapshot.state.entries.size > 0 };
     },
     setup(_, __, plugin) {
         const pivot = plugin.managers.snapshot.state.entries.get(0)!;
-        setPartialSnapshot(plugin, pivot, true);
+        setPartialSnapshot(plugin, pivot.snapshot, true);
     },
     getDuration: (_, plugin) => {
         return {
@@ -66,7 +75,8 @@ export const AnimateStateSnapshots = PluginStateAnimation.create({
         return {
             totalDuration: snapshots.reduce((a, b) => a + (b.snapshot.durationInMs ?? 0), 0),
             snapshots,
-            currentIndex: 0
+            currentIndex: 0,
+            currentTransitionFrame: 0,
         } as State;
     },
     async apply(animState: State, t, ctx) {
@@ -75,7 +85,9 @@ export const AnimateStateSnapshots = PluginStateAnimation.create({
         }
 
         let ctime = 0, i = 0;
+        let ftime = 0;
         for (const s of animState.snapshots) {
+            ftime = t.current - ctime;
             ctime += s.snapshot.durationInMs ?? 0;
             if (t.current < ctime) {
                 break;
@@ -85,12 +97,114 @@ export const AnimateStateSnapshots = PluginStateAnimation.create({
 
         if (i >= animState.snapshots.length) return { kind: 'finished' };
 
+        const { transition, camera, canvas3d } = animState.snapshots[i].snapshot;
+        const frameIndex = PluginState.getStateTransitionFrameIndex(animState.snapshots[i].snapshot, ftime);
+        if (transition && frameIndex !== undefined) {
+            if (i === animState.currentIndex && frameIndex === animState.currentTransitionFrame) {
+                return { kind: 'skip' };
+            }
+
+            if (frameIndex === 0 || i !== animState.currentIndex) {
+                await setPartialSnapshot(ctx.plugin, {
+                    ...transition.frames[frameIndex],
+                    camera,
+                    canvas3d,
+                });
+            } else {
+                await setPartialSnapshot(ctx.plugin, transition.frames[frameIndex]);
+            }
+
+            return { kind: 'next', state: { ...animState, currentIndex: i, currentAnimationFrame: frameIndex } };
+        }
+
         if (i === animState.currentIndex) {
             return { kind: 'skip' };
         }
 
-        await setPartialSnapshot(ctx.plugin, animState.snapshots[i]);
+        await setPartialSnapshot(ctx.plugin, animState.snapshots[i].snapshot);
+        return { kind: 'next', state: { ...animState, currentIndex: i, currentAnimationFrame: undefined } };
+    }
+});
 
-        return { kind: 'next', state: { ...animState, currentIndex: i } };
+export const AnimateStateSnapshotTransition = PluginStateAnimation.create({
+    name: 'built-in.animate-state-snapshot-transition',
+    display: { name: 'State Snapshot Transition' },
+    isExportable: true,
+    params: () => ({}),
+    canApply(plugin) {
+        const { snapshot } = plugin.managers;
+        const { current } = snapshot;
+
+        if (!current?.snapshot.transition) {
+            return { canApply: false, reason: 'No transition found' };
+        }
+
+        return { canApply: true };
+    },
+    setup(_, __, plugin) {
+        const { current } = plugin.managers.snapshot;
+        if (!current) return;
+        setPartialSnapshot(plugin, current.snapshot.transition?.frames[0] ?? current.snapshot, true);
+    },
+    getDuration: (_, plugin) => {
+        const { current } = plugin.managers.snapshot;
+        if (!current?.snapshot.transition) return { kind: 'fixed', durationMs: 0 };
+
+        if (current.snapshot.transition?.loop) {
+            return { kind: 'infinite' };
+        }
+
+        return {
+            kind: 'fixed',
+            durationMs: PluginState.getStateTransitionDuration(current.snapshot) ?? 0
+        };
+    },
+    initialState: (_, plugin) => {
+        const { current } = plugin.managers.snapshot;
+        if (!current) return;
+
+        return {
+            totalDuration: current.snapshot.transition?.loop ? Number.MAX_VALUE : (PluginState.getStateTransitionDuration(current.snapshot) ?? 0),
+            snapshots: [current],
+            currentIndex: 0,
+            currentTransitionFrame: undefined,
+            isInitial: true,
+        } as State;
+    },
+    async apply(animState: State, t, ctx) {
+        const snapshot = animState.snapshots[0]?.snapshot;
+
+        if (t.current >= animState.totalDuration) {
+            if (snapshot?.transition && animState.isInitial) {
+                const frameIndex = snapshot.transition.frames.length - 1;
+                ctx.plugin.managers.snapshot.setSnapshotAnimationFrame(animState.totalDuration, false);
+                await setPartialSnapshot(ctx.plugin, snapshot.transition.frames[frameIndex]);
+            }
+            return { kind: 'finished' };
+        }
+
+        if (!snapshot) return { kind: 'finished' };
+
+        const { transition, camera, canvas3d } = snapshot;
+        const frameIndex = PluginState.getStateTransitionFrameIndex(snapshot, t.current);
+        if (!transition || frameIndex === undefined) {
+            return { kind: 'finished' };
+        }
+
+        if (frameIndex === animState.currentTransitionFrame) {
+            return { kind: 'skip' };
+        }
+
+        ctx.plugin.managers.snapshot.setSnapshotAnimationFrame(t.current, false);
+        if (frameIndex === 0) {
+            await setPartialSnapshot(ctx.plugin, {
+                ...transition.frames[frameIndex],
+                camera,
+                canvas3d,
+            });
+        } else {
+            await setPartialSnapshot(ctx.plugin, transition.frames[frameIndex]);
+        }
+        return { kind: 'next', state: { ...animState, currentAnimationFrame: frameIndex, isInitial: false } };
     }
 });

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  */
@@ -33,6 +33,10 @@ class PluginAnimationManager extends StatefulPluginComponent<PluginAnimationMana
 
     get animations() { return this._animations; }
 
+    get isAnimatingStateTransition() {
+        return this._current.anim.name === 'built-in.animate-state-snapshot-transition';
+    }
+
     private triggerUpdate() {
         this.events.updated.next(void 0);
     }
@@ -150,6 +154,11 @@ class PluginAnimationManager extends StatefulPluginComponent<PluginAnimationMana
         }
     }
 
+    stopStateTransitionAnimation() {
+        if (!this.isAnimatingStateTransition) return;
+        return this.stop();
+    }
+
     get isAnimating() {
         return this.state.animationState === 'playing';
     }

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

@@ -6,8 +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';
 
@@ -43,6 +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 }) => {
@@ -82,9 +97,141 @@ export const BuiltInMarkdownExtension: MarkdownExtension[] = [
             }
         }
     },
+    {
+        name: 'query',
+        execute: ({ event, args, manager }) => {
+            const expression = args['query'];
+            if (!expression?.length) return;
+
+            // supported languages: mol-script, pymol, vmd, jmol
+            const language = args['lang'] || 'mol-script';
+            // supported actions: highlight, focus
+            const action = parseArray(args['action'] || 'highlight');
+            const focusRadius = parseFloat(args['focus-radius'] || '3');
+
+            if (event === 'mouse-leave') {
+                if (action.includes('highlight')) {
+                    manager.plugin.managers.interactivity.lociHighlights.clearHighlights();
+                }
+                return;
+            }
+
+            let query: QueryFn<StructureSelection>;
+            try {
+                query = Script.toQuery({
+                    language: language as Script.Language,
+                    expression
+                });
+            } catch (e) {
+                console.warn(`Failed to parse query '${expression}' (${language})`, e);
+                return;
+            }
+
+            const structures = manager.plugin.state.data.selectQ(q => q.rootsOfType(PluginStateObject.Molecule.Structure));
+
+            if (event === 'mouse-enter') {
+                if (!action.includes('focus')) {
+                    return;
+                }
+                manager.plugin.managers.interactivity.lociHighlights.clearHighlights();
+                for (const structure of structures) {
+                    if (!structure.obj?.data) continue;
+                    const selection = query(new QueryContext(structure.obj.data));
+                    const loci = StructureSelection.toLociWithSourceUnits(selection);
+                    manager.plugin.managers.interactivity.lociHighlights.highlight({
+                        loci,
+                    }, false);
+                }
+            }
+
+            if (event === 'click') {
+                if (!action.includes('focus')) {
+                    return;
+                }
+                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;
+
+                    const loci = StructureSelection.toLociWithSourceUnits(selection);
+                    return StructureElement.Loci.getBoundary(loci).sphere;
+                }).filter(s => !!s);
+
+                if (spheres.length) {
+                    manager.plugin.managers.camera.focusSpheres(spheres, s => s, { extraRadius: focusRadius });
+                }
+            }
+        },
+    },
+    {
+        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
@@ -218,6 +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

@@ -19,20 +19,32 @@ import { PLUGIN_VERSION } from '../../mol-plugin/version';
 import { canvasToBlob } from '../../mol-canvas3d/util';
 import { Task } from '../../mol-task';
 import { StringLike } from '../../mol-io/common/string-like';
+import { SingleTaskQueue } from '../../mol-util/single-task-queue';
 
 export { PluginStateSnapshotManager };
 
-class PluginStateSnapshotManager extends StatefulPluginComponent<{
-    current?: UUID | undefined,
+interface StateManagerState {
+    current?: UUID,
+    currentAnimationTimeMs?: number,
     entries: List<PluginStateSnapshotManager.Entry>,
     isPlaying: boolean,
     nextSnapshotDelayInMs: number
-}> {
+}
+
+class PluginStateSnapshotManager extends StatefulPluginComponent<StateManagerState> {
     static DefaultNextSnapshotDelayInMs = 1500;
 
     private entryMap = new Map<string, PluginStateSnapshotManager.Entry>();
     private defaultSnapshotId: UUID | undefined = undefined;
 
+    protected updateState(state: Partial<StateManagerState>) {
+        if ('current' in state && !('currentAnimationTimeMs' in state)) {
+            return super.updateState({ ...state, currentAnimationTimeMs: 0 });
+        } else {
+            return super.updateState(state);
+        }
+    }
+
     readonly events = {
         changed: this.ev(),
         opened: this.ev(),
@@ -155,6 +167,26 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<{
         return e && e.snapshot;
     }
 
+    private animationFrameQueue = new SingleTaskQueue();
+    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(() => {
+                return this.plugin.state.setAnimationSnapshot(entry.snapshot, frameIndex ?? 0);
+            });
+        }
+
+        return frameIndex;
+    }
+
     getNextId(id: string | undefined, dir: -1 | 1) {
         const len = this.state.entries.size;
         if (!id) {
@@ -183,11 +215,6 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<{
     }
 
     async setStateSnapshot(snapshot: PluginStateSnapshotManager.StateSnapshot): Promise<PluginState.Snapshot | undefined> {
-        if (snapshot.version !== PLUGIN_VERSION) {
-            // TODO
-            // console.warn('state snapshot version mismatch');
-        }
-
         this.clear();
         const entries = List<PluginStateSnapshotManager.Entry>().asMutable();
         for (const e of snapshot.entries) {
@@ -211,7 +238,7 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<{
         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;
     }
 
@@ -343,10 +370,33 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<{
         if (this.state.isPlaying) this.timeoutHandle = setTimeout(this.next, delay);
     };
 
-    play(delayFirst: boolean = false) {
+    private async startPlayback() {
+        const { current } = this;
+        if (!current) return;
+
+        // If there is a transition associated with the current snapshot, replay it
+        if (current.snapshot.transition) {
+            const snapshot = this.setCurrent(this.state.current!)!;
+            await this.plugin.state.setSnapshot(snapshot);
+            const delay = typeof snapshot.durationInMs !== 'undefined' ? snapshot.durationInMs : this.state.nextSnapshotDelayInMs;
+            if (this.state.isPlaying) this.timeoutHandle = setTimeout(this.next, delay);
+        } else {
+            return this.next();
+        }
+    }
+
+    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();
@@ -357,23 +407,24 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<{
             const delay = typeof snapshot.durationInMs !== 'undefined' ? snapshot.durationInMs : this.state.nextSnapshotDelayInMs;
             this.timeoutHandle = setTimeout(this.next, delay);
         } else {
-            this.next();
+            this.startPlayback();
         }
     }
 
-    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-state/transforms/helpers.ts

@@ -49,18 +49,48 @@ export function getPlaneDataFromStructureSelections(s: ReadonlyArray<PluginState
     return { locis: s.map(v => v.loci) };
 }
 
-export function getTransformFromParams(src:
-    | { name: 'matrix', params: { data: Mat4, transpose?: boolean } }
-    | { name: 'components', params: { translation: Vec3, axis: Vec3, angle: number } }
-) {
+const GetTransformState = {
+    center: Vec3(),
+    rotation: Mat4(),
+    translationToCenter: Mat4(),
+    translationFromCenter: Mat4(),
+    translation: Mat4(),
+    local: Mat4(),
+};
+
+export function transformParamsNeedCentroid(src: TransformParam) {
+    if (src.name === 'components' && src.params.rotationCenter?.name === 'centroid') {
+        return true;
+    }
+    return false;
+}
+
+export function getTransformFromParams(src: TransformParam, centroid: Vec3) {
     if (src.name === 'matrix') {
         const transform = Mat4();
         Mat4.copy(transform, src.params.data);
         if (src.params.transpose) Mat4.transpose(transform, transform);
         return transform;
     } else {
-        const transform = Mat4.fromRotation(Mat4(), src.params.angle * Math.PI / 180, src.params.axis);
-        Mat4.setTranslation(transform, src.params.translation);
+        if (src.params.rotationCenter?.name === 'centroid') {
+            Vec3.copy(GetTransformState.center, centroid);
+        } else if (src.params.rotationCenter?.name === 'point') {
+            Vec3.copy(GetTransformState.center, src.params.rotationCenter.params.point);
+        } else {
+            Vec3.set(GetTransformState.center, 0, 0, 0);
+        }
+
+        Mat4.fromTranslation(GetTransformState.translationToCenter, GetTransformState.center);
+        Mat4.fromRotation(GetTransformState.rotation, src.params.angle * Math.PI / 180, src.params.axis);
+        Mat4.fromTranslation(GetTransformState.translationFromCenter, Vec3.negate(GetTransformState.center, GetTransformState.center));
+        const transform = Mat4.mul3(
+            Mat4(),
+            GetTransformState.translationToCenter,
+            GetTransformState.rotation,
+            GetTransformState.translationFromCenter,
+        );
+        Mat4.fromTranslation(GetTransformState.translation, src.params.translation);
+        Mat4.mul(transform, GetTransformState.translation, transform);
         return transform;
     }
 }
@@ -80,9 +110,15 @@ export const TransformParam = PD.MappedStatic(
                 translation: PD.Vec3(Vec3.create(0, 0, 0)),
                 axis: PD.Vec3(Vec3.create(1, 0, 0)),
                 angle: PD.Numeric(0, { min: -360, max: 360, step: 1 }, { description: 'Angle in Degrees' }),
+                rotationCenter: PD.MappedStatic('point', {
+                    point: PD.Group({ point: PD.Vec3(Vec3.create(0, 0, 0)) }, { isFlat: true }),
+                    centroid: PD.Group({})
+                }),
             },
             { isFlat: true }
         ),
     },
     { label: 'Kind' },
-);
+);
+
+export type TransformParam = (typeof TransformParam)['defaultValue']

src/mol-plugin-state/transforms/model.ts

@@ -55,7 +55,7 @@ import { parseNctraj } from '../../mol-io/reader/nctraj/parser';
 import { coordinatesFromNctraj } from '../../mol-model-formats/structure/nctraj';
 import { topologyFromPrmtop } from '../../mol-model-formats/structure/prmtop';
 import { topologyFromTop } from '../../mol-model-formats/structure/top';
-import { getTransformFromParams, TransformParam } from './helpers';
+import { getTransformFromParams, TransformParam, transformParamsNeedCentroid } from './helpers';
 
 export { CoordinatesFromDcd };
 export { CoordinatesFromXtc };
@@ -225,7 +225,7 @@ const TopologyFromTop = PluginStateTransform.BuiltIn({
     }
 });
 
-async function getTrajectory(ctx: RuntimeContext, obj: StateObject, coordinates: Coordinates) {
+export async function getTrajectory(ctx: RuntimeContext, obj: StateObject, coordinates: Coordinates) {
     if (obj.type === SO.Molecule.Topology.type) {
         const topology = obj.data as Topology;
         return await Model.trajectoryFromTopologyAndCoordinates(topology, coordinates).runInContext(ctx);
@@ -355,7 +355,7 @@ const TrajectoryFromPDB = PluginStateTransform.BuiltIn({
     from: [SO.Data.String],
     to: SO.Molecule.Trajectory,
     params: {
-        isPdbqt: PD.Boolean(false)
+        isPdbqt: PD.Boolean(false),
     }
 })({
     apply({ a, params }) {
@@ -578,7 +578,7 @@ const ModelFromTrajectory = PluginStateTransform.BuiltIn({
     isApplicable: a => a.data.frameCount > 0,
     apply({ a, params }) {
         return Task.create('Model from Trajectory', async ctx => {
-            let modelIndex = params.modelIndex % a.data.frameCount;
+            let modelIndex = Math.round(params.modelIndex) % a.data.frameCount;
             if (modelIndex < 0) modelIndex += a.data.frameCount;
             const model = await Task.resolveInContext(a.data.getFrameAtIndex(modelIndex), ctx);
             const label = `Model ${modelIndex + 1}`;
@@ -644,8 +644,6 @@ const StructureFromModel = PluginStateTransform.BuiltIn({
     }
 });
 
-const _translation = Vec3(), _m = Mat4(), _n = Mat4();
-
 type TransformStructureConformation = typeof TransformStructureConformation
 const TransformStructureConformation = PluginStateTransform.BuiltIn({
     name: 'transform-structure-conformation',
@@ -661,23 +659,8 @@ const TransformStructureConformation = PluginStateTransform.BuiltIn({
         return newParams.transform.name !== 'matrix';
     },
     apply({ a, params }) {
-        // TODO: optimze
-        // TODO: think of ways how to fast-track changes to this for animations
-
-        const transform = Mat4();
-
-        if (params.transform.name === 'components') {
-            const { axis, angle, translation } = params.transform.params;
-            const center = a.data.boundary.sphere.center;
-            Mat4.fromTranslation(_m, Vec3.negate(_translation, center));
-            Mat4.fromTranslation(_n, Vec3.add(_translation, center, translation));
-            const rot = Mat4.fromRotation(Mat4(), Math.PI / 180 * angle, Vec3.normalize(Vec3(), axis));
-            Mat4.mul3(transform, _n, rot, _m);
-        } else if (params.transform.name === 'matrix') {
-            Mat4.copy(transform, params.transform.params.data);
-            if (params.transform.params.transpose) Mat4.transpose(transform, transform);
-        }
-
+        const center = transformParamsNeedCentroid(params.transform) ? a.data.boundary.sphere.center : Vec3.unit;
+        const transform = getTransformFromParams(params.transform, center);
         const s = Structure.transform(a.data, transform);
         return new SO.Molecule.Structure(s, { label: a.label, description: `${a.description} [Transformed]` });
     },
@@ -715,7 +698,8 @@ const StructureInstances = PluginStateTransform.BuiltIn({
         return true;
     },
     apply({ a, params }) {
-        const instances = params.transforms.map(t => getTransformFromParams(t.transform));
+        const center = params.transforms.some(t => transformParamsNeedCentroid(t.transform)) ? a.data.boundary.sphere.center : Vec3.unit;
+        const instances = params.transforms.map(t => getTransformFromParams(t.transform, center));
         if (!instances.length) {
             return a;
         }

src/mol-plugin-state/transforms/volume.ts

@@ -20,7 +20,7 @@ import { Grid, Volume } from '../../mol-model/volume';
 import { PluginContext } from '../../mol-plugin/context';
 import { StateSelection } from '../../mol-state';
 import { volumeFromSegmentationData } from '../../mol-model-formats/volume/segmentation';
-import { getTransformFromParams, TransformParam } from './helpers';
+import { getTransformFromParams, TransformParam, transformParamsNeedCentroid } from './helpers';
 
 export { VolumeFromCcp4 };
 export { VolumeFromDsn6 };
@@ -248,7 +248,8 @@ export const VolumeTransform = PluginStateTransform.BuiltIn({
     },
     apply({ a, params }) {
         // similar to StateTransforms.Model.TransformStructureConformation;
-        const transform = getTransformFromParams(params.transform);
+        const center = transformParamsNeedCentroid(params.transform) ? Grid.getBoundingSphere(a.data.grid).center : Vec3.unit;
+        const transform = getTransformFromParams(params.transform, center);
         const gridTransform = {
             kind: 'matrix' as const,
             matrix: Mat4.mul(Mat4(), transform, Grid.getGridToCartesianTransform(a.data.grid)),
@@ -281,13 +282,14 @@ export const VolumeInstances = PluginStateTransform.BuiltIn({
         return true;
     },
     apply({ a, params }) {
-        const instances = params.transforms.map(t => ({ transform: getTransformFromParams(t.transform) }));
+        const center = params.transforms.some(t => transformParamsNeedCentroid(t.transform)) ? Grid.getBoundingSphere(a.data.grid).center : Vec3.unit;
+        const instances = params.transforms.map(t => ({ transform: getTransformFromParams(t.transform, center) }));
         if (!instances.length) {
             return a;
         }
         return new SO.Volume.Data({
             ...a.data,
-            instances: params.transforms.map(t => ({ transform: getTransformFromParams(t.transform) })),
+            instances,
         }, {
             label: a.label,
             description: `${a.description} [Instanced]`,

src/mol-plugin-ui/context.ts

@@ -11,6 +11,7 @@ import { StateTransformParameters } from './state/common';
 
 export class PluginUIContext extends PluginContext {
     readonly customParamEditors = new Map<string, StateTransformParameters.Class>();
+    readonly customUIState: Record<string, any> = {};
 
     private initCustomParamEditors() {
         if (!this.spec.customParamEditors) return;

src/mol-plugin-ui/controls.tsx

@@ -16,7 +16,7 @@ import { PluginCommands } from '../mol-plugin/commands';
 import { StateTransformer } from '../mol-state';
 import { PluginReactContext, PluginUIComponent } from './base';
 import { IconButton } from './controls/common';
-import { Icon, NavigateBeforeSvg, NavigateNextSvg, SkipPreviousSvg, StopSvg, PlayArrowSvg, SubscriptionsOutlinedSvg, BuildSvg } from './controls/icons';
+import { Icon, NavigateBeforeSvg, NavigateNextSvg, SkipPreviousSvg, StopSvg, PlayArrowSvg, SubscriptionsOutlinedSvg, BuildSvg, AnimationSvg, RefreshSvg } from './controls/icons';
 import { AnimationControls } from './state/animation';
 import { StructureComponentControls } from './structure/components';
 import { StructureMeasurementsControls } from './structure/measurements';
@@ -27,6 +27,9 @@ import { PluginConfig } from '../mol-plugin/config';
 import { StructureSuperpositionControls } from './structure/superposition';
 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: '' };
@@ -59,7 +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}`;
                 }
             }
         }
@@ -102,45 +105,19 @@ export class TrajectoryViewportControls extends PluginUIComponent<{}, { show: bo
     }
 }
 
-export class StateSnapshotViewportControls extends PluginUIComponent<{}, { isBusy: boolean, show: boolean }> {
-    state = { isBusy: false, show: true };
+export class StateSnapshotViewportControls extends PluginUIComponent<{}, { isBusy: boolean, show: boolean, showAnimation: boolean }> {
+    state = { isBusy: false, show: true, showAnimation: false };
 
     componentDidMount() {
-        // TODO: this needs to be diabled when the state is updating!
         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 });
@@ -168,27 +145,65 @@ export class StateSnapshotViewportControls extends PluginUIComponent<{}, { isBus
         this.plugin.managers.snapshot.togglePlay();
     };
 
+    toggleShowAnimation = () => {
+        this.setState({ showAnimation: !this.state.showAnimation });
+    };
+
+    toggleStateAnimation = () => {
+        if (this.state.isBusy) {
+            this.plugin.managers.animation.stop();
+            this.plugin.managers.markdownExtensions.audio.pause();
+        } else {
+            this.plugin.managers.animation.play(AnimateStateSnapshotTransition, {});
+        }
+    };
+
+    get isStateTransitionPlaying() {
+        return this.plugin.managers.animation.isAnimatingStateTransition;
+    }
+
     render() {
         const snapshots = this.plugin.managers.snapshot;
         const count = snapshots.state.entries.size;
 
-        if (count < 2 || !this.state.show) {
+        if (!count || !this.state.show) {
             return null;
         }
 
         const current = snapshots.state.current;
         const isPlaying = snapshots.state.isPlaying;
+        const entry = snapshots.getEntry(current);
+        const hasAnimation = !!entry?.snapshot.transition;
+
+        const disabled = isPlaying || (this.state.isBusy && !this.isStateTransitionPlaying);
 
         return <div className='msp-state-snapshot-viewport-controls'>
-            <select className='msp-form-control' value={current || 'none'} onChange={this.change} disabled={this.state.isBusy || isPlaying}>
+            <select className='msp-form-control' value={current || 'none'} onChange={this.change} disabled={disabled}>
                 {!current && <option key='none' value='none'></option>}
                 {snapshots.state.entries.valueSeq().map((e, i) => <option key={e!.snapshot.id} value={e!.snapshot.id}>{`[${i! + 1}/${count}]`} {e!.name || new Date(e!.timestamp).toLocaleString()}</option>)}
             </select>
             <IconButton svg={isPlaying ? StopSvg : PlayArrowSvg} title={isPlaying ? 'Pause' : 'Cycle States'} onClick={this.togglePlay}
-                disabled={isPlaying ? false : this.state.isBusy} />
+                disabled={isPlaying ? false : (this.state.isBusy && !this.isStateTransitionPlaying)} />
             {!isPlaying && <>
-                <IconButton svg={NavigateBeforeSvg} title='Previous State' onClick={this.prev} disabled={this.state.isBusy || isPlaying} />
-                <IconButton svg={NavigateNextSvg} title='Next State' onClick={this.next} disabled={this.state.isBusy || 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='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={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, true)}
+                        hideInput
+                        disabled={this.state.isBusy}
+                    />
+                    &nbsp;
+                </div>
+                <IconButton svg={this.state.isBusy ? StopSvg : RefreshSvg} title={this.state.isBusy ? 'Stop' : 'Replay'} onClick={this.toggleStateAnimation} toggleState={false} />
             </>}
         </div>;
     }

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -70,6 +70,8 @@ export function AccountTreeOutlinedSvg() { return _AccountTreeOutlined; }
 const _Add = <svg width='24px' height='24px' viewBox='0 0 24 24'><path d='M19 13h-6v6h-2v-6H5v-2h6V5h2v6h6v2z' /></svg>;
 export function AddSvg() { return _Add; }
 const _ArrowDownward = <svg width='24px' height='24px' viewBox='0 0 24 24'><path d='M20 12l-1.41-1.41L13 16.17V4h-2v12.17l-5.58-5.59L4 12l8 8 8-8z' /></svg>;
+export function AnimationSvg() { return _Animation; }
+const _Animation = <svg width='24px' height='24px' viewBox='0 0 24 24'><path d='M15 2c-2.71 0-5.05 1.54-6.22 3.78-1.28.67-2.34 1.72-3 3C3.54 9.95 2 12.29 2 15c0 3.87 3.13 7 7 7 2.71 0 5.05-1.54 6.22-3.78 1.28-.67 2.34-1.72 3-3C20.46 14.05 22 11.71 22 9c0-3.87-3.13-7-7-7M9 20c-2.76 0-5-2.24-5-5 0-1.12.37-2.16 1-3 0 3.87 3.13 7 7 7-.84.63-1.88 1-3 1m3-3c-2.76 0-5-2.24-5-5 0-1.12.37-2.16 1-3 0 3.86 3.13 6.99 7 7-.84.63-1.88 1-3 1m4.7-3.3c-.53.19-1.1.3-1.7.3-2.76 0-5-2.24-5-5 0-.6.11-1.17.3-1.7.53-.19 1.1-.3 1.7-.3 2.76 0 5 2.24 5 5 0 .6-.11 1.17-.3 1.7M19 12c0-3.86-3.13-6.99-7-7 .84-.63 1.87-1 3-1 2.76 0 5 2.24 5 5 0 1.12-.37 2.16-1 3' /></svg>;
 export function ArrowDownwardSvg() { return _ArrowDownward; }
 const _ArrowDropDown = <svg width='24px' height='24px' viewBox='0 0 24 24'><path d='M7 10l5 5 5-5z' /></svg>;
 export function ArrowDropDownSvg() { return _ArrowDropDown; }

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/controls/slider.tsx

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2024 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>
@@ -18,7 +18,8 @@ export class Slider extends React.Component<{
     onChange: (v: number) => void,
     onChangeImmediate?: (v: number) => void,
     disabled?: boolean,
-    onEnter?: () => void
+    onEnter?: () => void,
+    hideInput?: boolean
 }, { isChanging: boolean, current: number }> {
 
     state = { isChanging: false, current: 0 };
@@ -69,7 +70,7 @@ export class Slider extends React.Component<{
     render() {
         let step = this.props.step;
         if (step === void 0) step = 1;
-        return <div className='msp-slider'>
+        return <div className={!this.props.hideInput ? 'msp-slider' : 'msp-slider msp-slider-no-input'}>
             <div>
                 <SliderBase min={this.props.min} max={this.props.max} step={step} value={this.state.current} disabled={this.props.disabled}
                     onBeforeChange={this.begin}

src/mol-plugin-ui/sequence/chain.ts

@@ -47,7 +47,7 @@ export class ChainSequenceWrapper extends SequenceWrapper<StructureUnit> {
         return Interval.Empty;
     }
 
-    getLoci(seqIdx: number) {
+    override getLoci(seqIdx: number) {
         return this.loci;
     }
 

src/mol-plugin-ui/sequence/element.ts

@@ -50,7 +50,7 @@ export class ElementSequenceWrapper extends SequenceWrapper<StructureUnit> {
         return Interval.Empty;
     }
 
-    getLoci(seqIdx: number) {
+    override getLoci(seqIdx: number) {
         const { units } = this.data;
         const lociElements: StructureElement.Loci['elements'][0][] = [];
         let offset = 0;

src/mol-plugin-ui/sequence/hetero.ts

@@ -53,7 +53,7 @@ export class HeteroSequenceWrapper extends SequenceWrapper<StructureUnit> {
         return Interval.Empty;
     }
 
-    getLoci(seqIdx: number) {
+    override getLoci(seqIdx: number) {
         const elements: StructureElement.Loci['elements'][0][] = [];
         const rI = this.residueIndices.get(seqIdx);
         if (rI !== undefined) {

src/mol-plugin-ui/sequence/polymer.ts

@@ -67,7 +67,7 @@ export class PolymerSequenceWrapper extends SequenceWrapper<StructureUnit> {
         return Interval.Empty;
     }
 
-    getLoci(seqIdx: number) {
+    override getLoci(seqIdx: number) {
         const query = createResidueQuery(this.data.units[0].chainGroupId, this.data.units[0].conformation.operator.name, this.seqId(seqIdx));
         return StructureSelection.toLociWithSourceUnits(StructureQuery.run(query, this.data.structure));
     }

src/mol-plugin-ui/sequence/sequence.tsx

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2024 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>
@@ -7,16 +7,21 @@
  */
 
 import * as React from 'react';
-import { Subject } from 'rxjs';
+import { BehaviorSubject, Subject } from 'rxjs';
 import { throttleTime } from 'rxjs/operators';
 import { OrderedSet } from '../../mol-data/int';
+import { ColorTypeLocation } from '../../mol-geo/geometry/color-data';
 import { EveryLoci } from '../../mol-model/loci';
 import { StructureElement, StructureProperties, Unit } from '../../mol-model/structure';
 import { PluginCommands } from '../../mol-plugin/commands';
+import { PluginContext } from '../../mol-plugin/context';
 import { Representation } from '../../mol-repr/representation';
+import { Task } from '../../mol-task';
+import { ColorTheme, LocationColor } from '../../mol-theme/color';
 import { Color } from '../../mol-util/color';
 import { ButtonsType, getButton, getButtons, getModifiers, ModifiersKeys } from '../../mol-util/input/input-observer';
 import { MarkerAction } from '../../mol-util/marker-action';
+import { memoizeLatest } from '../../mol-util/memoize';
 import { PluginUIComponent } from '../base';
 import { SequenceWrapper } from './wrapper';
 
@@ -36,12 +41,19 @@ const DefaultMarkerColors = {
     focused: '',
 };
 
+type ColorThemeProvider = ColorTheme.Provider<any, string, ColorTypeLocation> | undefined
+
+
 // TODO: this is somewhat inefficient and should be done using a canvas.
 export class Sequence<P extends SequenceProps> extends PluginUIComponent<P> {
     protected parentDiv = React.createRef<HTMLDivElement>();
     protected lastMouseOverSeqIdx = -1;
     protected highlightQueue = new Subject<{ seqIdx: number, buttons: number, button: number, modifiers: ModifiersKeys }>();
     protected markerColors = { ...DefaultMarkerColors };
+    /** @experimental */
+    private customColorThemeWrapper: ColorThemeWrapper | undefined = undefined;
+    /** @experimental Custom function that assigns color to residues in the Sequence component (unless highlighted or selected) */
+    private customColorFunction: ((idx: number) => string) | undefined = undefined;
 
     protected lociHighlightProvider = (loci: Representation.Loci, action: MarkerAction) => {
         const changed = this.props.sequenceWrapper.markResidue(loci.loci, action);
@@ -81,6 +93,14 @@ export class Sequence<P extends SequenceProps> extends PluginUIComponent<P> {
             this.updateColors();
             this.updateMarker();
         });
+        const experimentalSequenceColorTheme: BehaviorSubject<ColorThemeProvider> | undefined = this.plugin.customUIState.experimentalSequenceColorTheme;
+        if (experimentalSequenceColorTheme) {
+            this.subscribe(experimentalSequenceColorTheme, theme => {
+                if (!theme && !this.customColorThemeWrapper) return;
+                this.customColorThemeWrapper = ColorThemeWrapper(this.plugin, theme, () => this.forceUpdate());
+                this.forceUpdate();
+            });
+        }
     }
 
     updateColors() {
@@ -199,9 +219,12 @@ export class Sequence<P extends SequenceProps> extends PluginUIComponent<P> {
 
     protected getBackgroundColor(seqIdx: number) {
         const seqWrapper = this.props.sequenceWrapper;
-        if (seqWrapper.isHighlighted(seqIdx)) return this.markerColors.highlighted;
-        if (seqWrapper.isSelected(seqIdx)) return this.markerColors.selected;
-        if (seqWrapper.isFocused(seqIdx)) return this.markerColors.focused;
+        if (seqWrapper.isHighlighted(seqIdx) && this.markerColors.highlighted) return this.markerColors.highlighted;
+        if (seqWrapper.isSelected(seqIdx) && this.markerColors.selected) return this.markerColors.selected;
+        if (seqWrapper.isFocused(seqIdx) && this.markerColors.focused) return this.markerColors.focused;
+        if (this.customColorFunction) {
+            return this.customColorFunction(seqIdx);
+        }
         return '';
     }
 
@@ -322,9 +345,12 @@ export class Sequence<P extends SequenceProps> extends PluginUIComponent<P> {
 
     render() {
         const sw = this.props.sequenceWrapper;
-
         const elems: JSX.Element[] = [];
 
+        if (this.customColorThemeWrapper) {
+            this.customColorFunction = this.customColorThemeWrapper.getColorFunction(sw);
+        }
+
         const hasNumbers = !this.props.hideSequenceNumbers, period = this.sequenceNumberPeriod;
         for (let i = 0, il = sw.length; i < il; ++i) {
             const label = sw.residueLabel(i);
@@ -355,3 +381,57 @@ export class Sequence<P extends SequenceProps> extends PluginUIComponent<P> {
         </div>;
     }
 }
+
+
+type ColorThemeWrapper = ReturnType<typeof ColorThemeWrapper>
+
+function ColorThemeWrapper(plugin: PluginContext, theme: ColorThemeProvider, forceUpdate: () => void) {
+    const tmpLocation = StructureElement.Location.create();
+
+    function computeColor(sequenceWrapper: SequenceWrapper.Any, idx: number, locationColor: LocationColor) {
+        const loci = sequenceWrapper.getLoci(idx);
+        if (!loci || StructureElement.Loci.isEmpty(loci)) return '';
+        StructureElement.Loci.getFirstLocation(loci, tmpLocation);
+        const color = locationColor(tmpLocation, false);
+        if (color < 0) return ''; // Color(-1) is used as special value NoColor
+        return Color.toHexStyle(color);
+    }
+
+    const getColorFunction = memoizeLatest((sequenceWrapper: SequenceWrapper.Any) => {
+        if (!theme) return undefined;
+        const structure = sequenceWrapper.getLoci(0)?.structure;
+        if (!structure) return undefined;
+
+        let themeColor: LocationColor | undefined = undefined;
+        if (theme.ensureCustomProperties) {
+            // The following task runs asynchronously
+            plugin.runTask(Task.create('Attach custom properties for coloring theme', async runtime => {
+                try {
+                    await theme.ensureCustomProperties?.attach({ assetManager: plugin.managers.asset, runtime }, { structure });
+                } catch (err) {
+                    console.warn(`Failed to attach custom properties needed for coloring theme ${theme.name}:`, err);
+                } finally {
+                    themeColor = theme.factory({ structure }, theme.defaultValues).color;
+                    forceUpdate();
+                }
+            }));
+        } else {
+            themeColor = theme.factory({ structure }, theme.defaultValues).color;
+        }
+
+        const cache: { [idx: number]: string } = {};
+
+        return (idx: number) => {
+            if (themeColor) { // custom properties ready
+                return cache[idx] ??= computeColor(sequenceWrapper, idx, themeColor);
+            } else { // custom properties not ready
+                return '';
+            }
+        };
+    });
+
+    return {
+        themeName: theme?.name,
+        getColorFunction,
+    };
+}

src/mol-plugin-ui/skin/base/components/controls.scss

@@ -133,6 +133,16 @@
             bottom: 0;
         }
 
+        &-no-input {
+            > div:first-child {
+                right: 18px;
+            }
+            > div:last-child {
+                visibility: hidden;
+                width: 0;
+            }
+        }
+
         input[type=text] {
             padding-right: 6px;
             padding-left: 4px;

src/mol-plugin-ui/skin/base/components/misc.scss

@@ -454,6 +454,17 @@
             }
         }
 
+        .msp-state-snapshot-animation-slider {
+            position: relative;
+            display: inline-block;
+            width: 120px;
+            line-height: $row-height;
+        }
+
+        .msp-state-snapshot-animation-button {
+            margin-left: $control-spacing;
+        }
+
         .msp-animation-viewport-controls {
             line-height: $row-height;
             float: left;
@@ -475,6 +486,7 @@
                 left: 0;
                 margin-top: $control-spacing;
                 background: $control-background;
+                z-index: 10001;
 
                 .msp-control-row:first-child {
                     margin-top: 0;

src/mol-plugin-ui/viewport.tsx

@@ -96,30 +96,32 @@ export class ViewportControls extends PluginUIComponent<ViewportControlsProps, V
     render() {
         return <div className={'msp-viewport-controls'}>
             <div className='msp-viewport-controls-buttons'>
-                <div className='msp-hover-box-wrapper'>
-                    <div className='msp-semi-transparent-background' />
-                    {this.icon(AutorenewSvg, this.resetCamera, 'Reset Zoom')}
-                    <div className='msp-hover-box-body'>
-                        <div className='msp-flex-column'>
-                            <div className='msp-flex-row'>
-                                <Button onClick={() => this.resetCamera()} disabled={!this.state.isCameraResetEnabled} title='Set camera zoom to fit the visible scene into view'>
-                                    Reset Zoom
-                                </Button>
-                            </div>
-                            <div className='msp-flex-row'>
-                                <Button onClick={() => PluginCommands.Camera.OrientAxes(this.plugin)} disabled={!this.state.isCameraResetEnabled} title='Align principal component axes of the loaded structures to the screen axes (“lay flat”)'>
-                                    Orient Axes
-                                </Button>
-                            </div>
-                            <div className='msp-flex-row'>
-                                <Button onClick={() => PluginCommands.Camera.ResetAxes(this.plugin)} disabled={!this.state.isCameraResetEnabled} title='Align Cartesian axes to the screen axes'>
-                                    Reset Axes
-                                </Button>
+                {this.plugin.config.get(PluginConfig.Viewport.ShowReset) &&
+                    <div className='msp-hover-box-wrapper'>
+                        <div className='msp-semi-transparent-background' />
+                        {this.icon(AutorenewSvg, this.resetCamera, 'Reset Zoom')}
+                        <div className='msp-hover-box-body'>
+                            <div className='msp-flex-column'>
+                                <div className='msp-flex-row'>
+                                    <Button onClick={() => this.resetCamera()} disabled={!this.state.isCameraResetEnabled} title='Set camera zoom to fit the visible scene into view'>
+                                        Reset Zoom
+                                    </Button>
+                                </div>
+                                <div className='msp-flex-row'>
+                                    <Button onClick={() => PluginCommands.Camera.OrientAxes(this.plugin)} disabled={!this.state.isCameraResetEnabled} title='Align principal component axes of the loaded structures to the screen axes (“lay flat”)'>
+                                        Orient Axes
+                                    </Button>
+                                </div>
+                                <div className='msp-flex-row'>
+                                    <Button onClick={() => PluginCommands.Camera.ResetAxes(this.plugin)} disabled={!this.state.isCameraResetEnabled} title='Align Cartesian axes to the screen axes'>
+                                        Reset Axes
+                                    </Button>
+                                </div>
                             </div>
                         </div>
+                        <div className='msp-hover-box-spacer'></div>
                     </div>
-                    <div className='msp-hover-box-spacer'></div>
-                </div>
+                }
                 {this.plugin.config.get(PluginConfig.Viewport.ShowScreenshotControls) && <div>
                     <div className='msp-semi-transparent-background' />
                     {this.icon(CameraOutlinedSvg, this.toggleScreenshotExpanded, 'Screenshot / State Snapshot', this.state.isScreenshotExpanded)}

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} />