0.7.1-dev.2

- so the build contains the correct version number

package-lock.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "0.7.0-dev.16",
+  "version": "0.7.1-dev.2",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "0.7.0-dev.16",
+  "version": "0.7.1-dev.2",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -34,7 +34,8 @@
     "model-server-watch": "nodemon --watch lib lib/servers/servers/model/server.js",
     "volume-server-test": "node lib/servers/servers/volume/server.js --idMap em 'test/${id}.mdb' --defaultPort 1336",
     "plugin-state": "node lib/servers/servers/plugin-state/index.js",
-    "preversion": "npm run test && npm run build",
+    "preversion": "npm run test",
+    "version": "npm run build",
     "postversion": "git push && git push --tags"
   },
   "files": [

src/apps/structure-info/model.ts

@@ -117,7 +117,7 @@ export function printSequence(model: Model) {
     for (const key of Object.keys(byEntityKey)) {
         const { sequence, entityId } = byEntityKey[+key];
         const { seqId, compId } = sequence;
-        console.log(`${entityId} (${sequence.kind} ${seqId.value(0)} (offset ${sequence.offset}), ${seqId.value(seqId.rowCount - 1)}) (${compId.value(0)}, ${compId.value(compId.rowCount - 1)})`);
+        console.log(`${entityId} (${sequence.kind} ${seqId.value(0)}, ${seqId.value(seqId.rowCount - 1)}) (${compId.value(0)}, ${compId.value(compId.rowCount - 1)})`);
         console.log(`${Sequence.getSequenceString(sequence)}`);
     }
     console.log();

src/apps/structure-info/volume.ts

@@ -8,38 +8,36 @@ import * as fs from 'fs';
 import * as argparse from 'argparse';
 import * as util from 'util';
 
-import { VolumeData, VolumeIsoValue } from '../../mol-model/volume';
+import { Volume } from '../../mol-model/volume';
 import { downloadCif } from './helpers';
 import { CIF } from '../../mol-io/reader/cif';
-import { DensityServer_Data_Database } from '../../mol-io/reader/cif/schema/density-server';
 import { Table } from '../../mol-data/db';
 import { StringBuilder } from '../../mol-util';
 import { Task } from '../../mol-task';
 import { createVolumeIsosurfaceMesh } from '../../mol-repr/volume/isosurface';
 import { Theme } from '../../mol-theme/theme';
-import { volumeFromDensityServerData } from '../../mol-model-formats/volume/density-server';
+import { volumeFromDensityServerData, DscifFormat } from '../../mol-model-formats/volume/density-server';
 
 require('util.promisify').shim();
 const writeFileAsync = util.promisify(fs.writeFile);
 
-type Volume = { source: DensityServer_Data_Database, volume: VolumeData }
-
 async function getVolume(url: string): Promise<Volume> {
     const cif = await downloadCif(url, true);
     const data = CIF.schema.densityServer(cif.blocks[1]);
-    return { source: data, volume: await volumeFromDensityServerData(data).run() };
+    return await volumeFromDensityServerData(data).run();
 }
 
-function print(data: Volume) {
-    const { volume_data_3d_info } = data.source;
+function print(volume: Volume) {
+    if (!DscifFormat.is(volume.sourceData)) return;
+    const { volume_data_3d_info } = volume.sourceData.data;
     const row = Table.getRow(volume_data_3d_info, 0);
     console.log(row);
-    if (data.volume.transform) console.log(data.volume.transform);
-    console.log(data.volume.dataStats);
+    console.log(volume.grid.transform);
+    console.log(volume.grid.stats);
 }
 
-async function doMesh(data: Volume, filename: string) {
-    const mesh = await Task.create('', runtime => createVolumeIsosurfaceMesh({ runtime }, data.volume, Theme.createEmpty(), { isoValue: VolumeIsoValue.absolute(1.5) } )).run();
+async function doMesh(volume: Volume, filename: string) {
+    const mesh = await Task.create('', runtime => createVolumeIsosurfaceMesh({ runtime }, volume, Theme.createEmpty(), { isoValue: Volume.IsoValue.absolute(1.5) } )).run();
     console.log({ vc: mesh.vertexCount, tc: mesh.triangleCount });
 
     // Export the mesh in OBJ format.

src/apps/viewer/embedded.html

@@ -21,8 +21,6 @@
         <script type="text/javascript" src="./molstar.js"></script>
         <script type="text/javascript">
             var viewer = new molstar.Viewer('app', {
-                extensions: [],
-
                 layoutIsExpanded: false,
                 layoutShowControls: false,
                 layoutShowRemoteState: false,

src/apps/viewer/index.html

@@ -45,17 +45,24 @@
                 return decodeURIComponent(((window.location.search || '').match(r) || [])[1] || '');
             }
 
+            var debugMode = getParam('debug-mode', '[^&]+').trim() === '1';
+            if (debugMode) molstar.setDebugMode(debugMode);
+
             var hideControls = getParam('hide-controls', '[^&]+').trim() === '1';
+            var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
+            var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
             var viewer = new molstar.Viewer('app', {
                 layoutShowControls: !hideControls,
                 viewportShowExpand: false,
+                pdbProvider: pdbProvider || 'pdbe',
+                emdbProvider: emdbProvider || 'pdbe',
             });
 
             var snapshotId = getParam('snapshot-id', '[^&]+').trim();
             if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
 
             var snapshotUrl = getParam('snapshot-url', '[^&]+').trim();
-            var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim();
+            var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj';
             if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType);
 
             var structureUrl = getParam('structure-url', '[^&]+').trim();

src/apps/viewer/index.ts

@@ -23,8 +23,12 @@ import { ObjectKeys } from '../../mol-util/type-helpers';
 import { PluginState } from '../../mol-plugin/state';
 import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
 import { PluginLayoutControlsDisplay } from '../../mol-plugin/layout';
+
 require('mol-plugin-ui/skin/light.scss');
 
+export { PLUGIN_VERSION as version } from '../../mol-plugin/version';
+export { setProductionMode, setDebugMode } from '../../mol-util/debug';
+
 const Extensions = {
     'cellpack': PluginSpec.Behavior(CellPack),
     'pdbe-structure-quality-report': PluginSpec.Behavior(PDBeStructureQualityReport),
@@ -83,18 +87,18 @@ export class Viewer {
                 ...DefaultPluginSpec.components,
                 remoteState: o.layoutShowRemoteState ? 'default' : 'none',
             },
-            config: DefaultPluginSpec.config
+            config: [
+                [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
+                [PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode],
+                [PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation],
+                [PluginConfig.State.DefaultServer, o.pluginStateServer],
+                [PluginConfig.State.CurrentServer, o.pluginStateServer],
+                [PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer],
+                [PluginConfig.Download.DefaultPdbProvider, o.pdbProvider],
+                [PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider]
+            ]
         };
 
-        spec.config?.set(PluginConfig.Viewport.ShowExpand, o.viewportShowExpand);
-        spec.config?.set(PluginConfig.Viewport.ShowSelectionMode, o.viewportShowSelectionMode);
-        spec.config?.set(PluginConfig.Viewport.ShowAnimation, o.viewportShowAnimation);
-        spec.config?.set(PluginConfig.State.DefaultServer, o.pluginStateServer);
-        spec.config?.set(PluginConfig.State.CurrentServer, o.pluginStateServer);
-        spec.config?.set(PluginConfig.VolumeStreaming.DefaultServer, o.volumeStreamingServer);
-        spec.config?.set(PluginConfig.Download.DefaultPdbProvider, o.pdbProvider);
-        spec.config?.set(PluginConfig.Download.DefaultEmdbProvider, o.emdbProvider);
-
         const element = document.getElementById(elementId);
         if (!element) throw new Error(`Could not get element with id '${elementId}'`);
         this.plugin = createPlugin(element, spec);
@@ -110,7 +114,7 @@ export class Viewer {
     }
 
     async loadStructureFromUrl(url: string, format = 'cif', isBinary = false) {
-        const params = DownloadStructure.createDefaultParams(undefined, this.plugin);
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
         return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
             source: {
                 name: 'url',
@@ -125,7 +129,7 @@ export class Viewer {
     }
 
     async loadPdb(pdb: string) {
-        const params = DownloadStructure.createDefaultParams(undefined, this.plugin);
+        const params = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
         const provider = this.plugin.config.get(PluginConfig.Download.DefaultPdbProvider)!;
         return this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
             source: {
@@ -145,12 +149,15 @@ export class Viewer {
     }
 
     async loadPdbDev(pdbDev: string) {
-        const params = DownloadStructure.createDefaultParams(undefined, this.plugin);
+        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-dev' as const,
                 params: {
-                    id: pdbDev,
+                    provider: {
+                        id: pdbDev,
+                        encoding: 'bcif',
+                    },
                     options: params.source.params.options,
                 }
             }

src/examples/basic-wrapper/superposition.ts

@@ -6,7 +6,7 @@
 
 import { Mat4 } from '../../mol-math/linear-algebra';
 import { QueryContext, StructureSelection } from '../../mol-model/structure';
-import { superposeStructures } from '../../mol-model/structure/structure/util/superposition';
+import { superpose } from '../../mol-model/structure/structure/util/superposition';
 import { PluginStateObject as PSO } from '../../mol-plugin-state/objects';
 import { PluginContext } from '../../mol-plugin/context';
 import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
@@ -79,7 +79,7 @@ export function dynamicSuperpositionTest(plugin: PluginContext, src: string[], c
         const xs = plugin.managers.structure.hierarchy.current.structures;
         const selections = xs.map(s => StructureSelection.toLociWithCurrentUnits(query(new QueryContext(s.cell.obj!.data))));
 
-        const transforms = superposeStructures(selections);
+        const transforms = superpose(selections);
 
         await siteVisual(plugin, xs[0].cell, pivot, rest);
         for (let i = 1; i < selections.length; i++) {

src/examples/proteopedia-wrapper/index.ts

@@ -249,9 +249,7 @@ class MolStarProteopediaWrapper {
     toggleSpin() {
         if (!this.plugin.canvas3d) return;
         const trackball = this.plugin.canvas3d.props.trackball;
-        const spinning = trackball.spin;
         PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { trackball: { ...trackball, spin: !trackball.spin } } });
-        if (!spinning) PluginCommands.Camera.Reset(this.plugin, { });
     }
 
     viewport = {

src/extensions/cellpack/color/generate.ts

@@ -4,29 +4,28 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { ThemeDataContext } from '../../mol-theme/theme';
-import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { Color } from '../../mol-util/color';
-import { getPalette } from '../../mol-util/color/palette';
-import { ColorTheme, LocationColor } from '../../mol-theme/color';
-import { ScaleLegend, TableLegend } from '../../mol-util/legend';
-import { StructureElement, Bond } from '../../mol-model/structure';
-import { Location } from '../../mol-model/location';
-import { CellPackInfoProvider } from './property';
-import { distinctColors } from '../../mol-util/color/distinct';
-import { Hcl } from '../../mol-util/color/spaces/hcl';
-
+import { ThemeDataContext } from '../../../mol-theme/theme';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { Color } from '../../../mol-util/color';
+import { getPalette } from '../../../mol-util/color/palette';
+import { ColorTheme, LocationColor } from '../../../mol-theme/color';
+import { ScaleLegend, TableLegend } from '../../../mol-util/legend';
+import { StructureElement, Bond } from '../../../mol-model/structure';
+import { Location } from '../../../mol-model/location';
+import { CellPackInfoProvider } from '../property';
+import { distinctColors } from '../../../mol-util/color/distinct';
+import { Hcl } from '../../../mol-util/color/spaces/hcl';
 
 const DefaultColor = Color(0xCCCCCC);
-const Description = 'Gives every model in a CellPack packing a unique color similar to other models in the packing.';
+const Description = 'Gives every model in a CellPack packing a unique generated color similar to other models in the packing.';
 
-export const CellPackColorThemeParams = {};
-export type CellPackColorThemeParams = typeof CellPackColorThemeParams
-export function getCellPackColorThemeParams(ctx: ThemeDataContext) {
-    return CellPackColorThemeParams; // TODO return copy
+export const CellPackGenerateColorThemeParams = {};
+export type CellPackGenerateColorThemeParams = typeof CellPackGenerateColorThemeParams
+export function getCellPackGenerateColorThemeParams(ctx: ThemeDataContext) {
+    return CellPackGenerateColorThemeParams; // TODO return copy
 }
 
-export function CellPackColorTheme(ctx: ThemeDataContext, props: PD.Values<CellPackColorThemeParams>): ColorTheme<CellPackColorThemeParams> {
+export function CellPackGenerateColorTheme(ctx: ThemeDataContext, props: PD.Values<CellPackGenerateColorThemeParams>): ColorTheme<CellPackGenerateColorThemeParams> {
     let color: LocationColor;
     let legend: ScaleLegend | TableLegend | undefined;
 
@@ -34,7 +33,8 @@ export function CellPackColorTheme(ctx: ThemeDataContext, props: PD.Values<CellP
 
     if (ctx.structure && info) {
         const colors = distinctColors(info.packingsCount);
-        const hcl = Hcl.fromColor(Hcl(), colors[info.packingIndex]);
+        let hcl = Hcl.fromColor(Hcl(), colors[info.packingIndex]);
+
         const hue = [Math.max(0, hcl[0] - 35), Math.min(360, hcl[0] + 35)] as [number, number];
 
         const { models } = ctx.structure.root;
@@ -70,7 +70,7 @@ export function CellPackColorTheme(ctx: ThemeDataContext, props: PD.Values<CellP
     }
 
     return {
-        factory: CellPackColorTheme,
+        factory: CellPackGenerateColorTheme,
         granularity: 'instance',
         color,
         props,
@@ -79,13 +79,13 @@ export function CellPackColorTheme(ctx: ThemeDataContext, props: PD.Values<CellP
     };
 }
 
-export const CellPackColorThemeProvider: ColorTheme.Provider<CellPackColorThemeParams, 'cellpack'> = {
-    name: 'cellpack',
-    label: 'CellPack',
+export const CellPackGenerateColorThemeProvider: ColorTheme.Provider<CellPackGenerateColorThemeParams, 'cellpack-generate'> = {
+    name: 'cellpack-generate',
+    label: 'CellPack Generate',
     category: ColorTheme.Category.Chain,
-    factory: CellPackColorTheme,
-    getParams: getCellPackColorThemeParams,
-    defaultValues: PD.getDefaultValues(CellPackColorThemeParams),
+    factory: CellPackGenerateColorTheme,
+    getParams: getCellPackGenerateColorThemeParams,
+    defaultValues: PD.getDefaultValues(CellPackGenerateColorThemeParams),
     isApplicable: (ctx: ThemeDataContext) => {
         return (
             !!ctx.structure && ctx.structure.elementCount > 0 &&
@@ -93,4 +93,5 @@ export const CellPackColorThemeProvider: ColorTheme.Provider<CellPackColorThemeP
             !!CellPackInfoProvider.get(ctx.structure).value
         );
     }
-};
+};
+

src/extensions/cellpack/color/provided.ts

@@ -0,0 +1,72 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ThemeDataContext } from '../../../mol-theme/theme';
+import { ParamDefinition as PD } from '../../../mol-util/param-definition';
+import { Color } from '../../../mol-util/color';
+import { ColorTheme, LocationColor } from '../../../mol-theme/color';
+import { ScaleLegend, TableLegend } from '../../../mol-util/legend';
+import { StructureElement } from '../../../mol-model/structure';
+import { Location } from '../../../mol-model/location';
+import { CellPackInfoProvider } from '../property';
+
+const DefaultColor = Color(0xCCCCCC);
+const Description = 'Gives every model in a CellPack the color provied in the packing data.';
+
+export const CellPackProvidedColorThemeParams = {};
+export type CellPackProvidedColorThemeParams = typeof CellPackProvidedColorThemeParams
+export function getCellPackProvidedColorThemeParams(ctx: ThemeDataContext) {
+    return CellPackProvidedColorThemeParams; // TODO return copy
+}
+
+export function CellPackProvidedColorTheme(ctx: ThemeDataContext, props: PD.Values<CellPackProvidedColorThemeParams>): ColorTheme<CellPackProvidedColorThemeParams> {
+    let color: LocationColor;
+    let legend: ScaleLegend | TableLegend | undefined;
+
+    const info = ctx.structure && CellPackInfoProvider.get(ctx.structure).value;
+
+    if (ctx.structure && info?.colors) {
+        const { models } = ctx.structure.root;
+        const modelColor = new Map<number, Color>();
+        for (let i = 0, il = models.length; i < il; ++i) {
+            const idx = models[i].trajectoryInfo.index;
+            modelColor.set(models[i].trajectoryInfo.index, info.colors[idx]);
+        }
+
+        color = (location: Location): Color => {
+            return StructureElement.Location.is(location)
+                ? modelColor.get(location.unit.model.trajectoryInfo.index)!
+                : DefaultColor;
+        };
+    } else {
+        color = () => DefaultColor;
+    }
+
+    return {
+        factory: CellPackProvidedColorTheme,
+        granularity: 'instance',
+        color,
+        props,
+        description: Description,
+        legend
+    };
+}
+
+export const CellPackProvidedColorThemeProvider: ColorTheme.Provider<CellPackProvidedColorThemeParams, 'cellpack-provided'> = {
+    name: 'cellpack-provided',
+    label: 'CellPack Provided',
+    category: ColorTheme.Category.Chain,
+    factory: CellPackProvidedColorTheme,
+    getParams: getCellPackProvidedColorThemeParams,
+    defaultValues: PD.getDefaultValues(CellPackProvidedColorThemeParams),
+    isApplicable: (ctx: ThemeDataContext) => {
+        return (
+            !!ctx.structure && ctx.structure.elementCount > 0 &&
+            ctx.structure.models[0].trajectoryInfo.size > 1 &&
+            !!CellPackInfoProvider.get(ctx.structure).value?.colors
+        );
+    }
+};

src/extensions/cellpack/curve.ts

@@ -191,8 +191,14 @@ function GetMiniFrame(points: Vec3[], normals: Vec3[]) {
 
 const rpTmpVec1 = Vec3();
 
-export function getMatFromResamplePoints(points: NumberArray, segmentLength: number) {
-    const new_points = ResampleControlPoints(points, segmentLength);
+export function getMatFromResamplePoints(points: NumberArray, segmentLength: number, resample: boolean) {
+    let new_points: Vec3[] = [];
+    if (resample) new_points = ResampleControlPoints(points, segmentLength);
+    else {
+        for (let idx = 0; idx < points.length / 3; ++idx){
+            new_points.push(Vec3.fromArray(Vec3.zero(), points, idx * 3));
+        }
+    }
     const npoints = new_points.length;
     const new_normal = GetSmoothNormals(new_points);
     const frames = GetMiniFrame(new_points, new_normal);

src/extensions/cellpack/data.ts

@@ -59,6 +59,7 @@ export interface Ingredient {
     radii?: [Radii];
     /** Number of `curveX` properties in the object where `X` is a 0-indexed number */
     nbCurve?: number;
+    uLength?: number;
     /** Curve properties are Vec3[] but that is not expressable in TypeScript */
     [curveX: string]: unknown;
     /** the orientation in the membrane */
@@ -66,6 +67,8 @@ export interface Ingredient {
     /** offset along membrane */
     offset?: Vec3;
     ingtype?: string;
+    color?: Vec3;
+    confidence?: number;
 }
 
 export interface IngredientSource {

src/extensions/cellpack/index.ts

@@ -5,9 +5,9 @@
  */
 
 import { PluginBehavior } from '../../mol-plugin/behavior';
-import { CellPackColorThemeProvider } from './color';
 import { LoadCellPackModel } from './model';
-
+import { CellPackGenerateColorThemeProvider } from './color/generate';
+import { CellPackProvidedColorThemeProvider } from './color/provided';
 
 export const CellPack = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
     name: 'cellpack',
@@ -19,12 +19,14 @@ export const CellPack = PluginBehavior.create<{ autoAttach: boolean, showTooltip
     ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showTooltip: boolean }> {
         register(): void {
             this.ctx.state.data.actions.add(LoadCellPackModel);
-            this.ctx.representation.structure.themes.colorThemeRegistry.add(CellPackColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(CellPackGenerateColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(CellPackProvidedColorThemeProvider);
         }
 
         unregister() {
             this.ctx.state.data.actions.remove(LoadCellPackModel);
-            this.ctx.representation.structure.themes.colorThemeRegistry.remove(CellPackColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(CellPackGenerateColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(CellPackProvidedColorThemeProvider);
         }
     }
 });

src/extensions/cellpack/model.ts

@@ -17,7 +17,7 @@ import { Mat4, Vec3, Quat } from '../../mol-math/linear-algebra';
 import { SymmetryOperator } from '../../mol-math/geometry';
 import { Task, RuntimeContext } from '../../mol-task';
 import { StateTransforms } from '../../mol-plugin-state/transforms';
-import { ParseCellPack, StructureFromCellpack, DefaultCellPackBaseUrl } from './state';
+import { ParseCellPack, StructureFromCellpack, DefaultCellPackBaseUrl, StructureFromAssemblies } from './state';
 import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
 import { getMatFromResamplePoints } from './curve';
 import { compile } from '../../mol-script/runtime/query/compiler';
@@ -27,6 +27,7 @@ import { Column } from '../../mol-data/db';
 import { createModels } from '../../mol-model-formats/structure/basic/parser';
 import { CellpackPackingPreset, CellpackMembranePreset } from './preset';
 import { Asset } from '../../mol-util/assets';
+import { Color } from '../../mol-util/color';
 import { readFromFile } from '../../mol-util/data-source';
 import { objectForEach } from '../../mol-util/object';
 
@@ -108,7 +109,7 @@ async function getStructure(plugin: PluginContext, model: Model, source: Ingredi
     }
     let query;
     if (source.selection){
-        const asymIds: string[] = source.selection.replace(' :', '').split(' or');
+        const asymIds: string[] = source.selection.replace(' ', '').replace(':', '').split('or');
         query = MS.struct.modifier.union([
             MS.struct.generator.atomGroups({
                 'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
@@ -155,11 +156,15 @@ function getResultTransforms(results: Ingredient['results'], legacy: boolean) {
 function getCurveTransforms(ingredient: Ingredient) {
     const n = ingredient.nbCurve || 0;
     const instances: Mat4[] = [];
-    const segmentLength = ingredient.radii
-        ? (ingredient.radii[0].radii
+    let segmentLength = 3.4;
+    if (ingredient.uLength){
+        segmentLength = ingredient.uLength;
+    } else if (ingredient.radii){
+        segmentLength = ingredient.radii[0].radii
             ? ingredient.radii[0].radii[0] * 2.0
-            : 3.4)
-        : 3.4;
+            : 3.4;
+    }
+    let resampling: boolean = false;
     for (let i = 0; i < n; ++i) {
         const cname = `curve${i}`;
         if (!(cname in ingredient)) {
@@ -171,12 +176,17 @@ function getCurveTransforms(ingredient: Ingredient) {
             // TODO handle curve with 2 or less points
             continue;
         }
+        // test for resampling
+        let distance: number = Vec3.distance(_points[0], _points[1]);
+        if (distance >= segmentLength + 2.0) {
+            console.info(distance);
+            resampling = true;
+        }
         const points = new Float32Array(_points.length * 3);
         for (let i = 0, il = _points.length; i < il; ++i) Vec3.toArray(_points[i], points, i * 3);
-        const newInstances = getMatFromResamplePoints(points, segmentLength);
+        const newInstances = getMatFromResamplePoints(points, segmentLength, resampling);
         instances.push(...newInstances);
     }
-
     return instances;
 }
 
@@ -290,7 +300,6 @@ function getCifCurve(name: string, transforms: Mat4[], model: Model) {
 
 async function getCurve(plugin: PluginContext, name: string, ingredient: Ingredient, transforms: Mat4[], model: Model) {
     const cif = getCifCurve(name, transforms, model);
-
     const curveModelTask = Task.create('Curve Model', async ctx => {
         const format = MmcifFormat.fromFrame(cif);
         const models = await createModels(format.data.db, format, ctx);
@@ -308,10 +317,10 @@ async function getIngredientStructure(plugin: PluginContext, ingredient: Ingredi
     const file = ingredientFiles[source.pdb];
     if (!file) {
         // TODO can these be added to the library?
-        if (name === 'HIV1_CAhex_0_1_0') return;
-        if (name === 'HIV1_CAhexCyclophilA_0_1_0') return;
-        if (name === 'iLDL') return;
-        if (name === 'peptides') return;
+        if (name === 'HIV1_CAhex_0_1_0') return; // 1VU4CtoH_hex.pdb
+        if (name === 'HIV1_CAhexCyclophilA_0_1_0') return; // 1AK4fitTo1VU4hex.pdb
+        if (name === 'iLDL') return; // EMD-5239
+        if (name === 'peptides') return; // peptide.pdb
         if (name === 'lypoglycane') return;
     }
 
@@ -369,12 +378,20 @@ export function createStructureFromCellPack(plugin: PluginContext, packing: Cell
         const assets: Asset.Wrapper[] = [];
         const trajCache = new TrajectoryCache();
         const structures: Structure[] = [];
+        const colors: Color[] = [];
+        let skipColors: boolean = false;
         for (const iName in ingredients) {
             if (ctx.shouldUpdate) await ctx.update(iName);
             const ingredientStructure = await getIngredientStructure(plugin, ingredients[iName], baseUrl, ingredientFiles, trajCache);
             if (ingredientStructure) {
                 structures.push(ingredientStructure.structure);
                 assets.push(...ingredientStructure.assets);
+                const c = ingredients[iName].color;
+                if (c){
+                    colors.push(Color.fromNormalizedRgb(c[0], c[1], c[2]));
+                } else {
+                    skipColors = true;
+                }
             }
         }
 
@@ -399,7 +416,7 @@ export function createStructureFromCellPack(plugin: PluginContext, packing: Cell
             trajectoryInfo.size = il;
             trajectoryInfo.index = i;
         }
-        return { structure, assets };
+        return { structure, assets, colors: skipColors ? undefined : colors };
     });
 }
 
@@ -435,11 +452,25 @@ async function loadMembrane(plugin: PluginContext, name: string, state: State, p
                 break;
             }
         }
+        if (!file){
+            // check for cif directly
+            const cifileName = `${name}.cif`;
+            for (const f of params.ingredients.files) {
+                if (cifileName === f.name) {
+                    file = f;
+                    break;
+                }
+            }
+        }
     }
 
     let b = state.build().toRoot();
     if (file) {
-        b = b.apply(StateTransforms.Data.ReadFile, { file, isBinary: true, label: file.name }, { state: { isGhost: true } });
+        if (file.name.endsWith('.cif')) {
+            b = b.apply(StateTransforms.Data.ReadFile, { file, isBinary: false, label: file.name }, { state: { isGhost: true } });
+        } else if (file.name.endsWith('.bcif')) {
+            b = b.apply(StateTransforms.Data.ReadFile, { file, isBinary: true, label: file.name }, { state: { isGhost: true } });
+        }
     } else {
         const url = Asset.getUrlAsset(plugin.managers.asset, `${params.baseUrl}/membranes/${name}.bcif`);
         b = b.apply(StateTransforms.Data.Download, { url, isBinary: true, label: name }, { state: { isGhost: true } });
@@ -448,12 +479,13 @@ async function loadMembrane(plugin: PluginContext, name: string, state: State, p
     const membrane = await b.apply(StateTransforms.Data.ParseCif, undefined, { state: { isGhost: true } })
         .apply(StateTransforms.Model.TrajectoryFromMmCif, undefined, { state: { isGhost: true } })
         .apply(StateTransforms.Model.ModelFromTrajectory, undefined, { state: { isGhost: true } })
-        .apply(StateTransforms.Model.StructureFromModel)
+        .apply(StructureFromAssemblies, undefined, { state: { isGhost: true } })
         .commit({ revertOnError: true });
 
     const membraneParams = {
         representation: params.preset.representation,
     };
+
     await CellpackMembranePreset.apply(membrane, membraneParams, plugin);
 }
 
@@ -510,7 +542,7 @@ async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, stat
             representation: params.preset.representation,
         };
         await CellpackPackingPreset.apply(packing, packingParams, plugin);
-        if ( packings[i].location === 'surface' ){
+        if ( packings[i].location === 'surface' && params.membrane){
             await loadMembrane(plugin, packings[i].name, state, params);
         }
     }
@@ -518,18 +550,21 @@ async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, stat
 
 const LoadCellPackModelParams = {
     source: PD.MappedStatic('id', {
-        'id': PD.Select('influenza_model1.json', [
-            ['blood_hiv_immature_inside.json', 'blood_hiv_immature_inside'],
-            ['BloodHIV1.0_mixed_fixed_nc1.cpr', 'BloodHIV1.0_mixed_fixed_nc1'],
-            ['HIV-1_0.1.6-8_mixed_radii_pdb.cpr', 'HIV-1_0.1.6-8_mixed_radii_pdb'],
-            ['hiv_lipids.bcif', 'hiv_lipids'],
-            ['influenza_model1.json', 'influenza_model1'],
-            ['ExosomeModel.json', 'ExosomeModel'],
-            ['Mycoplasma1.5_mixed_pdb_fixed.cpr', 'Mycoplasma1.5_mixed_pdb_fixed'],
+        'id': PD.Select('InfluenzaModel2.json', [
+            ['blood_hiv_immature_inside.json', 'Blood HIV immature'],
+            ['HIV_immature_model.json', 'HIV immature'],
+            ['BloodHIV1.0_mixed_fixed_nc1.cpr', 'Blood HIV'],
+            ['HIV-1_0.1.6-8_mixed_radii_pdb.cpr', 'HIV'],
+            ['influenza_model1.json', 'Influenza envelope'],
+            ['InfluenzaModel2.json', 'Influenza Complete'],
+            ['ExosomeModel.json', 'Exosome Model'],
+            ['Mycoplasma1.5_mixed_pdb_fixed.cpr', 'Mycoplasma simple'],
+            ['MycoplasmaModel.json', 'Mycoplasma WholeCell model'],
         ] as const, { description: 'Download the model definition with `id` from the server at `baseUrl.`' }),
         'file': PD.File({ accept: '.json,.cpr,.zip', description: 'Open model definition from .json/.cpr file or open .zip file containing model definition plus ingredients.' }),
     }, { options: [['id', 'Id'], ['file', 'File']] }),
     baseUrl: PD.Text(DefaultCellPackBaseUrl),
+    membrane: PD.Boolean(true),
     ingredients : PD.Group({
         files: PD.FileList({ accept: '.cif,.bcif,.pdb' })
     }, { isExpanded: true }),
@@ -545,9 +580,5 @@ export const LoadCellPackModel = StateAction.build({
     params: LoadCellPackModelParams,
     from: PSO.Root
 })(({ state, params }, ctx: PluginContext) => Task.create('CellPack Loader', async taskCtx => {
-    if (params.source.name === 'id' && params.source.params === 'hiv_lipids.bcif') {
-        await loadMembrane(ctx, 'hiv_lipids', state, params);
-    } else {
-        await loadPackings(ctx, taskCtx, state, params);
-    }
+    await loadPackings(ctx, taskCtx, state, params);
 }));

src/extensions/cellpack/preset.ts

@@ -8,7 +8,9 @@ import { StateObjectRef } from '../../mol-state';
 import { StructureRepresentationPresetProvider, presetStaticComponent } from '../../mol-plugin-state/builder/structure/representation-preset';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ColorNames } from '../../mol-util/color/names';
-import { CellPackColorThemeProvider } from './color';
+import { CellPackGenerateColorThemeProvider } from './color/generate';
+import { CellPackInfoProvider } from './property';
+import { CellPackProvidedColorThemeProvider } from './color/provided';
 
 export const CellpackPackingPresetParams = {
     traceOnly: PD.Boolean(true),
@@ -40,8 +42,10 @@ export const CellpackPackingPreset = StructureRepresentationPresetProvider({
             Object.assign(reprProps, { sizeFactor: 2 });
         }
 
+        const info = structureCell.obj?.data && CellPackInfoProvider.get(structureCell.obj?.data).value;
+        const color = info?.colors ? CellPackProvidedColorThemeProvider.name : CellPackGenerateColorThemeProvider.name;
+
         const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, {});
-        const color = CellPackColorThemeProvider.name;
         const representations = {
             polymer: builder.buildRepresentation<any>(update, components.polymer, { type: params.representation, typeParams: { ...typeParams, ...reprProps }, color }, { tag: 'polymer' })
         };
@@ -85,6 +89,7 @@ export const CellpackMembranePreset = StructureRepresentationPresetProvider({
         };
 
         await update.commit({ revertOnError: true });
+
         return { components, representations };
     }
 });

src/extensions/cellpack/property.ts

@@ -5,17 +5,20 @@
  */
 
 import { CustomStructureProperty } from '../../mol-model-props/common/custom-structure-property';
-import { Structure, CustomPropertyDescriptor } from '../../mol-model/structure';
+import { Structure } from '../../mol-model/structure';
 import { CustomProperty } from '../../mol-model-props/common/custom-property';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Color } from '../../mol-util/color';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 
 export type CellPackInfoValue = {
     packingsCount: number
     packingIndex: number
+    colors?: Color[]
 }
 
 const CellPackInfoParams = {
-    info: PD.Value<CellPackInfoValue>({ packingsCount: 1, packingIndex: 0 }, { isHidden: true })
+    info: PD.Value<CellPackInfoValue>({ packingsCount: 1, packingIndex: 0, colors: undefined }, { isHidden: true })
 };
 type CellPackInfoParams = PD.Values<typeof CellPackInfoParams>
 

src/extensions/cellpack/state.ts

@@ -13,6 +13,8 @@ import { IngredientFiles } from './util';
 import { Asset } from '../../mol-util/assets';
 import { PluginContext } from '../../mol-plugin/context';
 import { CellPackInfoProvider } from './property';
+import { Structure, StructureSymmetry, Unit } from '../../mol-model/structure';
+import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
 
 export const DefaultCellPackBaseUrl = 'https://mesoscope.scripps.edu/data/cellPACK_data/cellPACK_database_1.1.0/';
 
@@ -71,10 +73,9 @@ const StructureFromCellpack = PluginStateTransform.BuiltIn({
                     ingredientFiles[file.name] = file;
                 }
             }
-            const { structure, assets } = await createStructureFromCellPack(plugin, packing, params.baseUrl, ingredientFiles).runInContext(ctx);
-
+            const { structure, assets, colors } = await createStructureFromCellPack(plugin, packing, params.baseUrl, ingredientFiles).runInContext(ctx);
             await CellPackInfoProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, structure, {
-                info: { packingsCount: a.data.packings.length, packingIndex: params.packing }
+                info: { packingsCount: a.data.packings.length, packingIndex: params.packing, colors }
             });
 
             (cache as any).assets = assets;
@@ -94,4 +95,110 @@ const StructureFromCellpack = PluginStateTransform.BuiltIn({
             }
         }
     }
-});
+});
+
+export { StructureFromAssemblies };
+type StructureFromAssemblies = typeof StructureFromAssemblies
+const StructureFromAssemblies = PluginStateTransform.BuiltIn({
+    name: 'Structure from all assemblies',
+    display: { name: 'Structure from all assemblies' },
+    from: PSO.Molecule.Model,
+    to: PSO.Molecule.Structure,
+    params: {
+    }
+})({
+    canAutoUpdate({ newParams }) {
+        return true;
+    },
+    apply({ a, params }) {
+        return Task.create('Build Structure', async ctx => {
+            // TODO: optimze
+            // TODO: think of ways how to fast-track changes to this for animations
+            const model = a.data;
+            let initial_structure = Structure.ofModel(model);
+            const structures: Structure[] = [];
+            let structure: Structure = initial_structure;
+            // the list of asambly *?
+            const symmetry = ModelSymmetry.Provider.get(model);
+            if (symmetry && symmetry.assemblies.length !== 0){
+                for (const a of symmetry.assemblies) {
+                    const s = await StructureSymmetry.buildAssembly(initial_structure, a.id).runInContext(ctx);
+                    structures.push(s);
+                }
+                const builder = Structure.Builder({ label: name });
+                let offsetInvariantId = 0;
+                for (const s of structures) {
+                    let maxInvariantId = 0;
+                    for (const u of s.units) {
+                        const invariantId = u.invariantId + offsetInvariantId;
+                        if (u.invariantId > maxInvariantId) maxInvariantId = u.invariantId;
+                        builder.addUnit(u.kind, u.model, u.conformation.operator, u.elements, Unit.Trait.None, invariantId);
+                    }
+                    offsetInvariantId += maxInvariantId + 1;
+                }
+                structure = builder.getStructure();
+                for( let i = 0, il = structure.models.length; i < il; ++i) {
+                    const { trajectoryInfo } = structure.models[i];
+                    trajectoryInfo.size = il;
+                    trajectoryInfo.index = i;
+                }
+            }
+            return new PSO.Molecule.Structure(structure, { label: a.label, description: `${a.description}` });
+        });
+    },
+    dispose({ b }) {
+        b?.data.customPropertyDescriptors.dispose();
+    }
+});
+
+// export { GetAllAssamblyinOneStructure };
+// type GetAllAssamblyinOneStructure = typeof GetAllAssamblyinOneStructure
+// const GetAllAssamblyinOneStructure = PluginStateTransform.BuiltIn({
+//     name: 'get assambly from structure',
+//     display: { name: 'get assambly from structure' },
+//     isDecorator: true,
+//     from: PSO.Molecule.Structure,
+//     to: PSO.Molecule.Structure,
+//     params(a) {
+//         return { };
+//     }
+// })({
+//     apply({ a, params }) {
+//         return Task.create('Build Structure Assemblies', async ctx => {
+//             // TODO: optimze
+//             // TODO: think of ways how to fast-track changes to this for animations
+//             const initial_structure = a.data;
+//             const structures: Structure[] = [];
+//             let structure: Structure = initial_structure;
+//             // the list of asambly *?
+//             const symmetry = ModelSymmetry.Provider.get(initial_structure.model);
+//             if (symmetry){
+//                 if (symmetry.assemblies.length !== 0) {
+//                     for (const a of symmetry.assemblies) {
+//                         const s = await StructureSymmetry.buildAssembly(initial_structure, a.id!).runInContext(ctx);
+//                         structures.push(s);
+//                     }
+//                     const builder = Structure.Builder({ label: name });
+//                     let offsetInvariantId = 0;
+//                     for (const s of structures) {
+//                         let maxInvariantId = 0;
+//                         for (const u of s.units) {
+//                             const invariantId = u.invariantId + offsetInvariantId;
+//                             if (u.invariantId > maxInvariantId) maxInvariantId = u.invariantId;
+//                             builder.addUnit(u.kind, u.model, u.conformation.operator, u.elements, Unit.Trait.None, invariantId);
+//                         }
+//                         offsetInvariantId += maxInvariantId + 1;
+//                     }
+//                     structure = builder.getStructure();
+//                     for( let i = 0, il = structure.models.length; i < il; ++i) {
+//                         const { trajectoryInfo } = structure.models[i];
+//                         trajectoryInfo.size = il;
+//                         trajectoryInfo.index = i;
+//                     }
+//                 }
+//             }
+//             return new PSO.Molecule.Structure(structure, { label: a.label, description: `${a.description}` });
+//         });
+//     }
+// });
+

src/extensions/pdbe/preferred-assembly.ts

@@ -7,9 +7,10 @@
 import { Column, Table } from '../../mol-data/db';
 import { toTable } from '../../mol-io/reader/cif/schema';
 import { CifWriter } from '../../mol-io/writer/cif';
-import { Model, CustomPropertyDescriptor } from '../../mol-model/structure';
+import { Model } from '../../mol-model/structure';
 import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
 import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 
 export namespace PDBePreferredAssembly {
     export type Property = string

src/extensions/pdbe/struct-ref-domain.ts

@@ -7,9 +7,10 @@
 import { Column, Table } from '../../mol-data/db';
 import { toTable } from '../../mol-io/reader/cif/schema';
 import { CifWriter } from '../../mol-io/writer/cif';
-import { Model, CustomPropertyDescriptor } from '../../mol-model/structure';
+import { Model } from '../../mol-model/structure';
 import { PropertyWrapper } from '../../mol-model-props/common/wrapper';
 import { MmcifFormat } from '../../mol-model-formats/structure/mmcif';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 
 export namespace PDBeStructRefDomain {
     export type Property = PropertyWrapper<Table<Schema['pdbe_struct_ref_domain']> | undefined>

src/extensions/pdbe/structure-quality-report/prop.ts

@@ -9,7 +9,7 @@ import { Column, Table } from '../../../mol-data/db';
 import { toTable } from '../../../mol-io/reader/cif/schema';
 import { mmCIF_residueId_schema } from '../../../mol-io/reader/cif/schema/mmcif-extras';
 import { CifWriter } from '../../../mol-io/writer/cif';
-import { Model, CustomPropertyDescriptor, ResidueIndex, Unit, IndexedCustomProperty } from '../../../mol-model/structure';
+import { Model, ResidueIndex, Unit, IndexedCustomProperty } from '../../../mol-model/structure';
 import { residueIdFields } from '../../../mol-model/structure/export/categories/atom_site';
 import { StructureElement, CifExportContext, Structure } from '../../../mol-model/structure/structure';
 import { CustomPropSymbol } from '../../../mol-script/language/symbol';
@@ -22,6 +22,7 @@ import { PropertyWrapper } from '../../../mol-model-props/common/wrapper';
 import { CustomProperty } from '../../../mol-model-props/common/custom-property';
 import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
 import { Asset } from '../../../mol-util/assets';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 
 export { StructureQualityReport };
 

src/extensions/rcsb/assembly-symmetry/prop.ts

@@ -8,7 +8,7 @@ import { AssemblySymmetryQuery, AssemblySymmetryQueryVariables } from '../graphq
 import query from '../graphql/symmetry.gql';
 
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { CustomPropertyDescriptor, Structure, Model, StructureSelection, QueryContext } from '../../../mol-model/structure';
+import { Structure, Model, StructureSelection, QueryContext } from '../../../mol-model/structure';
 import { Database as _Database, Column } from '../../../mol-data/db';
 import { GraphQLClient } from '../../../mol-util/graphql-client';
 import { CustomProperty } from '../../../mol-model-props/common/custom-property';
@@ -19,6 +19,7 @@ import { ReadonlyVec3 } from '../../../mol-math/linear-algebra/3d/vec3';
 import { SetUtils } from '../../../mol-util/set';
 import { MolScriptBuilder as MS } from '../../../mol-script/language/builder';
 import { compile } from '../../../mol-script/runtime/query/compiler';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 
 const BiologicalAssemblyNames = new Set([
     'author_and_software_defined_assembly',

src/extensions/rcsb/assembly-symmetry/representation.ts

@@ -186,12 +186,22 @@ const getSymbolCage = memoize1((symbol: string): Cage | undefined => {
     if (symbol.startsWith('D') || symbol.startsWith('C')) {
         // z axis is prism axis, x/y axes cut through edge midpoints
         const fold = parseInt(symbol.substr(1));
+        let cage: Cage;
         if (fold === 2) {
-            return PrismCage(polygon(4, false));
+            cage = PrismCage(polygon(4, false));
         } else if (fold === 3) {
-            return WedgeCage();
+            cage = WedgeCage();
         } else if (fold > 3) {
-            return PrismCage(polygon(fold, false));
+            cage = PrismCage(polygon(fold, false));
+        } else {
+            return;
+        }
+        if (fold % 2 === 0) {
+            return cage;
+        } else {
+            const m = Mat4.identity();
+            Mat4.rotate(m, m, 1 / fold * Math.PI / 2, Vec3.unitZ);
+            return transformCage(cloneCage(cage), m);
         }
     } else if (symbol === 'O') {
         // x/y/z axes cut through order 4 vertices
@@ -237,7 +247,7 @@ function setSymbolTransform(t: Mat4, symbol: string, axes: AssemblySymmetry.Rota
             pair = axes.filter(a => a.order === 2);
         } else if (fold >= 3) {
             const aN = axes.filter(a => a.order === fold)[0];
-            const a2 = axes.filter(a => a.order === 2)[0];
+            const a2 = axes.filter(a => a.order === 2)[1];
             pair = [aN, a2];
         }
     } else if (symbol === 'O') {
@@ -267,7 +277,19 @@ function setSymbolTransform(t: Mat4, symbol: string, axes: AssemblySymmetry.Rota
             Vec3.sub(dir, eye, target);
             if (Vec3.dot(dir, up) < 0) Vec3.negate(up, up);
             Mat4.targetTo(t, eye, target, up);
-            Mat4.scaleUniformly(t, t, size * getSymbolScale(symbol));
+
+            if (symbol.startsWith('D')) {
+                const { sphere } = structure.lookup3d.boundary;
+                let sizeXY = (sphere.radius * 2) * 0.8; // fallback for missing extrema
+                if (Sphere3D.hasExtrema(sphere)) {
+                    const n = Mat3.directionTransform(Mat3(), t);
+                    const dirs = unitCircleDirections.map(d => Vec3.transformMat3(Vec3(), d, n));
+                    sizeXY = getMaxProjectedDistance(sphere.extrema, dirs, sphere.center) * 1.6;
+                }
+                Mat4.scale(t, t, Vec3.create(sizeXY, sizeXY, Vec3.distance(aA.start, aA.end) * 0.9));
+            } else {
+                Mat4.scaleUniformly(t, t, size * getSymbolScale(symbol));
+            }
         } else {
             if (Vec3.dot(Vec3.unitY, Vec3.sub(tmpV, aA.end, aA.start)) === 0) {
                 Vec3.copy(up, Vec3.unitY);
@@ -283,7 +305,6 @@ function setSymbolTransform(t: Mat4, symbol: string, axes: AssemblySymmetry.Rota
                 const dirs = unitCircleDirections.map(d => Vec3.transformMat3(Vec3(), d, n));
                 sizeXY = getMaxProjectedDistance(sphere.extrema, dirs, sphere.center);
             }
-
             Mat4.scale(t, t, Vec3.create(sizeXY, sizeXY, size * 0.9));
         }
     }

src/extensions/rcsb/validation-report/behavior.ts

@@ -222,12 +222,12 @@ function densityFitLabel(loci: Loci): string | undefined {
         if (rsrzSeen.size) {
             const rsrzCount = `<small>(${rsrzSeen.size} ${rsrzSeen.size > 1 ? 'Residues avg.' : 'Residue'})</small>`;
             const rsrzAvg = rsrzSum / rsrzSeen.size;
-            summary.push(`Real Space R ${rsrzCount}: ${rsrzAvg.toFixed(2)}`);
+            summary.push(`Real-Space R Z-score ${rsrzCount}: ${rsrzAvg.toFixed(2)}`);
         }
         if (rsccSeen.size) {
             const rsccCount = `<small>(${rsccSeen.size} ${rsccSeen.size > 1 ? 'Residues avg.' : 'Residue'})</small>`;
             const rsccAvg = rsccSum / rsccSeen.size;
-            summary.push(`Real Space Correlation Coefficient ${rsccCount}: ${rsccAvg.toFixed(2)}`);
+            summary.push(`Real-Space Correlation Coefficient ${rsccCount}: ${rsccAvg.toFixed(2)}`);
         }
 
         if (summary.length) {

src/extensions/rcsb/validation-report/prop.ts

@@ -5,7 +5,7 @@
  */
 
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { CustomPropertyDescriptor, Structure, Unit } from '../../../mol-model/structure';
+import { Structure, Unit } from '../../../mol-model/structure';
 import { CustomProperty } from '../../../mol-model-props/common/custom-property';
 import { CustomModelProperty } from '../../../mol-model-props/common/custom-model-property';
 import { Model, ElementIndex, ResidueIndex } from '../../../mol-model/structure/model';
@@ -21,6 +21,7 @@ import { QuerySymbolRuntime } from '../../../mol-script/runtime/query/compiler';
 import { CustomPropSymbol } from '../../../mol-script/language/symbol';
 import Type from '../../../mol-script/language/type';
 import { Asset } from '../../../mol-util/assets';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 
 export { ValidationReport };
 

src/mol-canvas3d/canvas3d.ts

@@ -36,6 +36,7 @@ import { Sphere3D } from '../mol-math/geometry';
 import { isDebugMode } from '../mol-util/debug';
 import { CameraHelperParams } from './helper/camera-helper';
 import { produce } from 'immer';
+import { HandleHelper, HandleHelperParams } from './helper/handle-helper';
 
 export const Canvas3DParams = {
     camera: PD.Group({
@@ -60,7 +61,8 @@ export const Canvas3DParams = {
     postprocessing: PD.Group(PostprocessingParams),
     renderer: PD.Group(RendererParams),
     trackball: PD.Group(TrackballControlsParams),
-    debug: PD.Group(DebugHelperParams)
+    debug: PD.Group(DebugHelperParams),
+    handle: PD.Group(HandleHelperParams),
 };
 export const DefaultCanvas3DParams = PD.getDefaultValues(Canvas3DParams);
 export type Canvas3DProps = PD.Values<typeof Canvas3DParams>
@@ -188,12 +190,13 @@ namespace Canvas3D {
         const controls = TrackballControls.create(input, camera, p.trackball);
         const renderer = Renderer.create(webgl, p.renderer);
         const debugHelper = new BoundingSphereHelper(webgl, scene, p.debug);
+        const handleHelper = new HandleHelper(webgl, p.handle);
         const interactionHelper = new Canvas3dInteractionHelper(identify, getLoci, input);
 
-        const drawPass = new DrawPass(webgl, renderer, scene, camera, debugHelper, {
+        const drawPass = new DrawPass(webgl, renderer, scene, camera, debugHelper, handleHelper, {
             cameraHelper: p.camera.helper
         });
-        const pickPass = new PickPass(webgl, renderer, scene, camera, 0.5);
+        const pickPass = new PickPass(webgl, renderer, scene, camera, handleHelper, 0.5);
         const postprocessing = new PostprocessingPass(webgl, camera, drawPass, p.postprocessing);
         const multiSample = new MultiSamplePass(webgl, camera, drawPass, postprocessing, p.multiSample);
 
@@ -205,6 +208,7 @@ namespace Canvas3D {
         function getLoci(pickingId: PickingId) {
             let loci: Loci = EmptyLoci;
             let repr: Representation.Any = Representation.Empty;
+            loci = handleHelper.getLoci(pickingId);
             reprRenderObjects.forEach((_, _repr) => {
                 const _loci = _repr.getLoci(pickingId);
                 if (!isEmptyLoci(_loci)) {
@@ -224,10 +228,12 @@ namespace Canvas3D {
             if (repr) {
                 changed = repr.mark(loci, action);
             } else {
+                changed = handleHelper.mark(loci, action);
                 reprRenderObjects.forEach((_, _repr) => { changed = _repr.mark(loci, action) || changed; });
             }
             if (changed) {
                 scene.update(void 0, true);
+                handleHelper.scene.update(void 0, true);
                 const prevPickDirty = pickPass.pickDirty;
                 draw(true);
                 pickPass.pickDirty = prevPickDirty; // marking does not change picking buffers
@@ -356,10 +362,19 @@ namespace Canvas3D {
 
             camera.setState({ radiusMax: scene.boundingSphere.radius }, 0);
             reprCount.next(reprRenderObjects.size);
+            if (isDebugMode) consoleStats();
 
             return true;
         }
 
+        function consoleStats() {
+            console.table(scene.renderables.map(r => ({
+                drawCount: r.values.drawCount.ref.value,
+                instanceCount: r.values.instanceCount.ref.value,
+                materialId: r.materialId,
+            })));
+        }
+
         function add(repr: Representation.Any) {
             registerAutoUpdate(repr);
 
@@ -378,6 +393,7 @@ namespace Canvas3D {
             reprRenderObjects.set(repr, newRO);
 
             scene.update(repr.renderObjects, false);
+            if (isDebugMode) consoleStats();
         }
 
         function remove(repr: Representation.Any) {
@@ -388,6 +404,7 @@ namespace Canvas3D {
                 renderObjects.forEach(o => scene.remove(o));
                 reprRenderObjects.delete(repr);
                 scene.update(repr.renderObjects, false, true);
+                if (isDebugMode) consoleStats();
             }
         }
 
@@ -428,7 +445,8 @@ namespace Canvas3D {
                 multiSample: { ...multiSample.props },
                 renderer: { ...renderer.props },
                 trackball: { ...controls.props },
-                debug: { ...debugHelper.props }
+                debug: { ...debugHelper.props },
+                handle: { ...handleHelper.props },
             };
         }
 
@@ -535,11 +553,12 @@ namespace Canvas3D {
                 if (props.renderer) renderer.setProps(props.renderer);
                 if (props.trackball) controls.setProps(props.trackball);
                 if (props.debug) debugHelper.setProps(props.debug);
+                if (props.handle) handleHelper.setProps(props.handle);
 
                 requestDraw(true);
             },
             getImagePass: (props: Partial<ImageProps> = {}) => {
-                return new ImagePass(webgl, renderer, scene, camera, debugHelper, props);
+                return new ImagePass(webgl, renderer, scene, camera, debugHelper, handleHelper, props);
             },
 
             get props() {
@@ -563,7 +582,8 @@ namespace Canvas3D {
                     multiSample: { ...multiSample.props },
                     renderer: { ...renderer.props },
                     trackball: { ...controls.props },
-                    debug: { ...debugHelper.props }
+                    debug: { ...debugHelper.props },
+                    handle: { ...handleHelper.props },
                 };
             },
             get input() {

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

@@ -0,0 +1,208 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { WebGLContext } from '../../mol-gl/webgl/context';
+import Scene from '../../mol-gl/scene';
+import { MeshBuilder } from '../../mol-geo/geometry/mesh/mesh-builder';
+import { Vec3, Mat4, Mat3 } from '../../mol-math/linear-algebra';
+import { addSphere } from '../../mol-geo/geometry/mesh/builder/sphere';
+import { GraphicsRenderObject } from '../../mol-gl/render-object';
+import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
+import { ColorNames } from '../../mol-util/color/names';
+import { addCylinder } from '../../mol-geo/geometry/mesh/builder/cylinder';
+import { ValueCell } from '../../mol-util';
+import { Sphere3D } from '../../mol-math/geometry';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import produce from 'immer';
+import { Shape } from '../../mol-model/shape';
+import { PickingId } from '../../mol-geo/geometry/picking';
+import { Camera } from '../camera';
+import { DataLoci, EmptyLoci, Loci } from '../../mol-model/loci';
+import { MarkerAction, MarkerActions } from '../../mol-util/marker-action';
+import { Visual } from '../../mol-repr/visual';
+import { Interval } from '../../mol-data/int';
+
+const HandleParams = {
+    ...Mesh.Params,
+    alpha: { ...Mesh.Params.alpha, defaultValue: 1 },
+    ignoreLight: { ...Mesh.Params.ignoreLight, defaultValue: true },
+    colorX: PD.Color(ColorNames.red, { isEssential: true }),
+    colorY: PD.Color(ColorNames.green, { isEssential: true }),
+    colorZ: PD.Color(ColorNames.blue, { isEssential: true }),
+    scale: PD.Numeric(0.33, { min: 0.1, max: 2, step: 0.1 }, { isEssential: true }),
+};
+type HandleParams = typeof HandleParams
+type HandleProps = PD.Values<HandleParams>
+
+export const HandleHelperParams = {
+    handle: PD.MappedStatic('off', {
+        on: PD.Group(HandleParams),
+        off: PD.Group({})
+    }, { cycle: true, description: 'Show handle tool' }),
+};
+export type HandleHelperParams = typeof HandleHelperParams
+export type HandleHelperProps = PD.Values<HandleHelperParams>
+
+export class HandleHelper {
+    scene: Scene
+    props: HandleHelperProps = {
+        handle: { name: 'off', params: {} }
+    }
+
+    private renderObject: GraphicsRenderObject | undefined
+
+    private _transform = Mat4();
+    getBoundingSphere(out: Sphere3D, instanceId: number) {
+        if (this.renderObject) {
+            Sphere3D.copy(out, this.renderObject.values.invariantBoundingSphere.ref.value);
+            Mat4.fromArray(this._transform, this.renderObject.values.aTransform.ref.value, instanceId * 16);
+            Sphere3D.transform(out, out, this._transform);
+        }
+        return out;
+    }
+
+    setProps(props: Partial<HandleHelperProps>) {
+        this.props = produce(this.props, p => {
+            if (props.handle !== undefined) {
+                p.handle.name = props.handle.name;
+                if (props.handle.name === 'on') {
+                    this.scene.clear();
+                    const params = { ...props.handle.params, scale: props.handle.params.scale * this.webgl.pixelRatio };
+                    this.renderObject = createHandleRenderObject(params);
+                    this.scene.add(this.renderObject);
+                    this.scene.commit();
+
+                    p.handle.params = { ...props.handle.params };
+                }
+            }
+        });
+    }
+
+    get isEnabled() {
+        return this.props.handle.name === 'on';
+    }
+
+    // TODO could be a lists of position/rotation if we want to show more than one handle tool,
+    //      they would be distingishable by their instanceId
+    update(camera: Camera, position: Vec3, rotation: Mat3) {
+        if (!this.renderObject) return;
+
+        Mat4.setTranslation(this.renderObject.values.aTransform.ref.value as unknown as Mat4, position);
+        Mat4.fromMat3(this.renderObject.values.aTransform.ref.value as unknown as Mat4, rotation);
+
+        // TODO make invariant to camera scaling by adjusting renderObject transform
+
+        ValueCell.update(this.renderObject.values.aTransform, this.renderObject.values.aTransform.ref.value);
+        this.scene.update([this.renderObject], true);
+    }
+
+    getLoci(pickingId: PickingId) {
+        const { objectId, groupId, instanceId } = pickingId;
+        if (!this.renderObject || objectId !== this.renderObject.id) return EmptyLoci;
+        return HandleLoci(this, groupId, instanceId);
+    }
+
+    private eachGroup = (loci: Loci, apply: (interval: Interval) => boolean): boolean => {
+        if (!this.renderObject) return false;
+        if (!isHandleLoci(loci)) return false;
+        let changed = false;
+        const groupCount = this.renderObject.values.uGroupCount.ref.value;
+        const { elements } = loci;
+        for (const { groupId, instanceId } of elements) {
+            const idx = instanceId * groupCount + groupId;
+            if (apply(Interval.ofSingleton(idx))) changed = true;
+        }
+        return changed;
+    }
+
+    mark(loci: Loci, action: MarkerAction) {
+        if (!MarkerActions.is(MarkerActions.Highlighting, action)) return false;
+        if (!isHandleLoci(loci)) return false;
+        if (loci.data !== this) return false;
+        return Visual.mark(this.renderObject, loci, action, this.eachGroup);
+    }
+
+    constructor(private webgl: WebGLContext, props: Partial<HandleHelperProps> = {}) {
+        this.scene = Scene.create(webgl);
+        this.setProps(props);
+    }
+}
+
+function createHandleMesh(scale: number, mesh?: Mesh) {
+    const state = MeshBuilder.createState(512, 256, mesh);
+    const radius = 0.05 * scale;
+    const x = Vec3.scale(Vec3(), Vec3.unitX, scale);
+    const y = Vec3.scale(Vec3(), Vec3.unitY, scale);
+    const z = Vec3.scale(Vec3(), Vec3.unitZ, scale);
+    const cylinderProps = { radiusTop: radius, radiusBottom: radius, radialSegments: 32 };
+
+    state.currentGroup = HandleGroup.TranslateScreenXY;
+    addSphere(state, Vec3.origin, radius * 3, 2);
+
+    state.currentGroup = HandleGroup.TranslateObjectX;
+    addSphere(state, x, radius, 2);
+    addCylinder(state, Vec3.origin, x, 1, cylinderProps);
+
+    state.currentGroup = HandleGroup.TranslateObjectY;
+    addSphere(state, y, radius, 2);
+    addCylinder(state, Vec3.origin, y, 1, cylinderProps);
+
+    state.currentGroup = HandleGroup.TranslateObjectZ;
+    addSphere(state, z, radius, 2);
+    addCylinder(state, Vec3.origin, z, 1, cylinderProps);
+
+    // TODO add more helper geometries for the other HandleGroup options
+    // TODO add props to create subset of geometries
+
+    return MeshBuilder.getMesh(state);
+}
+
+export const HandleGroup = {
+    None: 0,
+    TranslateScreenXY: 1,
+    // TranslateScreenZ: 2,
+    TranslateObjectX: 3,
+    TranslateObjectY: 4,
+    TranslateObjectZ: 5,
+    // TranslateObjectXY: 6,
+    // TranslateObjectXZ: 7,
+    // TranslateObjectYZ: 8,
+
+    // RotateScreenZ: 9,
+    // RotateObjectX: 10,
+    // RotateObjectY: 11,
+    // RotateObjectZ: 12,
+} as const;
+
+function HandleLoci(handleHelper: HandleHelper, groupId: number, instanceId: number) {
+    return DataLoci('handle', handleHelper, [{ groupId, instanceId }],
+        (boundingSphere: Sphere3D) => handleHelper.getBoundingSphere(boundingSphere, instanceId),
+        () => `Handle Helper | Group Id ${groupId} | Instance Id ${instanceId}`);
+}
+export type HandleLoci = ReturnType<typeof HandleLoci>
+export function isHandleLoci(x: Loci): x is HandleLoci {
+    return x.kind === 'data-loci' && x.tag === 'handle';
+}
+
+function getHandleShape(props: HandleProps, shape?: Shape<Mesh>) {
+    const scale = 10 * props.scale;
+    const mesh = createHandleMesh(scale, shape?.geometry);
+    mesh.setBoundingSphere(Sphere3D.create(Vec3.create(scale / 2, scale / 2, scale / 2), scale + scale / 4));
+    const getColor = (groupId: number) => {
+        switch (groupId) {
+            case HandleGroup.TranslateObjectX: return props.colorX;
+            case HandleGroup.TranslateObjectY: return props.colorY;
+            case HandleGroup.TranslateObjectZ: return props.colorZ;
+            default: return ColorNames.grey;
+        }
+    };
+    return Shape.create('handle', {}, mesh, getColor, () => 1, () => '');
+}
+
+function createHandleRenderObject(props: HandleProps) {
+    const shape = getHandleShape(props);
+    return Shape.createRenderObject(shape, props);
+}

src/mol-canvas3d/passes/draw.ts

@@ -13,6 +13,7 @@ import { Texture } from '../../mol-gl/webgl/texture';
 import { Camera } from '../camera';
 import { CameraHelper, CameraHelperParams } from '../helper/camera-helper';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { HandleHelper } from '../helper/handle-helper';
 
 export const DrawPassParams = {
     cameraHelper: PD.Group(CameraHelperParams)
@@ -29,7 +30,7 @@ export class DrawPass {
 
     private depthTarget: RenderTarget | null
 
-    constructor(private webgl: WebGLContext, private renderer: Renderer, private scene: Scene, private camera: Camera, private debugHelper: BoundingSphereHelper, props: Partial<DrawPassProps> = {}) {
+    constructor(private webgl: WebGLContext, private renderer: Renderer, private scene: Scene, private camera: Camera, private debugHelper: BoundingSphereHelper, private handleHelper: HandleHelper, props: Partial<DrawPassProps> = {}) {
         const { gl, extensions, resources } = webgl;
         const width = gl.drawingBufferWidth;
         const height = gl.drawingBufferHeight;
@@ -89,12 +90,15 @@ export class DrawPass {
     }
 
     private renderInternal(variant: 'color' | 'depth', transparentBackground: boolean) {
-        const { renderer, scene, camera, debugHelper, cameraHelper } = this;
+        const { renderer, scene, camera, debugHelper, cameraHelper, handleHelper } = this;
         renderer.render(scene, camera, variant, true, transparentBackground);
         if (debugHelper.isEnabled) {
             debugHelper.syncVisibility();
             renderer.render(debugHelper.scene, camera, variant, false, transparentBackground);
         }
+        if (handleHelper.isEnabled) {
+            renderer.render(handleHelper.scene, camera, variant, false, transparentBackground);
+        }
         if (cameraHelper.isEnabled) {
             cameraHelper.update(camera);
             renderer.render(cameraHelper.scene, cameraHelper.camera, variant, false, transparentBackground);

src/mol-canvas3d/passes/image.ts

@@ -15,6 +15,7 @@ import { PostprocessingPass, PostprocessingParams } from './postprocessing';
 import { MultiSamplePass, MultiSampleParams } from './multi-sample';
 import { Camera } from '../camera';
 import { Viewport } from '../camera/util';
+import { HandleHelper } from '../helper/handle-helper';
 
 export const ImageParams = {
     transparentBackground: PD.Boolean(false),
@@ -40,12 +41,12 @@ export class ImagePass {
     get width() { return this._width; }
     get height() { return this._height; }
 
-    constructor(webgl: WebGLContext, private renderer: Renderer, scene: Scene, private camera: Camera, debugHelper: BoundingSphereHelper, props: Partial<ImageProps>) {
+    constructor(webgl: WebGLContext, private renderer: Renderer, scene: Scene, private camera: Camera, debugHelper: BoundingSphereHelper, handleHelper: HandleHelper, props: Partial<ImageProps>) {
         const p = { ...PD.getDefaultValues(ImageParams), ...props };
 
         this._transparentBackground = p.transparentBackground;
 
-        this.drawPass = new DrawPass(webgl, renderer, scene, this._camera, debugHelper, p.drawPass);
+        this.drawPass = new DrawPass(webgl, renderer, scene, this._camera, debugHelper, handleHelper, p.drawPass);
         this.postprocessing = new PostprocessingPass(webgl, this._camera, this.drawPass, p.postprocessing);
         this.multiSample = new MultiSamplePass(webgl, this._camera, this.drawPass, this.postprocessing, p.multiSample);
 

src/mol-canvas3d/passes/pick.ts

@@ -11,6 +11,7 @@ import Scene from '../../mol-gl/scene';
 import { PickingId } from '../../mol-geo/geometry/picking';
 import { decodeFloatRGB } from '../../mol-util/float-packing';
 import { Camera } from '../camera';
+import { HandleHelper } from '../helper/handle-helper';
 
 export class PickPass {
     pickDirty = true
@@ -27,7 +28,7 @@ export class PickPass {
     private pickWidth: number
     private pickHeight: number
 
-    constructor(private webgl: WebGLContext, private renderer: Renderer, private scene: Scene, private camera: Camera, private pickBaseScale: number) {
+    constructor(private webgl: WebGLContext, private renderer: Renderer, private scene: Scene, private camera: Camera, private handleHelper: HandleHelper, private pickBaseScale: number) {
         const { gl } = webgl;
         const width = gl.drawingBufferWidth;
         const height = gl.drawingBufferHeight;
@@ -65,14 +66,18 @@ export class PickPass {
     }
 
     render() {
-        const { renderer, scene, camera } = this;
+        const { renderer, scene, camera, handleHelper: { scene: handleScene } } = this;
         renderer.setViewport(0, 0, this.pickWidth, this.pickHeight);
+
         this.objectPickTarget.bind();
         renderer.render(scene, camera, 'pickObject', true, false);
+        renderer.render(handleScene, camera, 'pickObject', false, false);
         this.instancePickTarget.bind();
         renderer.render(scene, camera, 'pickInstance', true, false);
+        renderer.render(handleScene, camera, 'pickInstance', false, false);
         this.groupPickTarget.bind();
         renderer.render(scene, camera, 'pickGroup', true, false);
+        renderer.render(handleScene, camera, 'pickGroup', false, false);
 
         this.pickDirty = false;
     }

src/mol-geo/geometry/points/points.ts

@@ -207,5 +207,6 @@ export namespace Points {
             !props.pointFilledCircle ||
             (props.pointFilledCircle && props.pointEdgeBleach === 0)
         );
+        state.writeDepth = state.opaque;
     }
 }

src/mol-geo/geometry/text/text.ts

@@ -283,6 +283,7 @@ export namespace Text {
         BaseGeometry.updateRenderableState(state, props);
         state.pickable = false;
         state.opaque = false;
+        state.writeDepth = true;
     }
 }
 

src/mol-gl/shader/chunks/apply-marker-color.glsl.ts

@@ -1,13 +1,10 @@
 export default `
-// only mark elements with an alpha above the picking threshold
-if (gl_FragColor.a >= uPickingAlphaThreshold) {
-    float marker = floor(vMarker * 255.0 + 0.5); // rounding required to work on some cards on win
-    if (marker > 0.1) {
-        if (intMod(marker, 2.0) > 0.1) {
-            gl_FragColor.rgb = mix(uHighlightColor, gl_FragColor.rgb, 0.3);
-        } else {
-            gl_FragColor.rgb = mix(uSelectColor, gl_FragColor.rgb, 0.3);
-        }
+float marker = floor(vMarker * 255.0 + 0.5); // rounding required to work on some cards on win
+if (marker > 0.1) {
+    if (intMod(marker, 2.0) > 0.1) {
+        gl_FragColor.rgb = mix(uHighlightColor, gl_FragColor.rgb, 0.3);
+    } else {
+        gl_FragColor.rgb = mix(uSelectColor, gl_FragColor.rgb, 0.3);
     }
 }
 `;

src/mol-model-formats/structure/basic/parser.ts

@@ -10,7 +10,7 @@ import { RuntimeContext } from '../../../mol-task';
 import UUID from '../../../mol-util/uuid';
 import { Model } from '../../../mol-model/structure/model/model';
 import { Entities } from '../../../mol-model/structure/model/properties/common';
-import { CustomProperties } from '../../../mol-model/structure';
+import { CustomProperties } from '../../../mol-model/custom-property';
 import { getAtomicHierarchyAndConformation } from './atomic';
 import { getCoarse, EmptyCoarse, CoarseData } from './coarse';
 import { getSequence } from './sequence';

src/mol-model-formats/structure/common/property.ts

@@ -4,8 +4,9 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { CustomPropertyDescriptor, Model } from '../../../mol-model/structure';
+import { Model } from '../../../mol-model/structure';
 import { ModelFormat } from '../../format';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 
 class FormatRegistry<T> {
     private map = new Map<ModelFormat['kind'], (model: Model) => T | undefined>()

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

@@ -5,7 +5,7 @@
  */
 
 import { Table, Column } from '../../../mol-data/db';
-import { CustomPropertyDescriptor } from '../../../mol-model/structure';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
 import { CifWriter } from '../../../mol-io/writer/cif';
 import { FormatPropertyProvider } from '../common/property';

src/mol-model-formats/structure/property/bonds/comp.ts

@@ -7,7 +7,7 @@
 
 import { Model } from '../../../../mol-model/structure/model/model';
 import { BondType } from '../../../../mol-model/structure/model/types';
-import { CustomPropertyDescriptor } from '../../../../mol-model/structure';
+import { CustomPropertyDescriptor } from '../../../../mol-model/custom-property';
 import { mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
 import { CifWriter } from '../../../../mol-io/writer/cif';
 import { Table } from '../../../../mol-data/db';

src/mol-model-formats/structure/property/bonds/index-pair.ts

@@ -4,7 +4,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { CustomPropertyDescriptor } from '../../../../mol-model/structure';
+import { CustomPropertyDescriptor } from '../../../../mol-model/custom-property';
 import { IntAdjacencyGraph } from '../../../../mol-math/graph';
 import { Column } from '../../../../mol-data/db';
 import { FormatPropertyProvider } from '../../common/property';

src/mol-model-formats/structure/property/bonds/struct_conn.ts

@@ -9,7 +9,7 @@ import { Model } from '../../../../mol-model/structure/model/model';
 import { Structure } from '../../../../mol-model/structure';
 import { BondType } from '../../../../mol-model/structure/model/types';
 import { Column, Table } from '../../../../mol-data/db';
-import { CustomPropertyDescriptor } from '../../../../mol-model/structure';
+import { CustomPropertyDescriptor } from '../../../../mol-model/custom-property';
 import { mmCIF_Schema } from '../../../../mol-io/reader/cif/schema/mmcif';
 import { SortedArray } from '../../../../mol-data/int';
 import { CifWriter } from '../../../../mol-io/writer/cif';

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

@@ -13,7 +13,7 @@ import { SecondaryStructure } from '../../../mol-model/structure/model/propertie
 import { Column, Table } from '../../../mol-data/db';
 import { ChainIndex, ResidueIndex } from '../../../mol-model/structure/model/indexing';
 import { FormatPropertyProvider } from '../common/property';
-import { CustomPropertyDescriptor } from '../../../mol-model/structure';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 
 export { ModelSecondaryStructure };
 

src/mol-model-formats/structure/property/symmetry.ts

@@ -10,7 +10,7 @@ import { Spacegroup, SpacegroupCell, SymmetryOperator } from '../../../mol-math/
 import { Tensor, Vec3, Mat3 } from '../../../mol-math/linear-algebra';
 import { Symmetry } from '../../../mol-model/structure/model/properties/symmetry';
 import { createAssemblies } from './assembly';
-import { CustomPropertyDescriptor } from '../../../mol-model/structure';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 import { FormatPropertyProvider } from '../common/property';
 import { Table } from '../../../mol-data/db';
 

src/mol-model-formats/volume/ccp4.ts

@@ -4,7 +4,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { VolumeData } from '../../mol-model/volume/data';
+import { Volume } from '../../mol-model/volume';
 import { Task } from '../../mol-task';
 import { SpacegroupCell, Box3D } from '../../mol-math/geometry';
 import { Tensor, Vec3 } from '../../mol-math/linear-algebra';
@@ -14,6 +14,7 @@ import { getCcp4ValueType } from '../../mol-io/reader/ccp4/parser';
 import { TypedArrayValueType } from '../../mol-io/common/typed-array';
 import { arrayMin, arrayRms, arrayMean, arrayMax } from '../../mol-util/array';
 import { ModelFormat } from '../format';
+import { CustomProperties } from '../../mol-model/custom-property';
 
 /** When available (e.g. in MRC files) use ORIGIN records instead of N[CRS]START */
 export function getCcp4Origin(header: Ccp4Header): Vec3 {
@@ -39,8 +40,8 @@ function getTypedArrayCtor(header: Ccp4Header) {
     throw Error(`${valueType} is not a supported value format.`);
 }
 
-export function volumeFromCcp4(source: Ccp4File, params?: { voxelSize?: Vec3, offset?: Vec3, label?: string }): Task<VolumeData> {
-    return Task.create<VolumeData>('Create Volume Data', async ctx => {
+export function volumeFromCcp4(source: Ccp4File, params?: { voxelSize?: Vec3, offset?: Vec3, label?: string }): Task<Volume> {
+    return Task.create<Volume>('Create Volume', async ctx => {
         const { header, values } = source;
         const size = Vec3.create(header.xLength, header.yLength, header.zLength);
         if (params && params.voxelSize) Vec3.mul(size, size, params.voxelSize);
@@ -69,15 +70,19 @@ export function volumeFromCcp4(source: Ccp4File, params?: { voxelSize?: Vec3, of
 
         return {
             label: params?.label,
-            transform: { kind: 'spacegroup', cell, fractionalBox: Box3D.create(origin_frac, Vec3.add(Vec3.zero(), origin_frac, dimensions_frac)) },
-            data,
-            dataStats: {
-                min: isNaN(header.AMIN) ? arrayMin(values) : header.AMIN,
-                max: isNaN(header.AMAX) ? arrayMax(values) : header.AMAX,
-                mean: isNaN(header.AMEAN) ? arrayMean(values) : header.AMEAN,
-                sigma: (isNaN(header.ARMS) || header.ARMS === 0) ? arrayRms(values) : header.ARMS
+            grid: {
+                transform: { kind: 'spacegroup', cell, fractionalBox: Box3D.create(origin_frac, Vec3.add(Vec3.zero(), origin_frac, dimensions_frac)) },
+                cells: data,
+                stats: {
+                    min: isNaN(header.AMIN) ? arrayMin(values) : header.AMIN,
+                    max: isNaN(header.AMAX) ? arrayMax(values) : header.AMAX,
+                    mean: isNaN(header.AMEAN) ? arrayMean(values) : header.AMEAN,
+                    sigma: (isNaN(header.ARMS) || header.ARMS === 0) ? arrayRms(values) : header.ARMS
+                },
             },
-            sourceData: Ccp4Format.create(source)
+            sourceData: Ccp4Format.create(source),
+            customProperties: new CustomProperties(),
+            _propertyData: Object.create(null),
         };
     });
 }

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

@@ -6,13 +6,14 @@
 
 import { CubeFile } from '../../mol-io/reader/cube/parser';
 import { Mat4, Tensor } from '../../mol-math/linear-algebra';
-import { VolumeData } from '../../mol-model/volume/data';
+import { Volume } from '../../mol-model/volume';
 import { Task } from '../../mol-task';
 import { arrayMax, arrayMean, arrayMin, arrayRms } from '../../mol-util/array';
 import { ModelFormat } from '../format';
+import { CustomProperties } from '../../mol-model/custom-property';
 
-export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number, label?: string }): Task<VolumeData> {
-    return Task.create<VolumeData>('Create Volume Data', async () => {
+export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number, label?: string }): Task<Volume> {
+    return Task.create<Volume>('Create Volume', async () => {
         const { header, values: sourceValues } = source;
         const space = Tensor.Space(header.dim, [0, 1, 2], Float64Array);
 
@@ -45,15 +46,19 @@ export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number,
 
         return {
             label: params?.label,
-            transform: { kind: 'matrix', matrix },
-            data,
-            dataStats: {
-                min: arrayMin(values),
-                max: arrayMax(values),
-                mean: arrayMean(values),
-                sigma: arrayRms(values)
+            grid: {
+                transform: { kind: 'matrix', matrix },
+                cells: data,
+                stats: {
+                    min: arrayMin(values),
+                    max: arrayMax(values),
+                    mean: arrayMean(values),
+                    sigma: arrayRms(values)
+                },
             },
-            sourceData: CubeFormat.create(source)
+            sourceData: CubeFormat.create(source),
+            customProperties: new CustomProperties(),
+            _propertyData: Object.create(null),
         };
     });
 }

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

@@ -5,14 +5,15 @@
  */
 
 import { DensityServer_Data_Database } from '../../mol-io/reader/cif/schema/density-server';
-import { VolumeData } from '../../mol-model/volume/data';
+import { Volume } from '../../mol-model/volume';
 import { Task } from '../../mol-task';
 import { SpacegroupCell, Box3D } from '../../mol-math/geometry';
 import { Tensor, Vec3 } from '../../mol-math/linear-algebra';
 import { ModelFormat } from '../format';
+import { CustomProperties } from '../../mol-model/custom-property';
 
-export function volumeFromDensityServerData(source: DensityServer_Data_Database): Task<VolumeData> {
-    return Task.create<VolumeData>('Create Volume Data', async ctx => {
+export function volumeFromDensityServerData(source: DensityServer_Data_Database): Task<Volume> {
+    return Task.create<Volume>('Create Volume', async ctx => {
         const { volume_data_3d_info: info, volume_data_3d: values } = source;
         const cell = SpacegroupCell.create(
             info.spacegroup_number.value(0),
@@ -35,15 +36,19 @@ export function volumeFromDensityServerData(source: DensityServer_Data_Database)
         const dimensions = Vec3.ofArray(normalizeOrder(info.dimensions.value(0)));
 
         return {
-            transform: { kind: 'spacegroup', cell, fractionalBox: Box3D.create(origin, Vec3.add(Vec3.zero(), origin, dimensions)) },
-            data,
-            dataStats: {
-                min: info.min_sampled.value(0),
-                max: info.max_sampled.value(0),
-                mean: info.mean_sampled.value(0),
-                sigma: info.sigma_sampled.value(0)
+            grid: {
+                transform: { kind: 'spacegroup', cell, fractionalBox: Box3D.create(origin, Vec3.add(Vec3.zero(), origin, dimensions)) },
+                cells: data,
+                stats: {
+                    min: info.min_sampled.value(0),
+                    max: info.max_sampled.value(0),
+                    mean: info.mean_sampled.value(0),
+                    sigma: info.sigma_sampled.value(0)
+                },
             },
-            sourceData: DscifFormat.create(source)
+            sourceData: DscifFormat.create(source),
+            customProperties: new CustomProperties(),
+            _propertyData: Object.create(null),
         };
     });
 }

src/mol-model-formats/volume/dsn6.ts

@@ -4,7 +4,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { VolumeData } from '../../mol-model/volume/data';
+import { Volume } from '../../mol-model/volume';
 import { Task } from '../../mol-task';
 import { SpacegroupCell, Box3D } from '../../mol-math/geometry';
 import { Tensor, Vec3 } from '../../mol-math/linear-algebra';
@@ -12,9 +12,10 @@ import { degToRad } from '../../mol-math/misc';
 import { Dsn6File } from '../../mol-io/reader/dsn6/schema';
 import { arrayMin, arrayMax, arrayMean, arrayRms } from '../../mol-util/array';
 import { ModelFormat } from '../format';
+import { CustomProperties } from '../../mol-model/custom-property';
 
-export function volumeFromDsn6(source: Dsn6File, params?: { voxelSize?: Vec3, label?: string }): Task<VolumeData> {
-    return Task.create<VolumeData>('Create Volume Data', async ctx => {
+export function volumeFromDsn6(source: Dsn6File, params?: { voxelSize?: Vec3, label?: string }): Task<Volume> {
+    return Task.create<Volume>('Create Volume', async ctx => {
         const { header, values } = source;
         const size = Vec3.create(header.xlen, header.ylen, header.zlen);
         if (params && params.voxelSize) Vec3.mul(size, size, params.voxelSize);
@@ -34,15 +35,19 @@ export function volumeFromDsn6(source: Dsn6File, params?: { voxelSize?: Vec3, la
 
         return {
             label: params?.label,
-            transform: { kind: 'spacegroup', cell, fractionalBox: Box3D.create(origin_frac, Vec3.add(Vec3.zero(), origin_frac, dimensions_frac)) },
-            data,
-            dataStats: {
-                min: arrayMin(values),
-                max: arrayMax(values),
-                mean: arrayMean(values),
-                sigma: header.sigma !== undefined ? header.sigma : arrayRms(values)
+            grid: {
+                transform: { kind: 'spacegroup', cell, fractionalBox: Box3D.create(origin_frac, Vec3.add(Vec3.zero(), origin_frac, dimensions_frac)) },
+                cells: data,
+                stats: {
+                    min: arrayMin(values),
+                    max: arrayMax(values),
+                    mean: arrayMean(values),
+                    sigma: header.sigma !== undefined ? header.sigma : arrayRms(values)
+                },
             },
-            sourceData: Dsn6Format.create(source)
+            sourceData: Dsn6Format.create(source),
+            customProperties: new CustomProperties(),
+            _propertyData: Object.create(null),
         };
     });
 }

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

@@ -6,13 +6,14 @@
 
 import { DxFile } from '../../mol-io/reader/dx/parser';
 import { Mat4, Tensor } from '../../mol-math/linear-algebra';
-import { VolumeData } from '../../mol-model/volume/data';
+import { Volume } from '../../mol-model/volume';
 import { Task } from '../../mol-task';
 import { arrayMax, arrayMean, arrayMin, arrayRms } from '../../mol-util/array';
 import { ModelFormat } from '../format';
+import { CustomProperties } from '../../mol-model/custom-property';
 
-export function volumeFromDx(source: DxFile, params?: { label?: string }): Task<VolumeData> {
-    return Task.create<VolumeData>('Create Volume Data', async () => {
+export function volumeFromDx(source: DxFile, params?: { label?: string }): Task<Volume> {
+    return Task.create<Volume>('Create Volume', async () => {
         const { header, values } = source;
         const space = Tensor.Space(header.dim, [0, 1, 2], Float64Array);
         const data = Tensor.create(space, Tensor.Data1(values));
@@ -22,15 +23,19 @@ export function volumeFromDx(source: DxFile, params?: { label?: string }): Task<
 
         return {
             label: params?.label,
-            transform: { kind: 'matrix', matrix },
-            data,
-            dataStats: {
-                min: arrayMin(values),
-                max: arrayMax(values),
-                mean: arrayMean(values),
-                sigma: arrayRms(values)
+            grid: {
+                transform: { kind: 'matrix', matrix },
+                cells: data,
+                stats: {
+                    min: arrayMin(values),
+                    max: arrayMax(values),
+                    mean: arrayMean(values),
+                    sigma: arrayRms(values)
+                },
             },
-            sourceData: DxFormat.create(source)
+            sourceData: DxFormat.create(source),
+            customProperties: new CustomProperties(),
+            _propertyData: Object.create(null),
         };
     });
 }

src/mol-model-props/common/custom-element-property.ts

@@ -5,7 +5,7 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { ElementIndex, Model, CustomPropertyDescriptor } from '../../mol-model/structure';
+import { ElementIndex, Model } from '../../mol-model/structure';
 import { StructureElement } from '../../mol-model/structure/structure';
 import { Location } from '../../mol-model/location';
 import { ThemeDataContext } from '../../mol-theme/theme';
@@ -16,6 +16,7 @@ import { OrderedSet } from '../../mol-data/int';
 import { CustomModelProperty } from './custom-model-property';
 import { CustomProperty } from './custom-property';
 import { LociLabelProvider } from '../../mol-plugin-state/manager/loci-label';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 
 export { CustomElementProperty };
 

src/mol-model-props/common/custom-model-property.ts

@@ -4,10 +4,11 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { CustomPropertyDescriptor, Model } from '../../mol-model/structure';
+import { Model } from '../../mol-model/structure';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ValueBox } from '../../mol-util';
 import { CustomProperty } from './custom-property';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 
 export { CustomModelProperty };
 

src/mol-model-props/common/custom-property.ts

@@ -5,7 +5,7 @@
  */
 
 import { RuntimeContext } from '../../mol-task';
-import { CustomPropertyDescriptor } from '../../mol-model/structure';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ValueBox } from '../../mol-util';
 import { OrderedMap } from 'immutable';

src/mol-model-props/common/custom-structure-property.ts

@@ -4,10 +4,11 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { CustomPropertyDescriptor, Structure } from '../../mol-model/structure';
+import { Structure } from '../../mol-model/structure';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ValueBox } from '../../mol-util';
 import { CustomProperty } from './custom-property';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 
 export { CustomStructureProperty };
 

src/mol-model-props/computed/accessible-surface-area.ts

@@ -7,12 +7,13 @@
 
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ShrakeRupleyComputationParams, AccessibleSurfaceArea } from './accessible-surface-area/shrake-rupley';
-import { Structure, CustomPropertyDescriptor, Unit } from '../../mol-model/structure';
+import { Structure, Unit } from '../../mol-model/structure';
 import { CustomStructureProperty } from '../common/custom-structure-property';
 import { CustomProperty } from '../common/custom-property';
 import { QuerySymbolRuntime } from '../../mol-script/runtime/query/compiler';
 import { CustomPropSymbol } from '../../mol-script/language/symbol';
 import Type from '../../mol-script/language/type';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 
 export const AccessibleSurfaceAreaParams = {
     ...ShrakeRupleyComputationParams

src/mol-model-props/computed/interactions.ts

@@ -4,11 +4,12 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { CustomPropertyDescriptor, Structure } from '../../mol-model/structure';
+import { Structure } from '../../mol-model/structure';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { computeInteractions, Interactions, InteractionsParams as _InteractionsParams } from './interactions/interactions';
 import { CustomStructureProperty } from '../common/custom-structure-property';
 import { CustomProperty } from '../common/custom-property';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 
 export const InteractionsParams = {
     ..._InteractionsParams

src/mol-model-props/computed/secondary-structure.ts

@@ -12,7 +12,7 @@ import { Unit } from '../../mol-model/structure/structure';
 import { CustomStructureProperty } from '../common/custom-structure-property';
 import { CustomProperty } from '../common/custom-property';
 import { ModelSecondaryStructure } from '../../mol-model-formats/structure/property/secondary-structure';
-import { CustomPropertyDescriptor } from '../../mol-model/structure/common/custom-property';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 import { Model } from '../../mol-model/structure/model';
 
 function getSecondaryStructureParams(data?: Structure) {

src/mol-model-props/computed/valence-model.ts

@@ -4,11 +4,12 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { CustomPropertyDescriptor, Structure } from '../../mol-model/structure';
+import { Structure } from '../../mol-model/structure';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { calcValenceModel, ValenceModel, ValenceModelParams as _ValenceModelParams } from './chemistry/valence-model';
 import { CustomStructureProperty } from '../common/custom-structure-property';
 import { CustomProperty } from '../common/custom-property';
+import { CustomPropertyDescriptor } from '../../mol-model/custom-property';
 
 export const ValenceModelParams = {
     ..._ValenceModelParams

src/mol-model-props/integrative/cross-link-restraint/format.ts

@@ -7,9 +7,10 @@
 import { Model } from '../../../mol-model/structure/model/model';
 import { Table } from '../../../mol-data/db';
 import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
-import { Unit, CustomPropertyDescriptor } from '../../../mol-model/structure';
+import { Unit } from '../../../mol-model/structure';
 import { ElementIndex } from '../../../mol-model/structure/model/indexing';
 import { FormatPropertyProvider } from '../../../mol-model-formats/structure/common/property';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 
 export { ModelCrossLinkRestraint };
 

src/mol-model-props/integrative/cross-link-restraint/property.ts

@@ -5,7 +5,7 @@
  */
 
 import { ModelCrossLinkRestraint } from './format';
-import { Unit, StructureElement, Structure, CustomPropertyDescriptor, Bond} from '../../../mol-model/structure';
+import { Unit, StructureElement, Structure, Bond} from '../../../mol-model/structure';
 import { PairRestraints, PairRestraint } from '../pair-restraints';
 import { CustomStructureProperty } from '../../common/custom-structure-property';
 import { CustomProperty } from '../../common/custom-property';
@@ -15,6 +15,7 @@ import { Sphere3D } from '../../../mol-math/geometry';
 import { CentroidHelper } from '../../../mol-math/geometry/centroid-helper';
 import { bondLabel } from '../../../mol-theme/label';
 import { Vec3 } from '../../../mol-math/linear-algebra';
+import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 
 export type CrossLinkRestraintValue = PairRestraints<CrossLinkRestraint>
 

src/mol-model/custom-property.ts

@@ -5,11 +5,11 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { CifWriter } from '../../../mol-io/writer/cif';
-import { CifExportContext } from '../export/mmcif';
-import { QuerySymbolRuntime } from '../../../mol-script/runtime/query/compiler';
-import { UUID } from '../../../mol-util';
-import { Asset } from '../../../mol-util/assets';
+import { CifWriter } from '../mol-io/writer/cif';
+import { CifExportContext } from './structure/export/mmcif';
+import { QuerySymbolRuntime } from '../mol-script/runtime/query/compiler';
+import { UUID } from '../mol-util';
+import { Asset } from '../mol-util/assets';
 
 export { CustomPropertyDescriptor, CustomProperties };
 

src/mol-model/loci.ts

@@ -255,11 +255,12 @@ namespace Loci {
     };
     export type Granularity = keyof typeof Granularity
     export const GranularityOptions = ParamDefinition.objectToOptions(Granularity, k => {
-        if (k.indexOf('Instances') > 0) return [stringToWords(k), 'With Symmetry'];
         switch (k) {
             case 'element': return'Atom/Coarse Element';
+            case 'elementInstances': return ['Atom/Coarse Element Instances', 'With Symmetry'];
             case 'structure': return'Structure/Shape';
-            default: return stringToWords(k);
+            default: return k.indexOf('Instances')
+                ? [stringToWords(k), 'With Symmetry'] : stringToWords(k);
         }
     });
 

src/mol-model/sequence/alignment/_spec/alignment.spec.ts

@@ -0,0 +1,26 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { align } from '../alignment';
+
+describe('Alignment', () => {
+    it('basic', () => {
+        // 3PQR: Rhodopsin
+        const seqA = 'MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA';
+        // 3SN6: Endolysin,Beta-2 adrenergic
+        const seqB = 'DYKDDDDAENLYFQGNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYAADEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILTKTWTFGNFWCEFWTSIDVLCVTASIETLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAEETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLQKIDKSEGRFHVQNLSQVEQDGRTGHGLRRSSKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCLRRSSLKAYGNGYSSNGNTGEQSG';
+
+        const { aliA, aliB, score } = align(seqA, seqB, {
+            gapPenalty: -11,
+            gapExtensionPenalty: -1,
+            substMatrix: 'blosum62'
+        });
+
+        expect(aliA).toEqual('------------------------------------------------------------------------------------------------------------------------------------------------MNGTEGPNFYVPFSNKTGVVRSPFEA---PQYYLAEPWQFSM--LAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLH---GYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMS-NFRFGENHAIMGVAFTWVMA-LACAAPPLVGWSRYI-PEGMQC----SCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLV----------------FTVKEAAAQQQESATTQ----------KAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA');
+        expect(aliB).toEqual('DYKDDDDAENLYFQGNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKS-RWYNQTPNRAKRVITTFRTGTWDAYAADEVWVVGMGIVMSLIVLAIVFG---NVLVITAIAKFERLQTVTNYFITSLACADLVM---GLAVVPFGAAHILTKTWTFGNFWCEFWTSIDVLCVTASIETLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAEETC-CDFFT------NQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLQKIDKSEGRFHVQNLSQVEQDGRTGHGLRRSSKFCLKEHKALKTLGIIMG-TFTLCWLPFF-IVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIY-CRSPDFRIAFQELLCLRRSSL--KAYGNGYSSNGNTGEQSG');
+        expect(score).toEqual(118);
+    });
+});

src/mol-model/sequence/alignment/alignment.ts

@@ -0,0 +1,196 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { SubstitutionMatrix, SubstitutionMatrices, SubstitutionMatrixData } from './substitution-matrix';
+
+const DefaultAlignmentOptions = {
+    gapPenalty: -11,
+    gapExtensionPenalty: -1,
+    substMatrix: 'default' as SubstitutionMatrix | 'default'
+};
+export type AlignmentOptions = typeof DefaultAlignmentOptions;
+
+export function align(seqA: ArrayLike<string>, seqB: ArrayLike<string>, options: Partial<AlignmentOptions> = {}) {
+    const o = { ...DefaultAlignmentOptions, ...options };
+    const alignment = new Alignment(seqA, seqB, o);
+    alignment.calculate();
+    return alignment.trace();
+}
+
+class Alignment {
+    readonly gapPenalty: number; readonly gapExtensionPenalty: number
+    readonly substMatrix: SubstitutionMatrixData | undefined
+
+    readonly n: number; readonly m: number
+    readonly S: number[][] = []; readonly V: number[][] = []; readonly H: number[][] = []
+
+    constructor (readonly seqA: ArrayLike<string>, readonly seqB: ArrayLike<string>, options: AlignmentOptions) {
+        this.gapPenalty = options.gapPenalty;
+        this.gapExtensionPenalty = options.gapExtensionPenalty;
+        this.substMatrix = options.substMatrix === 'default' ? undefined : SubstitutionMatrices[options.substMatrix];
+
+        this.n = this.seqA.length;
+        this.m = this.seqB.length;
+    }
+
+    private initMatrices () {
+        const { n, m, gapPenalty, S, V, H } = this;
+
+        for (let i = 0; i <= n; ++i) {
+            S[i] = [], V[i] = [], H[i] = [];
+
+            for (let j = 0; j <= m; ++j) {
+                S[i][j] = 0, V[i][j] = 0, H[i][j] = 0;
+            }
+        }
+
+        for (let i = 0; i <= n; ++i) {
+            S[i][0] = gapPenalty;
+            H[i][0] = -Infinity;
+        }
+
+        for (let j = 0; j <= m; ++j) {
+            S[0][j] = gapPenalty;
+            V[0][j] = -Infinity;
+        }
+
+        S[0][0] = 0;
+    }
+
+    private makeScoreFn () {
+        const { seqA, seqB, substMatrix } = this;
+
+        if (substMatrix) {
+            return function score (i: number, j: number) {
+                const cA = seqA[i];
+                const cB = seqB[j];
+                return substMatrix[cA]?.[cB] ?? -4;
+            };
+        } else {
+            return function scoreNoSubstMat (i: number, j: number) {
+                const cA = seqA[i];
+                const cB = seqB[j];
+                return cA === cB ? 5 : -3;
+            };
+        }
+    }
+
+    calculate () {
+        this.initMatrices();
+
+        const scoreFn = this.makeScoreFn();
+        const { V, H, S, n, m, gapExtensionPenalty, gapPenalty } = this;
+
+        let Vi1, Si1, Vi, Hi, Si;
+        for (let i = 1; i <= n; ++i) {
+            Si1 = S[i - 1], Vi1 = V[i - 1];
+            Vi = V[i], Hi = H[i], Si = S[i];
+
+            for (let j = 1; j <= m; ++j) {
+                Vi[j] = Math.max(
+                    Si1[j] + gapPenalty,
+                    Vi1[j] + gapExtensionPenalty
+                );
+
+                Hi[j] = Math.max(
+                    Si[j - 1] + gapPenalty,
+                    Hi[j - 1] + gapExtensionPenalty
+                );
+
+                Si[j] = Math.max(
+                    Si1[j - 1] + scoreFn(i - 1, j - 1), // match
+                    Vi[j], // del
+                    Hi[j]  // ins
+                );
+            }
+        }
+    }
+
+    trace (): { aliA: ArrayLike<string>, aliB: ArrayLike<string>, score: number } {
+        const scoreFn = this.makeScoreFn();
+        const { V, H, S, seqA, seqB, gapExtensionPenalty, gapPenalty } = this;
+
+        let i = this.n;
+        let j = this.m;
+        let mat: 'S' | 'V' | 'H';
+        let score: number;
+
+        let aliA = '';
+        let aliB = '';
+
+        if (S[i][j] >= V[i][j]) {
+            mat = 'S';
+            score = S[i][j];
+        } else if (V[i][j] >= H[i][j]) {
+            mat = 'V';
+            score = V[i][j];
+        } else {
+            mat = 'H';
+            score = H[i][j];
+        }
+
+        while (i > 0 && j > 0) {
+            if (mat === 'S') {
+                if (S[i][j] === S[i - 1][j - 1] + scoreFn(i - 1, j - 1)) {
+                    aliA = seqA[i - 1] + aliA;
+                    aliB = seqB[j - 1] + aliB;
+                    --i;
+                    --j;
+                    mat = 'S';
+                } else if (S[i][j] === V[i][j]) {
+                    mat = 'V';
+                } else if (S[i][j] === H[i][j]) {
+                    mat = 'H';
+                } else {
+                    --i;
+                    --j;
+                }
+            } else if (mat === 'V') {
+                if (V[i][j] === V[i - 1][j] + gapExtensionPenalty) {
+                    aliA = seqA[i - 1] + aliA;
+                    aliB = '-' + aliB;
+                    --i;
+                    mat = 'V';
+                } else if (V[i][j] === S[i - 1][j] + gapPenalty) {
+                    aliA = seqA[i - 1] + aliA;
+                    aliB = '-' + aliB;
+                    --i;
+                    mat = 'S';
+                } else {
+                    --i;
+                }
+            } else if (mat === 'H') {
+                if (H[i][j] === H[i][j - 1] + gapExtensionPenalty) {
+                    aliA = '-' + aliA;
+                    aliB = seqB[j - 1] + aliB;
+                    --j;
+                    mat = 'H';
+                } else if (H[i][j] === S[i][j - 1] + gapPenalty) {
+                    aliA = '-' + aliA;
+                    aliB = seqB[j - 1] + aliB;
+                    --j;
+                    mat = 'S';
+                } else {
+                    --j;
+                }
+            }
+        }
+
+        while (i > 0) {
+            aliA = seqA[i - 1] + aliA;
+            aliB = '-' + aliB;
+            --i;
+        }
+
+        while (j > 0) {
+            aliA = '-' + aliA;
+            aliB = seqB[j - 1] + aliB;
+            --j;
+        }
+
+        return { aliA, aliB, score };
+    }
+}

src/mol-model/sequence/alignment/sequence.ts

@@ -0,0 +1,110 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { StructureElement, Unit } from '../../structure/structure';
+import { AlignmentOptions, align } from './alignment';
+import { OrderedSet } from '../../../mol-data/int';
+
+export { AlignSequences };
+
+namespace AlignSequences {
+    export type Input = {
+        a: StructureElement.Loci.Element,
+        b: StructureElement.Loci.Element
+    }
+    /** `a` and `b` contain matching pairs, i.e. `a.indices[0]` aligns with `b.indices[0]` */
+    export type Result = {
+        a: StructureElement.Loci.Element,
+        b: StructureElement.Loci.Element,
+        score: number
+    }
+
+    function createSeqIdIndicesMap(element: StructureElement.Loci.Element) {
+        const seqIds = new Map<number, StructureElement.UnitIndex[]>();
+        if (Unit.isAtomic(element.unit)) {
+            const { label_seq_id } = element.unit.model.atomicHierarchy.residues;
+            const { residueIndex } = element.unit;
+            for (let i = 0, il = OrderedSet.size(element.indices); i < il; ++i) {
+                const uI = OrderedSet.getAt(element.indices, i);
+                const eI = element.unit.elements[uI];
+                const seqId = label_seq_id.value(residueIndex[eI]);
+                if (seqIds.has(seqId)) seqIds.get(seqId)!.push(uI);
+                else seqIds.set(seqId, [uI]);
+            }
+        } else if (Unit.isCoarse(element.unit)) {
+            const { seq_id_begin } = Unit.isSpheres(element.unit)
+                ? element.unit.model.coarseHierarchy.spheres
+                : element.unit.model.coarseHierarchy.gaussians;
+            for (let i = 0, il = OrderedSet.size(element.indices); i < il; ++i) {
+                const uI = OrderedSet.getAt(element.indices, i);
+                const eI = element.unit.elements[uI];
+                const seqId = seq_id_begin.value(eI);
+                seqIds.set(seqId, [uI]);
+            }
+        }
+        return seqIds;
+    }
+
+    export function compute(input: Input, options: Partial<AlignmentOptions> = {}): Result {
+        const seqA = getSequence(input.a.unit);
+        const seqB = getSequence(input.b.unit);
+
+        const seqIdIndicesA = createSeqIdIndicesMap(input.a);
+        const seqIdIndicesB = createSeqIdIndicesMap(input.b);
+
+        const indicesA: StructureElement.UnitIndex[] = [];
+        const indicesB: StructureElement.UnitIndex[] = [];
+        const { aliA, aliB, score } = align(seqA.code.toArray(), seqB.code.toArray(), options);
+
+        let seqIdxA = 0, seqIdxB = 0;
+        for (let i = 0, il = aliA.length; i < il; ++i) {
+            if (aliA[i] === '-' || aliB[i] === '-') {
+                if (aliA[i] !== '-') seqIdxA += 1;
+                if (aliB[i] !== '-') seqIdxB += 1;
+                continue;
+            }
+
+            const seqIdA = seqA.seqId.value(seqIdxA);
+            const seqIdB = seqB.seqId.value(seqIdxB);
+
+            if (seqIdIndicesA.has(seqIdA) && seqIdIndicesB.has(seqIdB)) {
+                const iA = seqIdIndicesA.get(seqIdA)!;
+                const iB = seqIdIndicesB.get(seqIdB)!;
+                // use min length to guard against alternate locations
+                for (let j = 0, jl = Math.min(iA.length, iB.length); j < jl; ++j) {
+                    indicesA.push(iA[j]);
+                    indicesB.push(iB[j]);
+                }
+            }
+
+            seqIdxA += 1, seqIdxB += 1;
+        }
+
+        const outA = OrderedSet.intersect(OrderedSet.ofSortedArray(indicesA), input.a.indices);
+        const outB = OrderedSet.intersect(OrderedSet.ofSortedArray(indicesB), input.b.indices);
+
+        return {
+            a: { unit: input.a.unit, indices: outA },
+            b: { unit: input.b.unit, indices: outB },
+            score
+        };
+    }
+}
+
+function entityKey(unit: Unit) {
+    switch (unit.kind) {
+        case Unit.Kind.Atomic:
+            return unit.model.atomicHierarchy.index.getEntityFromChain(unit.chainIndex[unit.elements[0]]);
+        case Unit.Kind.Spheres:
+            return unit.model.coarseHierarchy.spheres.entityKey[unit.elements[0]];
+        case Unit.Kind.Gaussians:
+            return unit.model.coarseHierarchy.gaussians.entityKey[unit.elements[0]];
+    }
+}
+
+function getSequence(unit: Unit) {
+    return unit.model.sequence.byEntityKey[entityKey(unit)].sequence;
+}

src/mol-model/sequence/alignment/substitution-matrix.ts

@@ -0,0 +1,81 @@
+/**
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Mutable } from '../../../mol-util/type-helpers';
+
+const aminoacidsX = 'ACDEFGHIKLMNPQRSTVWY';
+const aminoacids = 'ARNDCQEGHILKMFPSTWYVBZX';
+
+const blosum62x = [
+    [4, 0, -2, -1, -2, 0, -2, -1, -1, -1, -1, -2, -1, -1, -1, 1, 0, 0, -3, -2],        // A
+    [0, 9, -3, -4, -2, -3, -3, -1, -3, -1, -1, -3, -3, -3, -3, -1, -1, -1, -2, -2],    // C
+    [-2, -3, 6, 2, -3, -1, -1, -3, -1, -4, -3, 1, -1, 0, -2, 0, -1, -3, -4, -3],       // D
+    [-1, -4, 2, 5, -3, -2, 0, -3, 1, -3, -2, 0, -1, 2, 0, 0, -1, -2, -3, -2],          // E
+    [-2, -2, -3, -3, 6, -3, -1, 0, -3, 0, 0, -3, -4, -3, -3, -2, -2, -1, 1, 3],        // F
+    [0, -3, -1, -2, -3, 6, -2, -4, -2, -4, -3, 0, -2, -2, -2, 0, -2, -3, -2, -3],      // G
+    [-2, -3, -1, 0, -1, -2, 8, -3, -1, -3, -2, 1, -2, 0, 0, -1, -2, -3, -2, 2],        // H
+    [-1, -1, -3, -3, 0, -4, -3, 4, -3, 2, 1, -3, -3, -3, -3, -2, -1, 3, -3, -1],       // I
+    [-1, -3, -1, 1, -3, -2, -1, -3, 5, -2, -1, 0, -1, 1, 2, 0, -1, -2, -3, -2],        // K
+    [-1, -1, -4, -3, 0, -4, -3, 2, -2, 4, 2, -3, -3, -2, -2, -2, -1, 1, -2, -1],       // L
+    [-1, -1, -3, -2, 0, -3, -2, 1, -1, 2, 5, -2, -2, 0, -1, -1, -1, 1, -1, -1],        // M
+    [-2, -3, 1, 0, -3, 0, 1, -3, 0, -3, -2, 6, -2, 0, 0, 1, 0, -3, -4, -2],            // N
+    [-1, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -2, 7, -1, -2, -1, -1, -2, -4, -3],   // P
+    [-1, -3, 0, 2, -3, -2, 0, -3, 1, -2, 0, 0, -1, 5, 1, 0, -1, -2, -2, -1],           // Q
+    [-1, -3, -2, 0, -3, -2, 0, -3, 2, -2, -1, 0, -2, 1, 5, -1, -1, -3, -3, -2],        // R
+    [1, -1, 0, 0, -2, 0, -1, -2, 0, -2, -1, 1, -1, 0, -1, 4, 1, -2, -3, -2],           // S
+    [0, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 1, 5, 0, -2, -2],       // T
+    [0, -1, -3, -2, -1, -3, -3, 3, -2, 1, 1, -3, -2, -2, -3, -2, 0, 4, -3, -1],        // V
+    [-3, -2, -4, -3, 1, -2, -2, -3, -3, -2, -1, -4, -4, -2, -3, -3, -2, -3, 11, 2],    // W
+    [-2, -2, -3, -2, 3, -3, 2, -1, -2, -1, -1, -2, -3, -1, -2, -2, -2, -1, 2, 7]       // Y
+];
+
+const blosum62 = [
+    // A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X
+    [4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0, -2, -1, 0], // A
+    [-1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1], // R
+    [-2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1], // N
+    [-2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3, 4, 1, -1], // D
+    [0, -3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2], // C
+    [-1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2, 0, 3, -1], // Q
+    [-1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1], // E
+    [0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3, -1, -2, -1], // G
+    [-2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3, 0, 0, -1], // H
+    [-1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3, -3, -3, -1], // I
+    [-1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1, -4, -3, -1], // L
+    [-1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2, 0, 1, -1], // K
+    [-1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1, -3, -1, -1], // M
+    [-2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1, -3, -3, -1], // F
+    [-1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2, -2, -1, -2], // P
+    [1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2, 0, 0, 0], // S
+    [0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0, -1, -1, 0], // T
+    [-3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3, -4, -3, -2], // W
+    [-2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1, -3, -2, -1], // Y
+    [0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1], // V
+    [-2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1], // B
+    [-1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1], // Z
+    [0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1]  // X
+];
+
+export type SubstitutionMatrixData = Readonly<{ [k: string]: Readonly<{ [k: string]: number }> }>;
+
+function prepareMatrix (cellNames: string, mat: number[][]): SubstitutionMatrixData {
+    let j: number;
+    let i = 0;
+    const matDict: Mutable<SubstitutionMatrixData> = {};
+    mat.forEach(row => {
+        j = 0;
+        const rowDict: { [k: string]: number } = {};
+        row.forEach(elm => rowDict[cellNames[j++]] = elm);
+        matDict[cellNames[i++]] = rowDict;
+    });
+    return matDict;
+}
+
+export const SubstitutionMatrices = (() => ({
+    blosum62: prepareMatrix(aminoacids, blosum62),
+    blosum62x: prepareMatrix(aminoacidsX, blosum62x)
+}))();
+export type SubstitutionMatrix = keyof typeof SubstitutionMatrices;

src/mol-model/sequence/sequence.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 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>
@@ -9,7 +9,6 @@ import { AminoAlphabet, NuclecicAlphabet, getProteinOneLetterCode, getRnaOneLett
 import { Column } from '../../mol-data/db';
 
 // TODO add mapping support to other sequence spaces, e.g. uniprot
-// TODO sequence alignment (take NGL code as starting point)
 
 type Sequence = Sequence.Protein | Sequence.DNA | Sequence.RNA | Sequence.Generic
 
@@ -24,14 +23,18 @@ namespace Sequence {
     export interface Base<K extends Kind, Alphabet extends string> {
         readonly kind: K,
         readonly length: number,
-        readonly offset: number,
 
+        /** One letter code */
         readonly code: Column<Alphabet>
         readonly label: Column<string>
 
         readonly seqId: Column<number>
+        /** Component id */
         readonly compId: Column<string>
 
+        /** returns index for given seqId */
+        readonly index: (seqId: number) => number
+
         /** maps seqId to list of compIds */
         readonly microHet: ReadonlyMap<number, string[]>
     }
@@ -41,11 +44,6 @@ namespace Sequence {
     export interface DNA extends Base<Kind.DNA, NuclecicAlphabet> { }
     export interface Generic extends Base<Kind.Generic, 'X' | '-'> { }
 
-    export function create<K extends Kind, Alphabet extends string>(kind: K, code: Column<Alphabet>, label: Column<string>, seqId: Column<number>, compId: Column<string>, microHet: Map<number, string[]>, offset: number = 0): Base<K, Alphabet> {
-        const length = code.rowCount;
-        return { kind, code, label, seqId, compId, microHet, offset, length };
-    }
-
     export function getSequenceString(seq: Sequence) {
         const array = seq.code.toArray();
         return (array instanceof Array ? array : Array.from(array)).join('');
@@ -88,100 +86,60 @@ namespace Sequence {
     }
 
     class ResidueNamesImpl<K extends Kind, Alphabet extends string> implements Base<K, Alphabet> {
-        private _offset = 0;
-        private _length = 0;
-        private _microHet: ReadonlyMap<number, string[]> | undefined = void 0;
-        private _code: Column<Alphabet> | undefined = undefined
-        private _label: Column<string> | undefined = undefined
+        public length: number
+        public code: Column<Alphabet>
+        public label: Column<string>
+        public seqId: Column<number>
+        public compId: Column<string>
+        public microHet: ReadonlyMap<number, string[]> = new Map()
 
-        private codeFromName: (name: string) => string
-
-        get code(): Column<Alphabet> {
-            if (this._code !== void 0) return this._code;
-            this.create();
-            return this._code!;
+        private indexMap: Map<number, number>
+        index(seqId: number) {
+            return this.indexMap.get(seqId)!;
         }
 
-        get label(): Column<string> {
-            if (this._label !== void 0) return this._label;
-            this.create();
-            return this._label!;
-        }
+        constructor(public kind: K, compId: Column<string>, seqId: Column<number>) {
+            const codeFromName = codeProvider(kind);
+            const codes: string[] = [];
+            const compIds: string[] = [];
+            const seqIds: number[] = [];
+            const microHet = new Map<number, string[]>();
 
-        get offset() {
-            if (this._code !== void 0) return this._offset;
-            this.create();
-            return this._offset;
-        }
+            let idx = 0;
+            const indexMap = new Map<number, number>();
+            for (let i = 0, il = seqId.rowCount; i < il; ++i) {
+                const seq_id = seqId.value(i);
 
-        get length() {
-            if (this._code !== void 0) return this._length;
-            this.create();
-            return this._length;
-        }
-
-        get microHet(): ReadonlyMap<number, string[]> {
-            if (this._microHet !== void 0) return this._microHet;
-            this.create();
-            return this._microHet!;
-        }
-
-        private create() {
-            let maxSeqId = 0, minSeqId = Number.MAX_SAFE_INTEGER;
-            for (let i = 0, _i = this.seqId.rowCount; i < _i; i++) {
-                const id = this.seqId.value(i);
-                if (maxSeqId < id) maxSeqId = id;
-                if (id < minSeqId) minSeqId = id;
-            }
-
-            const count = maxSeqId - minSeqId + 1;
-            const sequenceArray = new Array<string>(maxSeqId + 1);
-            const labels = new Array<string[]>(maxSeqId + 1);
-            for (let i = 0; i < count; i++) {
-                sequenceArray[i] = '-';
-                labels[i] = [];
-            }
-
-            const compIds = new Array<string[]>(maxSeqId + 1);
-            for (let i = minSeqId; i <= maxSeqId; ++i) {
-                compIds[i] = [];
-            }
-
-            for (let i = 0, _i = this.seqId.rowCount; i < _i; i++) {
-                const seqId = this.seqId.value(i);
-                const idx = seqId - minSeqId;
-                const name = this.compId.value(i);
-                const code = this.codeFromName(name);
-                // in case of MICROHETEROGENEITY `sequenceArray[idx]` may already be set
-                if (!sequenceArray[idx] || sequenceArray[idx] === '-') {
-                    sequenceArray[idx] = code;
+                if (!indexMap.has(seq_id)) {
+                    indexMap.set(seq_id, idx);
+                    const comp_id = compId.value(i);
+                    compIds[idx] = comp_id;
+                    seqIds[idx] = seq_id;
+                    codes[idx] = codeFromName(comp_id);
+                    idx += 1;
+                } else {
+                    // micro-heterogeneity
+                    if (!microHet.has(seq_id)) {
+                        microHet.set(seq_id, [compIds[indexMap.get(seq_id)!], compId.value(i)]);
+                    } else {
+                        microHet.get(seq_id)!.push(compId.value(i));
+                    }
                 }
-                labels[idx].push(code === 'X' ? name : code);
-                compIds[seqId].push(name);
             }
 
-            const microHet = new Map();
-            for (let i = minSeqId; i <= maxSeqId; ++i) {
-                if (compIds[i].length > 1) microHet.set(i, compIds[i]);
+            const labels: string[] = [];
+            for (let i = 0, il = idx; i < il; ++i) {
+                const mh = microHet.get(seqIds[i]);
+                labels[i] = mh ? `(${mh.join('|')})` : codes[i];
             }
 
-            this._code = Column.ofStringArray(sequenceArray) as Column<Alphabet>;
-            this._label = Column.ofLambda({
-                value: i => {
-                    const l = labels[i];
-                    return l.length > 1 ? `(${l.join('|')})` : l.join('');
-                },
-                rowCount: labels.length,
-                schema: Column.Schema.str
-            });
-            this._microHet = microHet;
-            this._offset = minSeqId - 1;
-            this._length = count;
-        }
-
-        constructor(public kind: K, public compId: Column<string>, public seqId: Column<number>) {
-
-            this.codeFromName = codeProvider(kind);
+            this.length = idx;
+            this.code = Column.ofStringArray(codes) as Column<Alphabet>;
+            this.compId = Column.ofStringArray(compIds);
+            this.seqId = Column.ofIntArray(seqIds);
+            this.label = Column.ofStringArray(labels);
+            this.microHet = microHet;
+            this.indexMap = indexMap;
         }
     }
 
@@ -192,13 +150,17 @@ namespace Sequence {
     }
 
     class SequenceRangesImpl<K extends Kind, Alphabet extends string> implements Base<K, Alphabet> {
-        public offset: number
         public length: number
         public code: Column<Alphabet>
         public label: Column<string>
         public seqId: Column<number>
         public compId: Column<string>
-        public microHet: ReadonlyMap<number, string[]>
+        public microHet: ReadonlyMap<number, string[]> = new Map()
+
+        private minSeqId: number
+        index(seqId: number) {
+            return seqId - this.minSeqId;
+        }
 
         constructor(public kind: K, private seqIdStart: Column<number>, private seqIdEnd: Column<number>) {
             let maxSeqId = 0, minSeqId = Number.MAX_SAFE_INTEGER;
@@ -220,8 +182,8 @@ namespace Sequence {
             });
             this.compId = Column.ofConst('', count, Column.Schema.str);
 
-            this.offset = minSeqId - 1;
             this.length = count;
+            this.minSeqId = minSeqId;
         }
     }
 }

src/mol-model/structure.ts

@@ -9,5 +9,4 @@ export * from './structure/coordinates';
 export * from './structure/topology';
 export * from './structure/model';
 export * from './structure/structure';
-export * from './structure/query';
-export * from './structure/common/custom-property';
+export * from './structure/query';

src/mol-model/structure/export/mmcif.ts

@@ -15,7 +15,7 @@ import { _chem_comp, _pdbx_chem_comp_identifier, _pdbx_nonpoly_scheme } from './
 import { Model } from '../model';
 import { getUniqueEntityIndicesFromStructures, copy_mmCif_category, copy_source_mmCifCategory } from './categories/utils';
 import { _struct_asym, _entity_poly, _entity_poly_seq } from './categories/sequence';
-import { CustomPropertyDescriptor } from '../common/custom-property';
+import { CustomPropertyDescriptor } from '../../custom-property';
 import { atom_site_operator_mapping } from './categories/atom_site_operator_mapping';
 import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
 

src/mol-model/structure/model/model.ts

@@ -10,7 +10,7 @@ import StructureSequence from './properties/sequence';
 import { AtomicHierarchy, AtomicConformation, AtomicRanges } from './properties/atomic';
 import { CoarseHierarchy, CoarseConformation } from './properties/coarse';
 import { Entities, ChemicalComponentMap, MissingResidues, StructAsymMap } from './properties/common';
-import { CustomProperties } from '../common/custom-property';
+import { CustomProperties } from '../../custom-property';
 import { SaccharideComponentMap } from '../structure/carbohydrates/constants';
 import { ModelFormat } from '../../../mol-model-formats/format';
 import { calcModelCenter } from './util';

src/mol-model/structure/query/queries/modifiers.ts

@@ -340,9 +340,6 @@ function expandConnected(ctx: QueryContext, structure: Structure) {
     const interBonds = inputStructure.interUnitBonds;
     const builder = new StructureUniqueSubsetBuilder(inputStructure);
 
-    // Note: each bond is visited twice so that bond.atom-a and bond.atom-b both get the "swapped values"
-    const visitedSourceUnits = new Set<number>();
-
     const atomicBond = ctx.atomicBond;
 
     // Process intra unit bonds
@@ -394,7 +391,6 @@ function expandConnected(ctx: QueryContext, structure: Structure) {
 
         // Process inter unit bonds
         for (const bondedUnit of interBonds.getConnectedUnits(inputUnitA)) {
-            if (visitedSourceUnits.has(bondedUnit.unitB.id)) continue;
             const currentUnitB = structure.unitMap.get(bondedUnit.unitB.id);
 
             for (const aI of bondedUnit.connectedIndices) {
@@ -422,8 +418,6 @@ function expandConnected(ctx: QueryContext, structure: Structure) {
                 }
             }
         }
-
-        visitedSourceUnits.add(inputUnitA.id);
     }
 
     return builder.getStructure();

src/mol-model/structure/structure/structure.ts

@@ -25,7 +25,7 @@ import { Vec3, Mat4 } from '../../../mol-math/linear-algebra';
 import { idFactory } from '../../../mol-util/id-factory';
 import { GridLookup3D } from '../../../mol-math/geometry';
 import { UUID } from '../../../mol-util';
-import { CustomProperties } from '../common/custom-property';
+import { CustomProperties } from '../../custom-property';
 import { AtomicHierarchy } from '../model/properties/atomic';
 import { StructureSelection } from '../query/selection';
 import { getBoundary } from '../../../mol-math/geometry/boundary';
@@ -956,6 +956,9 @@ namespace Structure {
             this.current.unit = this.structure.units[this.unitIndex];
             this.elements = this.current.unit.elements;
             this.maxIdx = this.elements.length - 1;
+            if (this.maxIdx === 0) {
+                this.hasNext = this.unitIndex + 1 < this.structure.units.length;
+            }
         }
 
         constructor(private structure: Structure) {
@@ -1057,14 +1060,19 @@ namespace Structure {
     //
 
     export const DefaultSizeThresholds = {
+        /** Must be lower to be small */
         smallResidueCount: 10,
+        /** Must be lower to be medium */
         mediumResidueCount: 3000,
-        /** large ribosomes like 4UG0 should still be `large` */
+        /** Must be lower to be large (big ribosomes like 4UG0 should still be `large`) */
         largeResidueCount: 20000,
+        /**
+         * Structures above `largeResidueCount` are consider huge when they have
+         * a `highSymmetryUnitCount` or gigantic when not
+         */
         highSymmetryUnitCount: 10,
+        /** Fiber-like structure are consider small when below this */
         fiberResidueCount: 15,
-
-        residueCountFactor: 1
     };
     export type SizeThresholds = typeof DefaultSizeThresholds
 
@@ -1094,9 +1102,13 @@ namespace Structure {
 
     export enum Size { Small, Medium, Large, Huge, Gigantic }
 
-    export function getSize(structure: Structure, thresholds: Partial<SizeThresholds> = {}): Size {
+    /**
+     * @param residueCountFactor - modifies the threshold counts, useful when estimating
+     *                             the size of a structure comprised of multiple models
+     */
+    export function getSize(structure: Structure, thresholds: Partial<SizeThresholds> = {}, residueCountFactor = 1): Size {
         const t = { ...DefaultSizeThresholds, ...thresholds };
-        if (structure.polymerResidueCount >= t.largeResidueCount * t.residueCountFactor) {
+        if (structure.polymerResidueCount >= t.largeResidueCount * residueCountFactor) {
             if (hasHighSymmetry(structure, t)) {
                 return Size.Huge;
             } else {
@@ -1104,9 +1116,9 @@ namespace Structure {
             }
         } else if (isFiberLike(structure, t)) {
             return Size.Small;
-        } else if (structure.polymerResidueCount < t.smallResidueCount * t.residueCountFactor) {
+        } else if (structure.polymerResidueCount < t.smallResidueCount * residueCountFactor) {
             return Size.Small;
-        } else if (structure.polymerResidueCount < t.mediumResidueCount * t.residueCountFactor) {
+        } else if (structure.polymerResidueCount < t.mediumResidueCount * residueCountFactor) {
             return Size.Medium;
         } else {
             return Size.Large;

src/mol-model/structure/structure/unit/bonds/inter-compute.ts

@@ -102,6 +102,10 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
             if (added) continue;
         }
 
+        // ignore atoms with zero occupancy (assuming they are not actually atoms)
+        const occA = occupancyA.value(aI);
+        if (hasOccupancy && occA === 0) continue;
+
         const { indices, count, squaredDistances } = lookup3d.find(imageA[0], imageA[1], imageA[2], MAX_RADIUS);
         if (count === 0) continue;
 
@@ -112,7 +116,6 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
         const metalA = MetalsSet.has(aeI);
         const atomIdA = label_atom_idA.value(aI);
         const compIdA = label_comp_idA.value(residueIndexA[aI]);
-        const occA = occupancyA.value(aI);
 
         for (let ni = 0; ni < count; ni++) {
             const _bI = indices[ni] as StructureElement.UnitIndex;

src/mol-model/structure/structure/unit/bonds/intra-compute.ts

@@ -37,9 +37,12 @@ function _computeBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUni
 
     const { x, y, z } = unit.model.atomicConformation;
     const atomCount = unit.elements.length;
-    const { elements: atoms, residueIndex } = unit;
+    const { elements: atoms, residueIndex, chainIndex } = unit;
     const { type_symbol, label_atom_id, label_alt_id } = unit.model.atomicHierarchy.atoms;
-    const { label_comp_id } = unit.model.atomicHierarchy.residues;
+    const { occupancy } = unit.model.atomicConformation;
+    const { label_comp_id, label_seq_id } = unit.model.atomicHierarchy.residues;
+    const { index } = unit.model.atomicHierarchy;
+    const { byEntityKey } = unit.model.sequence;
     const query3d = unit.lookup3d;
 
     const structConn = StructConn.Provider.get(unit.model);
@@ -101,13 +104,22 @@ function _computeBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUni
 
         if (!props.forceCompute && raI !== lastResidue) {
             if (!!component && component.entries.has(compId)) {
-                componentMap = component.entries.get(compId)!.map;
+                const entitySeq = byEntityKey[index.getEntityFromChain(chainIndex[aI])];
+                if (entitySeq && entitySeq.sequence.microHet.has(label_seq_id.value(raI))) {
+                    // compute for sequence positions with micro-heterogeneity
+                    componentMap = void 0;
+                } else {
+                    componentMap = component.entries.get(compId)!.map;
+                }
             } else {
                 componentMap = void 0;
             }
         }
         lastResidue = raI;
 
+        // ignore atoms with zero occupancy (assuming they are not actually atoms)
+        if (occupancy.isDefined && occupancy.value(aI) === 0) continue;
+
         const aeI = getElementIdx(type_symbol.value(aI));
         const atomIdA = label_atom_id.value(aI);
         const componentPairs = componentMap ? componentMap.get(atomIdA) : void 0;

src/mol-model/structure/structure/util/superposition.ts

@@ -1,19 +1,26 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 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>
  */
 
 import { MinimizeRmsd } from '../../../../mol-math/linear-algebra/3d/minimize-rmsd';
 import StructureElement from '../element';
 import { OrderedSet } from '../../../../mol-data/int';
+import { AlignSequences } from '../../../sequence/alignment/sequence';
+import StructureProperties from '../properties';
 
-export function superposeStructures(xs: StructureElement.Loci[]): MinimizeRmsd.Result[] {
+export function superpose(xs: StructureElement.Loci[]): MinimizeRmsd.Result[] {
     const ret: MinimizeRmsd.Result[] = [];
     if (xs.length <= 0) return ret;
 
     const n = getMinSize(xs);
-    const input: MinimizeRmsd.Input = { a: getPositionTable(xs[0], n), b: getPositionTable(xs[1], n) };
+    const input: MinimizeRmsd.Input = {
+        a: getPositionTable(xs[0], n),
+        b: getPositionTable(xs[1], n)
+    };
+
     ret[0] = MinimizeRmsd.compute(input);
     for (let i = 2; i < xs.length; i++) {
         input.b = getPositionTable(xs[i], n);
@@ -24,6 +31,39 @@ export function superposeStructures(xs: StructureElement.Loci[]): MinimizeRmsd.R
     return ret;
 }
 
+type AlignAndSuperposeResult = MinimizeRmsd.Result & { alignmentScore: number };
+const reProtein = /(polypeptide|cyclic-pseudo-peptide)/i;
+
+export function alignAndSuperpose(xs: StructureElement.Loci[]): AlignAndSuperposeResult[] {
+    const ret: AlignAndSuperposeResult[] = [];
+    if (xs.length <= 0) return ret;
+
+    const l = StructureElement.Loci.getFirstLocation(xs[0])!;
+    const subtype = StructureProperties.entity.subtype(l);
+    const substMatrix = subtype.match(reProtein) ? 'blosum62' : 'default';
+
+    for (let i = 1; i < xs.length; i++) {
+        const { a, b, score } = AlignSequences.compute({
+            a: xs[0].elements[0],
+            b: xs[i].elements[0],
+        }, { substMatrix });
+
+        const lociA = StructureElement.Loci(xs[0].structure, [a]);
+        const lociB = StructureElement.Loci(xs[i].structure, [b]);
+        const n = OrderedSet.size(a.indices);
+
+        ret.push({
+            ...MinimizeRmsd.compute({
+                a: getPositionTable(lociA, n),
+                b: getPositionTable(lociB, n)
+            }),
+            alignmentScore: score
+        });
+    }
+
+    return ret;
+}
+
 function getPositionTable(xs: StructureElement.Loci, n: number): MinimizeRmsd.Positions {
     const ret = MinimizeRmsd.Positions.empty(n);
     let o = 0;

src/mol-model/volume.ts

@@ -1,7 +1,9 @@
 /**
- * Copyright (c) 2018 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>
  */
 
-export * from './volume/data';
+export * from './volume/volume';
+export * from './volume/grid';

src/mol-model/volume/data.ts

@@ -1,96 +0,0 @@
-/**
- * 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>
- */
-
-import { SpacegroupCell, Box3D } from '../../mol-math/geometry';
-import { Tensor, Mat4, Vec3 } from '../../mol-math/linear-algebra';
-import { equalEps } from '../../mol-math/linear-algebra/3d/common';
-import { ModelFormat } from '../../mol-model-formats/format';
-
-/** The basic unit cell that contains the data. */
-interface VolumeDataBase {
-    readonly label?: string,
-    readonly transform: { kind: 'spacegroup', cell: SpacegroupCell, fractionalBox: Box3D } | { kind: 'matrix', matrix: Mat4 },
-    readonly data: Tensor,
-    readonly dataStats: Readonly<{
-        min: number,
-        max: number,
-        mean: number,
-        sigma: number
-    }>
-    readonly sourceData: ModelFormat,
-}
-
-interface VolumeData extends VolumeDataBase {
-    readonly colorVolume?: VolumeDataBase
-}
-
-namespace VolumeData {
-    export const One: VolumeData = {
-        transform: { kind: 'matrix', matrix: Mat4.identity() },
-        data: Tensor.create(Tensor.Space([1, 1, 1], [0, 1, 2]), Tensor.Data1([0])),
-        dataStats: { min: 0, max: 0, mean: 0, sigma: 0 },
-        sourceData: { kind: '', data: '', name: '' }
-    };
-
-    const _scale = Mat4.zero(), _translate = Mat4.zero();
-    export function getGridToCartesianTransform(volume: VolumeData) {
-        if (volume.transform.kind === 'matrix') {
-            return Mat4.copy(Mat4(), volume.transform.matrix);
-        }
-
-        if (volume.transform.kind === 'spacegroup') {
-            const { data: { space } } = volume;
-            const scale = Mat4.fromScaling(_scale, Vec3.div(Vec3.zero(), Box3D.size(Vec3.zero(), volume.transform.fractionalBox), Vec3.ofArray(space.dimensions)));
-            const translate = Mat4.fromTranslation(_translate, volume.transform.fractionalBox.min);
-            return Mat4.mul3(Mat4.zero(), volume.transform.cell.fromFractional, translate, scale);
-        }
-
-        return Mat4.identity();
-    }
-
-    export function areEquivalent(volA: VolumeData, volB: VolumeData) {
-        return volA === volB;
-    }
-}
-
-type VolumeIsoValue = VolumeIsoValue.Absolute | VolumeIsoValue.Relative
-
-namespace VolumeIsoValue {
-    export type Relative = Readonly<{ kind: 'relative', relativeValue: number }>
-    export type Absolute = Readonly<{ kind: 'absolute', absoluteValue: number }>
-
-    export function areSame(a: VolumeIsoValue, b: VolumeIsoValue, stats: VolumeData['dataStats']) {
-        return equalEps(toAbsolute(a, stats).absoluteValue, toAbsolute(b, stats).absoluteValue, stats.sigma / 100);
-    }
-
-    export function absolute(value: number): Absolute { return { kind: 'absolute', absoluteValue: value }; }
-    export function relative(value: number): Relative { return { kind: 'relative', relativeValue: value }; }
-
-    export function calcAbsolute(stats: VolumeData['dataStats'], relativeValue: number): number {
-        return relativeValue * stats.sigma + stats.mean;
-    }
-
-    export function calcRelative(stats: VolumeData['dataStats'], absoluteValue: number): number {
-        return stats.sigma === 0 ? 0 : ((absoluteValue - stats.mean) / stats.sigma);
-    }
-
-    export function toAbsolute(value: VolumeIsoValue, stats: VolumeData['dataStats']): Absolute {
-        return value.kind === 'absolute' ? value : { kind: 'absolute', absoluteValue: VolumeIsoValue.calcAbsolute(stats, value.relativeValue) };
-    }
-
-    export function toRelative(value: VolumeIsoValue, stats: VolumeData['dataStats']): Relative {
-        return value.kind === 'relative' ? value : { kind: 'relative', relativeValue: VolumeIsoValue.calcRelative(stats, value.absoluteValue) };
-    }
-
-    export function toString(value: VolumeIsoValue) {
-        return value.kind === 'relative'
-            ? `${value.relativeValue.toFixed(2)} σ`
-            : `${value.absoluteValue.toPrecision(4)}`;
-    }
-}
-
-export { VolumeData, VolumeIsoValue };

src/mol-model/volume/grid.ts

@@ -0,0 +1,57 @@
+/**
+ * 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>
+ */
+
+import { SpacegroupCell, Box3D } from '../../mol-math/geometry';
+import { Tensor, Mat4, Vec3 } from '../../mol-math/linear-algebra';
+
+/** The basic unit cell that contains the grid data. */
+interface Grid {
+    readonly transform: Grid.Transform,
+    readonly cells: Tensor,
+    readonly stats: Readonly<{
+        min: number,
+        max: number,
+        mean: number,
+        sigma: number
+    }>
+}
+
+namespace Grid {
+    export const One: Grid = {
+        transform: { kind: 'matrix', matrix: Mat4.identity() },
+        cells: Tensor.create(Tensor.Space([1, 1, 1], [0, 1, 2]), Tensor.Data1([0])),
+        stats: { min: 0, max: 0, mean: 0, sigma: 0 },
+    };
+
+    export type Transform = { kind: 'spacegroup', cell: SpacegroupCell, fractionalBox: Box3D } | { kind: 'matrix', matrix: Mat4 }
+
+    const _scale = Mat4.zero(), _translate = Mat4.zero();
+    export function getGridToCartesianTransform(grid: Grid) {
+        if (grid.transform.kind === 'matrix') {
+            return Mat4.copy(Mat4(), grid.transform.matrix);
+        }
+
+        if (grid.transform.kind === 'spacegroup') {
+            const { cells: { space } } = grid;
+            const scale = Mat4.fromScaling(_scale, Vec3.div(Vec3.zero(), Box3D.size(Vec3.zero(), grid.transform.fractionalBox), Vec3.ofArray(space.dimensions)));
+            const translate = Mat4.fromTranslation(_translate, grid.transform.fractionalBox.min);
+            return Mat4.mul3(Mat4.zero(), grid.transform.cell.fromFractional, translate, scale);
+        }
+
+        return Mat4.identity();
+    }
+
+    export function areEquivalent(gridA: Grid, gridB: Grid) {
+        return gridA === gridB;
+    }
+
+    export function isEmpty(grid: Grid) {
+        return grid.cells.data.length === 0;
+    }
+}
+
+export { Grid };

src/mol-model/volume/volume.ts

@@ -4,32 +4,105 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
-import { VolumeData, VolumeIsoValue } from './data';
+import { Grid } from './grid';
 import { OrderedSet } from '../../mol-data/int';
 import { Sphere3D } from '../../mol-math/geometry';
 import { Vec3, Mat4 } from '../../mol-math/linear-algebra';
 import { BoundaryHelper } from '../../mol-math/geometry/boundary-helper';
 import { CubeFormat } from '../../mol-model-formats/volume/cube';
+import { equalEps } from '../../mol-math/linear-algebra/3d/common';
+import { ModelFormat } from '../../mol-model-formats/format';
+import { CustomProperties } from '../custom-property';
+
+export interface Volume {
+    readonly label?: string
+    readonly grid: Grid
+    readonly sourceData: ModelFormat
+
+    // TODO use...
+    customProperties: CustomProperties
+
+    /**
+     * Not to be accessed directly, each custom property descriptor
+     * defines property accessors that use this field to store the data.
+     */
+    _propertyData: { [name: string]: any }
+
+    // TODO add as customProperty?
+    readonly colorVolume?: Volume
+}
 
 export namespace Volume {
     export type CellIndex = { readonly '@type': 'cell-index' } & number
 
-    export function isOrbitals(volume: VolumeData) {
+    export type IsoValue = IsoValue.Absolute | IsoValue.Relative
+
+    export namespace IsoValue {
+        export type Relative = Readonly<{ kind: 'relative', relativeValue: number }>
+        export type Absolute = Readonly<{ kind: 'absolute', absoluteValue: number }>
+
+        export function areSame(a: IsoValue, b: IsoValue, stats: Grid['stats']) {
+            return equalEps(toAbsolute(a, stats).absoluteValue, toAbsolute(b, stats).absoluteValue, stats.sigma / 100);
+        }
+
+        export function absolute(value: number): Absolute { return { kind: 'absolute', absoluteValue: value }; }
+        export function relative(value: number): Relative { return { kind: 'relative', relativeValue: value }; }
+
+        export function calcAbsolute(stats: Grid['stats'], relativeValue: number): number {
+            return relativeValue * stats.sigma + stats.mean;
+        }
+
+        export function calcRelative(stats: Grid['stats'], absoluteValue: number): number {
+            return stats.sigma === 0 ? 0 : ((absoluteValue - stats.mean) / stats.sigma);
+        }
+
+        export function toAbsolute(value: IsoValue, stats: Grid['stats']): Absolute {
+            return value.kind === 'absolute' ? value : { kind: 'absolute', absoluteValue: IsoValue.calcAbsolute(stats, value.relativeValue) };
+        }
+
+        export function toRelative(value: IsoValue, stats: Grid['stats']): Relative {
+            return value.kind === 'relative' ? value : { kind: 'relative', relativeValue: IsoValue.calcRelative(stats, value.absoluteValue) };
+        }
+
+        export function toString(value: IsoValue) {
+            return value.kind === 'relative'
+                ? `${value.relativeValue.toFixed(2)} σ`
+                : `${value.absoluteValue.toPrecision(4)}`;
+        }
+    }
+
+    export const One: Volume = {
+        label: '',
+        grid: Grid.One,
+        sourceData: { kind: '', name: '', data: {} },
+        customProperties: new CustomProperties(),
+        _propertyData: Object.create(null),
+    };
+
+    export function areEquivalent(volA: Volume, volB: Volume) {
+        return Grid.areEquivalent(volA.grid, volB.grid);
+    }
+
+    export function isEmpty(vol: Volume) {
+        return Grid.isEmpty(vol.grid);
+    }
+
+    export function isOrbitals(volume: Volume) {
         if (!CubeFormat.is(volume.sourceData)) return false;
         return volume.sourceData.data.header.orbitals;
     }
 
-    export interface Loci { readonly kind: 'volume-loci', readonly volume: VolumeData }
-    export function Loci(volume: VolumeData): Loci { return { kind: 'volume-loci', volume }; }
+    export interface Loci { readonly kind: 'volume-loci', readonly volume: Volume }
+    export function Loci(volume: Volume): Loci { return { kind: 'volume-loci', volume }; }
     export function isLoci(x: any): x is Loci { return !!x && x.kind === 'volume-loci'; }
     export function areLociEqual(a: Loci, b: Loci) { return a.volume === b.volume; }
-    export function isLociEmpty(loci: Loci) { return loci.volume.data.data.length === 0; }
+    export function isLociEmpty(loci: Loci) { return Grid.isEmpty(loci.volume.grid); }
 
-    export function getBoundingSphere(volume: VolumeData, boundingSphere?: Sphere3D) {
+    export function getBoundingSphere(volume: Volume, boundingSphere?: Sphere3D) {
         if (!boundingSphere) boundingSphere = Sphere3D();
 
-        const transform = VolumeData.getGridToCartesianTransform(volume);
-        const [x, y, z] = volume.data.space.dimensions;
+        const transform = Grid.getGridToCartesianTransform(volume.grid);
+        const [x, y, z] = volume.grid.cells.space.dimensions;
 
         const cpA = Vec3.create(0, 0, 0); Vec3.transformMat4(cpA, cpA, transform);
         const cpB = Vec3.create(x, y, z); Vec3.transformMat4(cpB, cpB, transform);
@@ -52,31 +125,31 @@ export namespace Volume {
     }
 
     export namespace Isosurface {
-        export interface Loci { readonly kind: 'isosurface-loci', readonly volume: VolumeData, readonly isoValue: VolumeIsoValue }
-        export function Loci(volume: VolumeData, isoValue: VolumeIsoValue): Loci { return { kind: 'isosurface-loci', volume, isoValue }; }
+        export interface Loci { readonly kind: 'isosurface-loci', readonly volume: Volume, readonly isoValue: Volume.IsoValue }
+        export function Loci(volume: Volume, isoValue: Volume.IsoValue): Loci { return { kind: 'isosurface-loci', volume, isoValue }; }
         export function isLoci(x: any): x is Loci { return !!x && x.kind === 'isosurface-loci'; }
-        export function areLociEqual(a: Loci, b: Loci) { return a.volume === b.volume && VolumeIsoValue.areSame(a.isoValue, b.isoValue, a.volume.dataStats); }
-        export function isLociEmpty(loci: Loci) { return loci.volume.data.data.length === 0; }
+        export function areLociEqual(a: Loci, b: Loci) { return a.volume === b.volume && Volume.IsoValue.areSame(a.isoValue, b.isoValue, a.volume.grid.stats); }
+        export function isLociEmpty(loci: Loci) { return loci.volume.grid.cells.data.length === 0; }
 
-        export function getBoundingSphere(volume: VolumeData, isoValue: VolumeIsoValue, boundingSphere?: Sphere3D) {
+        export function getBoundingSphere(volume: Volume, isoValue: Volume.IsoValue, boundingSphere?: Sphere3D) {
             // TODO get bounding sphere for subgrid with values >= isoValue
             return Volume.getBoundingSphere(volume, boundingSphere);
         }
     }
 
     export namespace Cell {
-        export interface Loci { readonly kind: 'cell-loci', readonly volume: VolumeData, readonly indices: OrderedSet<CellIndex> }
-        export function Loci(volume: VolumeData, indices: OrderedSet<CellIndex>): Loci { return { kind: 'cell-loci', volume, indices }; }
+        export interface Loci { readonly kind: 'cell-loci', readonly volume: Volume, readonly indices: OrderedSet<CellIndex> }
+        export function Loci(volume: Volume, indices: OrderedSet<CellIndex>): Loci { return { kind: 'cell-loci', volume, indices }; }
         export function isLoci(x: any): x is Loci { return !!x && x.kind === 'cell-loci'; }
         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; }
 
         const boundaryHelper = new BoundaryHelper('98');
         const tmpBoundaryPos = Vec3();
-        export function getBoundingSphere(volume: VolumeData, indices: OrderedSet<CellIndex>, boundingSphere?: Sphere3D) {
+        export function getBoundingSphere(volume: Volume, indices: OrderedSet<CellIndex>, boundingSphere?: Sphere3D) {
             boundaryHelper.reset();
-            const transform = VolumeData.getGridToCartesianTransform(volume);
-            const { getCoords } = volume.data.space;
+            const transform = Grid.getGridToCartesianTransform(volume.grid);
+            const { getCoords } = volume.grid.cells.space;
 
             for (let i = 0, _i = OrderedSet.size(indices); i < _i; i++) {
                 const o = OrderedSet.getAt(indices, i);

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

@@ -32,7 +32,7 @@ export const PdbDownloadProvider = {
         encoding: PD.Select('bcif', [['cif', 'cif'], ['bcif', 'bcif']] as ['cif' | 'bcif', string][]),
     }, { label: 'RCSB PDB', isFlat: true }),
     'pdbe': PD.Group({
-        variant: PD.Select('updated-bcif', [['updated-bcif', 'Updated (bcif)'], ['updated', 'Updated'], ['archival', 'Archival']] as ['updated' | 'archival', string][]),
+        variant: PD.Select('updated-bcif', [['updated-bcif', 'Updated (bcif)'], ['updated', 'Updated'], ['archival', 'Archival']] as ['updated' | 'updtaed-bcif' | 'archival', string][]),
     }, { label: 'PDBe', isFlat: true }),
 };
 export type PdbDownloadProvider = keyof typeof PdbDownloadProvider;
@@ -55,7 +55,10 @@ const DownloadStructure = StateAction.build({
                     options
                 }, { isFlat: true, label: 'PDB' }),
                 'pdb-dev': PD.Group({
-                    id: PD.Text('PDBDEV_00000001', { label: 'PDBDev Id(s)', description: 'One or more comma/space separated ids.' }),
+                    provider: PD.Group({
+                        id: PD.Text('PDBDEV_00000001', { label: 'PDBDev Id(s)', description: 'One or more comma/space separated ids.' }),
+                        encoding: PD.Select('bcif', [['cif', 'cif'], ['bcif', 'bcif']] as ['cif' | 'bcif', string][]),
+                    }, { pivot: 'id' }),
                     options
                 }, { isFlat: true, label: 'PDBDEV' }),
                 'bcif-static': PD.Group({
@@ -104,13 +107,15 @@ const DownloadStructure = StateAction.build({
             asTrajectory = !!src.params.options.asTrajectory;
             break;
         case 'pdb-dev':
-            downloadParams = getDownloadParams(src.params.id,
+            downloadParams = getDownloadParams(src.params.provider.id,
                 id => {
                     const nId = id.toUpperCase().startsWith('PDBDEV_') ? id : `PDBDEV_${id.padStart(8, '0')}`;
-                    return `https://pdb-dev.wwpdb.org/cif/${nId.toUpperCase()}.cif`;
+                    return src.params.provider.encoding === 'bcif'
+                        ? `https://pdb-dev.wwpdb.org/bcif/${nId.toUpperCase()}.bcif`
+                        : `https://pdb-dev.wwpdb.org/cif/${nId.toUpperCase()}.cif`;
                 },
                 id => id.toUpperCase().startsWith('PDBDEV_') ? id : `PDBDEV_${id.padStart(8, '0')}`,
-                false
+                src.params.provider.encoding === 'bcif'
             );
             asTrajectory = !!src.params.options.asTrajectory;
             break;

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

@@ -23,6 +23,15 @@ export const AnimateModelIndex = PluginStateAnimation.create({
         }, { options: [['palindrome', 'Palindrome'], ['loop', 'Loop'], ['once', 'Once']] }),
         maxFPS: PD.Numeric(15, { min: 1, max: 30, step: 1 })
     }),
+    canApply(ctx) {
+        const state = ctx.state.data;
+        const models = state.select(StateSelection.Generators.ofTransformer(StateTransforms.Model.ModelFromTrajectory));
+        for (const m of models) {
+            const parent = StateSelection.findAncestorOfType(state.tree, state.cells, m.transform.ref, [PluginStateObject.Molecule.Trajectory]);
+            if (parent && parent.obj && parent.obj.data.length > 1) return { canApply: true };
+        }
+        return { canApply: false, reason: 'No trajectory to animate' };
+    },
     initialState: () => ({} as { palindromeDirections?: { [id: string]: -1 | 1 | undefined } }),
     async apply(animState, t, ctx) {
         // limit fps
@@ -48,6 +57,8 @@ export const AnimateModelIndex = PluginStateAnimation.create({
             const parent = StateSelection.findAncestorOfType(state.tree, state.cells, m.transform.ref, [PluginStateObject.Molecule.Trajectory]);
             if (!parent || !parent.obj) continue;
             const traj = parent.obj;
+            if (traj.data.length <= 1) continue;
+
             update.to(m).update(old => {
                 const len = traj.data.length;
                 if (len !== 1) {
@@ -79,7 +90,9 @@ export const AnimateModelIndex = PluginStateAnimation.create({
             });
         }
 
-        await PluginCommands.State.Update(ctx.plugin, { state, tree: update, options: { doNotLogTiming: true } });
+        if (!allSingles) {
+            await PluginCommands.State.Update(ctx.plugin, { state, tree: update, options: { doNotLogTiming: true } });
+        }
 
         if (allSingles || (params.mode.name === 'once' && isEnd)) return { kind: 'finished' };
         if (params.mode.name === 'palindrome') return { kind: 'next', state: { palindromeDirections } };
@@ -104,6 +117,12 @@ export const AnimateAssemblyUnwind = PluginStateAnimation.create({
             target: PD.Select(targets[0][0], targets)
         };
     },
+    canApply(plugin) {
+        const state = plugin.state.data;
+        const root = StateTransform.RootRef;
+        const reprs = state.select(StateSelection.Generators.ofType(PluginStateObject.Molecule.Structure.Representation3D, root));
+        return { canApply: reprs.length > 0 };
+    },
     initialState: () => ({ t: 0 }),
     setup(params, plugin) {
         const state = plugin.state.data;
@@ -231,6 +250,9 @@ export const AnimateStateInterpolation = PluginStateAnimation.create({
     params: () => ({
         transtionDurationInMs: PD.Numeric(2000, { min: 100, max: 30000, step: 10 })
     }),
+    canApply(plugin) {
+        return { canApply: plugin.managers.snapshot.state.entries.size > 1 };
+    },
     initialState: () => ({ }),
     async apply(animState, t, ctx) {
 

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

@@ -15,7 +15,9 @@ export { PluginStateAnimation };
 interface PluginStateAnimation<P = any, S = any> {
     name: string,
     readonly display: { readonly name: string, readonly description?: string },
+
     params(ctx: PluginContext): PD.For<P>,
+    canApply?(ctx: PluginContext): { canApply: true } | { canApply: false, reason?: string },
     initialState(params: P, ctx: PluginContext): S,
 
     // TODO: support state in setup/teardown?

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

@@ -15,6 +15,7 @@ import { PluginContext } from '../../../mol-plugin/context';
 import { StateObjectRef, StateObjectSelector } from '../../../mol-state';
 import { StaticStructureComponentType } from '../../helpers/structure-component';
 import { StructureSelectionQueries as Q } from '../../helpers/structure-selection-query';
+import { PluginConfig } from '../../../mol-plugin/config';
 
 export interface StructureRepresentationPresetProvider<P = any, S extends _Result = _Result> extends PresetProvider<PluginStateObject.Molecule.Structure, P, S> { }
 export function StructureRepresentationPresetProvider<P, S extends _Result>(repr: StructureRepresentationPresetProvider<P, S>) { return repr; }
@@ -64,7 +65,9 @@ const auto = StructureRepresentationPresetProvider({
     apply(ref, params, plugin) {
         const structure = StateObjectRef.resolveAndCheck(plugin.state.data, ref)?.obj?.data;
         if (!structure) return { };
-        const size = Structure.getSize(structure);
+
+        const thresholds = plugin.config.get(PluginConfig.Structure.SizeThresholds) || Structure.DefaultSizeThresholds;
+        const size = Structure.getSize(structure, thresholds);
 
         switch (size) {
             case Structure.Size.Gigantic:

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

@@ -12,10 +12,9 @@ import { StateObjectSelector } from '../../mol-state';
 import { PluginStateObject } from '../objects';
 import { VolumeRepresentation3DHelpers } from '../transforms/representation';
 import { ColorNames } from '../../mol-util/color/names';
-import { VolumeIsoValue } from '../../mol-model/volume';
+import { Volume } from '../../mol-model/volume';
 import { createVolumeRepresentationParams } from '../helpers/volume-representation-params';
 import { objectForEach } from '../../mol-util/object';
-import { Volume } from '../../mol-model/volume/volume';
 
 const Category = 'Volume';
 
@@ -110,13 +109,13 @@ export const CubeProvider = DataFormatProvider({
         if (volumeData && Volume.isOrbitals(volumeData)) {
             const volumePos = surfaces.to(data.volume).apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(plugin, volumeData, {
                 type: 'isosurface',
-                typeParams: { isoValue: VolumeIsoValue.relative(1), alpha: 0.4 },
+                typeParams: { isoValue: Volume.IsoValue.relative(1), alpha: 0.4 },
                 color: 'uniform',
                 colorParams: { value: ColorNames.blue }
             }));
             const volumeNeg = surfaces.to(data.volume).apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(plugin, volumeData, {
                 type: 'isosurface',
-                typeParams: { isoValue: VolumeIsoValue.relative(-1), alpha: 0.4 },
+                typeParams: { isoValue: Volume.IsoValue.relative(-1), alpha: 0.4 },
                 color: 'uniform',
                 colorParams: { value: ColorNames.red }
             }));
@@ -124,7 +123,7 @@ export const CubeProvider = DataFormatProvider({
         } else {
             const volume = surfaces.to(data.volume).apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(plugin, volumeData, {
                 type: 'isosurface',
-                typeParams: { isoValue: VolumeIsoValue.relative(2), alpha: 0.4 },
+                typeParams: { isoValue: Volume.IsoValue.relative(2), alpha: 0.4 },
                 color: 'uniform',
                 colorParams: { value: ColorNames.grey }
             }));
@@ -176,13 +175,13 @@ export const DscifProvider = DataFormatProvider({
         if (volumes.length > 0) {
             visuals[0] = tree
                 .to(volumes[0])
-                .apply(StateTransforms.Representation.VolumeRepresentation3D, VolumeRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'isosurface', { isoValue: VolumeIsoValue.relative(1.5), alpha: 1 }, 'uniform', { value: ColorNames.teal }))
+                .apply(StateTransforms.Representation.VolumeRepresentation3D, VolumeRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'isosurface', { isoValue: Volume.IsoValue.relative(1.5), alpha: 1 }, 'uniform', { value: ColorNames.teal }))
                 .selector;
         }
 
         if (volumes.length > 1) {
-            const posParams = VolumeRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'isosurface', { isoValue: VolumeIsoValue.relative(3), alpha: 0.3 }, 'uniform', { value: ColorNames.green });
-            const negParams = VolumeRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'isosurface', { isoValue: VolumeIsoValue.relative(-3), alpha: 0.3 }, 'uniform', { value: ColorNames.red });
+            const posParams = VolumeRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'isosurface', { isoValue: Volume.IsoValue.relative(3), alpha: 0.3 }, 'uniform', { value: ColorNames.green });
+            const negParams = VolumeRepresentation3DHelpers.getDefaultParamsStatic(plugin, 'isosurface', { isoValue: Volume.IsoValue.relative(-3), alpha: 0.3 }, 'uniform', { value: ColorNames.red });
             visuals[visuals.length] = tree.to(volumes[1]).apply(StateTransforms.Representation.VolumeRepresentation3D, posParams).selector;
             visuals[visuals.length] = tree.to(volumes[1]).apply(StateTransforms.Representation.VolumeRepresentation3D, negParams).selector;
         }

src/mol-plugin-state/helpers/structure-selection-query.ts

@@ -74,7 +74,7 @@ function StructureSelectionQuery(label: string, expression: Expression, props: S
         ensureCustomProperties: props.ensureCustomProperties,
         async getSelection(plugin, runtime, structure) {
             const current = plugin.managers.structure.selection.getStructure(structure);
-            const currentSelection = current ? StructureSelection.Singletons(structure, current) : StructureSelection.Empty(structure);
+            const currentSelection = current ? StructureSelection.Sequence(structure, [current]) : StructureSelection.Empty(structure);
             if (props.ensureCustomProperties) {
                 await props.ensureCustomProperties({ runtime, assetManager: plugin.managers.asset }, structure);
             }
@@ -119,71 +119,132 @@ const trace = StructureSelectionQuery('Trace', MS.struct.modifier.union([
     ])
 ]), { category: StructureSelectionCategory.Structure });
 
-// TODO maybe pre-calculate atom properties like backbone/sidechain
+const _proteinEntityTest = MS.core.logic.and([
+    MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
+    MS.core.str.match([
+        MS.re('(polypeptide|cyclic-pseudo-peptide)', 'i'),
+        MS.ammp('entitySubtype')
+    ])
+]);
+
+const _nucleiEntityTest = MS.core.logic.and([
+    MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
+    MS.core.str.match([
+        MS.re('(nucleotide|peptide nucleic acid)', 'i'),
+        MS.ammp('entitySubtype')
+    ])
+]);
+
+/**
+ * this is to get non-polymer and peptide terminus components in polymer entities,
+ * - non-polymer, e.g. PXZ in 4HIV or generally ACE
+ * - carboxy terminus, e.g. FC0 in 4BP9, or ETA in 6DDE
+ * - amino terminus, e.g. ARF in 3K4V, or 4MM in 3EGV
+ */
+const _nonPolymerResidueTest = MS.core.str.match([
+    MS.re('non-polymer|(amino|carboxy) terminus|peptide-like', 'i'),
+    MS.ammp('chemCompType')
+]);
+
+// TODO maybe pre-calculate backbone atom properties
 const backbone = StructureSelectionQuery('Backbone', MS.struct.modifier.union([
     MS.struct.combinator.merge([
         MS.struct.modifier.union([
             MS.struct.generator.atomGroups({
-                'entity-test': MS.core.logic.and([
-                    MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
-                    MS.core.str.match([
-                        MS.re('(polypeptide|cyclic-pseudo-peptide)', 'i'),
-                        MS.ammp('entitySubtype')
-                    ])
-                ]),
+                'entity-test': _proteinEntityTest,
                 'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
+                'residue-test': MS.core.logic.not([_nonPolymerResidueTest]),
                 'atom-test': MS.core.set.has([MS.set(...SetUtils.toArray(ProteinBackboneAtoms)), MS.ammp('label_atom_id')])
             })
         ]),
         MS.struct.modifier.union([
             MS.struct.generator.atomGroups({
-                'entity-test': MS.core.logic.and([
-                    MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
-                    MS.core.str.match([
-                        MS.re('(nucleotide|peptide nucleic acid)', 'i'),
-                        MS.ammp('entitySubtype')
-                    ])
-                ]),
+                'entity-test': _nucleiEntityTest,
                 'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
+                'residue-test': MS.core.logic.not([_nonPolymerResidueTest]),
                 'atom-test': MS.core.set.has([MS.set(...SetUtils.toArray(NucleicBackboneAtoms)), MS.ammp('label_atom_id')])
             })
         ])
     ])
 ]), { category: StructureSelectionCategory.Structure });
 
-const protein = StructureSelectionQuery('Protein', MS.struct.modifier.union([
-    MS.struct.generator.atomGroups({
-        'entity-test': MS.core.logic.and([
-            MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
-            MS.core.str.match([
-                MS.re('(polypeptide|cyclic-pseudo-peptide)', 'i'),
-                MS.ammp('entitySubtype')
-            ])
+// TODO maybe pre-calculate sidechain atom property
+const sidechain = StructureSelectionQuery('Sidechain', MS.struct.modifier.union([
+    MS.struct.combinator.merge([
+        MS.struct.modifier.union([
+            MS.struct.generator.atomGroups({
+                'entity-test': _proteinEntityTest,
+                'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
+                'residue-test': MS.core.logic.not([_nonPolymerResidueTest]),
+                'atom-test': MS.core.logic.or([
+                    MS.core.logic.not([
+                        MS.core.set.has([MS.set(...SetUtils.toArray(ProteinBackboneAtoms)), MS.ammp('label_atom_id')])
+                    ])
+                ])
+            })
+        ]),
+        MS.struct.modifier.union([
+            MS.struct.generator.atomGroups({
+                'entity-test': _nucleiEntityTest,
+                'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
+                'residue-test': MS.core.logic.not([_nonPolymerResidueTest]),
+                'atom-test': MS.core.logic.or([
+                    MS.core.logic.not([
+                        MS.core.set.has([MS.set(...SetUtils.toArray(NucleicBackboneAtoms)), MS.ammp('label_atom_id')])
+                    ])
+                ])
+            })
         ])
-    })
+    ])
+]), { category: StructureSelectionCategory.Structure });
+
+// TODO maybe pre-calculate sidechain atom property
+const sidechainWithTrace = StructureSelectionQuery('Sidechain with Trace', MS.struct.modifier.union([
+    MS.struct.combinator.merge([
+        MS.struct.modifier.union([
+            MS.struct.generator.atomGroups({
+                'entity-test': _proteinEntityTest,
+                'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
+                'residue-test': MS.core.logic.not([_nonPolymerResidueTest]),
+                'atom-test': MS.core.logic.or([
+                    MS.core.logic.not([
+                        MS.core.set.has([MS.set(...SetUtils.toArray(ProteinBackboneAtoms)), MS.ammp('label_atom_id')])
+                    ]),
+                    MS.core.rel.eq([MS.ammp('label_atom_id'), 'CA']),
+                    MS.core.logic.and([
+                        MS.core.rel.eq([MS.ammp('auth_comp_id'), 'PRO']),
+                        MS.core.rel.eq([MS.ammp('label_atom_id'), 'N'])
+                    ])
+                ])
+            })
+        ]),
+        MS.struct.modifier.union([
+            MS.struct.generator.atomGroups({
+                'entity-test': _nucleiEntityTest,
+                'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
+                'residue-test': MS.core.logic.not([_nonPolymerResidueTest]),
+                'atom-test': MS.core.logic.or([
+                    MS.core.logic.not([
+                        MS.core.set.has([MS.set(...SetUtils.toArray(NucleicBackboneAtoms)), MS.ammp('label_atom_id')])
+                    ]),
+                    MS.core.rel.eq([MS.ammp('label_atom_id'), 'P'])
+                ])
+            })
+        ])
+    ])
+]), { category: StructureSelectionCategory.Structure });
+
+const protein = StructureSelectionQuery('Protein', MS.struct.modifier.union([
+    MS.struct.generator.atomGroups({ 'entity-test': _proteinEntityTest })
 ]), { category: StructureSelectionCategory.Type });
 
 const nucleic = StructureSelectionQuery('Nucleic', MS.struct.modifier.union([
-    MS.struct.generator.atomGroups({
-        'entity-test': MS.core.logic.and([
-            MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
-            MS.core.str.match([
-                MS.re('(nucleotide|peptide nucleic acid)', 'i'),
-                MS.ammp('entitySubtype')
-            ])
-        ])
-    })
+    MS.struct.generator.atomGroups({ 'entity-test': _nucleiEntityTest })
 ]), { category: StructureSelectionCategory.Type });
 
 const helix = StructureSelectionQuery('Helix', MS.struct.modifier.union([
     MS.struct.generator.atomGroups({
-        'entity-test': MS.core.logic.and([
-            MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
-            MS.core.str.match([
-                MS.re('(polypeptide|cyclic-pseudo-peptide)', 'i'),
-                MS.ammp('entitySubtype')
-            ])
-        ]),
+        'entity-test': _proteinEntityTest,
         'residue-test': MS.core.flags.hasAny([
             MS.ammp('secondaryStructureFlags'),
             MS.core.type.bitflags([SecondaryStructureType.Flag.Helix])
@@ -193,13 +254,7 @@ const helix = StructureSelectionQuery('Helix', MS.struct.modifier.union([
 
 const beta = StructureSelectionQuery('Beta Strand/Sheet', MS.struct.modifier.union([
     MS.struct.generator.atomGroups({
-        'entity-test': MS.core.logic.and([
-            MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
-            MS.core.str.match([
-                MS.re('(polypeptide|cyclic-pseudo-peptide)', 'i'),
-                MS.ammp('entitySubtype')
-            ])
-        ]),
+        'entity-test': _proteinEntityTest,
         'residue-test': MS.core.flags.hasAny([
             MS.ammp('secondaryStructureFlags'),
             MS.core.type.bitflags([SecondaryStructureType.Flag.Beta])
@@ -258,18 +313,11 @@ const ligand = StructureSelectionQuery('Ligand', MS.struct.modifier.union([
                 ])
             })
         ]),
-        // this is to get non-polymer and peptide terminus components in polymer entities,
-        // - non-polymer, e.g. PXZ in 4HIV or generally ACE
-        // - carboxy terminus, e.g. FC0 in 4BP9, or ETA in 6DDE
-        // - amino terminus, e.g. ARF in 3K4V, or 4MM in 3EGV
         MS.struct.modifier.union([
             MS.struct.generator.atomGroups({
                 'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
                 'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
-                'residue-test': MS.core.str.match([
-                    MS.re('non-polymer|(amino|carboxy) terminus|peptide-like', 'i'),
-                    MS.ammp('chemCompType')
-                ])
+                'residue-test': _nonPolymerResidueTest
             })
         ])
     ]),
@@ -373,7 +421,7 @@ const complement = StructureSelectionQuery('Inverse / Complement of Selection',
     referencesCurrent: true
 });
 
-const bonded = StructureSelectionQuery('Residues Bonded to Selection', MS.struct.modifier.union([
+const covalentlyBonded = StructureSelectionQuery('Residues Covalently Bonded to Selection', MS.struct.modifier.union([
     MS.struct.modifier.includeConnected({
         0: MS.internal.generator.current(), 'layer-count': 1, 'as-whole-residues': true
     })
@@ -383,6 +431,24 @@ const bonded = StructureSelectionQuery('Residues Bonded to Selection', MS.struct
     referencesCurrent: true
 });
 
+const covalentlyOrMetallicBonded = StructureSelectionQuery('Residues with Cov. or Metallic Bond to Selection', MS.struct.modifier.union([
+    MS.struct.modifier.includeConnected({
+        0: MS.internal.generator.current(),
+        'layer-count': 1,
+        'as-whole-residues': true,
+        'bond-test': MS.core.flags.hasAny([
+            MS.struct.bondProperty.flags(),
+            MS.core.type.bitflags([
+                BondType.Flag.Covalent | BondType.Flag.MetallicCoordination
+            ])
+        ])
+    })
+]), {
+    description: 'Select residues with covalent or metallic bond to current selection.',
+    category: StructureSelectionCategory.Manipulate,
+    referencesCurrent: true
+});
+
 const wholeResidues = StructureSelectionQuery('Whole Residues of Selection', MS.struct.modifier.union([
     MS.struct.modifier.wholeResidues({
         0: MS.internal.generator.current()
@@ -532,6 +598,8 @@ export const StructureSelectionQueries = {
     polymer,
     trace,
     backbone,
+    sidechain,
+    sidechainWithTrace,
     protein,
     nucleic,
     helix,
@@ -551,7 +619,8 @@ export const StructureSelectionQueries = {
     aromaticRing,
     surroundings,
     complement,
-    bonded,
+    covalentlyBonded,
+    covalentlyOrMetallicBonded,
     wholeResidues,
 };
 

src/mol-plugin-state/helpers/volume-representation-params.ts

@@ -4,7 +4,7 @@
  * @author David Sehnal <david.sehnal@gmail.com>
  */
 
-import { VolumeData } from '../../mol-model/volume';
+import { Volume } from '../../mol-model/volume';
 import { PluginContext } from '../../mol-plugin/context';
 import { RepresentationProvider } from '../../mol-repr/representation';
 import { VolumeRepresentationRegistry } from '../../mol-repr/volume/registry';
@@ -30,7 +30,7 @@ export interface VolumeRepresentationBuiltInProps<
 }
 
 export interface VolumeRepresentationProps<
-    R extends RepresentationProvider<VolumeData> = RepresentationProvider<VolumeData>,
+    R extends RepresentationProvider<Volume> = RepresentationProvider<Volume>,
     C extends ColorTheme.Provider = ColorTheme.Provider,
     S extends SizeTheme.Provider = SizeTheme.Provider> {
     type?: R,
@@ -41,43 +41,43 @@ export interface VolumeRepresentationProps<
     sizeParams?: Partial<SizeTheme.ParamValues<S>>
 }
 
-export function createVolumeRepresentationParams<R extends VolumeRepresentationRegistry.BuiltIn, C extends ColorTheme.BuiltIn, S extends SizeTheme.BuiltIn>(ctx: PluginContext, volume?: VolumeData, props?: VolumeRepresentationBuiltInProps<R, C, S>): StateTransformer.Params<VolumeRepresentation3D>
-export function createVolumeRepresentationParams<R extends RepresentationProvider<VolumeData>, C extends ColorTheme.Provider, S extends SizeTheme.Provider>(ctx: PluginContext, volume?: VolumeData, props?: VolumeRepresentationProps<R, C, S>): StateTransformer.Params<VolumeRepresentation3D>
-export function createVolumeRepresentationParams(ctx: PluginContext, volume?: VolumeData, props: any = {}): StateTransformer.Params<VolumeRepresentation3D>  {
+export function createVolumeRepresentationParams<R extends VolumeRepresentationRegistry.BuiltIn, C extends ColorTheme.BuiltIn, S extends SizeTheme.BuiltIn>(ctx: PluginContext, volume?: Volume, props?: VolumeRepresentationBuiltInProps<R, C, S>): StateTransformer.Params<VolumeRepresentation3D>
+export function createVolumeRepresentationParams<R extends RepresentationProvider<Volume>, C extends ColorTheme.Provider, S extends SizeTheme.Provider>(ctx: PluginContext, volume?: Volume, props?: VolumeRepresentationProps<R, C, S>): StateTransformer.Params<VolumeRepresentation3D>
+export function createVolumeRepresentationParams(ctx: PluginContext, volume?: Volume, props: any = {}): StateTransformer.Params<VolumeRepresentation3D>  {
     const p = props as VolumeRepresentationBuiltInProps;
-    if (typeof p.type === 'string' || typeof p.color === 'string' || typeof p.size === 'string') return createParamsByName(ctx, volume || VolumeData.One, props);
-    return createParamsProvider(ctx, volume || VolumeData.One, props);
+    if (typeof p.type === 'string' || typeof p.color === 'string' || typeof p.size === 'string') return createParamsByName(ctx, volume || Volume.One, props);
+    return createParamsProvider(ctx, volume || Volume.One, props);
 }
 
-export function getVolumeThemeTypes(ctx: PluginContext, volume?: VolumeData) {
+export function getVolumeThemeTypes(ctx: PluginContext, volume?: Volume) {
     const { themes: themeCtx } = ctx.representation.volume;
     if (!volume) return themeCtx.colorThemeRegistry.types;
     return themeCtx.colorThemeRegistry.getApplicableTypes({ volume });
 }
 
-export function createVolumeColorThemeParams<T extends ColorTheme.BuiltIn>(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName: T, params?: ColorTheme.BuiltInParams<T>): StateTransformer.Params<VolumeRepresentation3D>['colorTheme']
-export function createVolumeColorThemeParams(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['colorTheme']
-export function createVolumeColorThemeParams(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['colorTheme'] {
+export function createVolumeColorThemeParams<T extends ColorTheme.BuiltIn>(ctx: PluginContext, volume: Volume | undefined, typeName: string | undefined, themeName: T, params?: ColorTheme.BuiltInParams<T>): StateTransformer.Params<VolumeRepresentation3D>['colorTheme']
+export function createVolumeColorThemeParams(ctx: PluginContext, volume: Volume | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['colorTheme']
+export function createVolumeColorThemeParams(ctx: PluginContext, volume: Volume | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['colorTheme'] {
     const { registry, themes } = ctx.representation.volume;
     const repr = registry.get(typeName || registry.default.name);
     const color = themes.colorThemeRegistry.get(themeName || repr.defaultColorTheme.name);
-    const colorDefaultParams = PD.getDefaultValues(color.getParams({ volume: volume || VolumeData.One }));
+    const colorDefaultParams = PD.getDefaultValues(color.getParams({ volume: volume || Volume.One }));
     if (color.name === repr.defaultColorTheme.name) Object.assign(colorDefaultParams, repr.defaultColorTheme.props);
     return { name: color.name, params: Object.assign(colorDefaultParams, params) };
 }
 
-export function createVolumeSizeThemeParams<T extends SizeTheme.BuiltIn>(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName: T, params?: SizeTheme.BuiltInParams<T>): StateTransformer.Params<VolumeRepresentation3D>['sizeTheme']
-export function createVolumeSizeThemeParams(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['sizeTheme']
-export function createVolumeSizeThemeParams(ctx: PluginContext, volume: VolumeData | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['sizeTheme'] {
+export function createVolumeSizeThemeParams<T extends SizeTheme.BuiltIn>(ctx: PluginContext, volume: Volume | undefined, typeName: string | undefined, themeName: T, params?: SizeTheme.BuiltInParams<T>): StateTransformer.Params<VolumeRepresentation3D>['sizeTheme']
+export function createVolumeSizeThemeParams(ctx: PluginContext, volume: Volume | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['sizeTheme']
+export function createVolumeSizeThemeParams(ctx: PluginContext, volume: Volume | undefined, typeName: string | undefined, themeName?: string, params?: any): StateTransformer.Params<VolumeRepresentation3D>['sizeTheme'] {
     const { registry, themes } = ctx.representation.volume;
     const repr = registry.get(typeName || registry.default.name);
     const size = themes.sizeThemeRegistry.get(themeName || repr.defaultSizeTheme.name);
-    const sizeDefaultParams = PD.getDefaultValues(size.getParams({ volume: volume || VolumeData.One }));
+    const sizeDefaultParams = PD.getDefaultValues(size.getParams({ volume: volume || Volume.One }));
     if (size.name === repr.defaultSizeTheme.name) Object.assign(sizeDefaultParams, repr.defaultSizeTheme.props);
     return { name: size.name, params: Object.assign(sizeDefaultParams, params) };
 }
 
-function createParamsByName(ctx: PluginContext, volume: VolumeData, props: VolumeRepresentationBuiltInProps): StateTransformer.Params<VolumeRepresentation3D> {
+function createParamsByName(ctx: PluginContext, volume: Volume, props: VolumeRepresentationBuiltInProps): StateTransformer.Params<VolumeRepresentation3D> {
     const typeProvider = (props.type && ctx.representation.volume.registry.get(props.type))
         || ctx.representation.volume.registry.default.provider;
     const colorProvider = (props.color && ctx.representation.volume.themes.colorThemeRegistry.get(props.color))
@@ -95,7 +95,7 @@ function createParamsByName(ctx: PluginContext, volume: VolumeData, props: Volum
     });
 }
 
-function createParamsProvider(ctx: PluginContext, volume: VolumeData, props: VolumeRepresentationProps = {}): StateTransformer.Params<VolumeRepresentation3D> {
+function createParamsProvider(ctx: PluginContext, volume: Volume, props: VolumeRepresentationProps = {}): StateTransformer.Params<VolumeRepresentation3D> {
     const { themes: themeCtx } = ctx.representation.volume;
     const themeDataCtx = { volume };
 

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

@@ -204,9 +204,10 @@ namespace InteractivityManager {
         }
 
         selectOnly(current: Representation.Loci, applyGranularity = true) {
-            this.deselectAll();
             const normalized = this.normalizedLoci(current, applyGranularity);
             if (StructureElement.Loci.is(normalized.loci)) {
+                // only deselect for the structure of the given loci
+                this.deselect({ loci: Structure.toStructureElementLoci(normalized.loci.structure), repr: normalized.repr }, false);
                 this.sel.modify('set', normalized.loci);
             }
             this.mark(normalized, MarkerAction.Select);

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

@@ -231,6 +231,8 @@ class PluginStateSnapshotManager extends StatefulPluginComponent<{
 
                 if (PluginStateSnapshotManager.isStateSnapshot(snapshot)) {
                     return this.setStateSnapshot(snapshot);
+                } else if (PluginStateSnapshotManager.isStateSnapshot(snapshot.data)) {
+                    return this.setStateSnapshot(snapshot.data);
                 } else {
                     this.plugin.state.setSnapshot(snapshot);
                 }
@@ -330,7 +332,7 @@ namespace PluginStateSnapshotManager {
         snapshot: PluginState.Snapshot
     }
 
-    export function Entry(snapshot: PluginState.Snapshot, params: {name?: string, description?: string }): Entry {
+    export function Entry(snapshot: PluginState.Snapshot, params: { name?: string, description?: string }): Entry {
         return { timestamp: +new Date(), snapshot, ...params };
     }
 

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

@@ -13,13 +13,13 @@ import { EmptyLoci, Loci } from '../../../mol-model/loci';
 import { Structure, StructureElement, StructureSelection } from '../../../mol-model/structure';
 import { Boundary } from '../../../mol-model/structure/structure/util/boundary';
 import { PluginContext } from '../../../mol-plugin/context';
-import { StateObject, StateObjectRef } from '../../../mol-state';
+import { StateObjectRef } from '../../../mol-state';
 import { Task } from '../../../mol-task';
 import { structureElementStatsLabel } from '../../../mol-theme/label';
 import { arrayRemoveAtInPlace } from '../../../mol-util/array';
 import { StatefulPluginComponent } from '../../component';
 import { StructureSelectionQuery } from '../../helpers/structure-selection-query';
-import { PluginStateObject } from '../../objects';
+import { PluginStateObject as PSO } from '../../objects';
 import { UUID } from '../../../mol-util';
 import { StructureRef } from './hierarchy-state';
 
@@ -30,17 +30,23 @@ interface StructureSelectionManagerState {
 }
 
 const boundaryHelper = new BoundaryHelper('98');
-const HISTORY_CAPACITY = 8;
+const HISTORY_CAPACITY = 24;
 
 export type StructureSelectionModifier = 'add' | 'remove' | 'intersect' | 'set'
 
 export class StructureSelectionManager extends StatefulPluginComponent<StructureSelectionManagerState> {
     readonly events = {
         changed: this.ev<undefined>(),
-        additionsHistoryUpdated: this.ev<undefined>()
+        additionsHistoryUpdated: this.ev<undefined>(),
+
+        loci: {
+            add: this.ev<StructureElement.Loci>(),
+            remove: this.ev<StructureElement.Loci>(),
+            clear: this.ev<undefined>()
+        }
     }
 
-    private referenceLoci: Loci | undefined
+    private referenceLoci: StructureElement.Loci | undefined
 
     get entries() { return this.state.entries; }
     get additionsHistory() { return this.state.additionsHistory; }
@@ -51,7 +57,8 @@ export class StructureSelectionManager extends StatefulPluginComponent<Structure
     }
 
     private getEntry(s: Structure) {
-        const cell = this.plugin.helpers.substructureParent.get(s);
+        // ignore decorators to get stable ref
+        const cell = this.plugin.helpers.substructureParent.get(s, true);
         if (!cell) return;
         const ref = cell.transform.ref;
         if (!this.entries.has(ref)) {
@@ -94,6 +101,7 @@ export class StructureSelectionManager extends StatefulPluginComponent<Structure
         entry.selection = StructureElement.Loci.union(entry.selection, loci);
         this.tryAddHistory(loci);
         this.referenceLoci = loci;
+        this.events.loci.add.next(loci);
         return !StructureElement.Loci.areEqual(sel, entry.selection);
     }
 
@@ -107,6 +115,7 @@ export class StructureSelectionManager extends StatefulPluginComponent<Structure
         entry.selection = StructureElement.Loci.subtract(entry.selection, loci);
         // this.addHistory(loci);
         this.referenceLoci = loci;
+        this.events.loci.remove.next(loci);
         return !StructureElement.Loci.areEqual(sel, entry.selection);
     }
 
@@ -136,26 +145,34 @@ export class StructureSelectionManager extends StatefulPluginComponent<Structure
         return !StructureElement.Loci.areEqual(sel, entry.selection);
     }
 
-    modifyHistory(entry: StructureSelectionHistoryEntry, action: 'remove' | 'up' | 'down', modulus?: number) {
-        const idx = this.additionsHistory.indexOf(entry);
+    modifyHistory(entry: StructureSelectionHistoryEntry, action: 'remove' | 'up' | 'down', modulus?: number, groupByStructure = false) {
+        const history = this.additionsHistory;
+        const idx = history.indexOf(entry);
         if (idx < 0) return;
 
         let swapWith: number | undefined = void 0;
 
         switch (action) {
-            case 'remove': arrayRemoveAtInPlace(this.additionsHistory, idx); break;
+            case 'remove': arrayRemoveAtInPlace(history, idx); break;
             case 'up': swapWith = idx - 1; break;
             case 'down': swapWith = idx + 1; break;
         }
 
         if (swapWith !== void 0) {
-            const mod = modulus ? Math.min(this.additionsHistory.length, modulus) : this.additionsHistory.length;
-            swapWith = swapWith % mod;
-            if (swapWith < 0) swapWith += mod;
+            const mod = modulus ? Math.min(history.length, modulus) : history.length;
+            while (true) {
+                swapWith = swapWith % mod;
+                if (swapWith < 0) swapWith += mod;
 
-            const t = this.additionsHistory[idx];
-            this.additionsHistory[idx] = this.additionsHistory[swapWith];
-            this.additionsHistory[swapWith] = t;
+                if (!groupByStructure || history[idx].loci.structure === history[swapWith].loci.structure) {
+                    const t = history[idx];
+                    history[idx] = history[swapWith];
+                    history[swapWith] = t;
+                    break;
+                } else {
+                    swapWith += action === 'up' ? -1 : +1;
+                }
+            }
         }
 
         this.events.additionsHistoryUpdated.next();
@@ -190,33 +207,88 @@ export class StructureSelectionManager extends StatefulPluginComponent<Structure
         this.events.additionsHistoryUpdated.next();
     }
 
-    private onRemove(ref: string) {
-        if (this.entries.has(ref)) {
-            this.entries.delete(ref);
-            // TODO: property update the latest loci
+    private clearHistory() {
+        if (this.state.additionsHistory.length !== 0) {
             this.state.additionsHistory = [];
-            this.referenceLoci = undefined;
+            this.events.additionsHistoryUpdated.next();
         }
     }
 
-    private onUpdate(ref: string, oldObj: StateObject | undefined, obj: StateObject) {
-        if (!PluginStateObject.Molecule.Structure.is(obj)) return;
+    private clearHistoryForStructure(structure: Structure) {
+        const historyEntryToRemove: StructureSelectionHistoryEntry[] = [];
+        for (const e of this.state.additionsHistory) {
+            if (e.loci.structure.root === structure.root) {
+                historyEntryToRemove.push(e);
+            }
+        }
+        for (const e of historyEntryToRemove) {
+            this.modifyHistory(e, 'remove');
+        }
+        if (historyEntryToRemove.length !== 0) {
+            this.events.additionsHistoryUpdated.next();
+        }
+    }
 
+    private onRemove(ref: string, obj: PSO.Molecule.Structure | undefined) {
         if (this.entries.has(ref)) {
-            if (!PluginStateObject.Molecule.Structure.is(oldObj) || oldObj === obj || oldObj.data === obj.data) return;
+            this.entries.delete(ref);
+            if (obj?.data) {
+                this.clearHistoryForStructure(obj.data);
+            }
+            if (this.referenceLoci?.structure === obj?.data) {
+                this.referenceLoci = undefined;
+            }
+            this.state.stats = void 0;
+            this.events.changed.next();
+        }
+    }
 
-            // TODO: property update the latest loci & reference loci
-            this.state.additionsHistory = [];
-            this.referenceLoci = undefined;
+    private onUpdate(ref: string, oldObj: PSO.Molecule.Structure | undefined, obj: PSO.Molecule.Structure) {
 
-            // remap the old selection to be related to the new object if possible.
-            if (Structure.areUnitAndIndicesEqual(oldObj.data, obj.data)) {
-                this.entries.set(ref, remapSelectionEntry(this.entries.get(ref)!, obj.data));
-                return;
+        // no change to structure
+        if (oldObj === obj || oldObj?.data === obj.data) return;
+
+        // ignore decorators to get stable ref
+        const cell = this.plugin.helpers.substructureParent.get(obj.data, true);
+        if (!cell) return;
+
+        ref = cell.transform.ref;
+        if (!this.entries.has(ref)) return;
+
+        // use structure from last decorator as reference
+        const structure = this.plugin.helpers.substructureParent.get(obj.data)?.obj?.data;
+        if (!structure) return;
+
+        // oldObj is not defined for inserts (e.g. TransformStructureConformation)
+        if (!oldObj || Structure.areUnitAndIndicesEqual(oldObj.data, obj.data)) {
+            this.entries.set(ref, remapSelectionEntry(this.entries.get(ref)!, structure));
+
+            // remap referenceLoci & prevHighlight if needed and possible
+            if (this.referenceLoci?.structure.root === structure.root) {
+                this.referenceLoci = StructureElement.Loci.remap(this.referenceLoci, structure);
             }
 
-            // clear the selection
-            this.entries.set(ref, new SelectionEntry(StructureElement.Loci(obj.data, [])));
+            // remap history locis if needed and possible
+            let changedHistory = false;
+            for (const e of this.state.additionsHistory) {
+                if (e.loci.structure.root === structure.root) {
+                    e.loci = StructureElement.Loci.remap(e.loci, structure);
+                    changedHistory = true;
+                }
+            }
+            if (changedHistory) this.events.additionsHistoryUpdated.next();
+        } else {
+            // clear the selection for ref
+            this.entries.set(ref, new SelectionEntry(StructureElement.Loci(structure, [])));
+
+            if (this.referenceLoci?.structure.root === structure.root) {
+                this.referenceLoci = undefined;
+            }
+
+            this.clearHistoryForStructure(structure);
+
+            this.state.stats = void 0;
+            this.events.changed.next();
         }
     }
 
@@ -234,6 +306,8 @@ export class StructureSelectionManager extends StatefulPluginComponent<Structure
         this.referenceLoci = undefined;
         this.state.stats = void 0;
         this.events.changed.next();
+        this.events.loci.clear.next();
+        this.clearHistory();
         return selections;
     }
 
@@ -276,7 +350,7 @@ export class StructureSelectionManager extends StatefulPluginComponent<Structure
         if (!xs) return;
 
         const ref = this.referenceLoci;
-        if (!ref || !StructureElement.Loci.is(ref) || ref.structure.root !== loci.structure.root) return;
+        if (!ref || !StructureElement.Loci.is(ref) || ref.structure !== loci.structure) return;
 
         let e: StructureElement.Loci['elements'][0] | undefined;
         for (const _e of ref.elements) {
@@ -289,26 +363,7 @@ export class StructureSelectionManager extends StatefulPluginComponent<Structure
 
         if (xs.unit !== e.unit) return;
 
-        return getElementRange(loci.structure.root, e, xs);
-    }
-
-    private prevHighlight: StructureElement.Loci | undefined = void 0;
-
-    accumulateInteractiveHighlight(loci: Loci) {
-        if (StructureElement.Loci.is(loci)) {
-            if (this.prevHighlight) {
-                this.prevHighlight = StructureElement.Loci.union(this.prevHighlight, loci);
-            } else {
-                this.prevHighlight = loci;
-            }
-        }
-        return this.prevHighlight;
-    }
-
-    clearInteractiveHighlight() {
-        const ret = this.prevHighlight;
-        this.prevHighlight = void 0;
-        return ret || EmptyLoci;
+        return getElementRange(loci.structure, e, xs);
     }
 
     /** Count of all selected elements */
@@ -411,11 +466,11 @@ export class StructureSelectionManager extends StatefulPluginComponent<Structure
         }));
     }
 
-    fromSelections(ref: StateObjectRef<PluginStateObject.Molecule.Structure.Selections>) {
+    fromSelections(ref: StateObjectRef<PSO.Molecule.Structure.Selections>) {
         const cell = StateObjectRef.resolveAndCheck(this.plugin.state.data, ref);
         if (!cell || !cell.obj) return;
 
-        if (!PluginStateObject.Molecule.Structure.Selections.is(cell.obj)) {
+        if (!PSO.Molecule.Structure.Selections.is(cell.obj)) {
             console.warn('fromSelections applied to wrong object type.', cell.obj);
             return;
         }
@@ -429,8 +484,9 @@ export class StructureSelectionManager extends StatefulPluginComponent<Structure
     constructor(private plugin: PluginContext) {
         super({ entries: new Map(), additionsHistory: [], stats: SelectionStats() });
 
-        plugin.state.data.events.object.removed.subscribe(e => this.onRemove(e.ref));
-        plugin.state.data.events.object.updated.subscribe(e => this.onUpdate(e.ref, e.oldObj, e.obj));
+        // listen to events from substructureParent helper to ensure it is updated
+        plugin.helpers.substructureParent.events.removed.subscribe(e => this.onRemove(e.ref, e.obj));
+        plugin.helpers.substructureParent.events.updated.subscribe(e => this.onUpdate(e.ref, e.oldObj, e.obj));
     }
 }
 

src/mol-plugin-state/objects.ts

@@ -14,7 +14,7 @@ import { PlyFile } from '../mol-io/reader/ply/schema';
 import { PsfFile } from '../mol-io/reader/psf/parser';
 import { ShapeProvider } from '../mol-model/shape/provider';
 import { Coordinates as _Coordinates, Model as _Model, Structure as _Structure, StructureElement, Topology as _Topology } from '../mol-model/structure';
-import { VolumeData } from '../mol-model/volume';
+import { Volume as _Volume } from '../mol-model/volume';
 import { PluginBehavior } from '../mol-plugin/behavior/behavior';
 import { Representation } from '../mol-repr/representation';
 import { ShapeRepresentation } from '../mol-repr/shape/representation';
@@ -121,7 +121,7 @@ export namespace PluginStateObject {
     }
 
     export namespace Volume {
-        export class Data extends Create<VolumeData>({ name: 'Volume Data', typeClass: 'Object' }) { }
+        export class Data extends Create<_Volume>({ name: 'Volume', typeClass: 'Object' }) { }
         export class Representation3D extends CreateRepresentation3D<VolumeRepresentation<any>>({ name: 'Volume 3D' }) { }
     }
 

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

@@ -6,7 +6,7 @@
  */
 
 import { Structure, StructureElement } from '../../mol-model/structure';
-import { VolumeData, VolumeIsoValue } from '../../mol-model/volume';
+import { Volume } from '../../mol-model/volume';
 import { PluginContext } from '../../mol-plugin/context';
 import { VolumeRepresentationRegistry } from '../../mol-repr/volume/registry';
 import { VolumeParams } from '../../mol-repr/volume/representation';
@@ -441,7 +441,7 @@ const TransparencyStructureRepresentation3DFromBundle = PluginStateTransform.Bui
 //
 
 export namespace VolumeRepresentation3DHelpers {
-    export function getDefaultParams(ctx: PluginContext, name: VolumeRepresentationRegistry.BuiltIn, volume: VolumeData, volumeParams?: Partial<PD.Values<VolumeParams>>): StateTransformer.Params<VolumeRepresentation3D> {
+    export function getDefaultParams(ctx: PluginContext, name: VolumeRepresentationRegistry.BuiltIn, volume: Volume, volumeParams?: Partial<PD.Values<VolumeParams>>): StateTransformer.Params<VolumeRepresentation3D> {
         const type = ctx.representation.volume.registry.get(name);
 
         const themeDataCtx = { volume };
@@ -467,7 +467,7 @@ export namespace VolumeRepresentation3DHelpers {
     }
 
     export function getDescription(props: any) {
-        return props.isoValue && VolumeIsoValue.toString(props.isoValue);
+        return props.isoValue && Volume.IsoValue.toString(props.isoValue);
     }
 }
 type VolumeRepresentation3D = typeof VolumeRepresentation3D
@@ -485,16 +485,16 @@ const VolumeRepresentation3D = PluginStateTransform.BuiltIn({
                 type: PD.Mapped<any>(
                     registry.default.name,
                     registry.types,
-                    name => PD.Group<any>(registry.get(name).getParams(themeCtx, VolumeData.One))),
+                    name => PD.Group<any>(registry.get(name).getParams(themeCtx, Volume.One))),
                 colorTheme: PD.Mapped<any>(
                     type.defaultColorTheme.name,
                     themeCtx.colorThemeRegistry.types,
-                    name => PD.Group<any>(themeCtx.colorThemeRegistry.get(name).getParams({ volume: VolumeData.One }))
+                    name => PD.Group<any>(themeCtx.colorThemeRegistry.get(name).getParams({ volume: Volume.One }))
                 ),
                 sizeTheme: PD.Mapped<any>(
                     type.defaultSizeTheme.name,
                     themeCtx.sizeThemeRegistry.types,
-                    name => PD.Group<any>(themeCtx.sizeThemeRegistry.get(name).getParams({ volume: VolumeData.One }))
+                    name => PD.Group<any>(themeCtx.sizeThemeRegistry.get(name).getParams({ volume: Volume.One }))
                 )
             };
         }

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

@@ -15,7 +15,7 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { PluginStateObject as SO, PluginStateTransform } from '../objects';
 import { volumeFromCube } from '../../mol-model-formats/volume/cube';
 import { volumeFromDx } from '../../mol-model-formats/volume/dx';
-import { VolumeData } from '../../mol-model/volume';
+import {  Volume } from '../../mol-model/volume';
 import { PluginContext } from '../../mol-plugin/context';
 import { StateSelection } from '../../mol-state';
 
@@ -42,7 +42,7 @@ const VolumeFromCcp4 = PluginStateTransform.BuiltIn({
     apply({ a, params }) {
         return Task.create('Create volume from CCP4/MRC/MAP', async ctx => {
             const volume = await volumeFromCcp4(a.data, { ...params, label: a.data.name || a.label }).runInContext(ctx);
-            const props = { label: volume.label || 'Volume', description: 'Volume' };
+            const props = { label: volume.label || 'Volume', description: `Volume ${a.data.header.NX}\u00D7${a.data.header.NX}\u00D7${a.data.header.NX}` };
             return new SO.Volume.Data(volume, props);
         });
     }
@@ -63,7 +63,7 @@ const VolumeFromDsn6 = PluginStateTransform.BuiltIn({
     apply({ a, params }) {
         return Task.create('Create volume from DSN6/BRIX', async ctx => {
             const volume = await volumeFromDsn6(a.data, { ...params, label: a.data.name || a.label }).runInContext(ctx);
-            const props = { label: volume.label || 'Volume', description: 'Volume' };
+            const props = { label: volume.label || 'Volume', description: `Volume ${a.data.header.xExtent}\u00D7${a.data.header.yExtent}\u00D7${a.data.header.zExtent}` };
             return new SO.Volume.Data(volume, props);
         });
     }
@@ -85,7 +85,7 @@ const VolumeFromCube = PluginStateTransform.BuiltIn({
     apply({ a, params }) {
         return Task.create('Create volume from Cube', async ctx => {
             const volume = await volumeFromCube(a.data, { ...params, label: a.data.name || a.label }).runInContext(ctx);
-            const props = { label: volume.label || 'Volume', description: 'Volume' };
+            const props = { label: volume.label || 'Volume', description: `Volume ${a.data.header.dim[0]}\u00D7${a.data.header.dim[1]}\u00D7${a.data.header.dim[2]}` };
             return new SO.Volume.Data(volume, props);
         });
     }
@@ -102,8 +102,7 @@ const VolumeFromDx = PluginStateTransform.BuiltIn({
         return Task.create('Parse DX', async ctx => {
             console.log(a);
             const volume = await volumeFromDx(a.data, { label: a.data.name || a.label }).runInContext(ctx);
-            console.log(volume);
-            const props = { label: volume.label || 'Volume', description: 'Volume' };
+            const props = { label: volume.label || 'Volume', description: `Volume ${a.data.header.dim[0]}\u00D7${a.data.header.dim[1]}\u00D7${a.data.header.dim[2]}` };
             return new SO.Volume.Data(volume, props);
         });
     }
@@ -135,7 +134,8 @@ const VolumeFromDensityServerCif = PluginStateTransform.BuiltIn({
             if (!block) throw new Error(`Data block '${[header]}' not found.`);
             const densityServerCif = CIF.schema.densityServer(block);
             const volume = await volumeFromDensityServerData(densityServerCif).runInContext(ctx);
-            const props = { label: densityServerCif.volume_data_3d_info.name.value(0), description: `${densityServerCif.volume_data_3d_info.name.value(0)}` };
+            const [x, y, z] = volume.grid.cells.space.dimensions;
+            const props = { label: densityServerCif.volume_data_3d_info.name.value(0), description: `Volume ${x}\u00D7${y}\u00D7${z}` };
             return new SO.Volume.Data(volume, props);
         });
     }
@@ -160,8 +160,8 @@ const AssignColorVolume = PluginStateTransform.BuiltIn({
             if (!dependencies || !dependencies[params.ref]) {
                 throw new Error('Dependency not available.');
             }
-            const colorVolume = dependencies[params.ref].data as VolumeData;
-            const volume: VolumeData = {
+            const colorVolume = dependencies[params.ref].data as Volume;
+            const volume: Volume = {
                 ...a.data,
                 colorVolume
             };

src/mol-plugin-ui/controls.tsx

@@ -30,6 +30,7 @@ import { StructureSelectionActionsControls } from './structure/selection';
 import { StructureSourceControls } from './structure/source';
 import { VolumeStreamingControls, VolumeSourceControls } from './structure/volume';
 import { PluginConfig } from '../mol-plugin/config';
+import { StructureSuperpositionControls } from './structure/superposition';
 
 export class TrajectoryViewportControls extends PluginUIComponent<{}, { show: boolean, label: string }> {
     state = { show: false, label: '' }
@@ -296,6 +297,7 @@ export class DefaultStructureTools extends PluginUIComponent {
 
             <StructureSourceControls />
             <StructureMeasurementsControls />
+            <StructureSuperpositionControls />
             <StructureComponentControls />
             <VolumeStreamingControls />
             <VolumeSourceControls />

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

@@ -34,10 +34,22 @@ export class CombinedColorControl extends React.PureComponent<ParamProps<PD.Colo
         }
     }
 
-    onChangeText = (value: Color) => {
-        if (value !== this.props.value) {
-            this.update(value);
-        }
+    onR = (v: number) => {
+        const [, g, b] = Color.toRgb(this.props.value);
+        const value = Color.fromRgb(v, g, b);
+        if (value !== this.props.value) this.update(value);
+    }
+
+    onG = (v: number) => {
+        const [r, , b] = Color.toRgb(this.props.value);
+        const value = Color.fromRgb(r, v, b);
+        if (value !== this.props.value) this.update(value);
+    }
+
+    onB = (v: number) => {
+        const [r, g, ] = Color.toRgb(this.props.value);
+        const value = Color.fromRgb(r, g, v);
+        if (value !== this.props.value) this.update(value);
     }
 
     swatch() {
@@ -49,44 +61,23 @@ export class CombinedColorControl extends React.PureComponent<ParamProps<PD.Colo
 
     render() {
         const label = this.props.param.label || camelCaseToWords(this.props.name);
+        const [r, g, b] = Color.toRgb(this.props.value);
         return <>
             <ControlRow title={this.props.param.description}
                 label={label}
                 control={<Button onClick={this.toggleExpanded} inline className='msp-combined-color-button' style={{ background: Color.toStyle(this.props.value) }} />} />
             {this.state.isExpanded && <div className='msp-control-offset'>
                 {this.swatch()}
-                <ControlRow label='RGB'
-                    control={<TextInput onChange={this.onChangeText} value={this.props.value}
-                        fromValue={formatColorRGB} toValue={getColorFromString} isValid={isValidColorString}
-                        className='msp-form-control' onEnter={this.props.onEnter} blurOnEnter={true} blurOnEscape={true}
-                        placeholder='e.g. 127 127 127' delayMs={250} />} />
+                <ControlRow label='RGB' control={<div style={{ display: 'flex', textAlignLast: 'center' }}>
+                    <TextInput onChange={this.onR} numeric value={r} delayMs={250} style={{ order: 1, flex: '1 1 auto', minWidth: 0 }} className='msp-form-control' onEnter={this.props.onEnter} blurOnEnter={true} blurOnEscape={true} />
+                    <TextInput onChange={this.onG} numeric value={g} delayMs={250} style={{ order: 2, flex: '1 1 auto', minWidth: 0 }} className='msp-form-control' onEnter={this.props.onEnter} blurOnEnter={true} blurOnEscape={true} />
+                    <TextInput onChange={this.onB} numeric value={b} delayMs={250} style={{ order: 3, flex: '1 1 auto', minWidth: 0 }} className='msp-form-control' onEnter={this.props.onEnter} blurOnEnter={true} blurOnEscape={true} />
+                </div>}/>
             </div>}
         </>;
     }
 }
 
-function formatColorRGB(c: Color) {
-    const [r, g, b] = Color.toRgb(c);
-    return `${r} ${g} ${b}`;
-}
-
-function getColorFromString(s: string) {
-    const cs = s.split(/\s+/g);
-    return Color.fromRgb(+cs[0], +cs[1], +cs[2]);
-}
-
-function isValidColorString(s: string) {
-    const cs = s.split(/\s+/g);
-    if (cs.length !== 3 && !(cs.length === 4 && cs[3] === '')) return false;
-    for (const c of cs) {
-        if (c === '') continue;
-        const n = +c;
-        if ('' + n !== c) return false;
-        if (n < 0 || n > 255) return false;
-    }
-    return true;
-}
-
 let _colors: React.ReactFragment | undefined = void 0;
 export function ColorOptions() {
     if (_colors) return _colors;

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

@@ -24,7 +24,8 @@ export class ControlGroup extends React.Component<{
     headerLeftMargin?: string,
     onHeaderClick?: () => void,
     noTopMargin?: boolean,
-    childrenClassName?: string
+    childrenClassName?: string,
+    maxHeight?: string
 }, { isExpanded: boolean }> {
     state = { isExpanded: !!this.props.initialExpanded }
 
@@ -49,7 +50,7 @@ export class ControlGroup extends React.Component<{
                     <b>{this.props.header}</b>
                 </Button>
             </div>
-            {this.state.isExpanded && <div className={groupClassName} style={{ display: this.state.isExpanded ? 'block' : 'none' }}>
+            {this.state.isExpanded && <div className={groupClassName} style={{ display: this.state.isExpanded ? 'block' : 'none', maxHeight: this.props.maxHeight, overflow: 'hidden', overflowY: 'auto' }}>
                 {this.props.children}
             </div>}
         </div>;

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

@@ -21,13 +21,14 @@ export function Icon(props: {
 
 //
 
-export function Union() { return _union; }
-export function Subtract() { return _subtract; }
-export function Intersect() { return _intersect; }
+export function UnionSvg() { return _union; }
+export function SubtractSvg() { return _subtract; }
+export function IntersectSvg() { return _intersect; }
 export function SetSvg() { return _set; }
 export function MoleculeSvg() { return _molecule; }
 export function RulerSvg() { return _ruler; }
 export function CubeSvg() { return _cube; }
+export function CursorSvg() { return _cursor; }
 
 const circleLeft = <circle r="6px" id="circle-left" cy="12px" cx="8px" strokeWidth="1" />;
 const circleRight = <circle r="6px" id="circle-right" cy="12px" cx="16px" strokeWidth="1" />;
@@ -87,64 +88,25 @@ const _set = <svg width="24px" height="24px" viewBox="0 0 24 24">
 
 const _molecule = <svg width="17px" height="17px" viewBox="0 0 299.463 299.463">
     <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"/>
+        <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 _ruler = <svg viewBox="0 0 508.073 508.073" width="17px" height="17px">
     <g>
-        <path d="M470.459,378.925c-0.7-2.1-1.9-4-3.4-5.5l-113.9-113.9l149.8-149.8c10-10,2.6-17.3,0-19.9l-85.7-85.7
-			c-5.5-5.5-14.4-5.5-19.9,0l-149.8,149.8l-134.7-134.7c-25.5-25.5-67.8-25.6-93.4,0c-25.8,25.8-25.8,67.7,0,93.5l134.6,134.7
-			l-149.9,149.9c-5.5,5.5-5.5,14.4,0,19.9l85.6,85.7c2.6,2.6,10,10,19.9,0l150-149.9l113.9,113.9c1.5,1.5,3.4,2.7,5.5,3.4
-			l110.4,36.9c6,2,10.7,0.3,14.4-3.4c3.8-3.8,5.1-9.4,3.4-14.4L470.459,378.925z M276.159,165.225l29.9,29.9
-			c5.5,5.5,14.4,5.5,19.9,0c5-5,5.5-14.4,0-19.9l-29.9-29.9l23.7-23.7l13,13c5.5,5.5,14.4,5.5,19.9,0c5.2-5.2,6.2-13.7,0-19.9
-			l-13-13l23.7-23.7l29.4,29.4c5.5,5.5,14.4,5.5,19.9,0c5.6-5.6,5.5-14.4,0-19.9l-29.4-29.5l24-24l65.8,65.7l-139.8,139.9
-			l-65.8-65.8L276.159,165.225z M39.359,92.825c-14.8-14.8-14.8-38.8,0-53.6c14.1-14.1,38.8-14.7,53.6,0l15.5,15.5l-53.6,53.6
-			L39.359,92.825z M99.759,473.025l-65.7-65.7l24-24l13.2,13.2c5.5,5.5,14.4,5.6,19.9,0c5.5-5.5,5.5-14.4,0-19.9l-13.1-13.3
-			l23.7-23.7l29.6,29.6c6.2,6.2,14.7,5.2,19.9,0c5.5-5.5,5.5-14.4,0-19.9l-29.6-29.6l23.7-23.7l13.2,13.2c5.5,5.5,14.9,5,19.9,0
-			c5.5-5.5,5.5-14.4,0-19.9l-13.2-13.2l8.8-8.8l65.8,65.7L99.759,473.025z M74.759,128.225l53.6-53.6l308.7,308.7l-53.6,53.6
-			L74.759,128.225z M409.659,450.725l41.3-41.3l20.7,61.9L409.659,450.725z"/>
+        <path d="M470.459,378.925c-0.7-2.1-1.9-4-3.4-5.5l-113.9-113.9l149.8-149.8c10-10,2.6-17.3,0-19.9l-85.7-85.7 c-5.5-5.5-14.4-5.5-19.9,0l-149.8,149.8l-134.7-134.7c-25.5-25.5-67.8-25.6-93.4,0c-25.8,25.8-25.8,67.7,0,93.5l134.6,134.7 l-149.9,149.9c-5.5,5.5-5.5,14.4,0,19.9l85.6,85.7c2.6,2.6,10,10,19.9,0l150-149.9l113.9,113.9c1.5,1.5,3.4,2.7,5.5,3.4 l110.4,36.9c6,2,10.7,0.3,14.4-3.4c3.8-3.8,5.1-9.4,3.4-14.4L470.459,378.925z M276.159,165.225l29.9,29.9 c5.5,5.5,14.4,5.5,19.9,0c5-5,5.5-14.4,0-19.9l-29.9-29.9l23.7-23.7l13,13c5.5,5.5,14.4,5.5,19.9,0c5.2-5.2,6.2-13.7,0-19.9 l-13-13l23.7-23.7l29.4,29.4c5.5,5.5,14.4,5.5,19.9,0c5.6-5.6,5.5-14.4,0-19.9l-29.4-29.5l24-24l65.8,65.7l-139.8,139.9 l-65.8-65.8L276.159,165.225z M39.359,92.825c-14.8-14.8-14.8-38.8,0-53.6c14.1-14.1,38.8-14.7,53.6,0l15.5,15.5l-53.6,53.6 L39.359,92.825z M99.759,473.025l-65.7-65.7l24-24l13.2,13.2c5.5,5.5,14.4,5.6,19.9,0c5.5-5.5,5.5-14.4,0-19.9l-13.1-13.3 l23.7-23.7l29.6,29.6c6.2,6.2,14.7,5.2,19.9,0c5.5-5.5,5.5-14.4,0-19.9l-29.6-29.6l23.7-23.7l13.2,13.2c5.5,5.5,14.9,5,19.9,0 c5.5-5.5,5.5-14.4,0-19.9l-13.2-13.2l8.8-8.8l65.8,65.7L99.759,473.025z M74.759,128.225l53.6-53.6l308.7,308.7l-53.6,53.6 L74.759,128.225z M409.659,450.725l41.3-41.3l20.7,61.9L409.659,450.725z"/>
     </g>
 </svg>;
 
 const _cube = <svg viewBox="0 0 270.06 270.06" width="17px" height="17px">
     <g>
-        <path d="M264.898,0.007
-c-0.181,0.006-0.362,0.023-0.541,0.049H84.996c-1.326,0-2.598,0.527-3.535,1.465l-80,80C0.525,82.459-0.001,83.73,0,85.056v180
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-M87.066,10.056h165.859l-70,70H17.066L87.066,10.056z M259.996,17.126v165.859l-70,70V87.126L259.996,17.126L259.996,17.126z
-M84.92,19.985c-2.759,0.042-4.963,2.311-4.924,5.07v40c-0.039,2.761,2.168,5.032,4.929,5.071s5.032-2.168,5.071-4.929
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-c-1.992,1.913-2.057,5.078-0.144,7.07c1.913,1.992,5.078,2.057,7.07,0.144c0.049-0.047,0.097-0.095,0.144-0.144l18.535-18.535h17.93
-c2.761,0.039,5.032-2.168,5.071-4.929s-2.168-5.032-4.929-5.071c-0.047-0.001-0.094-0.001-0.141,0h-15v-15
-c0.039-2.761-2.168-5.031-4.93-5.07C85.018,159.984,84.969,159.984,84.92,159.985z M134.996,180.055
-c-2.761-0.039-5.032,2.168-5.071,4.929c-0.039,2.761,2.168,5.032,4.929,5.071c0.047,0.001,0.094,0.001,0.141,0h30
-c2.761,0.039,5.032-2.168,5.071-4.929c0.039-2.761-2.168-5.032-4.929-5.071c-0.047-0.001-0.094-0.001-0.141,0H134.996z
-M204.996,180.055c-2.761-0.039-5.032,2.168-5.071,4.929c-0.039,2.761,2.168,5.032,4.929,5.071c0.047,0.001,0.094,0.001,0.141,0h40
-c2.761,0.039,5.032-2.168,5.071-4.929s-2.168-5.032-4.929-5.071c-0.047-0.001-0.094-0.001-0.141,0H204.996z M44.898,220.007
-c-1.299,0.039-2.532,0.582-3.438,1.514l-20,20c-1.992,1.913-2.057,5.078-0.144,7.07c1.913,1.992,5.078,2.057,7.07,0.144
-c0.049-0.047,0.097-0.095,0.144-0.144l20-20c1.98-1.925,2.025-5.091,0.1-7.071C47.654,220.514,46.3,219.965,44.898,220.007z"/>
+        <path d="M264.898,0.007 c-0.181,0.006-0.362,0.023-0.541,0.049H84.996c-1.326,0-2.598,0.527-3.535,1.465l-80,80C0.525,82.459-0.001,83.73,0,85.056v180 c0,2.761,2.239,5,5,5h180c1.326,0,2.598-0.527,3.535-1.465l80-80c0.938-0.938,1.465-2.209,1.465-3.535V5.819 c0.14-0.893,0.035-1.807-0.303-2.645c-0.016-0.045-0.033-0.09-0.051-0.135c-0.808-1.89-2.69-3.093-4.744-3.033L264.898,0.007z M87.066,10.056h165.859l-70,70H17.066L87.066,10.056z M259.996,17.126v165.859l-70,70V87.126L259.996,17.126L259.996,17.126z M84.92,19.985c-2.759,0.042-4.963,2.311-4.924,5.07v40c-0.039,2.761,2.168,5.032,4.929,5.071s5.032-2.168,5.071-4.929 c0.001-0.047,0.001-0.094,0-0.141v-40c0.039-2.761-2.168-5.031-4.93-5.07C85.018,19.984,84.969,19.984,84.92,19.985z M9.996,90.056 h170v170h-170V90.056L9.996,90.056z M84.92,99.985c-2.759,0.042-4.963,2.311-4.924,5.07v30c-0.039,2.761,2.168,5.032,4.929,5.071 s5.032-2.168,5.071-4.929c0.001-0.047,0.001-0.094,0-0.141v-30c0.039-2.761-2.168-5.031-4.93-5.07 C85.018,99.984,84.969,99.984,84.92,99.985z M84.92,159.985c-2.759,0.042-4.963,2.311-4.924,5.07v17.93L61.461,201.52 c-1.992,1.913-2.057,5.078-0.144,7.07c1.913,1.992,5.078,2.057,7.07,0.144c0.049-0.047,0.097-0.095,0.144-0.144l18.535-18.535h17.93 c2.761,0.039,5.032-2.168,5.071-4.929s-2.168-5.032-4.929-5.071c-0.047-0.001-0.094-0.001-0.141,0h-15v-15 c0.039-2.761-2.168-5.031-4.93-5.07C85.018,159.984,84.969,159.984,84.92,159.985z M134.996,180.055 c-2.761-0.039-5.032,2.168-5.071,4.929c-0.039,2.761,2.168,5.032,4.929,5.071c0.047,0.001,0.094,0.001,0.141,0h30 c2.761,0.039,5.032-2.168,5.071-4.929c0.039-2.761-2.168-5.032-4.929-5.071c-0.047-0.001-0.094-0.001-0.141,0H134.996z M204.996,180.055c-2.761-0.039-5.032,2.168-5.071,4.929c-0.039,2.761,2.168,5.032,4.929,5.071c0.047,0.001,0.094,0.001,0.141,0h40 c2.761,0.039,5.032-2.168,5.071-4.929s-2.168-5.032-4.929-5.071c-0.047-0.001-0.094-0.001-0.141,0H204.996z M44.898,220.007 c-1.299,0.039-2.532,0.582-3.438,1.514l-20,20c-1.992,1.913-2.057,5.078-0.144,7.07c1.913,1.992,5.078,2.057,7.07,0.144 c0.049-0.047,0.097-0.095,0.144-0.144l20-20c1.98-1.925,2.025-5.091,0.1-7.071C47.654,220.514,46.3,219.965,44.898,220.007z"/>
     </g>
+</svg>;
+
+// Icons below are adapted from https://materialdesignicons.com/ and
+// licensed with https://github.com/Templarian/MaterialDesign/blob/master/LICENSE
+
+const _cursor = <svg width="24px" height="24px" viewBox="0 0 24 24">
+    <path d="M10.07,14.27C10.57,14.03 11.16,14.25 11.4,14.75L13.7,19.74L15.5,18.89L13.19,13.91C12.95,13.41 13.17,12.81 13.67,12.58L13.95,12.5L16.25,12.05L8,5.12V15.9L9.82,14.43L10.07,14.27M13.64,21.97C13.14,22.21 12.54,22 12.31,21.5L10.13,16.76L7.62,18.78C7.45,18.92 7.24,19 7,19A1,1 0 0,1 6,18V3A1,1 0 0,1 7,2C7.24,2 7.47,2.09 7.64,2.23L7.65,2.22L19.14,11.86C19.57,12.22 19.62,12.85 19.27,13.27C19.12,13.45 18.91,13.57 18.7,13.61L15.54,14.23L17.74,18.96C18,19.46 17.76,20.05 17.26,20.28L13.64,21.97Z" />
 </svg>;

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

@@ -1073,7 +1073,7 @@ export class MappedControl extends React.PureComponent<ParamProps<PD.Mapped<any>
 
 type ObjectListEditorProps = { params: PD.Params, value: object, isUpdate?: boolean, apply: (value: any) => void, isDisabled?: boolean }
 class ObjectListEditor extends React.PureComponent<ObjectListEditorProps, { current: object }> {
-    state = { current: void 0 as any };
+    state = { current: this.props.value };
 
     onChangeParam: ParamOnChange = e => {
         this.setState({ current: { ...this.state.current, [e.name]: e.value } });

src/mol-plugin-ui/custom/volume.tsx

@@ -12,7 +12,7 @@ import { ExpandableControlRow, IconButton } from '../controls/common';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ParameterControls, ParamOnChange } from '../controls/parameters';
 import { Slider } from '../controls/slider';
-import { VolumeIsoValue, VolumeData } from '../../mol-model/volume';
+import { Volume, Grid } from '../../mol-model/volume';
 import { Vec3 } from '../../mol-math/linear-algebra';
 import { ColorNames } from '../../mol-util/color/names';
 import { toPrecision } from '../../mol-util/number';
@@ -28,17 +28,25 @@ const ChannelParams = {
 };
 type ChannelParams = PD.Values<typeof ChannelParams>
 
+const Bounds = new Map<VolumeStreaming.ChannelType, [number, number]>([
+    ['em', [-5, 5]],
+    ['2fo-fc', [0, 3]],
+    ['fo-fc(+ve)', [1, 5]],
+    ['fo-fc(-ve)', [-5, -1]],
+]);
+
 class Channel extends PluginUIComponent<{
     label: string,
     name: VolumeStreaming.ChannelType,
     channels: { [k: string]: VolumeStreaming.ChannelParams },
     isRelative: boolean,
     params: StateTransformParameters.Props,
-    stats: VolumeData['dataStats'],
+    stats: Grid['stats'],
     changeIso: (name: string, value: number, isRelative: boolean) => void,
     changeParams: (name: string, param: string, value: any) => void,
     bCell: StateObjectCell,
-    isDisabled?: boolean
+    isDisabled?: boolean,
+    isUnbounded?: boolean
 }> {
     private ref = StateSelection.findTagInSubtree(this.plugin.state.data.tree, this.props.bCell!.transform.ref, this.props.name);
 
@@ -73,15 +81,31 @@ class Channel extends PluginUIComponent<{
 
         const { min, max, mean, sigma } = stats;
         const value = Math.round(100 * (channel.isoValue.kind === 'relative' ? channel.isoValue.relativeValue : channel.isoValue.absoluteValue)) / 100;
-        const relMin = (min - mean) / sigma;
-        const relMax = (max - mean) / sigma;
-        const step = toPrecision(isRelative ? Math.round(((max - min) / sigma)) / 100 : sigma / 100, 2);
+        let relMin = (min - mean) / sigma;
+        let relMax = (max - mean) / sigma;
+
+        if (!this.props.isUnbounded) {
+            const bounds = Bounds.get(this.props.name)!;
+            if (this.props.name === 'em') {
+                relMin = Math.max(bounds[0], relMin);
+                relMax = Math.min(bounds[1], relMax);
+            } else {
+                relMin = bounds[0];
+                relMax = bounds[1];
+            }
+        }
+
+        const vMin = mean + sigma * relMin, vMax = mean + sigma * relMax;
+
+        const step = toPrecision(isRelative ? Math.round(((vMax - vMin) / sigma)) / 100 : sigma / 100, 2);
+        const ctrlMin = isRelative ? relMin : vMin;
+        const ctrlMax = isRelative ? relMax : vMax;
 
         return <ExpandableControlRow
             label={props.label + (props.isRelative ? ' \u03C3' : '')}
             colorStripe={channel.color}
             pivot={<div className='msp-volume-channel-inline-controls'>
-                <Slider value={value} min={isRelative ? relMin : min} max={isRelative ? relMax : max} step={step}
+                <Slider value={value} min={ctrlMin} max={ctrlMax} step={step}
                     onChange={v => props.changeIso(props.name, v, isRelative)} disabled={props.params.isDisabled} onEnter={props.params.events.onEnter} />
                 <IconButton svg={this.getVisible() ? VisibilityOutlined : VisibilityOffOutlined} onClick={this.toggleVisible} toggleState={false} disabled={props.params.isDisabled} />
             </div>}
@@ -111,7 +135,7 @@ export class VolumeStreamingCustomControls extends PluginUIComponent<StateTransf
                         ...old.entry.params.channels,
                         [name]: {
                             ...(old.entry.params.channels as any)[name],
-                            isoValue: isRelative ? VolumeIsoValue.relative(value) : VolumeIsoValue.absolute(value)
+                            isoValue: isRelative ? Volume.IsoValue.relative(value) : Volume.IsoValue.absolute(value)
                         }
                     }
                 }
@@ -139,11 +163,11 @@ export class VolumeStreamingCustomControls extends PluginUIComponent<StateTransf
         });
     };
 
-    convert(channel: any, stats: VolumeData['dataStats'], isRelative: boolean) {
+    convert(channel: any, stats: Grid['stats'], isRelative: boolean) {
         return {
             ...channel, isoValue: isRelative
-                ? VolumeIsoValue.toRelative(channel.isoValue, stats)
-                : VolumeIsoValue.toAbsolute(channel.isoValue, stats)
+                ? Volume.IsoValue.toRelative(channel.isoValue, stats)
+                : Volume.IsoValue.toAbsolute(channel.isoValue, stats)
         };
     }
 
@@ -163,6 +187,7 @@ export class VolumeStreamingCustomControls extends PluginUIComponent<StateTransf
             const isEM = b.info.kind === 'em';
 
             const isRelative = value.params.isRelative;
+
             const sampling = b.info.header.sampling[0];
             const oldChannels = old.entry.params.channels as any;
 
@@ -180,6 +205,7 @@ export class VolumeStreamingCustomControls extends PluginUIComponent<StateTransf
                 viewParams.bottomLeft = value.params.bottomLeft;
                 viewParams.topRight = value.params.topRight;
             }
+            viewParams.isUnbounded = !!value.params.isUnbounded;
 
             this.newParams({
                 ...old,
@@ -215,34 +241,41 @@ export class VolumeStreamingCustomControls extends PluginUIComponent<StateTransf
         const params = this.props.params as VolumeStreaming.Params;
         const detailLevel = ((this.props.info.params as VolumeStreaming.ParamDefinition)
             .entry.map(params.entry.name) as PD.Group<VolumeStreaming.EntryParamDefinition>).params.detailLevel;
-        const isRelative = ((params.entry.params.channels as any)[pivot].isoValue as VolumeIsoValue).kind === 'relative';
+        const isRelative = ((params.entry.params.channels as any)[pivot].isoValue as Volume.IsoValue).kind === 'relative';
 
         const sampling = b.info.header.sampling[0];
 
         const isRelativeParam = PD.Boolean(isRelative, { description: 'Use normalized or absolute isocontour scale.', label: 'Normalized' });
 
+        const isUnbounded = !!(params.entry.params.view.params as any).isUnbounded;
+        const isUnboundedParam = PD.Boolean(isUnbounded, { description: 'Show full/limited range of iso-values for more fine-grained control.', label: 'Unbounded' });
+
         const isOff = params.entry.params.view.name === 'off';
         // TODO: factor common things out, cache
         const OptionsParams = {
             entry: PD.Select(params.entry.name, b.data.entries.map(info => [info.dataId, info.dataId] as [string, string]), { isHidden: isOff, description: 'Which entry with volume data to display.' }),
             view: PD.MappedStatic(params.entry.params.view.name, {
                 'off': PD.Group({
-                    isRelative: PD.Boolean(isRelative, { isHidden: true })
+                    isRelative: PD.Boolean(isRelative, { isHidden: true }),
+                    isUnbounded: PD.Boolean(isUnbounded, { isHidden: true }),
                 }, { description: 'Display off.' }),
                 'box': PD.Group({
                     bottomLeft: PD.Vec3(Vec3.zero()),
                     topRight: PD.Vec3(Vec3.zero()),
                     detailLevel,
-                    isRelative: isRelativeParam
+                    isRelative: isRelativeParam,
+                    isUnbounded: isUnboundedParam,
                 }, { description: 'Static box defined by cartesian coords.' }),
                 'selection-box': PD.Group({
                     radius: PD.Numeric(5, { min: 0, max: 50, step: 0.5 }, { description: 'Radius in \u212B within which the volume is shown.' }),
                     detailLevel,
-                    isRelative: isRelativeParam
+                    isRelative: isRelativeParam,
+                    isUnbounded: isUnboundedParam,
                 }, { description: 'Box around focused element.' }),
                 'cell': PD.Group({
                     detailLevel,
-                    isRelative: isRelativeParam
+                    isRelative: isRelativeParam,
+                    isUnbounded: isUnboundedParam,
                 }, { description: 'Box around the structure\'s bounding box.' }),
                 // 'auto': PD.Group({  }), // TODO based on camera distance/active selection/whatever, show whole structure or slice.
             }, { options: VolumeStreaming.ViewTypeOptions, description: 'Controls what of the volume is displayed. "Off" hides the volume alltogether. "Bounded box" shows the volume inside the given box. "Around Focus" shows the volume around the element/atom last interacted with. "Whole Structure" shows the volume for the whole structure.' })
@@ -256,7 +289,8 @@ export class VolumeStreamingCustomControls extends PluginUIComponent<StateTransf
                     radius: (params.entry.params.view.params as any).radius,
                     bottomLeft: (params.entry.params.view.params as any).bottomLeft,
                     topRight: (params.entry.params.view.params as any).topRight,
-                    isRelative
+                    isRelative,
+                    isUnbounded
                 }
             }
         };
@@ -266,10 +300,10 @@ export class VolumeStreamingCustomControls extends PluginUIComponent<StateTransf
         }
 
         return <>
-            {!isEM && <Channel label='2Fo-Fc' name='2fo-fc' bCell={this.props.bCell!} channels={params.entry.params.channels} changeIso={this.changeIso} changeParams={this.changeParams} isRelative={isRelative} params={this.props} stats={sampling.valuesInfo[0]} />}
-            {!isEM && <Channel label='Fo-Fc(+ve)' name='fo-fc(+ve)' bCell={this.props.bCell!} channels={params.entry.params.channels} changeIso={this.changeIso} changeParams={this.changeParams} isRelative={isRelative} params={this.props} stats={sampling.valuesInfo[1]} />}
-            {!isEM && <Channel label='Fo-Fc(-ve)' name='fo-fc(-ve)' bCell={this.props.bCell!} channels={params.entry.params.channels} changeIso={this.changeIso} changeParams={this.changeParams} isRelative={isRelative} params={this.props} stats={sampling.valuesInfo[1]} />}
-            {isEM && <Channel label='EM' name='em' bCell={this.props.bCell!} channels={params.entry.params.channels} changeIso={this.changeIso} changeParams={this.changeParams} isRelative={isRelative} params={this.props} stats={sampling.valuesInfo[0]} />}
+            {!isEM && <Channel label='2Fo-Fc' name='2fo-fc' bCell={this.props.bCell!} channels={params.entry.params.channels} changeIso={this.changeIso} changeParams={this.changeParams} isRelative={isRelative} params={this.props} stats={sampling.valuesInfo[0]} isUnbounded={isUnbounded} />}
+            {!isEM && <Channel label='Fo-Fc(+ve)' name='fo-fc(+ve)' bCell={this.props.bCell!} channels={params.entry.params.channels} changeIso={this.changeIso} changeParams={this.changeParams} isRelative={isRelative} params={this.props} stats={sampling.valuesInfo[1]} isUnbounded={isUnbounded} />}
+            {!isEM && <Channel label='Fo-Fc(-ve)' name='fo-fc(-ve)' bCell={this.props.bCell!} channels={params.entry.params.channels} changeIso={this.changeIso} changeParams={this.changeParams} isRelative={isRelative} params={this.props} stats={sampling.valuesInfo[1]} isUnbounded={isUnbounded} />}
+            {isEM && <Channel label='EM' name='em' bCell={this.props.bCell!} channels={params.entry.params.channels} changeIso={this.changeIso} changeParams={this.changeParams} isRelative={isRelative} params={this.props} stats={sampling.valuesInfo[0]} isUnbounded={isUnbounded} />}
 
             <ParameterControls onChange={this.changeOption} params={OptionsParams} values={options} onEnter={this.props.events.onEnter} isDisabled={this.props.isDisabled} />
         </>;

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

@@ -44,18 +44,18 @@ export class PolymerSequenceWrapper extends SequenceWrapper<StructureUnit> {
     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 false;
             loci = StructureElement.Loci.remap(loci, structure);
 
-            const { offset } = this.sequence;
             for (const e of loci.elements) {
                 if (!this.unitMap.has(e.unit.id)) continue;
 
                 if (Unit.isAtomic(e.unit)) {
-                    changed = applyMarkerAtomic(e, action, this.markerArray, offset) || changed;
+                    changed = applyMarkerAtomic(e, action, this.markerArray, index) || changed;
                 } else {
-                    changed = applyMarkerCoarse(e, action, this.markerArray, offset) || changed;
+                    changed = applyMarkerCoarse(e, action, this.markerArray, index) || changed;
                 }
             }
         } else if (Structure.isLoci(loci)) {
@@ -117,27 +117,28 @@ function createResidueQuery(chainGroupId: number, operatorName: string, label_se
     });
 }
 
-function applyMarkerAtomic(e: StructureElement.Loci.Element, action: MarkerAction, markerArray: Uint8Array, offset: number) {
+function applyMarkerAtomic(e: StructureElement.Loci.Element, action: MarkerAction, markerArray: Uint8Array, index: (seqId: number) => number) {
     const { model, elements } = e.unit;
-    const { index } = model.atomicHierarchy.residueAtomSegments;
+    const { index: residueIndex } = model.atomicHierarchy.residueAtomSegments;
     const { label_seq_id } = model.atomicHierarchy.residues;
 
     let changed = false;
-    OrderedSet.forEachSegment(e.indices, i => index[elements[i]], rI => {
+    OrderedSet.forEachSegment(e.indices, i => residueIndex[elements[i]], rI => {
         const seqId = label_seq_id.value(rI);
-        changed = applyMarkerActionAtPosition(markerArray, seqId - 1 - offset, action) || changed;
+        changed = applyMarkerActionAtPosition(markerArray, index(seqId), action) || changed;
     });
     return changed;
 }
 
-function applyMarkerCoarse(e: StructureElement.Loci.Element, action: MarkerAction, markerArray: Uint8Array, offset: 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;
 
     let changed = false;
     OrderedSet.forEach(e.indices, i => {
-        for (let s = begin.value(elements[i]) - 1 - offset, e = end.value(elements[i]) - 1 - offset; s <= e; s++) {
+        const eI = elements[i];
+        for (let s = index(begin.value(eI)), e = index(end.value(eI)); s <= e; s++) {
             changed = applyMarkerActionAtPosition(markerArray, s, action) || changed;
         }
     });

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

@@ -239,7 +239,7 @@
 // TODO : get rid of the important
 .msp-control-group-header {
     background: $default-background;
-    > button {
+    > button, div {
         padding-left: 4px; // $control-spacing / 2 !important;
         text-align: left;
         height: 24px !important; // 2 * $row-height / 3 !important;

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

@@ -427,8 +427,7 @@
     position: relative;
     // display: inline-block;
     margin: $control-spacing auto 0 auto;
-    width: 400px;
-    line-height: $row-height;
+    width: 430px;
 
     &-actions {
         position: absolute;

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

@@ -100,15 +100,16 @@
   }
 
   &-disabled {
-    background-color: #e9e9e9;
-
-    .msp-slider-base-track {
-      background-color: $slider-disabledColor;
-    }
-
+    background: $default-background;
+    opacity: 0.35;
+    
+    // .msp-slider-base-track {
+    //   background-color: $slider-disabledColor;
+    // }
+    
     .msp-slider-base-handle, .msp-slider-base-dot {
-      border-color: $slider-disabledColor;
-      background-color: #fff;
+      // border-color: $slider-disabledColor;
+      // background-color: color-lower-contrast($font-color, 10%);
       cursor: not-allowed;
     }
 

src/mol-plugin-ui/state/animation.tsx

@@ -37,14 +37,15 @@ export class AnimationControls extends PluginUIComponent<{ onStart?: () => void
         if (anim.isEmpty) return null;
 
         const isDisabled = anim.state.animationState === 'playing';
+        const canApply = anim.current.anim.canApply?.(this.plugin);
 
         return <>
             <ParameterControls params={anim.getParams()} values={anim.state.params} onChange={this.updateParams} isDisabled={isDisabled} />
             <ParameterControls params={anim.current.params} values={anim.current.paramValues} onChange={this.updateCurrentParams} isDisabled={isDisabled} />
 
             <div className='msp-flex-row'>
-                <Button icon={anim.state.animationState !== 'playing' ? void 0 : PlayArrow} onClick={this.startOrStop}>
-                    {anim.state.animationState === 'playing' ? 'Stop' : 'Start'}
+                <Button icon={anim.state.animationState !== 'playing' ? void 0 : PlayArrow} onClick={this.startOrStop} disabled={canApply !== void 0 && canApply.canApply === false}>
+                    {anim.state.animationState === 'playing' ? 'Stop' : canApply === void 0 || canApply.canApply ? 'Start' : canApply.reason || 'Start'}
                 </Button>
             </div>
         </>;