tweaks

CHANGELOG.md

@@ -5,43 +5,18 @@ Note that since we don't clearly distinguish between a public and private interf
 
 ## [Unreleased]
 
-## [v4.11.0] - 2025-01-26
-
-- Fix for tubular helices issue (Fixes #1422)
 - Volume UI improvements
-    - Render all volume entries instead of selecting them one-by-one
-    - Toggle visibility of all volumes
-    - More accessible iso value control
+  - Render all volume entries instead of selecting them one-by-one
+  - Toggle visibility of all volumes
+  - More accessible iso value control
 - Support wheel event on sliders
 - MolViewSpec extension:
-    - Add validation for discriminated union params
-    - Primitives: remove triangle_colors, line_colors, have implicit grouping instead; rename many parameters
-- UI configuration options
-    - Support removal of independent selection controls in the viewport
-    - Support custom selection controls
-    - Support for custom granularity dropdown options
-    - Support for custom Sequence Viewer mode options
+  - Add validation for discriminated union params
+  - Primitives: remove triangle_colors, line_colors, have implicit grouping instead; rename many parameters
 - Add `external-structure` theme that colors any geometry by structure properties
 - Support float and half-float data type for direct-volume rendering and GPU isosurface extraction
 - Minor documentation updates
-- Add support for position-location to `volume-value` color theme
-- Add support for color themes to `slice` representation
-- Improve/fix palette support in volume color themes
-- Fix `Plane3D.projectPoint`
-- Fix marking related image rendering issues
-    - Handle pixels without a group
-    - Take fog into account
-- MolViewSpec extension: Initial support for customizable representation parameters
-- Quick Styles section reorganized
-- UI color improvements (scrollbar contrast, toggle button hover color)
-- Add `overrideWater` param for entity-id color theme
-- Renames PDB-Dev to PDB-IHM and adjusts data source
-- Fix vertex based themes for spheres shader
-- Add volume dot representation
-- Add volume-value size theme
-- Sequence panel: Mark focused loci (bold+underline)
-- Change modifier key behavior in Normal Mode (default = select only, Ctrl/Cmd = add to selection, Shift = extend last selected range)
-- Handle Firefox's limit on vertex ids per draw (#1116)
+- Fix plugin mouse interactions when CSS `scale` transform is applied
 
 ## [v4.10.0] - 2024-12-15
 
@@ -109,7 +84,7 @@ Note that since we don't clearly distinguish between a public and private interf
 - Fix `findPredecessorIndex` bug when repeating values
 - MolViewSpec: Support for transparency and custom properties
 - MolViewSpec: MVP Support for geometrical primitives (mesh, lines, line, label, distance measurement)
-- Mesoscale Explorer: Add support for 4-character PDB IDs (e.g., 8ZZC) in PDB-IHM/PDB-Dev loader
+- Mesoscale Explorer: Add support for 4-character PDB IDs (e.g., 8ZZC) in PDB-Dev loader
 - Fix Sequence View in Safari 18
 - Improve performance of `IndexPairBonds` assignment when operator keys are available
 - ModelArchive QualityAssessment extension:
@@ -162,7 +137,7 @@ Note that since we don't clearly distinguish between a public and private interf
 - Improve entity-id coloring for structures with multiple models from the same source (#1221)
 - Wrap screenshot & image generation in a `Task`
 - AlphaFold DB: Add BinaryCIF support when fetching data
-- PDB-IHM/PDB-Dev: Add support for 4-character PDB IDs (e.g., 8ZZC)
+- PDB-Dev: Add support for 4-character PDB IDs (e.g., 8ZZC)
 - Fix polymer-gap visual coloring with cartoon theme
 - Add formal-charge color theme (#328)
 - Add more coloring options to cartoon theme

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "4.11.0",
+  "version": "4.10.0",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -114,8 +114,7 @@
     "Eric E <etongfu@outlook.com>",
     "Xavier Martinez <xavier.martinez.xm@gmail.com>",
     "Alex Chan <smalldirkalex@gmail.com>",
-    "Simeon Borko <simeon.borko@gmail.com>",
-    "Ventura Rivera <venturaxrivera@gmail.com>"
+    "Simeon Borko <simeon.borko@gmail.com>"
   ],
   "license": "MIT",
   "devDependencies": {
@@ -123,19 +122,19 @@
     "@types/gl": "^6.0.5",
     "@types/jest": "^29.5.14",
     "@types/pngjs": "^6.0.5",
-    "@types/react": "^18.3.18",
+    "@types/react": "^18.3.16",
     "@types/react-dom": "^18.3.5",
     "@typescript-eslint/eslint-plugin": "^7.18.0",
     "@typescript-eslint/parser": "^7.18.0",
     "benchmark": "^2.1.4",
-    "concurrently": "^9.1.2",
+    "concurrently": "^9.1.0",
     "cpx2": "^8.0.0",
     "crypto-browserify": "^3.12.1",
     "css-loader": "^7.1.2",
     "eslint": "^8.57.1",
     "extra-watch-webpack-plugin": "^1.0.3",
     "file-loader": "^6.2.0",
-    "fs-extra": "^11.3.0",
+    "fs-extra": "^11.2.0",
     "http-server": "^14.1.1",
     "jest": "^29.7.0",
     "jpeg-js": "^0.4.4",
@@ -144,22 +143,22 @@
     "raw-loader": "^4.0.2",
     "react": "^18.3.1",
     "react-dom": "^18.3.1",
-    "sass": "^1.83.4",
+    "sass": "^1.83.0",
     "sass-loader": "^16.0.4",
     "simple-git": "^3.27.0",
     "stream-browserify": "^3.0.0",
     "style-loader": "^4.0.0",
     "ts-jest": "^29.2.5",
-    "typescript": "^5.7.3",
+    "typescript": "^5.7.2",
     "webpack": "^5.97.1",
-    "webpack-cli": "^6.0.1"
+    "webpack-cli": "^5.1.4"
   },
   "dependencies": {
     "@types/argparse": "^2.0.17",
     "@types/benchmark": "^2.1.5",
     "@types/compression": "1.7.5",
     "@types/express": "^5.0.0",
-    "@types/node": "^18.19.74",
+    "@types/node": "^18.19.68",
     "@types/node-fetch": "^2.6.12",
     "@types/swagger-ui-dist": "3.30.5",
     "argparse": "^2.0.1",
@@ -171,11 +170,11 @@
     "immutable": "^5.0.3",
     "io-ts": "^2.2.22",
     "node-fetch": "^2.7.0",
-    "react-markdown": "^9.0.3",
+    "react-markdown": "^9.0.1",
     "rxjs": "^7.8.1",
     "swagger-ui-dist": "^5.18.2",
     "tslib": "^2.8.1",
-    "util.promisify": "^1.1.3",
+    "util.promisify": "^1.1.2",
     "xhr2": "^0.2.1"
   },
   "peerDependencies": {

src/apps/mesoscale-explorer/app.ts

@@ -25,7 +25,7 @@ import { MesoFocusLoci } from './behavior/camera';
 import { GraphicsMode, MesoscaleState } from './data/state';
 import { MesoSelectLoci } from './behavior/select';
 import { Transparency } from '../../mol-gl/webgl/render-item';
-import { LoadModel, loadExampleEntry, loadPdb, loadPdbIhm, loadUrl, openState } from './ui/states';
+import { LoadModel, loadExampleEntry, loadPdb, loadPdbDev, loadUrl, openState } from './ui/states';
 import { Asset } from '../../mol-util/assets';
 import { AnimateCameraSpin } from '../../mol-plugin-state/animation/built-in/camera-spin';
 import { AnimateCameraRock } from '../../mol-plugin-state/animation/built-in/camera-rock';
@@ -120,15 +120,8 @@ export class MesoscaleExplorer {
         await loadPdb(this.plugin, id);
     }
 
-    /**
-     * @deprecated Scheduled for removal in v5. Use {@link loadPdbIhm | loadPdbIhm(id: string)} instead.
-     */
     async loadPdbDev(id: string) {
-        await this.loadPdbIhm(id);
-    }
-
-    async loadPdbIhm(id: string) {
-        await loadPdbIhm(this.plugin, id);
+        await loadPdbDev(this.plugin, id);
     }
 
     static async create(elementOrId: string | HTMLElement, options: Partial<MesoscaleExplorerOptions> = {}) {

src/apps/mesoscale-explorer/index.html

@@ -93,15 +93,9 @@
                     return;
                 }
 
-                var pdbihm = getParam('pdbihm', '[^&]+').trim();
-                if (pdbihm) {
-                    me.loadPdbIhm(pdbihm);
-                    return;
-                }
-                // support for deprecated pdb-dev param
                 var pdbdev = getParam('pdbdev', '[^&]+').trim();
                 if (pdbdev) {
-                    me.loadPdbIhm(pdbdev);
+                    me.loadPdbDev(pdbdev);
                     return;
                 }
                 window.addEventListener('unload', () => {

src/apps/mesoscale-explorer/ui/states.tsx

@@ -211,15 +211,15 @@ export async function loadPdb(ctx: PluginContext, id: string) {
     await createHierarchy(ctx, data.ref);
 }
 
-export async function loadPdbIhm(ctx: PluginContext, id: string) {
+export async function loadPdbDev(ctx: PluginContext, id: string) {
     await reset(ctx);
     let url: string;
     // 4 character PDB id, TODO: support extended PDB ID
     if (id.match(/^[1-9][A-Z0-9]{3}$/i) !== null) {
-        url = `https://pdb-ihm.org/bcif/${id.toLowerCase()}.bcif`;
+        url = `https://pdb-dev.wwpdb.org/bcif/${id.toLowerCase()}.bcif`;
     } else {
         const nId = id.toUpperCase().startsWith('PDBDEV_') ? id : `PDBDEV_${id.padStart(8, '0')}`;
-        url = `https://pdb-ihm.org/bcif/${nId.toUpperCase()}.bcif`;
+        url = `https://pdb-dev.wwpdb.org/bcif/${nId.toUpperCase()}.bcif`;
     }
     const data = await ctx.builders.data.download({ url, isBinary: true });
     await createHierarchy(ctx, data.ref);
@@ -231,7 +231,7 @@ export const LoadDatabase = StateAction.build({
     display: { name: 'Database', description: 'Load from Database' },
     params: (a, ctx: PluginContext) => {
         return {
-            source: PD.Select('pdb', PD.objectToOptions({ pdb: 'PDB', pdbIhm: 'PDB-IHM' })),
+            source: PD.Select('pdb', PD.objectToOptions({ pdb: 'PDB', pdbDev: 'PDB-Dev' })),
             entry: PD.Text(''),
         };
     },
@@ -239,8 +239,8 @@ export const LoadDatabase = StateAction.build({
 })(({ params }, ctx: PluginContext) => Task.create('Loading from database...', async taskCtx => {
     if (params.source === 'pdb') {
         await loadPdb(ctx, params.entry);
-    } else if (params.source === 'pdbIhm') {
-        await loadPdbIhm(ctx, params.entry);
+    } else if (params.source === 'pdbDev') {
+        await loadPdbDev(ctx, params.entry);
     }
 }));
 
@@ -426,7 +426,7 @@ export class ExplorerInfo extends PluginUIComponent<{}, { isDisabled: boolean, s
         driver.setSteps([
             // Left panel
             { element: '#explorerinfo', popover: { title: 'Explorer Header Info', description: 'This section displays the explorer header with version information, documentation access, and tour navigation. Use the right and left arrow keys to navigate the tour.', side: 'left', align: 'start' } },
-            { element: '#database', popover: { title: 'Import from PDB', description: 'Load structures directly from PDB and PDB-IHM databases.', side: 'bottom', align: 'start' } },
+            { element: '#database', popover: { title: 'Import from PDB', description: 'Load structures directly from PDB and PDB-DEV databases.', side: 'bottom', align: 'start' } },
             { element: '#loader', popover: { title: 'Import from File', description: 'Load local files (.molx, .molj, .zip, .cif, .bcif) using this option.', side: 'bottom', align: 'start' } },
             { element: '#example', popover: { title: 'Example Models and Tours', description: 'Select from a range of example models and tours provided.', side: 'left', align: 'start' } },
             { element: '#session', popover: { title: 'Session Management', description: 'Download the current session in .molx format.', side: 'top', align: 'start' } },

src/apps/viewer/app.ts

@@ -288,21 +288,14 @@ export class Viewer {
         }));
     }
 
-    /**
-     * @deprecated Scheduled for removal in v5. Use {@link loadPdbIhm | loadPdbIhm(pdbIhm: string)} instead.
-     */
     loadPdbDev(pdbDev: string) {
-        return this.loadPdbIhm(pdbDev);
-    }
-
-    loadPdbIhm(pdbIhm: string) {
         const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
         return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
             source: {
-                name: 'pdb-ihm' as const,
+                name: 'pdb-dev' as const,
                 params: {
                     provider: {
-                        id: pdbIhm,
+                        id: pdbDev,
                         encoding: 'bcif',
                     },
                     options: params.source.params.options,

src/apps/viewer/index.html

@@ -111,11 +111,8 @@
                 var pdb = getParam('pdb', '[^&]+').trim();
                 if (pdb) viewer.loadPdb(pdb);
 
-                var pdbIhm = getParam('pdb-ihm', '[^&]+').trim();
-                if (pdbIhm) viewer.loadPdbIhm(pdbIhm);
-                // support for deprecated pdb-dev param
                 var pdbDev = getParam('pdb-dev', '[^&]+').trim();
-                if (pdbDev) viewer.loadPdbIhm(pdbDev);
+                if (pdbDev) viewer.loadPdbDev(pdbDev);
 
                 var emdb = getParam('emdb', '[^&]+').trim();
                 if (emdb) viewer.loadEmdb(emdb);

src/extensions/mvs/load-helpers.ts

@@ -285,21 +285,19 @@ export function componentFromXProps(node: MolstarNode<'component_from_uri' | 'co
 /** Create props for `StructureRepresentation3D` transformer from a representation node. */
 export function representationProps(node: MolstarSubtree<'representation'>): Partial<StateTransformer.Params<StructureRepresentation3D>> {
     const alpha = alphaForNode(node);
-    const params = node.params;
-    switch (params.type) {
+    switch (node.params.type) {
         case 'cartoon':
             return {
-                type: { name: 'cartoon', params: { alpha, tubularHelices: params.tubular_helices } },
-                sizeTheme: { name: 'uniform', params: { value: params.size_factor } },
+                type: { name: 'cartoon', params: { alpha } },
             };
         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 } },
+                type: { name: 'ball-and-stick', params: { sizeFactor: 0.5, sizeAspectRatio: 0.5, alpha } },
             };
         case 'surface':
             return {
-                type: { name: 'molecular-surface', params: { alpha, ignoreHydrogens: params.ignore_hydrogens } },
-                sizeTheme: { name: 'physical', params: { scale: params.size_factor } },
+                type: { name: 'molecular-surface', params: { alpha } },
+                sizeTheme: { name: 'physical', params: { scale: 1 } },
             };
         default:
             throw new Error('NotImplementedError');

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

@@ -1,39 +0,0 @@
-/**
- * Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import { bool, float, OptionalField } from '../generic/field-schema';
-import { SimpleParamsSchema, UnionParamsSchema } from '../generic/params-schema';
-
-const Cartoon = {
-    /** Scales the corresponding visuals */
-    size_factor: OptionalField(float, 1, 'Scales the corresponding visuals.'),
-    /** Simplify corkscrew helices to tubes. */
-    tubular_helices: OptionalField(bool, false, 'Simplify corkscrew helices to tubes.'),
-};
-
-const BallAndStick = {
-    /** 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 Surface = {
-    /** 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.'),
-};
-
-export const MVSRepresentationParams = UnionParamsSchema(
-    'type',
-    'Representation type',
-    {
-        cartoon: SimpleParamsSchema(Cartoon),
-        ball_and_stick: SimpleParamsSchema(BallAndStick),
-        surface: SimpleParamsSchema(Surface),
-    },
-);

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2023-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2023-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Adam Midlik <midlik@gmail.com>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -8,9 +8,8 @@
 import { float, int, list, literal, nullable, OptionalField, RequiredField, str, tuple, union } from '../generic/field-schema';
 import { SimpleParamsSchema } from '../generic/params-schema';
 import { NodeFor, ParamsOfKind, SubtreeOfKind, TreeFor, TreeSchema, TreeSchemaWithAllRequired } from '../generic/tree-schema';
-import { MVSRepresentationParams } from './mvs-tree-representations';
 import { MVSPrimitiveParams } from './mvs-tree-primitives';
-import { ColorT, ComponentExpressionT, ComponentSelectorT, Matrix, ParseFormatT, SchemaFormatT, SchemaT, StrList, StructureTypeT, Vector3 } from './param-types';
+import { ColorT, ComponentExpressionT, ComponentSelectorT, Matrix, ParseFormatT, RepresentationTypeT, SchemaFormatT, SchemaT, StrList, StructureTypeT, Vector3 } from './param-types';
 
 
 const _DataFromUriParams = {
@@ -143,7 +142,10 @@ export const MVSTreeSchema = TreeSchema({
         representation: {
             description: 'This node instructs to create a visual representation of a component.',
             parent: ['component', 'component_from_uri', 'component_from_source'],
-            params: MVSRepresentationParams,
+            params: SimpleParamsSchema({
+                /** Method of visual representation of the component. */
+                type: RequiredField(RepresentationTypeT, 'Method of visual representation of the component.'),
+            }),
         },
         /** This node instructs to apply color to a visual representation. */
         color: {

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

@@ -45,6 +45,9 @@ export const ComponentExpressionT = iots.partial({
 });
 export type ComponentExpressionT = ValueFor<typeof ComponentExpressionT>
 
+/** `type` parameter values for `representation` node in MVS tree */
+export const RepresentationTypeT = literal('ball_and_stick', 'cartoon', 'surface');
+
 /** `schema` parameter values for `*_from_uri` and `*_from_source` nodes in MVS tree */
 export const SchemaT = literal('whole_structure', 'entity', 'chain', 'auth_chain', 'residue', 'auth_residue', 'residue_range', 'auth_residue_range', 'atom', 'auth_atom', 'all_atomic');
 

src/mol-canvas3d/canvas3d.ts

@@ -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>
@@ -392,6 +392,8 @@ namespace Canvas3D {
         let y = 0;
         let width = 128;
         let height = 128;
+        let canvasScaleRatioX = 1;
+        let canvasScaleRatioY = 1;
 
         let forceNextRender = false;
         let currentTime = 0;
@@ -645,7 +647,7 @@ namespace Canvas3D {
 
         function identify(x: number, y: number): PickData | undefined {
             const cam = p.camera.stereo.name === 'on' ? stereoCamera : camera;
-            return webgl.isContextLost ? undefined : pickHelper.identify(x, y, cam);
+            return webgl.isContextLost ? undefined : pickHelper.identify(x / canvasScaleRatioX, y / canvasScaleRatioY, cam);
         }
 
         function commit(isSynchronous: boolean = false) {
@@ -1158,6 +1160,12 @@ namespace Canvas3D {
         function updateViewport() {
             const oldX = x, oldY = y, oldWidth = width, oldHeight = height;
 
+            const canvasRect = canvas?.getBoundingClientRect();
+            canvasScaleRatioX = (canvasRect?.width ?? gl.drawingBufferWidth) / gl.drawingBufferWidth;
+            if (!canvasScaleRatioX) canvasScaleRatioX = 1;
+            canvasScaleRatioY = (canvasRect?.height ?? gl.drawingBufferHeight) / gl.drawingBufferHeight;
+            if (!canvasScaleRatioY) canvasScaleRatioY = 1;
+
             if (p.viewport.name === 'canvas') {
                 x = 0;
                 y = 0;
@@ -1184,7 +1192,7 @@ namespace Canvas3D {
             pickHelper.setViewport(x, y, width, height);
             renderer.setViewport(x, y, width, height);
             Viewport.set(camera.viewport, x, y, width, height);
-            Viewport.set(controls.viewport, x, y, width, height);
+            Viewport.set(controls.viewport, x, y, width * canvasScaleRatioX, height * canvasScaleRatioY);
             hiZ.setViewport(x, y, width, height);
         }
     }

src/mol-geo/geometry/color-data.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 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>
@@ -24,7 +24,6 @@ export type ColorData = {
     uColor: ValueCell<Vec3>,
     tColor: ValueCell<TextureImage<Uint8Array>>,
     tColorGrid: ValueCell<Texture>,
-    uPaletteDomain: ValueCell<Vec2>,
     tPalette: ValueCell<TextureImage<Uint8Array>>,
     uColorTexDim: ValueCell<Vec2>,
     uColorGridDim: ValueCell<Vec3>,
@@ -37,8 +36,6 @@ export function createColors(locationIt: LocationIterator, positionIt: LocationI
     const data = _createColors(locationIt, positionIt, colorTheme, colorData);
     if (colorTheme.palette) {
         ValueCell.updateIfChanged(data.dUsePalette, true);
-        const [min, max] = colorTheme.palette.domain || [0, 1];
-        ValueCell.update(data.uPaletteDomain, Vec2.set(data.uPaletteDomain.ref.value, min, max));
         updatePaletteTexture(colorTheme.palette, data.tPalette);
     } else {
         ValueCell.updateIfChanged(data.dUsePalette, false);
@@ -106,7 +103,6 @@ export function createValueColor(value: Color, colorData?: ColorData): ColorData
             uColor: ValueCell.create(Color.toVec3Normalized(Vec3(), value)),
             tColor: ValueCell.create({ array: new Uint8Array(3), width: 1, height: 1 }),
             tColorGrid: ValueCell.create(createNullTexture()),
-            uPaletteDomain: ValueCell.create(Vec2.create(0, 1)),
             tPalette: ValueCell.create({ array: new Uint8Array(3), width: 1, height: 1 }),
             uColorTexDim: ValueCell.create(Vec2.create(1, 1)),
             uColorGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
@@ -135,7 +131,6 @@ export function createTextureColor(colors: TextureImage<Uint8Array>, type: Color
             uColor: ValueCell.create(Vec3()),
             tColor: ValueCell.create(colors),
             tColorGrid: ValueCell.create(createNullTexture()),
-            uPaletteDomain: ValueCell.create(Vec2.create(0, 1)),
             tPalette: ValueCell.create({ array: new Uint8Array(3), width: 1, height: 1 }),
             uColorTexDim: ValueCell.create(Vec2.create(colors.width, colors.height)),
             uColorGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
@@ -238,7 +233,6 @@ export function createGridColor(grid: ColorVolume, type: ColorType, colorData?:
             uColor: ValueCell.create(Vec3()),
             tColor: ValueCell.create({ array: new Uint8Array(3), width: 1, height: 1 }),
             tColorGrid: ValueCell.create(colors),
-            uPaletteDomain: ValueCell.create(Vec2.create(0, 1)),
             tPalette: ValueCell.create({ array: new Uint8Array(3), width: 1, height: 1 }),
             uColorTexDim: ValueCell.create(Vec2.create(width, height)),
             uColorGridDim: ValueCell.create(Vec3.clone(dimension)),
@@ -261,7 +255,6 @@ function createDirectColor(colorData?: ColorData): ColorData {
             uColor: ValueCell.create(Vec3()),
             tColor: ValueCell.create({ array: new Uint8Array(3), width: 1, height: 1 }),
             tColorGrid: ValueCell.create(createNullTexture()),
-            uPaletteDomain: ValueCell.create(Vec2.create(0, 1)),
             tPalette: ValueCell.create({ array: new Uint8Array(3), width: 1, height: 1 }),
             uColorTexDim: ValueCell.create(Vec2.create(1, 1)),
             uColorGridDim: ValueCell.create(Vec3.create(1, 1, 1)),

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

@@ -1,25 +0,0 @@
-/**
- * Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { Vec3, Mat4 } from '../../../../mol-math/linear-algebra';
-import { SegmentedPlane } from '../../../primitive/plane';
-import { MeshBuilder } from '../mesh-builder';
-
-const tmpPlaneMat = Mat4.identity();
-const tmpVec = Vec3();
-
-function setPlaneMat(m: Mat4, center: Vec3, dirMajor: Vec3, dirMinor: Vec3, scale: Vec3) {
-    Vec3.add(tmpVec, center, dirMajor);
-    Mat4.targetTo(m, center, tmpVec, dirMinor);
-    Mat4.setTranslation(m, center);
-    Mat4.mul(m, m, Mat4.rotY90);
-    return Mat4.scale(m, m, scale);
-}
-
-export function addPlane(state: MeshBuilder.State, center: Vec3, dirMajor: Vec3, dirMinor: Vec3, scale: Vec3, widthSegments: number, heightSegments: number) {
-    const plane = SegmentedPlane(widthSegments, heightSegments);
-    MeshBuilder.addPrimitive(state, setPlaneMat(tmpPlaneMat, center, dirMajor, dirMinor, scale), plane);
-}

src/mol-geo/primitive/plane.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -37,53 +37,4 @@ export function Plane(): Primitive {
 
 export function PlaneCage(): Cage {
     return planeCage;
-}
-
-//
-
-export function SegmentedPlane(widthSegments: number, heightSegments: number): Primitive {
-    const widthSegments1 = widthSegments + 1;
-    const heightSegments1 = heightSegments + 1;
-
-    const segmentWidth = 1 / widthSegments;
-    const segmentHeight = 1 / heightSegments;
-
-    const vertices = new Float32Array(widthSegments1 * heightSegments1 * 3);
-    const normals = new Float32Array(widthSegments1 * heightSegments1 * 3);
-    const indices = new Uint32Array(widthSegments * heightSegments * 6);
-
-    let i = 0;
-    for (let iy = 0; iy < heightSegments1; ++iy) {
-        const y = iy * segmentHeight - 0.5;
-        for (let ix = 0; ix < widthSegments1; ++ix) {
-            const x = ix * segmentWidth - 0.5;
-            vertices[i] = x;
-            vertices[i + 1] = -y;
-            vertices[i + 2] = 0;
-            normals[i] = 0;
-            normals[i + 1] = 0;
-            normals[i + 2] = 1;
-            i += 3;
-        }
-    }
-
-    let j = 0;
-    for (let iy = 0; iy < heightSegments; ++iy) {
-        for (let ix = 0; ix < widthSegments; ++ix) {
-            const a = ix + widthSegments1 * iy;
-            const b = ix + widthSegments1 * (iy + 1);
-            const c = (ix + 1) + widthSegments1 * (iy + 1);
-            const d = (ix + 1) + widthSegments1 * iy;
-
-            indices[j] = a;
-            indices[j + 1] = b;
-            indices[j + 2] = d;
-            indices[j + 3] = b;
-            indices[j + 4] = c;
-            indices[j + 5] = d;
-            j += 6;
-        }
-    }
-
-    return { vertices, normals, indices };
-}
+}

src/mol-gl/renderable/schema.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Gianluca Tomasello <giagitom@gmail.com>
@@ -203,7 +203,6 @@ export const ColorSchema = {
     uColorTexDim: UniformSpec('v2'),
     uColorGridDim: UniformSpec('v3'),
     uColorGridTransform: UniformSpec('v4'),
-    uPaletteDomain: UniformSpec('v2'),
     tColor: TextureSpec('image-uint8', 'rgb', 'ubyte', 'nearest'),
     tPalette: TextureSpec('image-uint8', 'rgb', 'ubyte', 'nearest'),
     tColorGrid: TextureSpec('texture', 'rgb', 'ubyte', 'linear'),

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

@@ -29,9 +29,9 @@ export const assign_color_varying = `
             vColor.rgb = readFromTexture(tColor, aInstance * float(uGroupCount) + group, uColorTexDim).rgb;
         #endif
     #elif defined(dColorType_vertex)
-        vColor.rgb = readFromTexture(tColor, vertexId, uColorTexDim).rgb;
+        vColor.rgb = readFromTexture(tColor, VertexID, uColorTexDim).rgb;
     #elif defined(dColorType_vertexInstance)
-        vColor.rgb = readFromTexture(tColor, int(aInstance) * uVertexCount + vertexId, uColorTexDim).rgb;
+        vColor.rgb = readFromTexture(tColor, int(aInstance) * uVertexCount + VertexID, uColorTexDim).rgb;
     #elif defined(dColorType_volume)
         vec3 cgridPos = (uColorGridTransform.w * (position - uColorGridTransform.xyz)) / uColorGridDim;
         vColor.rgb = texture3dFrom2dLinear(tColorGrid, cgridPos, uColorGridDim, uColorTexDim).rgb;
@@ -50,7 +50,7 @@ export const assign_color_varying = `
         #elif defined(dOverpaintType_groupInstance)
             vOverpaint = readFromTexture(tOverpaint, aInstance * float(uGroupCount) + group, uOverpaintTexDim);
         #elif defined(dOverpaintType_vertexInstance)
-            vOverpaint = readFromTexture(tOverpaint, int(aInstance) * uVertexCount + vertexId, uOverpaintTexDim);
+            vOverpaint = readFromTexture(tOverpaint, int(aInstance) * uVertexCount + VertexID, uOverpaintTexDim);
         #elif defined(dOverpaintType_volumeInstance)
             vec3 ogridPos = (uOverpaintGridTransform.w * (vModelPosition - uOverpaintGridTransform.xyz)) / uOverpaintGridDim;
             vOverpaint = texture3dFrom2dLinear(tOverpaintGrid, ogridPos, uOverpaintGridDim, uOverpaintTexDim);
@@ -71,7 +71,7 @@ export const assign_color_varying = `
         #elif defined(dEmissiveType_groupInstance)
             vEmissive = readFromTexture(tEmissive, aInstance * float(uGroupCount) + group, uEmissiveTexDim).a;
         #elif defined(dEmissiveType_vertexInstance)
-            vEmissive = readFromTexture(tEmissive, int(aInstance) * uVertexCount + vertexId, uEmissiveTexDim).a;
+            vEmissive = readFromTexture(tEmissive, int(aInstance) * uVertexCount + VertexID, uEmissiveTexDim).a;
         #elif defined(dEmissiveType_volumeInstance)
             vec3 egridPos = (uEmissiveGridTransform.w * (vModelPosition - uEmissiveGridTransform.xyz)) / uEmissiveGridDim;
             vEmissive = texture3dFrom2dLinear(tEmissiveGrid, egridPos, uEmissiveGridDim, uEmissiveTexDim).a;
@@ -85,7 +85,7 @@ export const assign_color_varying = `
         #elif defined(dSubstanceType_groupInstance)
             vSubstance = readFromTexture(tSubstance, aInstance * float(uGroupCount) + group, uSubstanceTexDim);
         #elif defined(dSubstanceType_vertexInstance)
-            vSubstance = readFromTexture(tSubstance, int(aInstance) * uVertexCount + vertexId, uSubstanceTexDim);
+            vSubstance = readFromTexture(tSubstance, int(aInstance) * uVertexCount + VertexID, uSubstanceTexDim);
         #elif defined(dSubstanceType_volumeInstance)
             vec3 sgridPos = (uSubstanceGridTransform.w * (vModelPosition - uSubstanceGridTransform.xyz)) / uSubstanceGridDim;
             vSubstance = texture3dFrom2dLinear(tSubstanceGrid, sgridPos, uSubstanceGridDim, uSubstanceTexDim);
@@ -102,7 +102,7 @@ export const assign_color_varying = `
         #elif defined(dEmissiveType_groupInstance)
             vEmissive = readFromTexture(tEmissive, aInstance * float(uGroupCount) + group, uEmissiveTexDim).a;
         #elif defined(dEmissiveType_vertexInstance)
-            vEmissive = readFromTexture(tEmissive, int(aInstance) * uVertexCount + vertexId, uEmissiveTexDim).a;
+            vEmissive = readFromTexture(tEmissive, int(aInstance) * uVertexCount + VertexID, uEmissiveTexDim).a;
         #elif defined(dEmissiveType_volumeInstance)
             vec3 egridPos = (uEmissiveGridTransform.w * (vModelPosition - uEmissiveGridTransform.xyz)) / uEmissiveGridDim;
             vEmissive = texture3dFrom2dLinear(tEmissiveGrid, egridPos, uEmissiveGridDim, uEmissiveTexDim).a;
@@ -131,7 +131,7 @@ export const assign_color_varying = `
     #elif defined(dTransparencyType_groupInstance)
         vTransparency = readFromTexture(tTransparency, aInstance * float(uGroupCount) + group, uTransparencyTexDim).a;
     #elif defined(dTransparencyType_vertexInstance)
-        vTransparency = readFromTexture(tTransparency, int(aInstance) * uVertexCount + vertexId, uTransparencyTexDim).a;
+        vTransparency = readFromTexture(tTransparency, int(aInstance) * uVertexCount + VertexID, uTransparencyTexDim).a;
     #elif defined(dTransparencyType_volumeInstance)
         vec3 tgridPos = (uTransparencyGridTransform.w * (vModelPosition - uTransparencyGridTransform.xyz)) / uTransparencyGridDim;
         vTransparency = texture3dFrom2dLinear(tTransparencyGrid, tgridPos, uTransparencyGridDim, uTransparencyTexDim).a;

src/mol-gl/shader/chunks/assign-group.glsl.ts

@@ -1,6 +1,6 @@
 export const assign_group = `
 #ifdef dGeometryType_textureMesh
-    float group = unpackRGBToInt(readFromTexture(tGroup, vertexId, uGeoTexDim).rgb);
+    float group = unpackRGBToInt(readFromTexture(tGroup, VertexID, uGeoTexDim).rgb);
 #else
     float group = aGroup;
 #endif

src/mol-gl/shader/chunks/assign-position.glsl.ts

@@ -2,7 +2,7 @@ export const assign_position = `
 mat4 model = uModel * aTransform;
 mat4 modelView = uView * model;
 #ifdef dGeometryType_textureMesh
-    vec3 position = readFromTexture(tPosition, vertexId, uGeoTexDim).xyz;
+    vec3 position = readFromTexture(tPosition, VertexID, uGeoTexDim).xyz;
 #else
     vec3 position = aPosition;
 #endif

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -38,8 +38,6 @@ uniform float uIsOrtho;
 uniform vec3 uCameraDir;
 
 void main() {
-    int vertexId = VertexID;
-
     #include assign_group
     #include assign_color_varying
     #include assign_marker_varying

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Michael Krone <michael.krone@uni-tuebingen.de>
@@ -122,7 +122,6 @@ uniform mat4 uCartnToUnit;
 #endif
 
 #ifdef dUsePalette
-    uniform vec2 uPaletteDomain;
     uniform sampler2D tPalette;
 #endif
 
@@ -272,8 +271,7 @@ vec4 raymarch(vec3 startLoc, vec3 step, vec3 rayDir) {
         #endif
 
         #if defined(dColorType_direct) && defined(dUsePalette)
-            float paletteValue = (value - uPaletteDomain[0]) / (uPaletteDomain[1] - uPaletteDomain[0]);
-            material.rgb = texture2D(tPalette, vec2(clamp(paletteValue, 0.0, 1.0), 0.0)).rgb;
+            material.rgb = texture2D(tPalette, vec2(value, 0.0)).rgb;
         #elif defined(dColorType_uniform)
             material.rgb = uColor;
         #elif defined(dColorType_instance)

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -25,10 +25,6 @@ uniform sampler2D tMarker;
 varying vec2 vUv;
 varying float vInstance;
 
-#ifdef dUsePalette
-    uniform sampler2D tPalette;
-#endif
-
 #if defined(dInterpolation_catmulrom) || defined(dInterpolation_mitchell) || defined(dInterpolation_bspline)
     #define dInterpolation_cubic
 #endif
@@ -94,19 +90,6 @@ varying float vInstance;
     }
 #endif
 
-#if defined(dNeedsMarker)
-    float getMarker() {
-        if (uMarker != -1.0) return uMarker;
-
-        vec3 packedGroup = texture2D(tGroupTex, vUv).rgb;
-        if (packedGroup == vec3(0.0)) return 0.0;
-
-        float group = unpackRGBToInt(packedGroup);
-        float marker = readFromTexture(tMarker, vInstance * float(uGroupCount) + group, uMarkerTexDim).a;
-        return floor(marker * 255.0 + 0.5); // rounding required to work on some cards on win
-    }
-#endif
-
 void main() {
     #include fade_lod
     #include clip_pixel
@@ -116,9 +99,12 @@ void main() {
     #else
         vec4 imageData = texture2D(tImageTex, vUv);
     #endif
-    if (imageData.a < 0.5) discard;
+    imageData.a = clamp(imageData.a, 0.0, 1.0);
+    if (imageData.a > 0.9) imageData.a = 1.0;
 
-    imageData.a = uAlpha;
+    imageData.a *= uAlpha;
+    if (imageData.a < 0.05)
+        discard;
 
     float fragmentDepth = gl_FragCoord.z;
 
@@ -129,7 +115,8 @@ void main() {
     }
 
     #if defined(dRenderVariant_pick)
-        #include check_picking_alpha
+        if (imageData.a < 0.3)
+            discard;
         #ifdef requiredDrawBuffers
             gl_FragColor = vec4(packIntToRGB(float(uObjectId)), 1.0);
             gl_FragData[1] = vec4(packIntToRGB(vInstance), 1.0);
@@ -146,41 +133,46 @@ void main() {
             }
         #endif
     #elif defined(dRenderVariant_depth)
+        if (imageData.a < 0.05)
+            discard;
         if (uRenderMask == MaskOpaque) {
             gl_FragColor = packDepthToRGBA(fragmentDepth);
         } else if (uRenderMask == MaskTransparent) {
             gl_FragColor = packDepthWithAlphaToRGBA(fragmentDepth, imageData.a);
         }
     #elif defined(dRenderVariant_marking)
-        float marker = getMarker();
+        float marker = uMarker;
+        if (uMarker == -1.0) {
+            float group = unpackRGBToInt(texture2D(tGroupTex, vUv).rgb);
+            marker = readFromTexture(tMarker, vInstance * float(uGroupCount) + group, uMarkerTexDim).a;
+            marker = floor(marker * 255.0 + 0.5); // rounding required to work on some cards on win
+        }
         if (uMarkingType == 1) {
-            if (marker > 0.0)
+            if (marker > 0.0 || imageData.a < 0.05)
                 discard;
             gl_FragColor = packDepthToRGBA(fragmentDepth);
         } else {
-            if (marker == 0.0)
+            if (marker == 0.0 || imageData.a < 0.05)
                 discard;
             float depthTest = 1.0;
             if (uMarkingDepthTest) {
                 depthTest = (fragmentDepth >= getDepthPacked(gl_FragCoord.xy / uDrawingBufferSize)) ? 1.0 : 0.0;
             }
             bool isHighlight = intMod(marker, 2.0) > 0.1;
-            float viewZ = depthToViewZ(uIsOrtho, fragmentDepth, uNear, uFar);
-            float fogFactor = smoothstep(uFogNear, uFogFar, abs(viewZ));
-            if (fogFactor == 1.0)
-                discard;
-            gl_FragColor = vec4(0.0, depthTest, isHighlight ? 1.0 : 0.0, 1.0 - fogFactor);
+            gl_FragColor = vec4(0.0, depthTest, isHighlight ? 1.0 : 0.0, 1.0);
         }
     #elif defined(dRenderVariant_emissive)
         gl_FragColor = vec4(0.0);
     #elif defined(dRenderVariant_color) || defined(dRenderVariant_tracing)
-        #ifdef dUsePalette
-            float v = ((imageData.r * 256.0 * 256.0 * 255.0 + imageData.g * 256.0 * 255.0 + imageData.b * 255.0) - 1.0) / 16777215.0;
-            imageData.rgb = texture2D(tPalette, vec2(v, 0.0)).rgb;
-        #endif
         gl_FragColor = imageData;
 
-        float marker = getMarker();
+        float marker = uMarker;
+        if (uMarker == -1.0) {
+            float group = unpackRGBToInt(texture2D(tGroupTex, vUv).rgb);
+            marker = readFromTexture(tMarker, vInstance * float(uGroupCount) + group, uMarkerTexDim).a;
+            marker = floor(marker * 255.0 + 0.5); // rounding required to work on some cards on win
+        }
+
         #include apply_marker_color
 
         #if defined(dRenderVariant_color)

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -19,8 +19,6 @@ varying vec2 vUv;
 varying float vInstance;
 
 void main() {
-    int vertexId = VertexID;
-
     #include assign_position
 
     vUv = aUv;

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  *
@@ -40,7 +40,6 @@ void trimSegment(const in vec4 start, inout vec4 end) {
 
 void main(){
     float aspect = uViewport.z / uViewport.w;
-    int vertexId = VertexID;
 
     #include assign_group
     #include assign_color_varying

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -32,8 +32,6 @@ attribute float aInstance;
 varying vec3 vNormal;
 
 void main(){
-    int vertexId = VertexID;
-
     #include assign_group
     #include assign_marker_varying
     #include assign_clipping_varying
@@ -42,7 +40,7 @@ void main(){
     #include clip_instance
 
     #ifdef dGeometryType_textureMesh
-        vec3 normal = readFromTexture(tNormal, vertexId, uGeoTexDim).xyz;
+        vec3 normal = readFromTexture(tNormal, VertexID, uGeoTexDim).xyz;
     #else
         vec3 normal = aNormal;
     #endif

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -24,8 +24,6 @@ attribute float aInstance;
 attribute float aGroup;
 
 void main(){
-    int vertexId = VertexID;
-
     #include assign_group
     #include assign_color_varying
     #include assign_marker_varying

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -70,9 +70,7 @@ void main(void){
         mapping = vec2(1.0, -1.0);
     }
 
-    int vertexId = VertexID / 6;
-
-    vec4 positionGroup = readFromTexture(tPositionGroup, vertexId, uTexDim);
+    vec4 positionGroup = readFromTexture(tPositionGroup, VertexID / 6, uTexDim);
     vec3 position = positionGroup.rgb;
     float group = positionGroup.a;
 

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -38,8 +38,6 @@ varying vec2 vTexCoord;
 #include matrix_scale
 
 void main(void){
-    int vertexId = VertexID;
-
     #include assign_group
     #include assign_color_varying
     #include assign_marker_varying

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Gianluca Tomasello <giagitom@gmail.com>
@@ -21,10 +21,6 @@ import { fillSerial } from '../../mol-util/array';
 import { deepClone } from '../../mol-util/object';
 import { cloneUniformValues, UniformsList } from './uniform';
 
-// Handle Firefox's preference [webgl.max-vert-ids-per-draw] which defaults to 30_000_000
-// since FF119, see https://bugzilla.mozilla.org/show_bug.cgi?id=1849433
-const MaxDrawCount = 30_000_000;
-
 const getNextRenderItemId = idFactory();
 
 export type DrawMode = 'points' | 'lines' | 'line-strip' | 'line-loop' | 'triangles' | 'triangle-strip' | 'triangle-fan'
@@ -315,16 +311,10 @@ export function createRenderItem<T extends string>(ctx: WebGLContext, drawMode:
                     }
                 }
             } else {
-                let offset = 0;
-                while (true) {
-                    const count = Math.min(drawCount - offset, MaxDrawCount);
-                    if (elementsBuffer) {
-                        instancedArrays.drawElementsInstanced(glDrawMode, count, elementsBuffer._dataType, offset * elementsBuffer._bpe, instanceCount);
-                    } else {
-                        instancedArrays.drawArraysInstanced(glDrawMode, offset, count, instanceCount);
-                    }
-                    offset += count;
-                    if (offset >= drawCount) break;
+                if (elementsBuffer) {
+                    instancedArrays.drawElementsInstanced(glDrawMode, drawCount, elementsBuffer._dataType, 0, instanceCount);
+                } else {
+                    instancedArrays.drawArraysInstanced(glDrawMode, 0, drawCount, instanceCount);
                 }
                 if (isTimingMode) {
                     stats.calls.drawInstanced += 1;

src/mol-gl/webgl/uniform.ts

@@ -1,10 +1,10 @@
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { Mat3, Mat4, Quat, Vec2, Vec3, Vec4 } from '../../mol-math/linear-algebra';
+import { Mat3, Mat4, Vec2, Vec3, Vec4 } from '../../mol-math/linear-algebra';
 import { ValueCell } from '../../mol-util';
 import { GLRenderingContext } from './compat';
 import { RenderableSchema } from '../../mol-gl/renderable/schema';
@@ -18,7 +18,6 @@ export type UniformKindValue = {
     'v2': Vec2; 'v2[]': number[]
     'v3': Vec3; 'v3[]': number[]
     'v4': Vec4; 'v4[]': number[]
-    'q': Quat; 'q[]': number[]
     'iv2': Vec2; 'iv2[]': number[]
     'iv3': Vec3; 'iv3[]': number[]
     'iv4': Vec4; 'iv4[]': number[]
@@ -40,7 +39,6 @@ export function getUniformType(gl: GLRenderingContext, kind: UniformKind) {
         case 'v2': case 'v2[]': return gl.FLOAT_VEC2;
         case 'v3': case 'v3[]': return gl.FLOAT_VEC3;
         case 'v4': case 'v4[]': return gl.FLOAT_VEC4;
-        case 'q': case 'q[]': return gl.FLOAT_VEC4;
         case 'iv2': case 'iv2[]': return gl.INT_VEC2;
         case 'iv3': case 'iv3[]': return gl.INT_VEC3;
         case 'iv4': case 'iv4[]': return gl.INT_VEC4;
@@ -79,7 +77,6 @@ function getUniformSetter(kind: UniformKind): UniformSetter {
         case 'v2': case 'v2[]': return uniform2fv;
         case 'v3': case 'v3[]': return uniform3fv;
         case 'v4': case 'v4[]': return uniform4fv;
-        case 'q': case 'q[]': return uniform4fv;
         case 'iv2': case 'iv2[]': return uniform2iv;
         case 'iv3': case 'iv3[]': return uniform3iv;
         case 'iv4': case 'iv4[]': return uniform4iv;
@@ -110,7 +107,6 @@ export function getUniformGlslType(kind: UniformKind): string {
         case 'v2': return 'vec2';
         case 'v3': return 'vec3';
         case 'v4': return 'vec4';
-        case 'q': return 'vec4';
         case 'm3': return 'mat3';
         case 'm4': return 'mat4';
     }

src/mol-io/reader/cif/schema/bird.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.401, IHM 1.27, MA 1.4.7.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.399, IHM 1.27, MA 1.4.6.
  *
  * @author molstar/ciftools package
  */

src/mol-io/reader/cif/schema/ccd.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.401, IHM 1.27, MA 1.4.7.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.399, IHM 1.27, MA 1.4.6.
  *
  * @author molstar/ciftools package
  */

src/mol-io/reader/cif/schema/mmcif.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.401, IHM 1.27, MA 1.4.7.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.399, IHM 1.27, MA 1.4.6.
  *
  * @author molstar/ciftools package
  */
@@ -705,7 +705,7 @@ export const mmCIF_Schema = {
         /**
          * An abbreviation that identifies the database.
          */
-        database_id: Aliased<'alphafolddb' | 'cas' | 'csd' | 'emdb' | 'icsd' | 'modelarchive' | 'mdf' | 'modbase' | 'ndb' | 'nbs' | 'pdb' | 'pdb-dev' | 'pdf' | 'rcsb' | 'swiss-model_repository' | 'ebi' | 'pdbe' | 'bmrb' | 'wwpdb' | 'pdb_acc'>(lstr),
+        database_id: Aliased<'alphafolddb' | 'cas' | 'csd' | 'emdb' | 'icsd' | 'modelarchive' | 'mdf' | 'modbase' | 'ndb' | 'nbs' | 'pdb' | 'pdf' | 'rcsb' | 'swiss-model_repository' | 'ebi' | 'pdbe' | 'bmrb' | 'wwpdb' | 'pdb_acc'>(lstr),
         /**
          * The code assigned by the database identified in
          * _database_2.database_id.
@@ -884,7 +884,7 @@ export const mmCIF_Schema = {
          * (DT) for Thymidine-5'-monophosphate
          * (MSE) for Selenomethionine
          * (SEP) for Phosphoserine
-         * (TPO) for Phosphothreonine
+         * (PTO) for Phosphothreonine
          * (PTR) for Phosphotyrosine
          * (PCA) for Pyroglutamic acid
          * (UNK) for Unknown amino acid
@@ -2098,7 +2098,7 @@ export const mmCIF_Schema = {
         /**
          * The name of the database containing the related entry.
          */
-        db_name: Aliased<'BIOISIS' | 'BMCD' | 'BMRB' | 'EMDB' | 'NDB' | 'PDB' | 'PDB-Dev' | 'SASBDB' | 'TargetDB' | 'TargetTrack'>(str),
+        db_name: str,
         /**
          * A description of the related entry.
          */
@@ -4939,19 +4939,25 @@ export const mmCIF_Schema = {
      */
     ma_model_list: {
         /**
-         * A unique identifier for the structural model being deposited.
+         * A unique identifier for the model / model group combination.
          */
         ordinal_id: int,
         /**
          * A unique identifier for the structural model being deposited.
-         * This data item was practically a duplicate of _ma_model_list.ordinal_id
-         * and has been deprecated with dictionary version 1.4.7.
          */
         model_id: int,
         /**
          * An identifier to group structural models into collections or sets.
-         * This data item has been deprecated with dictionary version 1.4.7.
-         * See ma_model_group category.
+         * A cluster of models and its representative can either be grouped together
+         * or can be separate groups in the ma_model_list table. The choice between
+         * the two options should be decided based on how the modeling was carried out
+         * and how the representative was chosen. If the representative is a member of
+         * the ensemble (i.e., best scoring model), then it is recommended that the
+         * representative and the ensemble belong to the same model group. If the
+         * representative is calculated from the ensemble (i.e., centroid), then it is
+         * recommended that the representative be separated into a different group.
+         * If the models do not need to be grouped into collections, then the
+         * _ma_model_list.model_group_id is the same as _ma_model_list.model_id.
          */
         model_group_id: int,
         /**
@@ -4960,8 +4966,6 @@ export const mmCIF_Schema = {
         model_name: str,
         /**
          * A decsriptive name for the model group.
-         * This data item has been deprecated with dictionary version 1.4.7.
-         * See ma_model_group category.
          */
         model_group_name: str,
         /**
@@ -5127,11 +5131,11 @@ export const mmCIF_Schema = {
         /**
          * The type of QA metric.
          */
-        type: Aliased<'zscore' | 'energy' | 'distance' | 'normalized score' | 'pLDDT' | 'pLDDT in [0,1]' | 'pLDDT all-atom' | 'pLDDT all-atom in [0,1]' | 'pLDDT to polymer' | 'PAE' | 'pTM' | 'ipTM' | 'contact probability' | 'boolean' | 'other'>(str),
+        type: Aliased<'zscore' | 'energy' | 'distance' | 'normalized score' | 'pLDDT' | 'pLDDT in [0,1]' | 'pLDDT all-atom' | 'pLDDT all-atom in [0,1]' | 'PAE' | 'pTM' | 'ipTM' | 'contact probability' | 'other'>(str),
         /**
          * The mode of calculation of the QA metric.
          */
-        mode: Aliased<'local' | 'global' | 'local-pairwise' | 'per-feature' | 'per-feature-pair'>(str),
+        mode: Aliased<'local' | 'global' | 'local-pairwise'>(str),
         /**
          * Identifier to the set of software used to calculate the QA metric.
          * This data item is a pointer to the _ma_software_group.group_id in the
@@ -5150,7 +5154,7 @@ export const mmCIF_Schema = {
         ordinal_id: int,
         /**
          * The identifier for the structural model, for which global QA metric is provided.
-         * This data item is a pointer to _ma_model_list.ordinal_id
+         * This data item is a pointer to _ma_model_list.model_id
          * in the MA_MODEL_LIST category.
          */
         model_id: int,
@@ -5168,10 +5172,6 @@ export const mmCIF_Schema = {
     /**
      * Data items in the MA_QA_METRIC_LOCAL category captures the
      * details of the local QA metrics, calculated at the residue-level.
-     * Data in this category can be extracted into a separate file which
-     * is linked to the main file using the categories
-     * ma_associated_archive_file_details or ma_entry_associated_files
-     * with file_content set to "QA metrics".
      */
     ma_qa_metric_local: {
         /**
@@ -5180,7 +5180,7 @@ export const mmCIF_Schema = {
         ordinal_id: int,
         /**
          * The identifier for the structural model, for which local QA metric is provided.
-         * This data item is a pointer to _ma_model_list.ordinal_id
+         * This data item is a pointer to _ma_model_list.model_id
          * in the MA_MODEL_LIST category.
          */
         model_id: int,
@@ -5219,15 +5219,6 @@ export const mmCIF_Schema = {
     /**
      * Data items in the MA_QA_METRIC_LOCAL_PAIRWISE category captures the
      * details of the local QA metrics, calculated at the pairwise residue level.
-     * In cases where the metric is symmetric, it is enough to store just one value per pair.
-     * For asymmetric metrics, the order of residues is expected to be meaningful
-     * (e.g. PAE where PAE_ij is defined by aligning residue i (label_*_1) and measuring
-     * the error on residue j (label_*_2)).
-     * In all cases, it is perfectly valid to only provide values for a subset of residue pairs.
-     * Data in this category is expected to be very large and can be extracted into a
-     * separate file which is linked to the main file using the categories
-     * ma_associated_archive_file_details or ma_entry_associated_files with file_content
-     * set to "QA metrics".
      */
     ma_qa_metric_local_pairwise: {
         /**
@@ -5236,7 +5227,7 @@ export const mmCIF_Schema = {
         ordinal_id: int,
         /**
          * The identifier for the structural model, for which local QA metric is provided.
-         * This data item is a pointer to _ma_model_list.ordinal_id
+         * This data item is a pointer to _ma_model_list.model_id
          * in the MA_MODEL_LIST category.
          */
         model_id: int,

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 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>
@@ -129,12 +129,6 @@ namespace Box3D {
         return out;
     }
 
-    export function expandUniformly(out: Box3D, box: Box3D, delta: number): Box3D {
-        Vec3.subScalar(out.min, box.min, delta);
-        Vec3.addScalar(out.max, box.max, delta);
-        return out;
-    }
-
     export function scale(out: Box3D, box: Box3D, scale: number) {
         Vec3.scale(out.min, box.min, scale);
         Vec3.scale(out.max, box.max, scale);
@@ -224,18 +218,6 @@ namespace Box3D {
         Vec3.scale(out, dir, tmin);
         return Vec3.set(out, out[0] + x, out[1] + y, out[2] + z);
     }
-
-    export function center(out: Vec3, box: Box3D): Vec3 {
-        return Vec3.center(out, box.max, box.min);
-    }
-
-    export function exactEquals(a: Box3D, b: Box3D) {
-        return Vec3.exactEquals(a.min, b.min) && Vec3.exactEquals(a.max, b.max);
-    }
-
-    export function equals(a: Box3D, b: Box3D) {
-        return Vec3.equals(a.min, b.min) && Vec3.equals(a.max, b.max);
-    }
 }
 
 export { Box3D };

src/mol-math/geometry/primitives/plane3d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2022-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2022-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  *
@@ -86,7 +86,7 @@ namespace Plane3D {
     }
 
     export function projectPoint(out: Vec3, plane: Plane3D, point: Vec3) {
-        return Vec3.scaleAndAdd(out, point, plane.normal, -distanceToPoint(plane, point));
+        return Vec3.scaleAndAdd(out, out, plane.normal, -distanceToPoint(plane, point));
     }
 }
 

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2023 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>
@@ -27,7 +27,6 @@ import { Vec3 } from './vec3';
 import { EPSILON } from './common';
 import { assertUnreachable, NumberArray } from '../../../mol-util/type-helpers';
 import { Euler } from './euler';
-import { Mat4 } from './mat4';
 
 interface Quat extends Array<number> { [d: number]: number, '@type': 'quat', length: 4 }
 interface ReadonlyQuat extends Array<number> { readonly [d: number]: number, '@type': 'quat', length: 4 }
@@ -283,12 +282,6 @@ namespace Quat {
         return out;
     }
 
-    const m3tmp = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] as unknown as Mat3;
-    export function fromMat4(out: Quat, m: Mat4) {
-        Mat3.fromMat4(m3tmp, m);
-        return fromMat3(out, m3tmp);
-    }
-
     export function fromEuler(out: Quat, euler: Euler, order: Euler.Order) {
         const [x, y, z] = euler;
 
@@ -374,12 +367,6 @@ namespace Quat {
         return out;
     }
 
-    const m4tmp = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] as unknown as Mat4;
-    export function fromBasis(out: Quat, x: Vec3, y: Vec3, z: Vec3) {
-        Mat4.fromBasis(m4tmp, x, y, z);
-        return fromMat4(out, m4tmp);
-    }
-
     export function clone(a: Quat) {
         const out = zero();
         out[0] = a[0];

src/mol-math/linear-algebra/3d/vec3.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2023 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>
@@ -645,11 +645,6 @@ namespace Vec3 {
         return normalize(out, cross(out, triangleNormalTmpAB, triangleNormalTmpAC));
     }
 
-    const centerTmpV = zero();
-    export function center(out: Vec3, a: Vec3, b: Vec3): Vec3 {
-        return Vec3.scaleAndAdd(out, a, Vec3.sub(centerTmpV, b, a), 0.5);
-    }
-
     export function toString(a: Vec3, precision?: number) {
         return `[${a[0].toPrecision(precision)} ${a[1].toPrecision(precision)} ${a[2].toPrecision(precision)}]`;
     }

src/mol-model/location.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -31,17 +31,4 @@ export function isDataLocation(x: any): x is DataLocation {
     return !!x && x.kind === 'data-location';
 }
 
-/**
- * A direct Location.
- *
- * For it, the location is implicitly clear from context and is not explicitly given.
- * This is used for themes with direct-volume rendering where the location is the volume
- * grid cell itself and coloring is applied in a shader on the GPU.
- */
-export const DirectLocation = { kind: 'direct-location' as const };
-export type DirectLocation = typeof DirectLocation
-export function isDirectLocation(x: any): x is DirectLocation {
-    return !!x && x.kind === 'direct-location';
-}
-
-export type Location = StructureElement.Location | Bond.Location | ShapeGroup.Location | PositionLocation | DataLocation | NullLocation | DirectLocation | Volume.Cell.Location | Volume.Segment.Location
+export type Location = StructureElement.Location | Bond.Location | ShapeGroup.Location | PositionLocation | DataLocation | NullLocation | Volume.Segment.Location

src/mol-model/volume/grid.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 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>
@@ -8,7 +8,6 @@
 import { SpacegroupCell, Box3D, Sphere3D } from '../../mol-math/geometry';
 import { Tensor, Mat4, Vec3 } from '../../mol-math/linear-algebra';
 import { Histogram, calculateHistogram } from '../../mol-math/histogram';
-import { lerp } from '../../mol-math/interpolate';
 
 /** The basic unit cell that contains the grid data. */
 interface Grid {
@@ -77,59 +76,6 @@ namespace Grid {
         }
         return histograms[binCount];
     }
-
-    export function makeGetTrilinearlyInterpolated(grid: Grid, transform: 'none' | 'relative') {
-        const cartnToGrid = Grid.getGridToCartesianTransform(grid);
-        Mat4.invert(cartnToGrid, cartnToGrid);
-        const gridCoords = Vec3();
-
-        const { stats } = grid;
-        const { dimensions, get } = grid.cells.space;
-        const data = grid.cells.data;
-
-        const [mi, mj, mk] = dimensions;
-
-        return function getTrilinearlyInterpolated(position: Vec3): number {
-            Vec3.copy(gridCoords, position);
-            Vec3.transformMat4(gridCoords, gridCoords, cartnToGrid);
-
-            const i = Math.trunc(gridCoords[0]);
-            const j = Math.trunc(gridCoords[1]);
-            const k = Math.trunc(gridCoords[2]);
-
-            if (i < 0 || i >= mi || j < 0 || j >= mj || k < 0 || k >= mk) {
-                return Number.NaN;
-            }
-
-            const u = gridCoords[0] - i;
-            const v = gridCoords[1] - j;
-            const w = gridCoords[2] - k;
-
-            // Tri-linear interpolation for the value
-            const ii = Math.min(i + 1, mi - 1);
-            const jj = Math.min(j + 1, mj - 1);
-            const kk = Math.min(k + 1, mk - 1);
-
-            let a = get(data, i, j, k);
-            let b = get(data, ii, j, k);
-            let c = get(data, i, jj, k);
-            let d = get(data, ii, jj, k);
-            const x = lerp(lerp(a, b, u), lerp(c, d, u), v);
-
-            a = get(data, i, j, kk);
-            b = get(data, ii, j, kk);
-            c = get(data, i, jj, kk);
-            d = get(data, ii, jj, kk);
-            const y = lerp(lerp(a, b, u), lerp(c, d, u), v);
-
-            const value = lerp(x, y, w);
-            if (transform === 'relative') {
-                return (value - stats.mean) / stats.sigma;
-            } else {
-                return value;
-            }
-        };
-    }
 }
 
 export { Grid };

src/mol-model/volume/volume.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -220,18 +220,6 @@ export namespace Volume {
         export function areLociEqual(a: Loci, b: Loci) { return a.volume === b.volume && OrderedSet.areEqual(a.indices, b.indices); }
         export function isLociEmpty(loci: Loci) { return OrderedSet.size(loci.indices) === 0; }
 
-        export interface Location {
-            readonly kind: 'cell-location',
-            volume: Volume
-            cell: CellIndex
-        }
-        export function Location(volume?: Volume, cell?: CellIndex): Location {
-            return { kind: 'cell-location', volume: volume as any, cell: cell as any };
-        }
-        export function isLocation(x: any): x is Location {
-            return !!x && x.kind === 'cell-location';
-        }
-
         const boundaryHelper = new BoundaryHelper('98');
         const tmpBoundaryPos = Vec3();
         export function getBoundingSphere(volume: Volume, indices: OrderedSet<CellIndex>, boundingSphere?: Sphere3D) {

src/mol-plugin-state/actions/structure.ts

@@ -63,13 +63,13 @@ const DownloadStructure = StateAction.build({
                     }, { pivot: 'id' }),
                     options
                 }, { isFlat: true, label: 'PDB' }),
-                'pdb-ihm': PD.Group({
+                'pdb-dev': PD.Group({
                     provider: PD.Group({
-                        id: PD.Text('8zzc', { label: 'PDB-IHM Id(s)', description: 'One or more comma/space separated ids.' }),
+                        id: PD.Text('PDBDEV_00000001', { label: 'PDB-Dev Id(s)', description: 'One or more comma/space separated ids.' }),
                         encoding: PD.Select('bcif', PD.arrayToOptions(['cif', 'bcif'] as const)),
                     }, { pivot: 'id' }),
                     options
-                }, { isFlat: true, label: 'PDB-IHM' }),
+                }, { isFlat: true, label: 'PDB-Dev' }),
                 'swissmodel': PD.Group({
                     id: PD.Text('Q9Y2I8', { label: 'UniProtKB AC(s)', description: 'One or more comma/space separated ACs.' }),
                     options
@@ -124,22 +124,22 @@ const DownloadStructure = StateAction.build({
             );
             asTrajectory = !!src.params.options.asTrajectory;
             break;
-        case 'pdb-ihm':
+        case 'pdb-dev':
             const map = (id: string) => id.startsWith('PDBDEV_') ? id : `PDBDEV_${id.padStart(8, '0')}`;
             downloadParams = await getDownloadParams(src.params.provider.id,
                 id => {
                     // 4 character PDB id, TODO: support extended PDB ID
                     if (id.match(/^[1-9][A-Z0-9]{3}$/i) !== null) {
                         return src.params.provider.encoding === 'bcif'
-                            ? `https://pdb-ihm.org/bcif/${id.toLowerCase()}.bcif`
-                            : `https://pdb-ihm.org/cif/${id.toLowerCase()}.cif`;
+                            ? `https://pdb-dev.wwpdb.org/bcif/${id.toLowerCase()}.bcif`
+                            : `https://pdb-dev.wwpdb.org/cif/${id.toLowerCase()}.cif`;
                     }
                     const nId = map(id.toUpperCase());
                     return src.params.provider.encoding === 'bcif'
-                        ? `https://pdb-ihm.org/bcif/${nId}.bcif`
-                        : `https://pdb-ihm.org/cif/${nId}.cif`;
+                        ? `https://pdb-dev.wwpdb.org/bcif/${nId}.bcif`
+                        : `https://pdb-dev.wwpdb.org/cif/${nId}.cif`;
                 },
-                id => { const nId = id.toUpperCase(); return nId.match(/^[1-9][A-Z0-9]{3}$/) ? `PDB-IHM: ${nId}` : map(nId); },
+                id => { const nId = id.toUpperCase(); return nId.match(/^[1-9][A-Z0-9]{3}$/) ? `PDB-Dev: ${nId}` : map(nId); },
                 src.params.provider.encoding === 'bcif'
             );
             asTrajectory = !!src.params.options.asTrajectory;

src/mol-plugin-state/builder/structure/representation-preset.ts

@@ -1,9 +1,8 @@
 /**
- * Copyright (c) 2019-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2024 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>
  */
 
 import { PresetProvider } from '../preset-provider';
@@ -122,7 +121,7 @@ const auto = StructureRepresentationPresetProvider({
     params: () => CommonParams,
     apply(ref, params, plugin) {
         const structure = StateObjectRef.resolveAndCheck(plugin.state.data, ref)?.obj?.data;
-        if (!structure) return {};
+        if (!structure) return { };
 
         const thresholds = plugin.config.get(PluginConfig.Structure.SizeThresholds) || Structure.DefaultSizeThresholds;
         const size = Structure.getSize(structure, thresholds);
@@ -152,7 +151,7 @@ const empty = StructureRepresentationPresetProvider({
     id: 'preset-structure-representation-empty',
     display: { name: 'Empty', description: 'Removes all existing representations.' },
     async apply(ref, params, plugin) {
-        return {};
+        return { };
     }
 });
 
@@ -397,9 +396,12 @@ const illustrative = StructureRepresentationPresetProvider({
     id: 'preset-structure-representation-illustrative',
     display: {
         name: 'Illustrative', group: 'Miscellaneous',
-        description: 'Show everything in spacefill representation with illustrative colors and ignore light.'
+        description: '...'
     },
-    params: () => CommonParams,
+    params: () => ({
+        ...CommonParams,
+        showCarbohydrateSymbol: PD.Boolean(false)
+    }),
     async apply(ref, params, plugin) {
         const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
         if (!structureCell) return {};
@@ -414,47 +416,7 @@ const illustrative = StructureRepresentationPresetProvider({
         const { update, builder, typeParams, color } = reprBuilder(plugin, params, structure);
 
         const representations = {
-            all: builder.buildRepresentation(update, components.all, {
-                type: 'spacefill',
-                typeParams: { ...typeParams, ignoreLight: true },
-                color: 'illustrative',
-                colorParams: { style: { name: 'entity-id', params: { overrideWater: true } } },
-            }, { tag: 'all' }),
-        };
-        await update.commit({ revertOnError: true });
-        await updateFocusRepr(plugin, structure, params.theme?.focus?.name ?? color, params.theme?.focus?.params);
-
-        return { components, representations };
-    }
-});
-
-const molecularSurface = StructureRepresentationPresetProvider({
-    id: 'preset-structure-representation-molecular-surface',
-    display: {
-        name: 'Molecular Surface', group: 'Miscellaneous',
-        description: 'Show everything in molecular surface representation with illustrative colors.'
-    },
-    params: () => CommonParams,
-    async apply(ref, params, plugin) {
-        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
-        if (!structureCell) return {};
-
-        const components = {
-            all: await presetStaticComponent(plugin, structureCell, 'all'),
-            branched: undefined
-        };
-
-        const structure = structureCell.obj!.data;
-
-        const { update, builder, typeParams, color } = reprBuilder(plugin, params, structure);
-
-        const representations = {
-            all: builder.buildRepresentation(update, components.all, {
-                type: 'molecular-surface',
-                typeParams,
-                color: 'entity-id',
-                colorParams: { overrideWater: true },
-            }, { tag: 'all' }),
+            all: builder.buildRepresentation(update, components.all, { type: 'spacefill', typeParams: { ...typeParams, ignoreLight: true }, color: 'illustrative' }, { tag: 'all' }),
         };
         await update.commit({ revertOnError: true });
         await updateFocusRepr(plugin, structure, params.theme?.focus?.name ?? color, params.theme?.focus?.params);
@@ -512,7 +474,6 @@ export const PresetStructureRepresentations = {
     'protein-and-nucleic': proteinAndNucleic,
     'coarse-surface': coarseSurface,
     illustrative,
-    'molecular-surface': molecularSurface,
     'auto-lod': autoLod,
 };
 export type PresetStructureRepresentations = typeof PresetStructureRepresentations;

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

@@ -1,9 +1,8 @@
 /**
- * Copyright (c) 2019-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 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>
- * @author Adam Midlik <midlik@gmail.com>
  */
 
 import { EveryLoci, isEmptyLoci, Loci } from '../../mol-model/loci';
@@ -179,9 +178,8 @@ namespace InteractivityManager {
         highlightOnlyExtend(current: Representation.Loci, applyGranularity = true) {
             const normalized = this.normalizedLoci(current, applyGranularity);
             if (StructureElement.Loci.is(normalized.loci)) {
-                const range = this.ctx.selectionMode ? this.sel.tryGetRange(normalized.loci) : this.ctx.managers.structure.focus.tryGetRange(normalized.loci);
                 const extended = {
-                    loci: range ?? normalized.loci,
+                    loci: this.sel.tryGetRange(normalized.loci) || normalized.loci,
                     repr: normalized.repr
                 };
                 if (!this.isHighlighted(extended)) {
@@ -295,4 +293,4 @@ namespace InteractivityManager {
             }
         }
     }
-}
+}

src/mol-plugin-state/manager/structure/focus.ts

@@ -1,22 +1,20 @@
 /**
- * Copyright (c) 2020-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020 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>
- * @author Adam Midlik <midlik@gmail.com>
  */
 
-import { Sphere3D } from '../../../mol-math/geometry';
-import { Vec3 } from '../../../mol-math/linear-algebra';
-import { Loci } from '../../../mol-model/loci';
-import { Structure, StructureElement } from '../../../mol-model/structure';
-import { PluginContext } from '../../../mol-plugin/context';
-import { StateSelection } from '../../../mol-state';
-import { lociLabel } from '../../../mol-theme/label';
-import { arrayRemoveAtInPlace } from '../../../mol-util/array';
 import { StatefulPluginComponent } from '../../component';
+import { PluginContext } from '../../../mol-plugin/context';
+import { arrayRemoveAtInPlace } from '../../../mol-util/array';
+import { StructureElement, Structure } from '../../../mol-model/structure';
+import { Loci } from '../../../mol-model/loci';
+import { lociLabel } from '../../../mol-theme/label';
 import { PluginStateObject } from '../../objects';
-import { getLociRange } from './selection';
+import { StateSelection } from '../../../mol-state';
+import { Vec3 } from '../../../mol-math/linear-algebra';
+import { Sphere3D } from '../../../mol-math/geometry';
 
 export type FocusEntry = {
     label: string
@@ -52,9 +50,6 @@ export class StructureFocusManager extends StatefulPluginComponent<StructureFocu
     get current() { return this.state.current; }
     get history() { return this.state.history; }
 
-    /** Last added or removed loci */
-    private referenceLoci: StructureElement.Loci | undefined;
-
     private tryAddHistory(entry: FocusEntry) {
         if (StructureElement.Loci.isEmpty(entry.loci)) return;
 
@@ -89,10 +84,6 @@ export class StructureFocusManager extends StatefulPluginComponent<StructureFocu
         }
     }
 
-    tryGetRange(loci: Loci): StructureElement.Loci | undefined {
-        return getLociRange(this.referenceLoci, loci);
-    }
-
     setFromLoci(anyLoci: Loci) {
         const loci = Loci.normalize(anyLoci);
         if (!StructureElement.Loci.is(loci) || StructureElement.Loci.isEmpty(loci)) {
@@ -101,7 +92,6 @@ export class StructureFocusManager extends StatefulPluginComponent<StructureFocu
         }
 
         this.set({ loci, label: lociLabel(loci, { reverse: true, hidePrefix: true, htmlStyling: false }) });
-        this.referenceLoci = loci;
     }
 
     addFromLoci(anyLoci: Loci) {
@@ -109,21 +99,6 @@ export class StructureFocusManager extends StatefulPluginComponent<StructureFocu
             ? StructureElement.Loci.union(anyLoci, this.state.current.loci)
             : anyLoci;
         this.setFromLoci(union);
-        const refLoci = Loci.normalize(anyLoci);
-        this.referenceLoci = StructureElement.Loci.is(refLoci) ? refLoci : undefined;
-    }
-
-    toggleFromLoci(anyLoci: Loci) {
-        const { kind, loci } = toggleLoci(this.state.current?.loci, anyLoci);
-        this.setFromLoci(loci);
-        const refLoci = Loci.normalize(anyLoci);
-        this.referenceLoci = StructureElement.Loci.is(refLoci) && kind !== 'subtract' ? refLoci : undefined;
-    }
-
-    extendFromLoci(anyLoci: Loci) {
-        const range = this.tryGetRange(anyLoci) ?? anyLoci;
-        this.toggleFromLoci(range);
-
     }
 
     clear() {
@@ -131,7 +106,6 @@ export class StructureFocusManager extends StatefulPluginComponent<StructureFocu
             this.state.current = undefined;
             this.behaviors.current.next(void 0);
         }
-        this.referenceLoci = undefined;
     }
 
     getSnapshot(): StructureFocusSnapshot {
@@ -217,17 +191,4 @@ export class StructureFocusManager extends StatefulPluginComponent<StructureFocu
             }
         });
     }
-}
-
-/** Return union of `currentLoci` and `newLoci`; or subtract `newLoci` from `currentLoci` if `newLoci` is a subset of `currentLoci`. */
-function toggleLoci(currentLoci: StructureElement.Loci | undefined, newLoci: Loci) {
-    if (currentLoci && StructureElement.Loci.is(newLoci) && newLoci.structure === currentLoci.structure) {
-        if (StructureElement.Loci.isSubset(currentLoci, newLoci)) {
-            return { kind: 'subtract', loci: StructureElement.Loci.subtract(currentLoci, newLoci) };
-        } else {
-            return { kind: 'add', loci: StructureElement.Loci.union(newLoci, currentLoci) };
-        }
-    } else {
-        return { kind: 'new', loci: newLoci };
-    }
-}
+}

src/mol-plugin-state/manager/structure/selection.ts

@@ -1,9 +1,8 @@
 /**
- * Copyright (c) 2019-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2023 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>
  */
 
 import { OrderedSet } from '../../../mol-data/int';
@@ -352,9 +351,28 @@ export class StructureSelectionManager extends StatefulPluginComponent<Structure
 
     tryGetRange(loci: Loci): StructureElement.Loci | undefined {
         if (!StructureElement.Loci.is(loci)) return;
-        if (!this.getEntry(loci.structure)) return;
+        if (loci.elements.length !== 1) return;
+        const entry = this.getEntry(loci.structure);
+        if (!entry) return;
 
-        return getLociRange(this.referenceLoci, loci);
+        const xs = loci.elements[0];
+        if (!xs) return;
+
+        const ref = this.referenceLoci;
+        if (!ref || !StructureElement.Loci.is(ref) || ref.structure !== loci.structure) return;
+
+        let e: StructureElement.Loci['elements'][0] | undefined;
+        for (const _e of ref.elements) {
+            if (xs.unit === _e.unit) {
+                e = _e;
+                break;
+            }
+        }
+        if (!e) return;
+
+        if (xs.unit !== e.unit) return;
+
+        return getElementRange(loci.structure, e, xs);
     }
 
     /** Count of all selected elements */
@@ -551,31 +569,6 @@ function remapSelectionEntry(e: SelectionEntry, s: Structure): SelectionEntry {
     return new SelectionEntry(StructureElement.Loci.remap(e.selection, s));
 }
 
-/** Return loci spanning the range between `fromLoci` and `toLoci` (including both) if they belong to the same unit in the same structure */
-export function getLociRange(fromLoci: Loci | undefined, toLoci: Loci | undefined): StructureElement.Loci | undefined {
-    if (!StructureElement.Loci.is(fromLoci)) return;
-    if (!StructureElement.Loci.is(toLoci)) return;
-    if (fromLoci.structure !== toLoci.structure) return;
-
-    if (toLoci.elements.length !== 1) return;
-
-    const xs = toLoci.elements[0];
-    if (!xs) return;
-
-    let e: StructureElement.Loci['elements'][0] | undefined;
-    for (const _e of fromLoci.elements) {
-        if (xs.unit === _e.unit) {
-            e = _e;
-            break;
-        }
-    }
-    if (!e) return;
-
-    if (xs.unit !== e.unit) return;
-
-    return getElementRange(toLoci.structure, e, xs);
-}
-
 /**
  * Assumes `ref` and `ext` belong to the same unit in the same structure
  */
@@ -587,4 +580,4 @@ function getElementRange(structure: Structure, ref: StructureElement.Loci['eleme
         unit: ref.unit,
         indices: OrderedSet.ofRange(min as StructureElement.UnitIndex, max as StructureElement.UnitIndex)
     }]);
-}
+}

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

@@ -1015,7 +1015,7 @@ const VolumeRepresentation3D = PluginStateTransform.BuiltIn({
             const provider = plugin.representation.volume.registry.get(params.type.name);
             if (provider.ensureCustomProperties) await provider.ensureCustomProperties.attach(propertyCtx, a.data);
             const repr = provider.factory({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.volume.themes }, provider.getParams);
-            repr.setTheme(Theme.create(plugin.representation.volume.themes, { volume: a.data, locationKinds: provider.locationKinds }, params));
+            repr.setTheme(Theme.create(plugin.representation.volume.themes, { volume: a.data }, params));
 
             const props = params.type.params || {};
             await repr.createOrUpdate(props, a.data).runInContext(ctx);
@@ -1024,13 +1024,13 @@ const VolumeRepresentation3D = PluginStateTransform.BuiltIn({
     },
     update({ a, b, oldParams, newParams }, plugin: PluginContext) {
         return Task.create('Volume Representation', async ctx => {
-            const oldProvider = plugin.representation.volume.registry.get(oldParams.type.name);
             if (newParams.type.name !== oldParams.type.name) {
+                const oldProvider = plugin.representation.volume.registry.get(oldParams.type.name);
                 oldProvider.ensureCustomProperties?.detach(a.data);
                 return StateTransformer.UpdateResult.Recreate;
             }
             const props = { ...b.data.repr.props, ...newParams.type.params };
-            b.data.repr.setTheme(Theme.create(plugin.representation.volume.themes, { volume: a.data, locationKinds: oldProvider.locationKinds }, newParams));
+            b.data.repr.setTheme(Theme.create(plugin.representation.volume.themes, { volume: a.data }, newParams));
             await b.data.repr.createOrUpdate(props, a.data).runInContext(ctx);
             b.data.sourceData = a.data;
             b.description = VolumeRepresentation3DHelpers.getDescription(props);

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

@@ -32,7 +32,7 @@ const _Intersect = <svg width='24px' height='24px' viewBox='0 0 24 24'><defs>{ci
 export function IntersectSvg() { return _Intersect; }
 const _Set = <svg width='24px' height='24px' viewBox='0 0 24 24'><defs>{circleLeft}{circleRight}</defs><g><use href='#circle-left' className='msp-shape-empty' /><use href='#circle-right' className='msp-shape-filled' /></g></svg>;
 export function SetSvg() { return _Set; }
-const _Molecule = <svg width='17px' height='17px' viewBox='0 0 299.463 299.463' strokeWidth='6px'><g><path d='M256.851,173.832v-48.201c22.916-4.918,34.151-30.668,22.556-50.771c-11.547-20.004-39.486-23.251-55.242-5.844 l-41.746-24.106C189.618,22.603,172.861,0,149.734,0c-23.132,0-39.881,22.609-32.685,44.911L75.305,69.016 C59.522,51.586,31.597,54.88,20.061,74.863c-11.63,20.163-0.298,45.862,22.557,50.769v48.2 c-22.821,4.898-34.195,30.591-22.556,50.771c11.529,19.972,39.454,23.285,55.242,5.845l41.746,24.106 c-7.199,22.308,9.559,44.911,32.685,44.911c23.132,0,39.88-22.609,32.685-44.911l41.745-24.106 c15.817,17.469,43.73,14.099,55.242-5.844c0,0,0-0.001,0.001-0.002c4.587-7.953,5.805-17.213,3.431-26.076 C279.392,185.657,269.129,176.461,256.851,173.832z M249.62,72.088c20.568,0,27.428,27.191,10.008,37.239 c-0.003,0.002-0.006,0.003-0.009,0.005c-10.04,5.81-22.85,1.762-27.877-8.475C225.206,87.548,234.938,72.088,249.62,72.088z M149.734,14.4c11.005,0,19.958,8.954,19.958,19.959c0,11.127-9.077,19.958-19.958,19.958c-10.95,0-19.958-8.9-19.958-19.958 C129.776,23.354,138.729,14.4,149.734,14.4z M39.84,109.328c-17.451-10.067-10.534-37.24,10.01-37.24 c15.311,0,24.922,16.653,17.251,29.942C61.681,111.397,49.517,114.925,39.84,109.328z M59.802,224.702 c-9.535,5.503-21.768,2.229-27.268-7.298c-7.639-13.242,1.887-29.945,17.236-29.945c0.013,0,0.027,0,0.04,0 C70.07,187.48,77.49,214.469,59.802,224.702z M149.734,285.062c-11.005,0-19.958-8.954-19.958-19.958 c0-11.127,9.077-19.958,19.958-19.958c10.954,0,19.958,8.903,19.958,19.958C169.693,276.109,160.74,285.062,149.734,285.062z M216.953,217.982l-41.727,24.095c-13.778-15.22-37.459-14.94-50.983,0l-41.728-24.096c6.196-19.289-5.541-39.835-25.498-44.149 V125.63c19.752-4.268,31.762-24.65,25.498-44.149l41.727-24.095c13.629,15.055,37.32,15.093,50.983,0l41.728,24.096 c-6.196,19.29,5.534,39.835,25.498,44.149v48.202C222.61,178.123,210.721,198.581,216.953,217.982z M266.935,217.404 c-5.501,9.528-17.732,12.802-27.261,7.302c-17.682-10.23-10.301-37.247,10.032-37.247 C264.984,187.459,274.602,204.112,266.935,217.404z' /></g></svg>;
+const _Molecule = <svg width='17px' height='17px' viewBox='0 0 299.463 299.463' strokeWidth='6px'><g><path d='M256.851,173.832v-48.201c22.916-4.918,34.151-30.668,22.556-50.771c-11.547-20.004-39.486-23.251-55.242-5.844 l-41.746-24.106C189.618,22.603,172.861,0,149.734,0c-23.132,0-39.881,22.609-32.685,44.911L75.305,69.016 C59.522,51.586,31.597,54.88,20.061,74.863c-11.63,20.163-0.298,45.862,22.557,50.769v48.2 c-22.821,4.898-34.195,30.591-22.556,50.771c11.529,19.972,39.454,23.285,55.242,5.845l41.746,24.106 c-7.199,22.308,9.559,44.911,32.685,44.911c23.132,0,39.88-22.609,32.685-44.911l41.745-24.106 c15.817,17.469,43.73,14.099,55.242-5.844c0,0,0-0.001,0.001-0.002c4.587-7.953,5.805-17.213,3.431-26.076 C279.392,185.657,269.129,176.461,256.851,173.832z M249.62,72.088c20.568,0,27.428,27.191,10.008,37.239 c-0.003,0.002-0.006,0.003-0.009,0.005c-10.04,5.81-22.85,1.762-27.877-8.475C225.206,87.548,234.938,72.088,249.62,72.088z M149.734,14.4c11.005,0,19.958,8.954,19.958,19.959c0,11.127-9.077,19.958-19.958,19.958c-10.95,0-19.958-8.9-19.958-19.958 C129.776,23.354,138.729,14.4,149.734,14.4z M39.84,109.328c-17.451-10.067-10.534-37.24,10.01-37.24 c15.311,0,24.922,16.653,17.251,29.942C61.681,111.397,49.517,114.925,39.84,109.328z M59.802,224.702 c-9.535,5.503-21.768,2.229-27.268-7.298c-7.639-13.242,1.887-29.945,17.236-29.945c0.013,0,0.027,0,0.04,0 C70.07,187.48,77.49,214.469,59.802,224.702z M149.734,285.062c-11.005,0-19.958-8.954-19.958-19.958 c0-11.127,9.077-19.958,19.958-19.958c10.954,0,19.958,8.903,19.958,19.958C169.693,276.109,160.74,285.062,149.734,285.062z M216.953,217.982l-41.727,24.095c-13.778-15.22-37.459-14.94-50.983,0l-41.728-24.096c6.196-19.289-5.541-39.835-25.498-44.149 V125.63c19.752-4.268,31.762-24.65,25.498-44.149l41.727-24.095c13.629,15.055,37.32,15.093,50.983,0l41.728,24.096 c-6.196,19.29,5.534,39.835,25.498,44.149v48.202C222.61,178.123,210.721,198.581,216.953,217.982z M266.935,217.404 c-5.501,9.528-17.732,12.802-27.261,7.302c-17.682-10.23-10.301-37.247,10.032-37.247 C264.984,187.459,274.602,204.112,266.935,217.404z'/></g></svg>;
 export function MoleculeSvg() { return _Molecule; }
 
 // The following icons are adapted from https://materialdesignicons.com/ and

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2024 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>
@@ -695,33 +695,15 @@ const colorGradientInterpolated = memoize1((colors: ColorListEntry[]) => {
 
 const colorGradientBanded = memoize1((colors: ColorListEntry[]) => {
     const n = colors.length;
-    const styles: string[] = [];
-
-    const hasOffsets = colors.every(c => Array.isArray(c));
-    if (hasOffsets) {
-        const off = colors as [Color, number][];
-        styles.push(`${Color.toStyle(off[0][0])} ${(100 * off[0][1]).toFixed(2)}%`);
-        for (let i = 0, il = off.length - 1; i < il; ++i) {
-            const [c0, o0] = off[i];
-            const [c1, o1] = off[i + 1];
-            const o = o0 + (o1 - o0) / 2;
-            styles.push(
-                `${Color.toStyle(c0)} ${(100 * o).toFixed(2)}%`,
-                `${Color.toStyle(c1)} ${(100 * o).toFixed(2)}%`
-            );
-        }
-        styles.push(`${Color.toStyle(off[off.length - 1][0])} ${(100 * off[off.length - 1][1]).toFixed(2)}%`);
-    } else {
-        const styles: string[] = [`${colorEntryToStyle(colors[0])} ${100 * (1 / n)}%`];
-        for (let i = 1, il = n - 1; i < il; ++i) {
-            styles.push(
-                `${colorEntryToStyle(colors[i])} ${100 * (i / n)}%`,
-                `${colorEntryToStyle(colors[i])} ${100 * ((i + 1) / n)}%`
-            );
-        }
-        styles.push(`${colorEntryToStyle(colors[n - 1])} ${100 * ((n - 1) / n)}%`);
+    const styles: string[] = [`${colorEntryToStyle(colors[0])} ${100 * (1 / n)}%`];
+    // TODO: does this need to support offsets?
+    for (let i = 1, il = n - 1; i < il; ++i) {
+        styles.push(
+            `${colorEntryToStyle(colors[i])} ${100 * (i / n)}%`,
+            `${colorEntryToStyle(colors[i])} ${100 * ((i + 1) / n)}%`
+        );
     }
-
+    styles.push(`${colorEntryToStyle(colors[n - 1])} ${100 * ((n - 1) / n)}%`);
     return `linear-gradient(to right, ${styles.join(', ')})`;
 });
 

src/mol-plugin-ui/plugin.tsx

@@ -4,7 +4,6 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Christian Dominguez <christian.99dominguez@gmail.com>
- * @author Ventura Rivera <venturaxrivera@gmail.com>
  */
 
 import { List } from 'immutable';
@@ -269,7 +268,6 @@ export class ControlsWrapper extends PluginUIComponent {
 export class DefaultViewport extends PluginUIComponent {
     render() {
         const VPControls = this.plugin.spec.components?.viewport?.controls || ViewportControls;
-        const SVPControls = this.plugin.spec.components?.selectionTools?.controls || SelectionViewportControls;
         const SnapshotDescription = this.plugin.spec.components?.viewport?.snapshotDescription || ViewportSnapshotDescription;
 
         return <>
@@ -280,7 +278,7 @@ export class DefaultViewport extends PluginUIComponent {
                 <StateSnapshotViewportControls />
                 <SnapshotDescription />
             </div>
-            <SVPControls />
+            <SelectionViewportControls />
             <VPControls />
             <BackgroundTaskProgress />
             <div className='msp-highlight-toast-wrapper'>

src/mol-plugin-ui/sequence.tsx

@@ -3,7 +3,6 @@
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
- * @author Ventura Rivera <venturaxrivera@gmail.com>
  */
 
 import * as React from 'react';
@@ -216,12 +215,11 @@ type SequenceViewState = {
     modelEntityId: string,
     chainGroupId: number,
     operatorKey: string,
-    mode: SequenceViewMode,
-    sequenceViewModeParam: typeof SequenceViewModeParam,
+    mode: SequenceViewMode
 }
 
 export class SequenceView extends PluginUIComponent<{ defaultMode?: SequenceViewMode }, SequenceViewState> {
-    state: SequenceViewState = { structureOptions: { options: [], all: [] }, structure: Structure.Empty, structureRef: '', modelEntityId: '', chainGroupId: -1, operatorKey: '', mode: 'single', sequenceViewModeParam: SequenceViewModeParam };
+    state: SequenceViewState = { structureOptions: { options: [], all: [] }, structure: Structure.Empty, structureRef: '', modelEntityId: '', chainGroupId: -1, operatorKey: '', mode: 'single' };
 
     componentDidMount() {
         if (this.plugin.state.data.select(StateSelection.Generators.rootsOfType(PSO.Molecule.Structure)).length > 0) this.setState(this.getInitialState());
@@ -243,16 +241,6 @@ export class SequenceView extends PluginUIComponent<{ defaultMode?: SequenceView
                 this.sync();
             }
         });
-
-        const modeOptions = this.plugin.spec.components?.sequenceViewer?.modeOptions;
-        if (modeOptions) {
-            const modeSet = new Set(modeOptions);
-            const sequenceViewModeParam = {
-                ...SequenceViewModeParam,
-                options: SequenceViewModeParam.options.filter(([firstItem]) => modeSet.has(firstItem)),
-            };
-            this.setState({ sequenceViewModeParam: sequenceViewModeParam });
-        }
     }
 
     private sync() {
@@ -312,9 +300,7 @@ export class SequenceView extends PluginUIComponent<{ defaultMode?: SequenceView
             chainGroupId = this.state.chainGroupId;
             operatorKey = this.state.operatorKey;
         }
-        const defaultMode = this.plugin.spec.components?.sequenceViewer?.defaultMode;
-        const initialMode = this.props.defaultMode ?? defaultMode ?? 'single';
-        return { structureOptions, structure, structureRef, modelEntityId, chainGroupId, operatorKey, mode: initialMode, sequenceViewModeParam: this.state.sequenceViewModeParam };
+        return { structureOptions, structure, structureRef, modelEntityId, chainGroupId, operatorKey, mode: this.props.defaultMode ?? 'single' };
     }
 
     private get params() {
@@ -327,7 +313,7 @@ export class SequenceView extends PluginUIComponent<{ defaultMode?: SequenceView
             entity: PD.Select(entityOptions[0][0], entityOptions, { shortLabel: true }),
             chain: PD.Select(chainOptions[0][0], chainOptions, { shortLabel: true, twoColumns: true, label: 'Chain' }),
             operator: PD.Select(operatorOptions[0][0], operatorOptions, { shortLabel: true, twoColumns: true }),
-            mode: this.state.sequenceViewModeParam,
+            mode: SequenceViewModeParam
         };
     }
 
@@ -393,11 +379,11 @@ export class SequenceView extends PluginUIComponent<{ defaultMode?: SequenceView
         return <div className='msp-sequence'>
             <div className='msp-sequence-select'>
                 <Icon svg={HelpOutlineSvg} style={{ cursor: 'help', position: 'absolute', right: 0, top: 0 }}
-                    title='This shows a single sequence. Use the controls to show a different sequence. &#10;Use Ctrl or Cmd key to add a sequence range to focus; use Shift key to extend last focused/selected range.' />
+                    title='This shows a single sequence. Use the controls to show a different sequence.' />
 
                 <span>Sequence of</span>
                 <PureSelectControl title={`[Structure] ${PD.optionLabel(params.structure, values.structure)}`} param={params.structure} name='structure' value={values.structure} onChange={this.setParamProps} />
-                <PureSelectControl title={`[Mode]`} param={this.state.sequenceViewModeParam} name='mode' value={values.mode} onChange={this.setParamProps} />
+                <PureSelectControl title={`[Mode]`} param={SequenceViewModeParam} name='mode' value={values.mode} onChange={this.setParamProps} />
                 {values.mode === 'single' && <PureSelectControl title={`[Entity] ${PD.optionLabel(params.entity, values.entity)}`} param={params.entity} name='entity' value={values.entity} onChange={this.setParamProps} />}
                 {values.mode === 'single' && <PureSelectControl title={`[Chain] ${PD.optionLabel(params.chain, values.chain)}`} param={params.chain} name='chain' value={values.chain} onChange={this.setParamProps} />}
                 {params.operator.options.length > 1 && <>

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

@@ -1,15 +1,15 @@
 /**
- * Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author Adam Midlik <midlik@gmail.com>
  */
 
-import { Interval, OrderedSet } from '../../mol-data/int';
-import { Loci } from '../../mol-model/loci';
 import { Structure, StructureElement, StructureProperties } from '../../mol-model/structure';
-import { ColorNames } from '../../mol-util/color/names';
 import { SequenceWrapper, StructureUnit } from './wrapper';
+import { OrderedSet, Interval } from '../../mol-data/int';
+import { Loci } from '../../mol-model/loci';
+import { ColorNames } from '../../mol-util/color/names';
+import { MarkerAction, applyMarkerAction } from '../../mol-util/marker-action';
 
 export class ChainSequenceWrapper extends SequenceWrapper<StructureUnit> {
     private label: string;
@@ -26,25 +26,27 @@ export class ChainSequenceWrapper extends SequenceWrapper<StructureUnit> {
         return 'msp-sequence-present';
     }
 
-    override getSeqIndices(loci: Loci): OrderedSet {
+    mark(loci: Loci, action: MarkerAction) {
+        let changed = false;
         const { structure } = this.data;
         if (StructureElement.Loci.is(loci)) {
-            if (!Structure.areRootsEquivalent(loci.structure, structure)) return Interval.Empty;
+            if (!Structure.areRootsEquivalent(loci.structure, structure)) return false;
             loci = StructureElement.Loci.remap(loci, structure);
 
             for (const e of loci.elements) {
                 const indices = this.unitIndices.get(e.unit.id);
                 if (indices) {
                     if (OrderedSet.isSubset(indices, e.indices)) {
-                        return Interval.ofSingleton(0);
+                        if (applyMarkerAction(this.markerArray, Interval.ofSingleton(0), action)) changed = true;
                     }
                 }
             }
         } else if (Structure.isLoci(loci)) {
-            if (!Structure.areRootsEquivalent(loci.structure, structure)) return Interval.Empty;
-            return Interval.ofSingleton(0);
+            if (!Structure.areRootsEquivalent(loci.structure, structure)) return false;
+
+            if (applyMarkerAction(this.markerArray, Interval.ofSingleton(0), action)) changed = true;
         }
-        return Interval.Empty;
+        return changed;
     }
 
     getLoci(seqIdx: number) {
@@ -76,11 +78,12 @@ export class ChainSequenceWrapper extends SequenceWrapper<StructureUnit> {
         counts.push(`${elementCount} elements`);
 
         const length = 1;
+        const markerArray = new Uint8Array(length);
 
-        super(data, length);
+        super(data, markerArray, length);
 
         this.label = `Whole Chain (${counts.join(', ')})`;
         this.unitIndices = unitIndices;
         this.loci = StructureElement.Loci(this.data.structure, lociElements);
     }
-}
+}

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

@@ -1,15 +1,15 @@
 /**
- * Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author Adam Midlik <midlik@gmail.com>
  */
 
-import { Interval, OrderedSet } from '../../mol-data/int';
-import { Loci } from '../../mol-model/loci';
 import { Structure, StructureElement } from '../../mol-model/structure';
-import { ColorNames } from '../../mol-util/color/names';
 import { SequenceWrapper, StructureUnit } from './wrapper';
+import { OrderedSet, Interval } from '../../mol-data/int';
+import { Loci } from '../../mol-model/loci';
+import { ColorNames } from '../../mol-util/color/names';
+import { MarkerAction, applyMarkerAction } from '../../mol-util/marker-action';
 
 export class ElementSequenceWrapper extends SequenceWrapper<StructureUnit> {
     private unitIndices: Map<number, Interval<StructureElement.UnitIndex>>;
@@ -24,30 +24,30 @@ export class ElementSequenceWrapper extends SequenceWrapper<StructureUnit> {
         return 'msp-sequence-present';
     }
 
-    override getSeqIndices(loci: Loci): OrderedSet {
+    mark(loci: Loci, action: MarkerAction) {
+        let changed = false;
         const { structure, units } = this.data;
         if (StructureElement.Loci.is(loci)) {
-            if (!Structure.areRootsEquivalent(loci.structure, structure)) return Interval.Empty;
+            if (!Structure.areRootsEquivalent(loci.structure, structure)) return false;
             loci = StructureElement.Loci.remap(loci, structure);
 
             for (const e of loci.elements) {
                 const indices = this.unitIndices.get(e.unit.id);
                 if (indices) {
                     if (OrderedSet.isSubset(indices, e.indices)) {
-                        // this assumes this SequnceWrapper has only a single unit, otherwise we'd need to collect indices from all units and apply offsets
-                        return e.indices;
+                        if (applyMarkerAction(this.markerArray, e.indices, action)) changed = true;
                     }
                 }
             }
         } else if (Structure.isLoci(loci)) {
-            if (!Structure.areRootsEquivalent(loci.structure, structure)) return Interval.Empty;
+            if (!Structure.areRootsEquivalent(loci.structure, structure)) return false;
 
             for (let i = 0, il = units.length; i < il; ++i) {
                 const indices = this.unitIndices.get(units[i].id)!;
-                return indices;
+                if (applyMarkerAction(this.markerArray, indices, action)) changed = true;
             }
         }
-        return Interval.Empty;
+        return changed;
     }
 
     getLoci(seqIdx: number) {
@@ -79,9 +79,10 @@ export class ElementSequenceWrapper extends SequenceWrapper<StructureUnit> {
             unitIndices.set(unit.id, indices);
             lociElements.push({ unit, indices });
         }
+        const markerArray = new Uint8Array(length);
 
-        super(data, length);
+        super(data, markerArray, length);
 
         this.unitIndices = unitIndices;
     }
-}
+}

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

@@ -1,15 +1,15 @@
 /**
- * Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author Adam Midlik <midlik@gmail.com>
  */
 
-import { Interval, OrderedSet, Segmentation, SortedArray } from '../../mol-data/int';
-import { Loci } from '../../mol-model/loci';
-import { ResidueIndex, Structure, StructureElement, Unit } from '../../mol-model/structure';
-import { ColorNames } from '../../mol-util/color/names';
+import { Structure, StructureElement, ResidueIndex, Unit } from '../../mol-model/structure';
 import { SequenceWrapper, StructureUnit } from './wrapper';
+import { OrderedSet, Segmentation, Interval, SortedArray } from '../../mol-data/int';
+import { Loci } from '../../mol-model/loci';
+import { ColorNames } from '../../mol-util/color/names';
+import { MarkerAction, applyMarkerAction } from '../../mol-util/marker-action';
 
 export class HeteroSequenceWrapper extends SequenceWrapper<StructureUnit> {
     private readonly unitMap: Map<number, Unit>;
@@ -28,29 +28,29 @@ export class HeteroSequenceWrapper extends SequenceWrapper<StructureUnit> {
         return 'msp-sequence-present';
     }
 
-    override getSeqIndices(loci: Loci): OrderedSet {
+    mark(loci: Loci, action: MarkerAction) {
+        let changed = false;
         const { structure } = this.data;
         if (StructureElement.Loci.is(loci)) {
-            if (!Structure.areRootsEquivalent(loci.structure, structure)) return Interval.Empty;
+            if (!Structure.areRootsEquivalent(loci.structure, structure)) return false;
             loci = StructureElement.Loci.remap(loci, structure);
 
-            const out: number[] = [];
             for (const e of loci.elements) {
                 const unit = this.unitMap.get(e.unit.id);
                 if (unit) {
                     const { index: residueIndex } = e.unit.model.atomicHierarchy.residueAtomSegments;
                     OrderedSet.forEach(e.indices, v => {
                         const seqIdx = this.sequenceIndices.get(residueIndex[unit.elements[v]]);
-                        if (seqIdx !== undefined) out.push(seqIdx);
+                        if (seqIdx !== undefined && applyMarkerAction(this.markerArray, Interval.ofSingleton(seqIdx), action)) changed = true;
                     });
                 }
             }
-            return SortedArray.deduplicate(SortedArray.ofSortedArray(out));
         } else if (Structure.isLoci(loci)) {
-            if (!Structure.areRootsEquivalent(loci.structure, structure)) return Interval.Empty;
-            return Interval.ofBounds(0, this.length);
+            if (!Structure.areRootsEquivalent(loci.structure, structure)) return false;
+
+            if (applyMarkerAction(this.markerArray, Interval.ofBounds(0, this.length), action)) changed = true;
         }
-        return Interval.Empty;
+        return changed;
     }
 
     getLoci(seqIdx: number) {
@@ -86,8 +86,9 @@ export class HeteroSequenceWrapper extends SequenceWrapper<StructureUnit> {
         }
 
         const length = sequence.length;
+        const markerArray = new Uint8Array(length);
 
-        super(data, length);
+        super(data, markerArray, length);
 
         this.unitMap = new Map();
         for (const unit of data.units) this.unitMap.set(unit.id, unit);
@@ -97,4 +98,4 @@ export class HeteroSequenceWrapper extends SequenceWrapper<StructureUnit> {
         this.residueIndices = residueIndices;
         this.seqToUnit = seqToUnit;
     }
-}
+}

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

@@ -1,17 +1,17 @@
 /**
- * Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author Adam Midlik <midlik@gmail.com>
  */
 
-import { Interval, OrderedSet, SortedArray } from '../../mol-data/int';
+import { StructureSelection, StructureQuery, Structure, Queries, StructureProperties as SP, StructureElement, Unit } from '../../mol-model/structure';
+import { SequenceWrapper, StructureUnit } from './wrapper';
+import { OrderedSet, Interval, SortedArray } from '../../mol-data/int';
 import { Loci } from '../../mol-model/loci';
 import { Sequence } from '../../mol-model/sequence';
-import { Queries, StructureProperties as SP, Structure, StructureElement, StructureQuery, StructureSelection, Unit } from '../../mol-model/structure';
 import { MissingResidues } from '../../mol-model/structure/model/properties/common';
 import { ColorNames } from '../../mol-util/color/names';
-import { SequenceWrapper, StructureUnit } from './wrapper';
+import { MarkerAction, applyMarkerAction, applyMarkerActionAtPosition } from '../../mol-util/marker-action';
 
 export class PolymerSequenceWrapper extends SequenceWrapper<StructureUnit> {
     private readonly unitMap: Map<number, Unit>;
@@ -41,30 +41,28 @@ export class PolymerSequenceWrapper extends SequenceWrapper<StructureUnit> {
             : 'msp-sequence-present';
     }
 
-    override getSeqIndices(loci: Loci): OrderedSet {
+    mark(loci: Loci, action: MarkerAction): boolean {
+        let changed = false;
         const { structure } = this.data;
         const index = (seqId: number) => this.sequence.index(seqId);
-
         if (StructureElement.Loci.is(loci)) {
-            if (!Structure.areRootsEquivalent(loci.structure, structure)) return Interval.Empty;
+            if (!Structure.areRootsEquivalent(loci.structure, structure)) return false;
             loci = StructureElement.Loci.remap(loci, structure);
 
-            const out: number[] = [];
             for (const e of loci.elements) {
                 if (!this.unitMap.has(e.unit.id)) continue;
 
                 if (Unit.isAtomic(e.unit)) {
-                    collectSeqIdxAtomic(out, e, index);
+                    changed = applyMarkerAtomic(e, action, this.markerArray, index) || changed;
                 } else {
-                    collectSeqIdxCoarse(out, e, index);
+                    changed = applyMarkerCoarse(e, action, this.markerArray, index) || changed;
                 }
             }
-            return SortedArray.deduplicate(SortedArray.ofSortedArray(out));
         } else if (Structure.isLoci(loci)) {
-            if (!Structure.areRootsEquivalent(loci.structure, structure)) return Interval.Empty;
-            return this.observed;
+            if (!Structure.areRootsEquivalent(loci.structure, structure)) return false;
+            if (applyMarkerAction(this.markerArray, this.observed, action)) changed = true;
         }
-        return Interval.Empty;
+        return changed;
     }
 
     getLoci(seqIdx: number) {
@@ -77,8 +75,9 @@ export class PolymerSequenceWrapper extends SequenceWrapper<StructureUnit> {
         const entitySeq = data.units[0].model.sequence.byEntityKey[SP.entity.key(l)];
 
         const length = entitySeq.sequence.length;
+        const markerArray = new Uint8Array(length);
 
-        super(data, length);
+        super(data, markerArray, length);
 
         this.unitMap = new Map();
         for (const unit of data.units) this.unitMap.set(unit.id, unit);
@@ -118,20 +117,19 @@ function createResidueQuery(chainGroupId: number, operatorName: string, label_se
     });
 }
 
-function collectSeqIdxAtomic(out: number[], e: StructureElement.Loci.Element, index: (seqId: number) => number) {
+function applyMarkerAtomic(e: StructureElement.Loci.Element, action: MarkerAction, markerArray: Uint8Array, index: (seqId: number) => number) {
     const { model, elements } = e.unit;
     const { index: residueIndex } = model.atomicHierarchy.residueAtomSegments;
     const { label_seq_id } = model.atomicHierarchy.residues;
 
     OrderedSet.forEachSegment(e.indices, i => residueIndex[elements[i]], rI => {
         const seqId = label_seq_id.value(rI);
-        const seqIdx = index(seqId);
-        out.push(seqIdx);
+        applyMarkerActionAtPosition(markerArray, index(seqId), action);
     });
     return true;
 }
 
-function collectSeqIdxCoarse(out: number[], e: StructureElement.Loci.Element, index: (seqId: number) => number) {
+function applyMarkerCoarse(e: StructureElement.Loci.Element, action: MarkerAction, markerArray: Uint8Array, index: (seqId: number) => number) {
     const { model, elements } = e.unit;
     const begin = Unit.isSpheres(e.unit) ? model.coarseHierarchy.spheres.seq_id_begin : model.coarseHierarchy.gaussians.seq_id_begin;
     const end = Unit.isSpheres(e.unit) ? model.coarseHierarchy.spheres.seq_id_end : model.coarseHierarchy.gaussians.seq_id_end;
@@ -139,8 +137,8 @@ function collectSeqIdxCoarse(out: number[], e: StructureElement.Loci.Element, in
     OrderedSet.forEach(e.indices, i => {
         const eI = elements[i];
         for (let s = index(begin.value(eI)), e = index(end.value(eI)); s <= e; s++) {
-            out.push(s);
+            applyMarkerActionAtPosition(markerArray, s, action);
         }
     });
     return true;
-}
+}

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

@@ -1,26 +1,21 @@
 /**
- * Copyright (c) 2018-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2020 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>
- * @author Adam Midlik <midlik@gmail.com>
  */
 
 import * as React from 'react';
 import { Subject } from 'rxjs';
 import { throttleTime } from 'rxjs/operators';
 import { OrderedSet } from '../../mol-data/int';
-import { EveryLoci } from '../../mol-model/loci';
 import { StructureElement, StructureProperties, Unit } from '../../mol-model/structure';
-import { PluginCommands } from '../../mol-plugin/commands';
 import { Representation } from '../../mol-repr/representation';
-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 { PluginUIComponent } from '../base';
 import { SequenceWrapper } from './wrapper';
 
-
 type SequenceProps = {
     sequenceWrapper: SequenceWrapper.Any,
     sequenceNumberPeriod?: number,
@@ -30,18 +25,11 @@ type SequenceProps = {
 /** Note, if this is changed, the CSS for `msp-sequence-number` needs adjustment too */
 const MaxSequenceNumberSize = 5;
 
-const DefaultMarkerColors = {
-    selected: 'rgb(51, 255, 25)',
-    highlighted: 'rgb(255, 102, 153)',
-    focused: '',
-};
-
 // 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 };
 
     protected lociHighlightProvider = (loci: Representation.Loci, action: MarkerAction) => {
         const changed = this.props.sequenceWrapper.markResidue(loci.loci, action);
@@ -71,33 +59,6 @@ export class Sequence<P extends SequenceProps> extends PluginUIComponent<P> {
             const loci = this.getLoci(e.seqIdx < 0 ? void 0 : e.seqIdx);
             this.hover(loci, e.buttons, e.button, e.modifiers);
         });
-        this.subscribe(this.plugin.managers.structure.focus.behaviors.current, focus => {
-            this.updateFocus(focus?.loci);
-            this.updateMarker();
-        });
-
-        this.updateColors();
-        PluginCommands.Canvas3D.SetSettings.subscribe(this.plugin, () => {
-            this.updateColors();
-            this.updateMarker();
-        });
-    }
-
-    updateColors() {
-        if (this.plugin.canvas3d) {
-            this.markerColors.highlighted = Color.toHexStyle(this.plugin.canvas3d.props.renderer.highlightColor);
-            this.markerColors.selected = Color.toHexStyle(this.plugin.canvas3d.props.renderer.selectColor);
-        } else {
-            this.markerColors.highlighted = DefaultMarkerColors.highlighted;
-            this.markerColors.selected = DefaultMarkerColors.selected;
-        }
-    }
-
-    updateFocus(loci: StructureElement.Loci | undefined) {
-        this.props.sequenceWrapper.markResidue(EveryLoci, 'unfocus');
-        if (loci) {
-            this.props.sequenceWrapper.markResidue(loci, 'focus');
-        }
     }
 
     componentWillUnmount() {
@@ -127,18 +88,6 @@ export class Sequence<P extends SequenceProps> extends PluginUIComponent<P> {
         const ev = { current: Representation.Loci.Empty, buttons, button, modifiers };
         if (loci !== undefined && !StructureElement.Loci.isEmpty(loci)) {
             ev.current = { loci };
-            if (this.mouseDownLoci) {
-                const ref = this.mouseDownLoci.elements[0];
-                const ext = loci.elements[0];
-                const min = Math.min(OrderedSet.min(ref.indices), OrderedSet.min(ext.indices));
-                const max = Math.max(OrderedSet.max(ref.indices), OrderedSet.max(ext.indices));
-
-                const range = StructureElement.Loci(loci.structure, [{
-                    unit: ref.unit,
-                    indices: OrderedSet.ofRange(min as StructureElement.UnitIndex, max as StructureElement.UnitIndex)
-                }]);
-                ev.current = { loci: range };
-            }
         }
         this.plugin.behaviors.interaction.hover.next(ev);
     }
@@ -162,6 +111,11 @@ export class Sequence<P extends SequenceProps> extends PluginUIComponent<P> {
 
         const seqIdx = this.getSeqIdx(e);
         const loci = this.getLoci(seqIdx);
+        const buttons = getButtons(e.nativeEvent);
+        const button = getButton(e.nativeEvent);
+        const modifiers = getModifiers(e.nativeEvent);
+
+        this.click(loci, buttons, button, modifiers);
         this.mouseDownLoci = loci;
     };
 
@@ -174,51 +128,44 @@ export class Sequence<P extends SequenceProps> extends PluginUIComponent<P> {
         const seqIdx = this.getSeqIdx(e);
         const loci = this.getLoci(seqIdx);
 
-        if (loci) {
+        if (loci && !StructureElement.Loci.areEqual(this.mouseDownLoci, loci)) {
             const buttons = getButtons(e.nativeEvent);
             const button = getButton(e.nativeEvent);
             const modifiers = getModifiers(e.nativeEvent);
 
-            let range = loci;
-            if (!StructureElement.Loci.areEqual(this.mouseDownLoci, loci)) {
-                const ref = this.mouseDownLoci.elements[0];
-                const ext = loci.elements[0];
-                const min = Math.min(OrderedSet.min(ref.indices), OrderedSet.min(ext.indices));
-                const max = Math.max(OrderedSet.max(ref.indices), OrderedSet.max(ext.indices));
+            const ref = this.mouseDownLoci.elements[0];
+            const ext = loci.elements[0];
+            const min = Math.min(OrderedSet.min(ref.indices), OrderedSet.min(ext.indices));
+            const max = Math.max(OrderedSet.max(ref.indices), OrderedSet.max(ext.indices));
 
-                range = StructureElement.Loci(loci.structure, [{
-                    unit: ref.unit,
-                    indices: OrderedSet.ofRange(min as StructureElement.UnitIndex, max as StructureElement.UnitIndex)
-                }]);
-            }
+            const range = StructureElement.Loci(loci.structure, [{
+                unit: ref.unit,
+                indices: OrderedSet.ofRange(min as StructureElement.UnitIndex, max as StructureElement.UnitIndex)
+            }]);
 
-            this.click(range, buttons, button, modifiers);
+            this.click(StructureElement.Loci.subtract(range, this.mouseDownLoci), buttons, button, modifiers);
         }
         this.mouseDownLoci = undefined;
     };
 
-    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;
-        return '';
+    protected getBackgroundColor(marker: number) {
+        // TODO: make marker color configurable
+        if (typeof marker === 'undefined') console.error('unexpected marker value');
+        return marker === 0
+            ? ''
+            : marker % 2 === 0
+                ? 'rgb(51, 255, 25)' // selected
+                : 'rgb(255, 102, 153)'; // highlighted
     }
 
     protected getResidueClass(seqIdx: number, label: string) {
-        const seqWrapper = this.props.sequenceWrapper;
-        const classes = [seqWrapper.residueClass(seqIdx)];
-        if (label.length > 1) {
-            classes.push(seqIdx === 0 ? 'msp-sequence-residue-long-begin' : 'msp-sequence-residue-long');
-        }
-        if (seqWrapper.isHighlighted(seqIdx)) classes.push('msp-sequence-residue-highlighted');
-        if (seqWrapper.isSelected(seqIdx)) classes.push('msp-sequence-residue-selected');
-        if (seqWrapper.isFocused(seqIdx)) classes.push('msp-sequence-residue-focused');
-        return classes.join(' ');
+        return label.length > 1
+            ? this.props.sequenceWrapper.residueClass(seqIdx) + (seqIdx === 0 ? ' msp-sequence-residue-long-begin' : ' msp-sequence-residue-long')
+            : this.props.sequenceWrapper.residueClass(seqIdx);
     }
 
-    protected residue(seqIdx: number, label: string) {
-        return <span key={seqIdx} data-seqid={seqIdx} style={{ backgroundColor: this.getBackgroundColor(seqIdx) }} className={this.getResidueClass(seqIdx, label)}>{`\u200b${label}\u200b`}</span>;
+    protected residue(seqIdx: number, label: string, marker: number) {
+        return <span key={seqIdx} data-seqid={seqIdx} style={{ backgroundColor: this.getBackgroundColor(marker) }} className={this.getResidueClass(seqIdx, label)}>{`\u200b${label}\u200b`}</span>;
     }
 
     protected getSequenceNumberClass(seqIdx: number, seqNum: string, label: string) {
@@ -261,23 +208,30 @@ export class Sequence<P extends SequenceProps> extends PluginUIComponent<P> {
     protected updateMarker() {
         if (!this.parentDiv.current) return;
         const xs = this.parentDiv.current.children;
+        const { markerArray } = this.props.sequenceWrapper;
         const hasNumbers = !this.props.hideSequenceNumbers, period = this.sequenceNumberPeriod;
 
-        const seqWrapper = this.props.sequenceWrapper;
-        const seqLength = seqWrapper.length;
+        // let first: HTMLSpanElement | undefined;
+
         let o = 0;
-        for (let i = 0; i < seqLength; i++) {
-            if (hasNumbers && i % period === 0 && i < seqLength) o++;
+        for (let i = 0, il = markerArray.length; i < il; i++) {
+            if (hasNumbers && i % period === 0 && i < il) o++;
             // o + 1 to account for help icon
             const span = xs[o] as HTMLSpanElement;
             if (!span) return;
             o++;
 
-            const className = this.getResidueClass(i, seqWrapper.residueLabel(i));
-            if (span.className !== className) span.className = className;
-            const backgroundColor = this.getBackgroundColor(i);
+            // if (!first && markerArray[i] > 0) {
+            //     first = span;
+            // }
+
+            const backgroundColor = this.getBackgroundColor(markerArray[i]);
             if (span.style.backgroundColor !== backgroundColor) span.style.backgroundColor = backgroundColor;
         }
+
+        // if (first) {
+        //     first.scrollIntoView({ block: 'nearest' });
+        // }
     }
 
     mouseMove = (e: React.MouseEvent) => {
@@ -301,7 +255,7 @@ export class Sequence<P extends SequenceProps> extends PluginUIComponent<P> {
             this.lastMouseOverSeqIdx = seqIdx;
             if (this.mouseDownLoci !== undefined) {
                 const loci = this.getLoci(seqIdx);
-                this.hover(loci, ButtonsType.Flag.None, ButtonsType.Flag.None, modifiers);
+                this.hover(loci, ButtonsType.Flag.None, ButtonsType.Flag.None, { ...modifiers, shift: true });
             } else {
                 this.highlightQueue.next({ seqIdx, buttons, button, modifiers });
             }
@@ -332,12 +286,9 @@ export class Sequence<P extends SequenceProps> extends PluginUIComponent<P> {
             if (hasNumbers && i % period === 0 && i < il) {
                 elems[elems.length] = this.getSequenceNumberSpan(i, label);
             }
-            elems[elems.length] = this.residue(i, label);
+            elems[elems.length] = this.residue(i, label, sw.markerArray[i]);
         }
 
-        // ensure the focus markers are updated after sequenceRender is recreated
-        this.updateFocus(this.plugin.managers.structure.focus.behaviors.current.value?.loci);
-
         // calling .updateMarker here is neccesary to ensure existing
         // residue spans are updated as react won't update them
         this.updateMarker();

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

@@ -1,15 +1,14 @@
 /**
- * Copyright (c) 2019-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author Adam Midlik <midlik@gmail.com>
  */
 
-import { Interval, OrderedSet } from '../../mol-data/int';
+import { Interval } from '../../mol-data/int';
 import { Loci, isEveryLoci } from '../../mol-model/loci';
-import { Structure, StructureElement, Unit } from '../../mol-model/structure';
-import { Color } from '../../mol-util/color';
 import { MarkerAction, applyMarkerAction } from '../../mol-util/marker-action';
+import { StructureElement, Structure, Unit } from '../../mol-model/structure';
+import { Color } from '../../mol-util/color';
 
 export type StructureUnit = { structure: Structure, units: Unit[] }
 
@@ -22,19 +21,9 @@ abstract class SequenceWrapper<D> {
 
     abstract getLoci(seqIdx: number): StructureElement.Loci
 
-    /** Return list of sequence viewer positions that correspond to `loci` */
-    abstract getSeqIndices(loci: Loci): OrderedSet;
-
-    mark(loci: Loci, action: MarkerAction): boolean {
-        const seqIdxs = this.getSeqIndices(loci);
-        if (OrderedSet.size(seqIdxs) === 0) return false;
-        return applyMarkerAction(this.markerArray, seqIdxs, action);
-    }
-
-    markResidue(loci: Loci, action: MarkerAction | 'focus' | 'unfocus'): boolean {
-        if (action === 'focus') return this.markResidueFocus(loci, true);
-        if (action === 'unfocus') return this.markResidueFocus(loci, false);
+    abstract mark(loci: Loci, action: MarkerAction): boolean;
 
+    markResidue(loci: Loci, action: MarkerAction) {
         if (isEveryLoci(loci)) {
             return applyMarkerAction(this.markerArray, Interval.ofLength(this.length), action);
         } else {
@@ -42,42 +31,11 @@ abstract class SequenceWrapper<D> {
         }
     }
 
-    private markResidueFocus(loci: Loci, focusState: boolean) {
-        const value = focusState ? 1 : 0;
-        if (isEveryLoci(loci)) {
-            this.focusMarkerArray.fill(value, 0, this.length);
-            return true;
-        } else {
-            const seqIdxs = this.getSeqIndices(loci);
-            OrderedSet.forEach(seqIdxs, seqIdx => this.focusMarkerArray[seqIdx] = value);
-            return OrderedSet.size(seqIdxs) > 0;
-        }
-    }
+    constructor(readonly data: D, readonly markerArray: Uint8Array, readonly length: number) {
 
-    /** Return true if the position `seqIndex` in sequence view is highlighted */
-    isHighlighted(seqIndex: number): boolean {
-        return !!(this.markerArray[seqIndex] & 1);
-    }
-    /** Return true if the position `seqIndex` in sequence view is selected */
-    isSelected(seqIndex: number): boolean {
-        return !!(this.markerArray[seqIndex] & 2);
-    }
-    /** Return true if the position `seqIndex` in sequence view is focused */
-    isFocused(seqIndex: number): boolean {
-        return !!(this.focusMarkerArray[seqIndex]);
-    }
-
-    /** Markers for "highlighted" and "selected" (2 bits per position) */
-    readonly markerArray: Uint8Array;
-    /** Markers for "focused" (1 bit per position) */
-    readonly focusMarkerArray: Uint8Array;
-
-    constructor(readonly data: D, readonly length: number) {
-        this.markerArray = new Uint8Array(length);
-        this.focusMarkerArray = new Uint8Array(length);
     }
 }
 
 namespace SequenceWrapper {
     export type Any = SequenceWrapper<any>
-}
+}

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

@@ -215,12 +215,8 @@
     color: $msp-btn-link-toggle-off-font-color !important;
 }
 
-.msp-btn-link-toggle-on:hover {
-    color: $msp-btn-link-toggle-on-hover-font-color !important;
-}
-
-.msp-btn-link-toggle-off:hover {
-    color: $msp-btn-link-toggle-off-hover-font-color !important;
+.msp-btn-link-toggle-off:hover,  .msp-btn-link-toggle-on:hover {
+    color: $hover-font-color !important;
 }
 
 @mixin msp-btn($name, $font, $bg) {

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

@@ -1,5 +1,4 @@
 @use "sass:math";
-@use "sass:color";
 
 .msp-control-row {
     position: relative;
@@ -333,7 +332,7 @@
 
 .msp-help:hover span {
     display: inline-block;
-    background: linear-gradient($default-background, color.change($default-background, $alpha: 0.8));
+    background: linear-gradient($default-background, change-color($default-background, $alpha: 0.8));
 }
 
 .msp-help-text {

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

@@ -8,7 +8,6 @@
 }
 
 $sequence-select-height: 24px;
-
 .msp-sequence-select {
     position: relative;
     height: $sequence-select-height;
@@ -85,11 +84,6 @@ $sequence-select-height: 24px;
         margin: 0em 0.2em 0em 0em;
     }
 
-    .msp-sequence-residue-focused {
-        font-weight: bold;
-        text-decoration: underline;
-    }
-
     .msp-sequence-label {
         color: $sequence-number-color;
         font-size: 90%;
@@ -97,7 +91,7 @@ $sequence-select-height: 24px;
         padding-bottom: 1em;
         padding-left: 0.2em;
     }
-
+    
     .msp-sequence-number {
         color: $sequence-number-color;
         word-break: keep-all;

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

@@ -21,11 +21,9 @@
 }
 
 ::-webkit-scrollbar-thumb {
-    border-radius: 10px;
+    border-radius: 0;
     //-webkit-box-shadow: inset 0 0 6px rgba(0,0,0,0.9);
-    background-color: color-increase-contrast($control-background, 16%);
-    border: solid 1px transparent;
-    background-clip: content-box;
+    background-color: color-lower-contrast($control-background, 8%);
 }
 
 @import 'components/controls-base';

src/mol-plugin-ui/skin/base/variables.scss

@@ -1,5 +1,3 @@
-@use "sass:color";
-
 // measures
 
 $control-label-width:   110px;
@@ -55,8 +53,6 @@ $msp-form-control-background: color-lower-contrast($default-background, 2.5%);
 $msp-btn-link-font-color: $font-color;
 $msp-btn-link-toggle-on-font-color: $font-color;
 $msp-btn-link-toggle-off-font-color: color-lower-contrast($font-color, 33%);
-$msp-btn-link-toggle-on-hover-font-color: $hover-font-color;
-$msp-btn-link-toggle-off-hover-font-color: color.adjust(color-lower-contrast($hover-font-color, 25%), $saturation: -30%, $space: hsl);
 
 // used for "actions" -- i.e. + in selection
 $msp-btn-remove-font-color: $font-color;

src/mol-plugin-ui/spec.ts

@@ -1,9 +1,8 @@
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2024 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 Ventura Rivera <venturaxrivera@gmail.com>
  */
 
 
@@ -12,8 +11,6 @@ import { CreateVolumeStreamingBehavior } from '../mol-plugin/behavior/dynamic/vo
 import { DefaultPluginSpec, PluginSpec } from '../mol-plugin/spec';
 import { StateAction, StateTransformer } from '../mol-state';
 import { VolumeStreamingCustomControls } from './custom/volume';
-import { Loci } from '../mol-model/loci';
-import { SequenceViewMode } from './sequence';
 
 export { PluginUISpec };
 
@@ -30,28 +27,9 @@ interface PluginUISpec extends PluginSpec {
         },
         sequenceViewer?: {
             view?: React.ComponentClass | React.FC
-            modeOptions?: SequenceViewMode[],
-            defaultMode?: SequenceViewMode,
         }
         hideTaskOverlay?: boolean,
         disableDragOverlay?: boolean,
-        selectionTools?: {
-            controls?: React.ComponentClass | React.FC,
-            granularityOptions?: Loci.Granularity[],
-            hide?: {
-                granularity?: boolean,
-                union?: boolean,
-                subtract?: boolean,
-                intersect?: boolean,
-                set?: boolean,
-                theme?: boolean,
-                componentAdd?: boolean,
-                componentRemove?: boolean,
-                undo?: boolean,
-                help?: boolean,
-                cancel?: boolean,
-            },
-        },
     },
 }
 

src/mol-plugin-ui/structure/quick-styles.tsx

@@ -1,21 +1,19 @@
 /**
- * Copyright (c) 2022-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2022-2024 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>
- * @author Adam Midlik <midlik@gmail.com>
  */
 
-import { PostprocessingParams } from '../../mol-canvas3d/passes/postprocessing';
 import { PresetStructureRepresentations } from '../../mol-plugin-state/builder/structure/representation-preset';
-import { PluginConfig } from '../../mol-plugin/config';
-import { PluginContext } from '../../mol-plugin/context';
 import { Color } from '../../mol-util/color';
-import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { CollapsableControls, PurePluginUIComponent } from '../base';
 import { Button } from '../controls/common';
 import { MagicWandSvg } from '../controls/icons';
-
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { PostprocessingParams } from '../../mol-canvas3d/passes/postprocessing';
+import { PluginConfig } from '../../mol-plugin/config';
+import { StructureComponentManager } from '../../mol-plugin-state/manager/structure/component';
 
 export class StructureQuickStylesControls extends CollapsableControls {
     defaultState() {
@@ -33,118 +31,65 @@ export class StructureQuickStylesControls extends CollapsableControls {
     }
 }
 
+export class QuickStyles extends PurePluginUIComponent {
+    async default() {
+        const { structures } = this.plugin.managers.structure.hierarchy.selection;
+        const preset = this.plugin.config.get(PluginConfig.Structure.DefaultRepresentationPreset) || PresetStructureRepresentations.auto.id;
+        const provider = this.plugin.builders.structure.representation.resolveProvider(preset);
+        await this.plugin.managers.structure.component.applyPreset(structures, provider);
 
-type PresetName = 'default' | 'cartoon' | 'spacefill' | 'surface';
-type StyleName = 'default' | 'illustrative';
+        this.plugin.managers.structure.component.setOptions(PD.getDefaultValues(StructureComponentManager.OptionsParams));
 
-interface QuickStylesState {
-    busy: boolean,
-    style: StyleName,
-}
-
-
-export class QuickStyles extends PurePluginUIComponent<{}, QuickStylesState> {
-    state: QuickStylesState = { busy: false, style: 'default' };
-
-    async applyRepresentation(preset: PresetName) {
-        this.setState({ busy: true });
-        await applyRepresentationPreset(this.plugin, preset);
-        await applyStyle(this.plugin, this.state.style); // reapplying current style is desired because some presets come with weird params (namely spacefill comes with ignoreLight:true)
-        this.setState({ busy: false });
-    }
-
-    async applyStyle(style: StyleName) {
-        this.setState({ busy: true });
-        await applyStyle(this.plugin, style);
-        this.setState({ busy: false, style });
-    }
-
-    render() {
-        return <>
-            <NoncollapsableGroup title='Apply Representation'>
-                <div className='msp-flex-row'>
-                    <Button title='Applies default representation preset (depends on structure size)'
-                        onClick={() => this.applyRepresentation('default')} disabled={this.state.busy} >
-                        Default
-                    </Button>
-                    <Button title='Applies cartoon polymer and ball-and-stick ligand representation preset'
-                        onClick={() => this.applyRepresentation('cartoon')} disabled={this.state.busy} >
-                        Cartoon
-                    </Button>
-                    <Button title='Applies spacefill representation preset'
-                        onClick={() => this.applyRepresentation('spacefill')} disabled={this.state.busy} >
-                        Spacefill
-                    </Button>
-                    <Button title='Applies molecular surface representation preset'
-                        onClick={() => this.applyRepresentation('surface')} disabled={this.state.busy} >
-                        Surface
-                    </Button>
-                </div>
-            </NoncollapsableGroup>
-            <NoncollapsableGroup title='Apply Style'>
-                <div className='msp-flex-row'>
-                    <Button title='Applies default appearance (no outline, no ignore-light)'
-                        onClick={() => this.applyStyle('default')} disabled={this.state.busy} >
-                        Default
-                    </Button>
-                    <Button title='Applies illustrative appearance (outline, ignore-light)'
-                        onClick={() => this.applyStyle('illustrative')} disabled={this.state.busy} >
-                        Illustrative
-                    </Button>
-                </div>
-            </NoncollapsableGroup>
-        </>;
-    }
-}
-
-
-/** Visually imitates `ControlGroup` but is always expanded */
-function NoncollapsableGroup(props: { title: string, children: any }): JSX.Element {
-    return <div className='msp-control-group-wrapper'>
-        <div className='msp-control-group-header'><div><b>{props.title}</b></div></div>
-        {props.children}
-    </div>;
-}
-
-async function applyRepresentationPreset(plugin: PluginContext, preset: PresetName) {
-    const { structures } = plugin.managers.structure.hierarchy.selection;
-
-    switch (preset) {
-        case 'default':
-            const defaultPreset = plugin.config.get(PluginConfig.Structure.DefaultRepresentationPreset) || PresetStructureRepresentations.auto.id;
-            const provider = plugin.builders.structure.representation.resolveProvider(defaultPreset);
-            await plugin.managers.structure.component.applyPreset(structures, provider);
-            break;
-        case 'spacefill':
-            await plugin.managers.structure.component.applyPreset(structures, PresetStructureRepresentations.illustrative);
-            break;
-        case 'cartoon':
-            await plugin.managers.structure.component.applyPreset(structures, PresetStructureRepresentations['polymer-and-ligand']);
-            break;
-        case 'surface':
-            await plugin.managers.structure.component.applyPreset(structures, PresetStructureRepresentations['molecular-surface']);
-            break;
-    }
-}
-
-async function applyStyle(plugin: PluginContext, style: StyleName) {
-    if (style === 'default') {
-        await plugin.managers.structure.component.setOptions({ ...plugin.managers.structure.component.state.options, ignoreLight: false });
-
-        if (plugin.canvas3d) {
+        if (this.plugin.canvas3d) {
             const p = PD.getDefaultValues(PostprocessingParams);
-            plugin.canvas3d.setProps({
-                postprocessing: { outline: p.outline, occlusion: p.occlusion, shadow: p.shadow }
+            this.plugin.canvas3d.setProps({
+                postprocessing: { outline: p.outline, occlusion: p.occlusion }
             });
         }
     }
 
-    if (style === 'illustrative') {
-        await plugin.managers.structure.component.setOptions({ ...plugin.managers.structure.component.state.options, ignoreLight: true });
+    async illustrative() {
+        const { structures } = this.plugin.managers.structure.hierarchy.selection;
+        await this.plugin.managers.structure.component.applyPreset(structures, PresetStructureRepresentations.illustrative);
 
-        if (plugin.canvas3d) {
-            const pp = plugin.canvas3d.props.postprocessing;
-            plugin.canvas3d.setProps({
+        if (this.plugin.canvas3d) {
+            this.plugin.canvas3d.setProps({
+                postprocessing: {
+                    outline: {
+                        name: 'on',
+                        params: {
+                            scale: 1,
+                            color: Color(0x000000),
+                            threshold: 0.25,
+                            includeTransparent: true,
+                        }
+                    },
+                    occlusion: {
+                        name: 'on',
+                        params: {
+                            multiScale: { name: 'off', params: {} },
+                            radius: 5,
+                            bias: 0.8,
+                            blurKernelSize: 15,
+                            blurDepthBias: 0.5,
+                            samples: 32,
+                            resolutionScale: 1,
+                            color: Color(0x000000),
+                            transparentThreshold: 0.4,
+                        }
+                    },
+                    shadow: { name: 'off', params: {} },
+                }
+            });
+        }
+    }
+
+    async stylized() {
+        this.plugin.managers.structure.component.setOptions({ ...this.plugin.managers.structure.component.state.options, ignoreLight: true });
+
+        if (this.plugin.canvas3d) {
+            const pp = this.plugin.canvas3d.props.postprocessing;
+            this.plugin.canvas3d.setProps({
                 postprocessing: {
                     outline: {
                         name: 'on',
@@ -178,4 +123,18 @@ async function applyStyle(plugin: PluginContext, style: StyleName) {
             });
         }
     }
-}
+
+    render() {
+        return <div className='msp-flex-row'>
+            <Button noOverflow title='Applies default representation preset and sets outline and occlusion effects to default' onClick={() => this.default()} style={{ width: 'auto' }}>
+                Default
+            </Button>
+            <Button noOverflow title='Applies illustrative representation preset and Stylize it' onClick={() => this.illustrative()} style={{ width: 'auto' }}>
+                Illustrative
+            </Button>
+            <Button noOverflow title='Does not change representation, enables outline and occlusion effects, enables ignore-light representation parameter' onClick={() => this.stylized()} style={{ width: 'auto' }}>
+                Stylize Current
+            </Button>
+        </div>;
+    }
+}

src/mol-plugin-ui/structure/selection.tsx

@@ -5,7 +5,6 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Jason Pattle <jpattle.exscientia.co.uk>
  * @author Ludovic Autin <ludovic.autin@gmail.com>
- * @author Ventura Rivera <venturaxrivera@gmail.com>
  */
 
 import * as React from 'react';
@@ -62,8 +61,6 @@ interface StructureSelectionActionsControlsState {
 
     action?: StructureSelectionModifier | 'theme' | 'add-component' | 'help',
     helper?: SelectionHelperType,
-
-    structureSelectionParams?: typeof StructureSelectionParams,
 }
 
 const ActionHeader = new Map<StructureSelectionModifier, string>([
@@ -81,8 +78,6 @@ export class StructureSelectionActionsControls extends PluginUIComponent<{}, Str
         isEmpty: true,
         isBusy: false,
         canUndo: false,
-
-        structureSelectionParams: StructureSelectionParams,
     };
 
     componentDidMount() {
@@ -107,20 +102,6 @@ export class StructureSelectionActionsControls extends PluginUIComponent<{}, Str
         this.subscribe(this.plugin.state.data.events.historyUpdated, ({ state }) => {
             this.setState({ canUndo: state.canUndo });
         });
-
-        // Update structureSelectionParams state if there are custom-defined granularityOptions
-        const granularityOptions = this.plugin.spec.components?.selectionTools?.granularityOptions;
-        if (granularityOptions) {
-            const granularitySet = new Set((granularityOptions));
-            const structureSelectionParams = {
-                ...StructureSelectionParams,
-                granularity: {
-                    ...StructureSelectionParams.granularity,
-                    options: StructureSelectionParams.granularity.options.filter(([firstItem]) => granularitySet.has(firstItem)),
-                },
-            };
-            this.setState({ structureSelectionParams: structureSelectionParams });
-        }
     }
 
     get isDisabled() {
@@ -237,7 +218,6 @@ export class StructureSelectionActionsControls extends PluginUIComponent<{}, Str
 
     render() {
         const granularity = this.plugin.managers.interactivity.props.granularity;
-        const hide = this.plugin.spec.components?.selectionTools?.hide;
         const undoTitle = this.state.canUndo
             ? `Undo ${this.plugin.state.data.latestUndoLabel}`
             : 'Some mistakes of the past can be undone.';
@@ -283,19 +263,19 @@ export class StructureSelectionActionsControls extends PluginUIComponent<{}, Str
 
         return <>
             <div className='msp-flex-row' style={{ background: 'none' }}>
-                {(!hide?.granularity) && <PureSelectControl title={`Picking Level for selecting and highlighting`} param={this.state.structureSelectionParams.granularity} name='granularity' value={granularity} onChange={this.setGranuality} isDisabled={this.isDisabled} />}
-                {(!hide?.union) && <ToggleButton icon={UnionSvg} title={`${ActionHeader.get('add')}. Hold shift key to keep menu open.`} toggle={this.toggleAdd} isSelected={this.state.action === 'add'} disabled={this.isDisabled} />}
-                {(!hide?.subtract) && <ToggleButton icon={SubtractSvg} title={`${ActionHeader.get('remove')}. Hold shift key to keep menu open.`} toggle={this.toggleRemove} isSelected={this.state.action === 'remove'} disabled={this.isDisabled} />}
-                {(!hide?.intersect) && <ToggleButton icon={IntersectSvg} title={`${ActionHeader.get('intersect')}. Hold shift key to keep menu open.`} toggle={this.toggleIntersect} isSelected={this.state.action === 'intersect'} disabled={this.isDisabled} />}
-                {(!hide?.set) && <ToggleButton icon={SetSvg} title={`${ActionHeader.get('set')}. Hold shift key to keep menu open.`} toggle={this.toggleSet} isSelected={this.state.action === 'set'} disabled={this.isDisabled} />}
+                <PureSelectControl title={`Picking Level for selecting and highlighting`} param={StructureSelectionParams.granularity} name='granularity' value={granularity} onChange={this.setGranuality} isDisabled={this.isDisabled} />
+                <ToggleButton icon={UnionSvg} title={`${ActionHeader.get('add')}. Hold shift key to keep menu open.`} toggle={this.toggleAdd} isSelected={this.state.action === 'add'} disabled={this.isDisabled} />
+                <ToggleButton icon={SubtractSvg} title={`${ActionHeader.get('remove')}. Hold shift key to keep menu open.`} toggle={this.toggleRemove} isSelected={this.state.action === 'remove'} disabled={this.isDisabled} />
+                <ToggleButton icon={IntersectSvg} title={`${ActionHeader.get('intersect')}. Hold shift key to keep menu open.`} toggle={this.toggleIntersect} isSelected={this.state.action === 'intersect'} disabled={this.isDisabled} />
+                <ToggleButton icon={SetSvg} title={`${ActionHeader.get('set')}. Hold shift key to keep menu open.`} toggle={this.toggleSet} isSelected={this.state.action === 'set'} disabled={this.isDisabled} />
 
-                {(!hide?.theme) && <ToggleButton icon={BrushSvg} title='Apply Theme to Selection' toggle={this.toggleTheme} isSelected={this.state.action === 'theme'} disabled={this.isDisabled} style={{ marginLeft: '10px' }} />}
-                {(!hide?.componentAdd) && <ToggleButton icon={CubeOutlineSvg} title='Create Component of Selection with Representation' toggle={this.toggleAddComponent} isSelected={this.state.action === 'add-component'} disabled={this.isDisabled} />}
-                {(!hide?.componentRemove) && <IconButton svg={RemoveSvg} title='Remove/subtract Selection from all Components' onClick={this.subtract} disabled={this.isDisabled} />}
-                {(!hide?.undo) && <IconButton svg={RestoreSvg} onClick={this.undo} disabled={!this.state.canUndo || this.isDisabled} title={undoTitle} />}
+                <ToggleButton icon={BrushSvg} title='Apply Theme to Selection' toggle={this.toggleTheme} isSelected={this.state.action === 'theme'} disabled={this.isDisabled} style={{ marginLeft: '10px' }} />
+                <ToggleButton icon={CubeOutlineSvg} title='Create Component of Selection with Representation' toggle={this.toggleAddComponent} isSelected={this.state.action === 'add-component'} disabled={this.isDisabled} />
+                <IconButton svg={RemoveSvg} title='Remove/subtract Selection from all Components' onClick={this.subtract} disabled={this.isDisabled} />
+                <IconButton svg={RestoreSvg} onClick={this.undo} disabled={!this.state.canUndo || this.isDisabled} title={undoTitle} />
 
-                {(!hide?.help) && <ToggleButton icon={HelpOutlineSvg} title='Show/hide help' toggle={this.toggleHelp} style={{ marginLeft: '10px' }} isSelected={this.state.action === 'help'} />}
-                {((!hide?.cancel) && this.plugin.config.get(PluginConfig.Viewport.ShowSelectionMode)) && (<IconButton svg={CancelOutlinedSvg} title='Turn selection mode off' onClick={this.turnOff} />)}
+                <ToggleButton icon={HelpOutlineSvg} title='Show/hide help' toggle={this.toggleHelp} style={{ marginLeft: '10px' }} isSelected={this.state.action === 'help'} />
+                {this.plugin.config.get(PluginConfig.Viewport.ShowSelectionMode) && (<IconButton svg={CancelOutlinedSvg} title='Turn selection mode off' onClick={this.turnOff} />)}
             </div>
             {children}
         </>;

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

@@ -28,7 +28,7 @@ export const DefaultClickResetCameraOnEmpty = Binding([
 export const DefaultClickResetCameraOnEmptySelectMode = Binding([
     Trigger(B.Flag.Secondary, M.create()),
     Trigger(B.Flag.Primary, M.create({ control: true }))
-], 'Reset camera focus (Selection Mode)', 'Click on nothing using ${triggers}');
+], 'Reset camera focus', 'Click on nothing using ${triggers}');
 
 type FocusLociBindings = {
     clickCenterFocus: Binding
@@ -45,7 +45,7 @@ export const DefaultFocusLociBindings: FocusLociBindings = {
     clickCenterFocusSelectMode: Binding([
         Trigger(B.Flag.Secondary, M.create()),
         Trigger(B.Flag.Primary, M.create({ control: true }))
-    ], 'Camera center and focus (Selection Mode)', 'Click element using ${triggers}'),
+    ], 'Camera center and focus', 'Click element using ${triggers}'),
     clickResetCameraOnEmpty: DefaultClickResetCameraOnEmpty,
     clickResetCameraOnEmptySelectMode: DefaultClickResetCameraOnEmptySelectMode,
 };
@@ -158,7 +158,7 @@ const DefaultCameraControlsBindings = {
     keyRockAnimation: Binding([Key('O')], 'Rock Animation', 'Press ${triggers}'),
     keyToggleFlyMode: Binding([Key('Space', M.create({ shift: true }))], 'Toggle Fly Mode', 'Press ${triggers}'),
     keyResetView: Binding([Key('T')], 'Reset View', 'Press ${triggers}'),
-    keyGlobalIllumination: Binding([Key('G')], 'Global Illumination', 'Press ${triggers}'),
+    keyGlobalIllumination: Binding([Key('G')], 'Gobal Illumination', 'Press ${triggers}'),
 };
 const CameraControlsParams = {
     bindings: PD.Value(DefaultCameraControlsBindings, { isHidden: true }),

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

@@ -1,10 +1,9 @@
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2024 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 Jason Pattle <jpattle.exscientia.co.uk>
- * @author Adam Midlik <midlik@gmail.com>
  */
 
 import { MarkerAction } from '../../../mol-util/marker-action';
@@ -96,9 +95,9 @@ export const HighlightLoci = PluginBehavior.create({
 
 export const DefaultSelectLociBindings = {
     clickSelect: Binding.Empty,
+    clickToggleExtend: Binding([Trigger(B.Flag.Primary, M.create({ shift: true }))], 'Toggle extended selection', 'Click on element using ${triggers} to extend selection along polymer'),
     clickSelectOnly: Binding.Empty,
     clickToggle: Binding([Trigger(B.Flag.Primary, M.create())], 'Toggle selection', 'Click on element using ${triggers}'),
-    clickToggleExtend: Binding([Trigger(B.Flag.Primary, M.create({ shift: true }))], 'Toggle extended selection', 'Click on element using ${triggers} to extend selection along polymer'),
     clickDeselect: Binding.Empty,
     clickDeselectAllOnEmpty: Binding([Trigger(B.Flag.Primary, M.create())], 'Deselect all', 'Click on nothing using ${triggers}'),
 };
@@ -243,21 +242,14 @@ export const DefaultFocusLociBindings = {
         Trigger(B.Flag.Primary, M.create()),
     ], 'Representation Focus', 'Click element using ${triggers}'),
     clickFocusAdd: Binding([
-        Trigger(B.Flag.Primary, M.create({ control: true })),
-        Trigger(B.Flag.Primary, M.create({ meta: true })),
-    ], 'Representation Focus Add', 'Click element using ${triggers}'),
-    clickFocusExtend: Binding([
         Trigger(B.Flag.Primary, M.create({ shift: true })),
-    ], 'Representation Focus Extend', 'Click on element using ${triggers}'),
+    ], 'Representation Focus Add', 'Click element using ${triggers}'),
     clickFocusSelectMode: Binding([
         // default is empty
-    ], 'Representation Focus (Selection Mode)', 'Click element using ${triggers}'),
+    ], 'Representation Focus', 'Click element using ${triggers}'),
     clickFocusAddSelectMode: Binding([
         // default is empty
-    ], 'Representation Focus Add (Selection Mode)', 'Click element using ${triggers}'),
-    clickFocusExtendSelectMode: Binding([
-        // default is empty
-    ], 'Representation Focus Extend (Selection Mode)', 'Click on element using ${triggers}'),
+    ], 'Representation Focus Add', 'Click element using ${triggers}'),
 };
 const FocusLociParams = {
     bindings: PD.Value(DefaultFocusLociBindings, { isHidden: true }),
@@ -270,19 +262,11 @@ export const FocusLoci = PluginBehavior.create<FocusLociProps>({
     ctor: class extends PluginBehavior.Handler<FocusLociProps> {
         register(): void {
             this.subscribeObservable(this.ctx.behaviors.interaction.click, ({ current, button, modifiers }) => {
-                const { clickFocus, clickFocusAdd, clickFocusExtend, clickFocusSelectMode, clickFocusAddSelectMode, clickFocusExtendSelectMode } = this.params.bindings;
+                const { clickFocus, clickFocusAdd, clickFocusSelectMode, clickFocusAddSelectMode } = this.params.bindings;
 
                 const binding = this.ctx.selectionMode ? clickFocusSelectMode : clickFocus;
                 const matched = Binding.match(binding, button, modifiers);
 
-                const bindingAdd = this.ctx.selectionMode ? clickFocusAddSelectMode : clickFocusAdd;
-                const matchedAdd = Binding.match(bindingAdd, button, modifiers);
-
-                const bindingExtend = this.ctx.selectionMode ? clickFocusExtendSelectMode : clickFocusExtend;
-                const matchedExtend = Binding.match(bindingExtend, button, modifiers);
-
-                if (!matched && !matchedAdd && !matchedExtend) return;
-
                 // Support snapshot key property, in which case ignore the focus functionality
                 const snapshotKey = current.repr?.props?.snapshotKey?.trim() ?? '';
                 if (!this.ctx.selectionMode && matched && snapshotKey) {
@@ -294,6 +278,10 @@ export const FocusLoci = PluginBehavior.create<FocusLociProps>({
                 const { granularity } = this.ctx.managers.interactivity.props;
                 if (granularity !== 'residue' && granularity !== 'element') return;
 
+                const bindingAdd = this.ctx.selectionMode ? clickFocusAddSelectMode : clickFocusAdd;
+                const matchedAdd = Binding.match(bindingAdd, button, modifiers);
+                if (!matched && !matchedAdd) return;
+
                 const loci = Loci.normalize(current.loci, 'residue');
                 const entry = this.ctx.managers.structure.focus.current;
                 if (entry && Loci.areEqual(entry.loci, loci)) {
@@ -302,13 +290,9 @@ export const FocusLoci = PluginBehavior.create<FocusLociProps>({
                     if (matched) {
                         this.ctx.managers.structure.focus.setFromLoci(loci);
                     } else {
-                        if (matchedExtend) {
-                            this.ctx.managers.structure.focus.extendFromLoci(loci);
-                        } else { // matchedAdd
-                            this.ctx.managers.structure.focus.toggleFromLoci(loci);
-                        }
+                        this.ctx.managers.structure.focus.addFromLoci(loci);
 
-                        // focus-add and focus-extend is not handled in camera behavior, doing it here
+                        // focus-add is not handled in camera behavior, doing it here
                         const current = this.ctx.managers.structure.focus.current?.loci;
                         if (current) this.ctx.managers.camera.focusLoci(current);
                     }
@@ -318,4 +302,4 @@ export const FocusLoci = PluginBehavior.create<FocusLociProps>({
     },
     params: () => FocusLociParams,
     display: { name: 'Representation Focus Loci on Canvas' }
-});
+});

src/mol-repr/representation.ts

@@ -27,7 +27,6 @@ import { SetUtils } from '../mol-util/set';
 import { cantorPairing } from '../mol-data/util';
 import { Substance } from '../mol-theme/substance';
 import { Emissive } from '../mol-theme/emissive';
-import { Location } from '../mol-model/location';
 
 export type RepresentationProps = { [k: string]: any }
 
@@ -58,13 +57,12 @@ export interface RepresentationProvider<D = any, P extends PD.Params = any, S ex
     }
     readonly getData?: (data: D, props: PD.Values<P>) => D
     readonly mustRecreate?: (oldProps: PD.Values<P>, newProps: PD.Values<P>) => boolean
-    readonly locationKinds?: ReadonlyArray<Location['kind']>
 }
 
 export namespace RepresentationProvider {
     export type ParamValues<R extends RepresentationProvider<any, any, any>> = R extends RepresentationProvider<any, infer P, any> ? PD.Values<P> : never;
 
-    export function getDefaultParams<R extends RepresentationProvider<D, any, any>, D>(r: R, ctx: ThemeRegistryContext, data: D) {
+    export function getDetaultParams<R extends RepresentationProvider<D, any, any>, D>(r: R, ctx: ThemeRegistryContext, data: D) {
         return PD.getDefaultValues(r.getParams(ctx, data));
     }
 }

src/mol-repr/structure/visual/polymer-trace-mesh.ts

@@ -83,22 +83,24 @@ function createPolymerTraceMesh(ctx: VisualContext, unit: Unit, structure: Struc
         const hasRoundCap = isHelix && tubularHelices && roundCap;
 
         let segmentCount = linearSegments;
-        if (v.initial) {
-            segmentCount = Math.max(Math.round(linearSegments * shift), 1);
-            const offset = linearSegments - segmentCount;
-            curvePoints.copyWithin(0, offset * 3);
-            binormalVectors.copyWithin(0, offset * 3);
-            normalVectors.copyWithin(0, offset * 3);
-            Vec3.fromArray(tmpV1, curvePoints, 3);
-            Vec3.normalize(tmpV1, Vec3.sub(tmpV1, v.p2, tmpV1));
-            Vec3.scaleAndAdd(tmpV1, v.p2, tmpV1, w1 * OverhangFactor);
-            Vec3.toArray(tmpV1, curvePoints, 0);
-        } else if (v.final) {
-            segmentCount = Math.max(Math.round(linearSegments * (1 - shift)), 1);
-            Vec3.fromArray(tmpV1, curvePoints, segmentCount * 3 - 3);
-            Vec3.normalize(tmpV1, Vec3.sub(tmpV1, v.p2, tmpV1));
-            Vec3.scaleAndAdd(tmpV1, v.p2, tmpV1, w1 * OverhangFactor);
-            Vec3.toArray(tmpV1, curvePoints, segmentCount * 3);
+        if (!hasRoundCap) {
+            if (v.initial) {
+                segmentCount = Math.max(Math.round(linearSegments * shift), 1);
+                const offset = linearSegments - segmentCount;
+                curvePoints.copyWithin(0, offset * 3);
+                binormalVectors.copyWithin(0, offset * 3);
+                normalVectors.copyWithin(0, offset * 3);
+                Vec3.fromArray(tmpV1, curvePoints, 3);
+                Vec3.normalize(tmpV1, Vec3.sub(tmpV1, v.p2, tmpV1));
+                Vec3.scaleAndAdd(tmpV1, v.p2, tmpV1, w1 * OverhangFactor);
+                Vec3.toArray(tmpV1, curvePoints, 0);
+            } else if (v.final) {
+                segmentCount = Math.max(Math.round(linearSegments * (1 - shift)), 1);
+                Vec3.fromArray(tmpV1, curvePoints, segmentCount * 3 - 3);
+                Vec3.normalize(tmpV1, Vec3.sub(tmpV1, v.p2, tmpV1));
+                Vec3.scaleAndAdd(tmpV1, v.p2, tmpV1, w1 * OverhangFactor);
+                Vec3.toArray(tmpV1, curvePoints, segmentCount * 3);
+            }
         }
 
         if (v.initial === true && v.final === true) {

src/mol-repr/structure/visual/util/polymer/trace-iterator.ts

@@ -281,7 +281,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
             const isHelixNext3 = isHelixSS(ssNext3);
 
             // handle positions for tubular helices
-            if (this.helixOrientationCenters && !(isHelix && value.secStrucFirst && value.secStrucLast)) {
+            if (this.helixOrientationCenters && !(value.secStrucFirst && value.secStrucLast)) {
                 if (isHelix !== isHelixPrev1) {
                     if (isHelix) {
                         Vec3.copy(this.p0, this.p3);
@@ -353,7 +353,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
                 this.setFromToVector(this.d34, residueIndexNext2, ssNext2);
             }
 
-            const helixFlag = isHelix && this.helixOrientationCenters;
+            const helixFlag = isHelix && this.helixOrientationCenters && !(value.secStrucFirst && value.secStrucLast);
 
             // extend termini
             const f = 1.5;

src/mol-repr/volume/direct-volume.ts

@@ -172,7 +172,7 @@ export function DirectVolumeVisual(materialId: number): VolumeVisual<DirectVolum
         geometryUtils: DirectVolume.Utils,
         dispose: (geometry: DirectVolume) => {
             geometry.gridTexture.ref.value.destroy();
-        },
+        }
     }, materialId);
 }
 
@@ -189,6 +189,5 @@ export const DirectVolumeRepresentationProvider = VolumeRepresentationProvider({
     defaultValues: PD.getDefaultValues(DirectVolumeParams),
     defaultColorTheme: { name: 'volume-value' },
     defaultSizeTheme: { name: 'uniform' },
-    locationKinds: ['position-location', 'direct-location'],
     isApplicable: (volume: Volume) => !Volume.isEmpty(volume) && !Volume.Segmentation.get(volume)
 });

src/mol-repr/volume/dot.ts

@@ -1,274 +0,0 @@
-/**
- * Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { Grid, Volume } from '../../mol-model/volume';
-import { VisualContext } from '../visual';
-import { Theme, ThemeRegistryContext } from '../../mol-theme/theme';
-import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
-import { VolumeVisual, VolumeRepresentation, VolumeRepresentationProvider, VolumeKey } from './representation';
-import { VisualUpdateState } from '../util';
-import { RepresentationContext, RepresentationParamsGetter, Representation } from '../representation';
-import { PickingId } from '../../mol-geo/geometry/picking';
-import { EmptyLoci, Loci } from '../../mol-model/loci';
-import { Interval } from '../../mol-data/int';
-import { createVolumeCellLocationIterator, eachVolumeLoci } from './util';
-import { WebGLContext } from '../../mol-gl/webgl/context';
-import { BaseGeometry } from '../../mol-geo/geometry/base';
-import { Spheres } from '../../mol-geo/geometry/spheres/spheres';
-import { MeshBuilder } from '../../mol-geo/geometry/mesh/mesh-builder';
-import { SpheresBuilder } from '../../mol-geo/geometry/spheres/spheres-builder';
-import { Vec3 } from '../../mol-math/linear-algebra/3d/vec3';
-import { addSphere } from '../../mol-geo/geometry/mesh/builder/sphere';
-import { sphereVertexCount } from '../../mol-geo/primitive/sphere';
-import { Points } from '../../mol-geo/geometry/points/points';
-import { PointsBuilder } from '../../mol-geo/geometry/points/points-builder';
-
-export const VolumeDotParams = {
-    isoValue: Volume.IsoValueParam,
-};
-export type VolumeDotParams = typeof VolumeDotParams
-export type VolumeDotProps = PD.Values<VolumeDotParams>
-
-//
-
-export const VolumeSphereParams = {
-    ...Spheres.Params,
-    ...Mesh.Params,
-    ...VolumeDotParams,
-    tryUseImpostor: PD.Boolean(true),
-    detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo),
-};
-export type VolumeSphereParams = typeof VolumeSphereParams
-export type VolumeSphereProps = PD.Values<VolumeSphereParams>
-
-export function VolumeSphereVisual(materialId: number, volume: Volume, key: number, props: PD.Values<VolumeSphereParams>, webgl?: WebGLContext) {
-    return props.tryUseImpostor && webgl && webgl.extensions.fragDepth && webgl.extensions.textureFloat
-        ? VolumeSphereImpostorVisual(materialId)
-        : VolumeSphereMeshVisual(materialId);
-}
-
-export function VolumeSphereImpostorVisual(materialId: number): VolumeVisual<VolumeSphereParams> {
-    return VolumeVisual<Spheres, VolumeSphereParams>({
-        defaultProps: PD.getDefaultValues(VolumeSphereParams),
-        createGeometry: createVolumeSphereImpostor,
-        createLocationIterator: createVolumeCellLocationIterator,
-        getLoci: getDotLoci,
-        eachLocation: eachDot,
-        setUpdateState: (state: VisualUpdateState, volume: Volume, newProps: PD.Values<VolumeSphereParams>, currentProps: PD.Values<VolumeSphereParams>) => {
-            state.createGeometry = (
-                !Volume.IsoValue.areSame(newProps.isoValue, currentProps.isoValue, volume.grid.stats)
-            );
-        },
-        geometryUtils: Spheres.Utils,
-        mustRecreate: (volumekey: VolumeKey, props: PD.Values<VolumeSphereParams>, webgl?: WebGLContext) => {
-            return !props.tryUseImpostor || !webgl;
-        }
-    }, materialId);
-}
-
-export function VolumeSphereMeshVisual(materialId: number): VolumeVisual<VolumeSphereParams> {
-    return VolumeVisual<Mesh, VolumeSphereParams>({
-        defaultProps: PD.getDefaultValues(VolumeSphereParams),
-        createGeometry: createVolumeSphereMesh,
-        createLocationIterator: createVolumeCellLocationIterator,
-        getLoci: getDotLoci,
-        eachLocation: eachDot,
-        setUpdateState: (state: VisualUpdateState, volume: Volume, newProps: PD.Values<VolumeSphereParams>, currentProps: PD.Values<VolumeSphereParams>) => {
-            state.createGeometry = (
-                !Volume.IsoValue.areSame(newProps.isoValue, currentProps.isoValue, volume.grid.stats) ||
-                newProps.sizeFactor !== currentProps.sizeFactor ||
-                newProps.detail !== currentProps.detail
-            );
-        },
-        geometryUtils: Mesh.Utils,
-        mustRecreate: (volumekey: VolumeKey, props: PD.Values<VolumeSphereParams>, webgl?: WebGLContext) => {
-            return props.tryUseImpostor && !!webgl;
-        }
-    }, materialId);
-}
-
-
-export function createVolumeSphereImpostor(ctx: VisualContext, volume: Volume, key: number, theme: Theme, props: VolumeSphereProps, spheres?: Spheres): Spheres {
-    const { cells: { space, data }, stats } = volume.grid;
-    const gridToCartn = Grid.getGridToCartesianTransform(volume.grid);
-    const isoVal = Volume.IsoValue.toAbsolute(props.isoValue, stats).absoluteValue;
-
-    const p = Vec3();
-    const [xn, yn, zn] = space.dimensions;
-
-    const count = Math.ceil((xn * yn * zn) / 10);
-    const builder = SpheresBuilder.create(count, Math.ceil(count / 2), spheres);
-
-    for (let z = 0; z < zn; ++z) {
-        for (let y = 0; y < yn; ++y) {
-            for (let x = 0; x < xn; ++x) {
-                if (space.get(data, x, y, z) < isoVal) continue;
-
-                Vec3.set(p, x, y, z);
-                Vec3.transformMat4(p, p, gridToCartn);
-                builder.add(p[0], p[1], p[2], space.dataOffset(x, y, z));
-            }
-        }
-    }
-
-    const s = builder.getSpheres();
-    s.setBoundingSphere(Volume.Isosurface.getBoundingSphere(volume, props.isoValue));
-    return s;
-}
-
-export function createVolumeSphereMesh(ctx: VisualContext, volume: Volume, key: number, theme: Theme, props: VolumeSphereProps, mesh?: Mesh): Mesh {
-    const { detail, sizeFactor } = props;
-
-    const { cells: { space, data }, stats } = volume.grid;
-    const gridToCartn = Grid.getGridToCartesianTransform(volume.grid);
-    const isoVal = Volume.IsoValue.toAbsolute(props.isoValue, stats).absoluteValue;
-
-    const p = Vec3();
-    const [xn, yn, zn] = space.dimensions;
-
-    const count = (xn * yn * zn) / 10;
-    const vertexCount = count * sphereVertexCount(detail);
-    const builderState = MeshBuilder.createState(vertexCount, vertexCount / 2, mesh);
-
-    const l = Volume.Cell.Location(volume);
-    const themeSize = theme.size.size;
-
-    for (let z = 0; z < zn; ++z) {
-        for (let y = 0; y < yn; ++y) {
-            for (let x = 0; x < xn; ++x) {
-                if (space.get(data, x, y, z) < isoVal) continue;
-
-                Vec3.set(p, x, y, z);
-                Vec3.transformMat4(p, p, gridToCartn);
-                builderState.currentGroup = space.dataOffset(x, y, z);
-                l.cell = builderState.currentGroup as Volume.CellIndex;
-                const size = themeSize(l);
-                addSphere(builderState, p, size * sizeFactor, detail);
-            }
-        }
-    }
-
-    const m = MeshBuilder.getMesh(builderState);
-    m.setBoundingSphere(Volume.Isosurface.getBoundingSphere(volume, props.isoValue));
-    return m;
-}
-
-//
-
-export const VolumePointParams = {
-    ...Points.Params,
-    ...VolumeDotParams,
-};
-export type VolumePointParams = typeof VolumePointParams
-export type VolumePointProps = PD.Values<VolumePointParams>
-
-export function VolumePointVisual(materialId: number): VolumeVisual<VolumePointParams> {
-    return VolumeVisual<Points, VolumePointParams>({
-        defaultProps: PD.getDefaultValues(VolumePointParams),
-        createGeometry: createVolumePoint,
-        createLocationIterator: createVolumeCellLocationIterator,
-        getLoci: getDotLoci,
-        eachLocation: eachDot,
-        setUpdateState: (state: VisualUpdateState, volume: Volume, newProps: PD.Values<VolumePointParams>, currentProps: PD.Values<VolumePointParams>) => {
-            state.createGeometry = (
-                !Volume.IsoValue.areSame(newProps.isoValue, currentProps.isoValue, volume.grid.stats)
-            );
-        },
-        geometryUtils: Points.Utils,
-    }, materialId);
-}
-
-export function createVolumePoint(ctx: VisualContext, volume: Volume, key: number, theme: Theme, props: VolumePointProps, points?: Points): Points {
-    const { cells: { space, data }, stats } = volume.grid;
-    const gridToCartn = Grid.getGridToCartesianTransform(volume.grid);
-    const isoVal = Volume.IsoValue.toAbsolute(props.isoValue, stats).absoluteValue;
-
-    const p = Vec3();
-    const [xn, yn, zn] = space.dimensions;
-
-    const count = Math.ceil((xn * yn * zn) / 10);
-    const builder = PointsBuilder.create(count, Math.ceil(count / 2), points);
-
-    for (let z = 0; z < zn; ++z) {
-        for (let y = 0; y < yn; ++y) {
-            for (let x = 0; x < xn; ++x) {
-                if (space.get(data, x, y, z) < isoVal) continue;
-
-                Vec3.set(p, x, y, z);
-                Vec3.transformMat4(p, p, gridToCartn);
-                builder.add(p[0], p[1], p[2], space.dataOffset(x, y, z));
-            }
-        }
-    }
-
-    const pt = builder.getPoints();
-    pt.setBoundingSphere(Volume.Isosurface.getBoundingSphere(volume, props.isoValue));
-    return pt;
-}
-
-//
-
-function getLoci(volume: Volume, props: VolumeDotProps) {
-    return Volume.Isosurface.Loci(volume, props.isoValue);
-}
-
-function getDotLoci(pickingId: PickingId, volume: Volume, key: number, props: VolumeDotProps, id: number) {
-    const { objectId, groupId } = pickingId;
-
-    if (id === objectId) {
-        const granularity = Volume.PickingGranularity.get(volume);
-        if (granularity === 'volume') {
-            return Volume.Loci(volume);
-        } else if (granularity === 'object') {
-            return Volume.Isosurface.Loci(volume, props.isoValue);
-        } else {
-            return Volume.Cell.Loci(volume, Interval.ofSingleton(groupId as Volume.CellIndex));
-        }
-    }
-    return EmptyLoci;
-}
-
-function eachDot(loci: Loci, volume: Volume, key: number, props: VolumeDotProps, apply: (interval: Interval) => boolean) {
-    return eachVolumeLoci(loci, volume, { isoValue: props.isoValue }, apply);
-}
-
-//
-
-const DotVisuals = {
-    'sphere': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Volume, VolumeSphereParams>) => VolumeRepresentation('Dot sphere', ctx, getParams, VolumeSphereVisual, getLoci),
-    'point': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Volume, VolumePointParams>) => VolumeRepresentation('Dot point', ctx, getParams, VolumePointVisual, getLoci),
-};
-
-export const DotParams = {
-    ...VolumeSphereParams,
-    ...VolumePointParams,
-    visuals: PD.MultiSelect(['sphere'], PD.objectToOptions(DotVisuals)),
-    bumpFrequency: PD.Numeric(1, { min: 0, max: 10, step: 0.1 }, BaseGeometry.ShadingCategory),
-};
-export type DotParams = typeof DotParams
-export function getDotParams(ctx: ThemeRegistryContext, volume: Volume) {
-    const p = PD.clone(DotParams);
-    p.isoValue = Volume.createIsoValueParam(Volume.IsoValue.relative(2), volume.grid.stats);
-    return p;
-}
-
-export type DotRepresentation = VolumeRepresentation<DotParams>
-export function DotRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<Volume, DotParams>): DotRepresentation {
-    return Representation.createMulti('Dot', ctx, getParams, Representation.StateBuilder, DotVisuals as unknown as Representation.Def<Volume, DotParams>);
-}
-
-export const DotRepresentationProvider = VolumeRepresentationProvider({
-    name: 'dot',
-    label: 'Dot',
-    description: 'Displays dots of volumetric data.',
-    factory: DotRepresentation,
-    getParams: getDotParams,
-    defaultValues: PD.getDefaultValues(DotParams),
-    defaultColorTheme: { name: 'uniform' },
-    defaultSizeTheme: { name: 'uniform' },
-    isApplicable: (volume: Volume) => !Volume.isEmpty(volume) && !Volume.Segmentation.get(volume)
-});

src/mol-repr/volume/registry.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -11,7 +11,6 @@ import { objectForEach } from '../../mol-util/object';
 import { SliceRepresentationProvider } from './slice';
 import { DirectVolumeRepresentationProvider } from './direct-volume';
 import { SegmentRepresentationProvider } from './segment';
-import { DotRepresentationProvider } from './dot';
 
 export class VolumeRepresentationRegistry extends RepresentationRegistry<Volume, Representation.State> {
     constructor() {
@@ -25,11 +24,10 @@ export class VolumeRepresentationRegistry extends RepresentationRegistry<Volume,
 
 export namespace VolumeRepresentationRegistry {
     export const BuiltIn = {
-        'direct-volume': DirectVolumeRepresentationProvider,
-        'dot': DotRepresentationProvider,
         'isosurface': IsosurfaceRepresentationProvider,
-        'segment': SegmentRepresentationProvider,
         'slice': SliceRepresentationProvider,
+        'direct-volume': DirectVolumeRepresentationProvider,
+        'segment': SegmentRepresentationProvider,
     };
 
     type _BuiltIn = typeof BuiltIn

src/mol-repr/volume/representation.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -35,7 +35,6 @@ import { isPromiseLike } from '../../mol-util/type-helpers';
 import { Substance } from '../../mol-theme/substance';
 import { createMarkers } from '../../mol-geo/geometry/marker-data';
 import { Emissive } from '../../mol-theme/emissive';
-import { SizeTheme } from '../../mol-theme/size';
 
 export type VolumeKey = { volume: Volume, key: number }
 export interface VolumeVisual<P extends VolumeParams> extends Visual<VolumeKey, P> { }
@@ -110,26 +109,15 @@ export function VolumeVisual<G extends Geometry, P extends VolumeParams & Geomet
 
         setUpdateState(updateState, volume, newProps, currentProps, newTheme, currentTheme);
 
-        if (!ColorTheme.areEqual(theme.color, currentTheme.color)) {
-            updateState.updateColor = true;
-        }
+        if (!ColorTheme.areEqual(theme.color, currentTheme.color)) updateState.updateColor = true;
 
-        if (!SizeTheme.areEqual(theme.size, currentTheme.size)) {
-            updateState.updateSize = true;
+        if (updateState.createGeometry) {
+            updateState.updateColor = true;
         }
 
         if (newProps.instanceGranularity !== currentProps.instanceGranularity) {
             updateState.updateTransform = true;
         }
-
-        if (updateState.updateSize && !('uSize' in renderObject!.values)) {
-            updateState.createGeometry = true;
-        }
-
-        if (updateState.createGeometry) {
-            updateState.updateColor = true;
-            updateState.updateSize = true;
-        }
     }
 
     function update(newGeometry?: G) {

src/mol-repr/volume/slice.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -9,7 +9,7 @@ import { Image } from '../../mol-geo/geometry/image/image';
 import { ThemeRegistryContext, Theme } from '../../mol-theme/theme';
 import { Grid, Volume } from '../../mol-model/volume';
 import { VolumeVisual, VolumeRepresentation, VolumeRepresentationProvider } from './representation';
-import { LocationIterator, PositionLocation } from '../../mol-geo/util/location-iterator';
+import { LocationIterator } from '../../mol-geo/util/location-iterator';
 import { VisualUpdateState } from '../util';
 import { NullLocation } from '../../mol-model/location';
 import { RepresentationContext, RepresentationParamsGetter } from '../representation';
@@ -23,20 +23,17 @@ import { Color } from '../../mol-util/color';
 import { ColorTheme } from '../../mol-theme/color';
 import { packIntToRGBArray } from '../../mol-util/number-packing';
 import { eachVolumeLoci } from './util';
-import { Vec3 } from '../../mol-math/linear-algebra/3d/vec3';
-import { equalEps } from '../../mol-math/linear-algebra/3d/common';
 
 export async function createImage(ctx: VisualContext, volume: Volume, key: number, theme: Theme, props: PD.Values<SliceParams>, image?: Image) {
     const { dimension: { name: dim }, isoValue } = props;
 
-    const { cells: { space, data }, stats } = volume.grid;
-    const { min, max } = stats;
-    const isoVal = Volume.IsoValue.toAbsolute(isoValue, stats).absoluteValue;
+    const { space, data } = volume.grid.cells;
+    const { min, max } = volume.grid.stats;
+    const isoVal = Volume.IsoValue.toAbsolute(isoValue, volume.grid.stats).absoluteValue;
 
-    const isUniform = theme.color.granularity === 'uniform';
-    const color = 'color' in theme.color && theme.color.color
-        ? theme.color.color
-        : () => Color(0xffffff);
+    // TODO more color themes
+    const color = 'color' in theme.color ? theme.color.color(NullLocation, false) : Color(0xffffff);
+    const [r, g, b] = Color.toRgbNormalized(color);
 
     const {
         width, height,
@@ -54,52 +51,17 @@ export async function createImage(ctx: VisualContext, volume: Volume, key: numbe
     const imageArray = new Uint8Array(width * height * 4);
     const groupArray = getPackedGroupArray(volume.grid, props);
 
-    const gridToCartn = Grid.getGridToCartesianTransform(volume.grid);
-    const l = PositionLocation(Vec3(), Vec3());
-
-    let v: (ix: number, iy: number, iz: number) => number;
-    if (equalEps(isoVal, stats.min, 0.001)) {
-        v = (_ix, _iy, _iz) => 255;
-    } else if (equalEps(isoVal, stats.max, 0.001)) {
-        v = (_ix, _iy, _iz) => 0;
-    } else {
-        v = (ix, iy, iz) => {
-            return (
-                (space.get(data, ix, iy, iz) >= isoVal ? 1 : 0) * 2 +
-                (space.get(data, ix + 1, iy, iz) >= isoVal ? 1 : 0) +
-                (space.get(data, ix - 1, iy, iz) >= isoVal ? 1 : 0) +
-                (space.get(data, ix, iy + 1, iz) >= isoVal ? 1 : 0) +
-                (space.get(data, ix, iy - 1, iz) >= isoVal ? 1 : 0) +
-                (space.get(data, ix, iy, iz + 1) >= isoVal ? 1 : 0) +
-                (space.get(data, ix, iy, iz - 1) >= isoVal ? 1 : 0) +
-                (space.get(data, ix + 1, iy + 1, iz + 1) >= isoVal ? 1 : 0) +
-                (space.get(data, ix - 1, iy + 1, iz + 1) >= isoVal ? 1 : 0) +
-                (space.get(data, ix + 1, iy - 1, iz + 1) >= isoVal ? 1 : 0) +
-                (space.get(data, ix + 1, iy + 1, iz - 1) >= isoVal ? 1 : 0) +
-                (space.get(data, ix - 1, iy - 1, iz + 1) >= isoVal ? 1 : 0) +
-                (space.get(data, ix - 1, iy + 1, iz - 1) >= isoVal ? 1 : 0) +
-                (space.get(data, ix + 1, iy - 1, iz - 1) >= isoVal ? 1 : 0) +
-                (space.get(data, ix - 1, iy - 1, iz - 1) >= isoVal ? 1 : 0)
-            ) / 16 * 255;
-        };
-    }
-
     let i = 0;
     for (let iy = y0; iy < ny; ++iy) {
         for (let ix = x0; ix < nx; ++ix) {
             for (let iz = z0; iz < nz; ++iz) {
-                Vec3.set(l.position, ix, iy, iz);
-                Vec3.transformMat4(l.position, l.position, gridToCartn);
-                Color.toArray(color(l, false), imageArray, i);
+                const val = space.get(data, ix, iy, iz);
+                const normVal = (val - min) / (max - min);
 
-                if (isUniform) {
-                    const val = space.get(data, ix, iy, iz);
-                    const normVal = (val - min) / (max - min);
-                    imageArray[i] *= normVal * 2;
-                    imageArray[i + 1] *= normVal * 2;
-                    imageArray[i + 2] *= normVal * 2;
-                }
-                imageArray[i + 3] = v(ix, iy, iz);
+                imageArray[i] = r * normVal * 2 * 255;
+                imageArray[i + 1] = g * normVal * 2 * 255;
+                imageArray[i + 2] = b * normVal * 2 * 255;
+                imageArray[i + 3] = val >= isoVal ? 255 : 0;
 
                 i += 4;
             }

src/mol-repr/volume/util.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -14,7 +14,6 @@ import { SetUtils } from '../../mol-util/set';
 import { Box3D } from '../../mol-math/geometry';
 import { toHalfFloat } from '../../mol-util/number-conversion';
 import { clamp } from '../../mol-math/interpolate';
-import { LocationIterator } from '../../mol-geo/util/location-iterator';
 
 // avoiding namespace lookup improved performance in Chrome (Aug 2020)
 const v3set = Vec3.set;
@@ -78,18 +77,6 @@ export function eachVolumeLoci(loci: Loci, volume: Volume, props: { isoValue?: V
     return changed;
 }
 
-export function createVolumeCellLocationIterator(volume: Volume): LocationIterator {
-    const [xn, yn, zn] = volume.grid.cells.space.dimensions;
-    const groupCount = xn * yn * zn;
-    const instanceCount = 1;
-    const location = Volume.Cell.Location(volume);
-    const getLocation = (groupIndex: number, _instanceIndex: number) => {
-        location.cell = groupIndex as Volume.CellIndex;
-        return location;
-    };
-    return LocationIterator(groupCount, instanceCount, 1, getLocation);
-}
-
 //
 
 export function getVolumeTexture2dLayout(dim: Vec3, padding = 0) {

src/mol-theme/color.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -35,7 +35,7 @@ import { OperatorHklColorThemeProvider } from './color/operator-hkl';
 import { PartialChargeColorThemeProvider } from './color/partial-charge';
 import { AtomIdColorThemeProvider } from './color/atom-id';
 import { EntityIdColorThemeProvider } from './color/entity-id';
-import type { Texture, TextureFilter } from '../mol-gl/webgl/texture';
+import { Texture, TextureFilter } from '../mol-gl/webgl/texture';
 import { VolumeValueColorThemeProvider } from './color/volume-value';
 import { Vec3, Vec4 } from '../mol-math/linear-algebra';
 import { ModelIndexColorThemeProvider } from './color/model-index';
@@ -46,10 +46,6 @@ import { ColorThemeCategory } from './color/categories';
 import { CartoonColorThemeProvider } from './color/cartoon';
 import { FormalChargeColorThemeProvider } from './color/formal-charge';
 import { ExternalStructureColorThemeProvider } from './color/external-structure';
-import { ColorListEntry } from '../mol-util/color/color';
-import { getPrecision } from '../mol-util/number';
-import { SortedArray } from '../mol-data/int/sorted-array';
-import { normalize } from '../mol-math/interpolate';
 
 export type LocationColor = (location: Location, isSecondary: boolean) => Color
 
@@ -98,55 +94,8 @@ namespace ColorTheme {
     export const Category = ColorThemeCategory;
 
     export interface Palette {
-        colors: Color[],
         filter?: TextureFilter,
-        domain?: [number, number],
-    }
-
-    export function Palette(list: ColorListEntry[], kind: 'set' | 'interpolate', domain?: [number, number]): Palette {
-        const colors: Color[] = [];
-
-        const hasOffsets = list.every(c => Array.isArray(c));
-        if (hasOffsets) {
-            let maxPrecision = 0;
-            for (const e of list) {
-                if (Array.isArray(e)) {
-                    const p = getPrecision(e[1]);
-                    if (p > maxPrecision) maxPrecision = p;
-                }
-            }
-            const count = Math.pow(10, maxPrecision);
-
-            const sorted = [...list] as [Color, number][];
-            sorted.sort((a, b) => a[1] - b[1]);
-
-            const src = sorted.map(c => c[0]);
-            const values = SortedArray.ofSortedArray(sorted.map(c => c[1]));
-
-            const _off: number[] = [];
-            for (let i = 0, il = values.length - 1; i < il; ++i) {
-                _off.push(values[i] + (values[i + 1] - values[i]) / 2);
-            }
-            _off.push(values[values.length - 1]);
-            const off = SortedArray.ofSortedArray(_off);
-
-            for (let i = 0, il = Math.max(count, list.length); i < il; ++i) {
-                const t = normalize(i, 0, count - 1);
-                const j = SortedArray.findPredecessorIndex(off, t);
-                colors[i] = src[j];
-            }
-        } else {
-            for (const e of list) {
-                if (Array.isArray(e)) colors.push(e[0]);
-                else colors.push(e);
-            }
-        }
-
-        return {
-            colors,
-            filter: kind === 'set' ? 'nearest' : 'linear',
-            domain,
-        };
+        colors: Color[],
     }
 
     export const PaletteScale = (1 << 24) - 1;

src/mol-theme/color/entity-id.ts

@@ -1,8 +1,7 @@
 /**
- * Copyright (c) 2021-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author Adam Midlik <midlik@gmail.com>
  */
 
 import { StructureProperties, StructureElement, Bond, Structure, Unit } from '../../mol-model/structure';
@@ -16,16 +15,12 @@ import { TableLegend, ScaleLegend } from '../../mol-util/legend';
 import { ColorThemeCategory } from './categories';
 import { ModelFormat } from '../../mol-model-formats/format';
 
-
 const DefaultList = 'many-distinct';
 const DefaultColor = Color(0xFAFAFA);
-const DefaultWaterColor = Color(0xFF0D0D);
 const Description = 'Gives every chain a color based on its `label_entity_id` value.';
 
 export const EntityIdColorThemeParams = {
     ...getPaletteParams({ type: 'colors', colorList: DefaultList }),
-    overrideWater: PD.Boolean(false, { description: 'Override the color for water molecules.' }),
-    waterColor: PD.Color(DefaultWaterColor, { hideIf: p => !p.overrideWater, description: 'Color for water molecules (if overrideWater is true).' }),
 };
 export type EntityIdColorThemeParams = typeof EntityIdColorThemeParams
 export function getEntityIdColorThemeParams(ctx: ThemeDataContext) {
@@ -99,25 +94,20 @@ export function EntityIdColorTheme(ctx: ThemeDataContext, props: PD.Values<Entit
         legend = palette.legend;
 
         color = (location: Location): Color => {
-            let structElemLoc: StructureElement.Location;
+            let serial: number | undefined = undefined;
             if (StructureElement.Location.is(location)) {
-                structElemLoc = location;
+                const entityId = getEntityId(location);
+                const sourceSerial = sourceSerialMap.get(location.unit.model.sourceData) ?? -1;
+                const k = key(entityId, sourceSerial);
+                serial = entityIdSerialMap.get(k);
             } else if (Bond.isLocation(location)) {
                 l.unit = location.aUnit;
                 l.element = location.aUnit.elements[location.aIndex];
-                structElemLoc = l;
-            } else {
-                return DefaultColor;
+                const entityId = getEntityId(l);
+                const sourceSerial = sourceSerialMap.get(l.unit.model.sourceData) ?? -1;
+                const k = key(entityId, sourceSerial);
+                serial = entityIdSerialMap.get(k);
             }
-            const entityId = getEntityId(structElemLoc);
-            const sourceSerial = sourceSerialMap.get(structElemLoc.unit.model.sourceData) ?? -1;
-            if (props.overrideWater) {
-                const entities = structElemLoc.unit.model.entities;
-                const entityType = entities.data.type.value(entities.getEntityIndex(entityId));
-                if (entityType === 'water') return props.waterColor;
-            }
-            const k = key(entityId, sourceSerial);
-            const serial = entityIdSerialMap.get(k);
             return serial === undefined ? DefaultColor : palette.color(serial);
         };
     } else {

src/mol-theme/color/external-volume.ts

@@ -1,21 +1,20 @@
 /**
- * Copyright (c) 2024-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Cai Huiyu <szmun.caihy@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
 import { Color, ColorScale } from '../../mol-util/color';
 import { Location } from '../../mol-model/location';
-import { ColorTheme, LocationColor } from '../color';
+import type { ColorTheme } from '../color';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ThemeDataContext } from '../theme';
 import { Grid, Volume } from '../../mol-model/volume';
 import { type PluginContext } from '../../mol-plugin/context';
 import { isPositionLocation } from '../../mol-geo/util/location-iterator';
-import { Vec3 } from '../../mol-math/linear-algebra';
-import { clamp } from '../../mol-math/interpolate';
+import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
+import { lerp } from '../../mol-math/interpolate';
 import { ColorThemeCategory } from './categories';
 
 const Description = `Assigns a color based on volume value at a given vertex.`;
@@ -31,7 +30,7 @@ export const ExternalVolumeColorThemeParams = {
     coloring: PD.MappedStatic('absolute-value', {
         'absolute-value': PD.Group({
             domain: PD.MappedStatic('auto', {
-                custom: PD.Interval([-1, 1], { step: 0.001 }),
+                custom: PD.Interval([-1, 1]),
                 auto: PD.Group({
                     symmetric: PD.Boolean(false, { description: 'If true the automatic range is determined as [-|max|, |max|].' })
                 })
@@ -40,7 +39,7 @@ export const ExternalVolumeColorThemeParams = {
         }),
         'relative-value': PD.Group({
             domain: PD.MappedStatic('auto', {
-                custom: PD.Interval([-1, 1], { step: 0.001 }),
+                custom: PD.Interval([-1, 1]),
                 auto: PD.Group({
                     symmetric: PD.Boolean(false, { description: 'If true the automatic range is determined as [-|max|, |max|].' })
                 })
@@ -50,7 +49,6 @@ export const ExternalVolumeColorThemeParams = {
     }),
     defaultColor: PD.Color(Color(0xcccccc)),
     normalOffset: PD.Numeric(0., { min: 0, max: 20, step: 0.1 }, { description: 'Offset vertex position along its normal by given amount.' }),
-    usePalette: PD.Boolean(false, { description: 'Use a palette to color at the pixel level.' }),
 };
 export type ExternalVolumeColorThemeParams = typeof ExternalVolumeColorThemeParams
 
@@ -65,11 +63,7 @@ export function ExternalVolumeColorTheme(ctx: ThemeDataContext, props: PD.Values
     // NOTE: this will currently be slow for with GPU/texture meshes due to slow iteration
     // TODO: create texture to be able to do the sampling on the GPU
 
-    let color: LocationColor;
-    let palette: ColorTheme.Palette | undefined;
-
-    const { normalOffset, defaultColor, usePalette } = props;
-
+    let color;
     if (volume) {
         const coloring = props.coloring.params;
         const { stats } = volume.grid;
@@ -81,7 +75,7 @@ export function ExternalVolumeColorTheme(ctx: ThemeDataContext, props: PD.Values
             domain[1] = (domain[1] - stats.mean) / stats.sigma;
         }
 
-        if (coloring.domain.name === 'auto' && coloring.domain.params.symmetric) {
+        if (props.coloring.params.domain.name === 'auto' && props.coloring.params.domain.params.symmetric) {
             const max = Math.max(Math.abs(domain[0]), Math.abs(domain[1]));
             domain[0] = -max;
             domain[1] = max;
@@ -89,37 +83,67 @@ export function ExternalVolumeColorTheme(ctx: ThemeDataContext, props: PD.Values
 
         const scale = ColorScale.create({ domain, listOrName: coloring.list.colors });
 
-        const position = Vec3();
-        const getTrilinearlyInterpolated = Grid.makeGetTrilinearlyInterpolated(volume.grid, isRelative ? 'relative' : 'none');
+        const cartnToGrid = Grid.getGridToCartesianTransform(volume.grid);
+        Mat4.invert(cartnToGrid, cartnToGrid);
+        const gridCoords = Vec3();
+
+        const { dimensions, get } = volume.grid.cells.space;
+        const data = volume.grid.cells.data;
+
+        const [mi, mj, mk] = dimensions;
 
         color = (location: Location): Color => {
             if (!isPositionLocation(location)) {
-                return defaultColor;
+                return props.defaultColor;
             }
 
             // Offset the vertex position along its normal
-            if (normalOffset > 0) {
-                Vec3.scaleAndAdd(position, location.position, location.normal, normalOffset);
-            } else {
-                Vec3.copy(position, location.position);
+            Vec3.copy(gridCoords, location.position);
+
+            if (props.normalOffset > 0) {
+                Vec3.scaleAndAdd(gridCoords, gridCoords, location.normal, props.normalOffset);
             }
 
-            const value = getTrilinearlyInterpolated(position);
-            if (isNaN(value)) return defaultColor;
+            Vec3.transformMat4(gridCoords, gridCoords, cartnToGrid);
 
-            if (usePalette) {
-                return (clamp((value - domain[0]) / (domain[1] - domain[0]), 0, 1) * ColorTheme.PaletteScale) as Color;
-            } else {
-                return scale.color(value);
+            const i = Math.floor(gridCoords[0]);
+            const j = Math.floor(gridCoords[1]);
+            const k = Math.floor(gridCoords[2]);
+
+            if (i < 0 || i >= mi || j < 0 || j >= mj || k < 0 || k >= mk) {
+                return props.defaultColor;
             }
+
+            const u = gridCoords[0] - i;
+            const v = gridCoords[1] - j;
+            const w = gridCoords[2] - k;
+
+            // Tri-linear interpolation for the value
+            const ii = Math.min(i + 1, mi - 1);
+            const jj = Math.min(j + 1, mj - 1);
+            const kk = Math.min(k + 1, mk - 1);
+
+            let a = get(data, i, j, k);
+            let b = get(data, ii, j, k);
+            let c = get(data, i, jj, k);
+            let d = get(data, ii, jj, k);
+            const x = lerp(lerp(a, b, u), lerp(c, d, u), v);
+
+            a = get(data, i, j, kk);
+            b = get(data, ii, j, kk);
+            c = get(data, i, jj, kk);
+            d = get(data, ii, jj, kk);
+            const y = lerp(lerp(a, b, u), lerp(c, d, u), v);
+
+            let value = lerp(x, y, w);
+            if (isRelative) {
+                value = (value - stats.mean) / stats.sigma;
+            }
+
+            return scale.color(value);
         };
-
-        palette = usePalette ? {
-            colors: coloring.list.colors.map(e => Array.isArray(e) ? e[0] : e),
-            filter: (coloring.list.kind === 'set' ? 'nearest' : 'linear') as 'nearest' | 'linear'
-        } : undefined;
     } else {
-        color = () => defaultColor;
+        color = () => props.defaultColor;
     }
 
     return {
@@ -127,7 +151,6 @@ export function ExternalVolumeColorTheme(ctx: ThemeDataContext, props: PD.Values
         granularity: 'vertex',
         preferSmoothing: true,
         color,
-        palette,
         props,
         description: Description,
         // TODO: figure out how to do legend for this

src/mol-theme/color/volume-value.ts

@@ -1,20 +1,17 @@
 /**
- * Copyright (c) 2021-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { ColorTheme } from '../color';
+import type { ColorTheme } from '../color';
+import { Color, ColorScale } from '../../mol-util/color';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ThemeDataContext } from '../theme';
 import { ColorNames } from '../../mol-util/color/names';
-import { Location } from '../../mol-model/location';
+import { ColorTypeDirect } from '../../mol-geo/geometry/color-data';
 import { Volume } from '../../mol-model/volume/volume';
 import { ColorThemeCategory } from './categories';
-import { clamp, normalize } from '../../mol-math/interpolate';
-import { Color } from '../../mol-util/color/color';
-import { Grid } from '../../mol-model/volume/grid';
-import { isPositionLocation } from '../../mol-geo/util/location-iterator';
 
 const Description = 'Assign color based on the given value of a volume cell.';
 
@@ -29,90 +26,30 @@ export const VolumeValueColorThemeParams = {
             [ColorNames.white, 1]
         ]
     }, { offsets: true, isEssential: true }),
-    domain: PD.MappedStatic('auto', {
-        custom: PD.Interval([-1, 1], { step: 0.001 }),
-        auto: PD.Group({
-            symmetric: PD.Boolean(false, { description: 'If true the automatic range is determined as [-|max|, |max|].' })
-        })
-    }),
-    isRelative: PD.Boolean(false, { description: 'If true the value is treated as relative to the volume mean and sigma.' }),
-    defaultColor: PD.Color(Color(0xcccccc)),
 };
 export type VolumeValueColorThemeParams = typeof VolumeValueColorThemeParams
 export function getVolumeValueColorThemeParams(ctx: ThemeDataContext) {
     return VolumeValueColorThemeParams; // TODO return copy
 }
 
-export function VolumeValueColorTheme(ctx: ThemeDataContext, props: PD.Values<VolumeValueColorThemeParams>): ColorTheme<VolumeValueColorThemeParams, any> {
-    if (ctx.volume) {
-        const { min, max, mean, sigma } = ctx.volume.grid.stats;
-        const domain: [number, number] = props.domain.name === 'custom' ? props.domain.params : [min, max];
-        const { colorList } = props;
+export function VolumeValueColorTheme(ctx: ThemeDataContext, props: PD.Values<VolumeValueColorThemeParams>): ColorTheme<VolumeValueColorThemeParams, ColorTypeDirect> {
+    const scale = ColorScale.create({ domain: [0, 1], listOrName: props.colorList.colors });
 
-        if (props.domain.name === 'auto' && props.isRelative) {
-            domain[0] = (domain[0] - mean) / sigma;
-            domain[1] = (domain[1] - mean) / sigma;
-        }
-
-        if (props.domain.name === 'auto' && props.domain.params.symmetric) {
-            const max = Math.max(Math.abs(domain[0]), Math.abs(domain[1]));
-            domain[0] = -max;
-            domain[1] = max;
-        }
-
-        if (ctx.locationKinds?.includes('direct-location')) {
-            // this is for direct-volume rendering where the location is the volume grid cell
-            // and we only need to provide the domain and palette here
-
-            const normalizedDomain = [
-                normalize(domain[0], min, max),
-                normalize(domain[1], min, max)
-            ] as [number, number];
-
-            const palette = ColorTheme.Palette(colorList.colors, colorList.kind, normalizedDomain);
-
-            return {
-                factory: VolumeValueColorTheme as any,
-                granularity: 'direct',
-                props,
-                description: Description,
-                palette,
-            };
-        } else {
-            const getTrilinearlyInterpolated = Grid.makeGetTrilinearlyInterpolated(ctx.volume.grid, 'none');
-
-            const color = (location: Location): Color => {
-                if (!isPositionLocation(location)) {
-                    return props.defaultColor;
-                }
-
-                const value = getTrilinearlyInterpolated(location.position);
-                if (isNaN(value)) return props.defaultColor;
-
-                return (clamp((value - domain[0]) / (domain[1] - domain[0]), 0, 1) * ColorTheme.PaletteScale) as Color;
-            };
-
-            const palette = ColorTheme.Palette(colorList.colors, colorList.kind);
-
-            return {
-                factory: VolumeValueColorTheme as any,
-                granularity: 'vertex',
-                preferSmoothing: true,
-                color,
-                palette,
-                props,
-                description: Description,
-            };
-        }
-    } else {
-        return {
-            factory: VolumeValueColorTheme as any,
-            granularity: 'uniform',
-            color: () => props.defaultColor,
-            props,
-            description: Description,
-        };
+    const colors: Color[] = [];
+    for (let i = 0; i < 256; ++i) {
+        colors[i] = scale.color(i / 255);
     }
+
+    const palette: ColorTheme.Palette = { colors, filter: 'linear' };
+
+    return {
+        factory: VolumeValueColorTheme,
+        granularity: 'direct',
+        props: props,
+        description: Description,
+        legend: scale.legend,
+        palette,
+    };
 }
 
 export const VolumeValueColorThemeProvider: ColorTheme.Provider<VolumeValueColorThemeParams, 'volume-value'> = {

src/mol-theme/size.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -12,7 +12,6 @@ import { PhysicalSizeThemeProvider } from './size/physical';
 import { deepEqual } from '../mol-util';
 import { ShapeGroupSizeThemeProvider } from './size/shape-group';
 import { UncertaintySizeThemeProvider } from './size/uncertainty';
-import { VolumeValueSizeThemeProvider } from './size/volume-value';
 
 export { SizeTheme };
 interface SizeTheme<P extends PD.Params> {
@@ -45,8 +44,7 @@ namespace SizeTheme {
         'physical': PhysicalSizeThemeProvider,
         'shape-group': ShapeGroupSizeThemeProvider,
         'uncertainty': UncertaintySizeThemeProvider,
-        'uniform': UniformSizeThemeProvider,
-        'volume-value': VolumeValueSizeThemeProvider,
+        'uniform': UniformSizeThemeProvider
     };
     type _BuiltIn = typeof BuiltIn
     export type BuiltIn = keyof _BuiltIn

src/mol-theme/size/volume-value.ts

@@ -1,63 +0,0 @@
-/**
- * Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-import type { SizeTheme } from '../size';
-import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { ThemeDataContext } from '../../mol-theme/theme';
-import { LocationSize } from '../../mol-geo/geometry/size-data';
-import { Volume } from '../../mol-model/volume/volume';
-import { Location } from '../../mol-model/location';
-
-const Description = 'Assign size based on the given value of a volume cell.';
-
-export const VolumeValueSizeThemeParams = {
-    scale: PD.Numeric(1, { min: 0.1, max: 5, step: 0.1 }),
-};
-export type VolumeValueSizeThemeParams = typeof VolumeValueSizeThemeParams
-export function getVolumeValueSizeThemeParams(ctx: ThemeDataContext) {
-    return VolumeValueSizeThemeParams; // TODO return copy
-}
-
-export function VolumeValueSizeTheme(ctx: ThemeDataContext, props: PD.Values<VolumeValueSizeThemeParams>): SizeTheme<VolumeValueSizeThemeParams> {
-    if (ctx.volume) {
-        const { data } = ctx.volume.grid.cells;
-
-        const isLocation = Volume.Cell.isLocation;
-        const size: LocationSize = (location: Location): number => {
-            if (isLocation(location)) {
-                return data[location.cell] * props.scale;
-            } else {
-                return 0;
-            }
-        };
-
-        return {
-            factory: VolumeValueSizeTheme,
-            granularity: 'group',
-            size,
-            props,
-            description: Description
-        };
-    } else {
-        return {
-            factory: VolumeValueSizeTheme,
-            granularity: 'uniform',
-            size: () => props.scale,
-            props,
-            description: Description
-        };
-    }
-}
-
-export const VolumeValueSizeThemeProvider: SizeTheme.Provider<VolumeValueSizeThemeParams, 'volume-value'> = {
-    name: 'volume-value',
-    label: 'Volume Value',
-    category: '',
-    factory: VolumeValueSizeTheme,
-    getParams: getVolumeValueSizeThemeParams,
-    defaultValues: PD.getDefaultValues(VolumeValueSizeThemeParams),
-    isApplicable: (ctx: ThemeDataContext) => !!ctx.volume && !Volume.Segmentation.get(ctx.volume),
-};

src/mol-theme/theme.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -13,7 +13,6 @@ import { Shape } from '../mol-model/shape';
 import { CustomProperty } from '../mol-model-props/common/custom-property';
 import { objectForEach } from '../mol-util/object';
 import { ColorType } from '../mol-geo/geometry/color-data';
-import { Location } from '../mol-model/location';
 
 export interface ThemeRegistryContext {
     colorThemeRegistry: ColorTheme.Registry
@@ -25,8 +24,6 @@ export interface ThemeDataContext {
     structure?: Structure
     volume?: Volume
     shape?: Shape
-    /** Hint to request support for specific kinds of locations */
-    locationKinds?: ReadonlyArray<Location['kind']>
 }
 
 export { Theme };