0.7.0-dev.12

package-lock.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "0.7.0-dev.7",
+  "version": "0.7.0-dev.12",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "0.7.0-dev.7",
+  "version": "0.7.0-dev.12",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {

src/examples/proteopedia-wrapper/index.html

@@ -92,6 +92,12 @@
             // var format = 'pdb';
             // var assemblyId = 'deposited';
 
+            function loadAndSnapshot(params) {
+                PluginWrapper.load(params).then(() => {
+                    setTimeout(() => snapshot = PluginWrapper.plugin.state.getSnapshot({ canvas3d: false /* do not save spinning state */ }), 500);
+                });
+            }
+
             var representationStyle = {
                 // sequence: { coloring: 'proteopedia-custom' }, // or just { }
                 hetGroups: { kind: 'ball-and-stick' }, // or 'spacefill
@@ -103,7 +109,7 @@
                 customColorList: CustomColors
             });
             PluginWrapper.setBackground(0xffffff);
-            PluginWrapper.load({ url: url, format: format, isBinary: isBinary, assemblyId: assemblyId, representationStyle: representationStyle });
+            loadAndSnapshot({ url: url, format: format, isBinary: isBinary, assemblyId: assemblyId, representationStyle: representationStyle });
             PluginWrapper.toggleSpin();
 
             PluginWrapper.events.modelInfo.subscribe(function (info) {
@@ -111,8 +117,8 @@
                 listHetGroups(info);
             });
 
-            addControl('Load Asym Unit', () => PluginWrapper.load({ url: url, format: format, isBinary }));
-            addControl('Load Assembly', () => PluginWrapper.load({ url: url, format: format, isBinary, assemblyId: assemblyId }));
+            addControl('Load Asym Unit', () => loadAndSnapshot({ url: url, format: format, isBinary }));
+            addControl('Load Assembly', () => loadAndSnapshot({ url: url, format: format, isBinary, assemblyId: assemblyId }));
 
             addSeparator();
 
@@ -185,10 +191,10 @@
                 PluginWrapper.snapshot.set(snapshot);
             });
             addControl('Download State', () => {
-                snapshot = PluginWrapper.snapshot.download('molj');
+                PluginWrapper.snapshot.download('molj');
             });
             addControl('Download Session', () => {
-                snapshot = PluginWrapper.snapshot.download('molx');
+                PluginWrapper.snapshot.download('molx');
             });
 
             ////////////////////////////////////////////////////////

src/examples/proteopedia-wrapper/index.ts

@@ -5,30 +5,29 @@
  */
 
 import * as ReactDOM from 'react-dom';
+import { Canvas3DProps, DefaultCanvas3DParams } from '../../mol-canvas3d/canvas3d';
 import { createPlugin, DefaultPluginSpec } from '../../mol-plugin';
-import './index.html';
-import { PluginContext } from '../../mol-plugin/context';
-import { PluginCommands } from '../../mol-plugin/commands';
-import { StateTransforms } from '../../mol-plugin-state/transforms';
-import { Color } from '../../mol-util/color';
-import { PluginStateObject as PSO, PluginStateObject } from '../../mol-plugin-state/objects';
 import { AnimateModelIndex } from '../../mol-plugin-state/animation/built-in';
-import { StateBuilder, StateObject, StateSelection } from '../../mol-state';
-import { EvolutionaryConservation } from './annotation';
-import { LoadParams, SupportedFormats, RepresentationStyle, ModelInfo, StateElements } from './helpers';
-import { RxEventHelper } from '../../mol-util/rx-event-helper';
-import { volumeStreamingControls } from './ui/controls';
-import { PluginState } from '../../mol-plugin/state';
-import { Scheduler } from '../../mol-task';
-import { createProteopediaCustomTheme } from './coloring';
-import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
-import { ColorNames } from '../../mol-util/color/names';
-import { InitVolumeStreaming, CreateVolumeStreamingInfo } from '../../mol-plugin/behavior/dynamic/volume-streaming/transformers';
-import { DefaultCanvas3DParams, Canvas3DProps } from '../../mol-canvas3d/canvas3d';
 import { createStructureRepresentationParams } from '../../mol-plugin-state/helpers/structure-representation-params';
-import { download } from '../../mol-util/download';
-import { getFormattedTime } from '../../mol-util/date';
+import { PluginStateObject, PluginStateObject as PSO } from '../../mol-plugin-state/objects';
+import { StateTransforms } from '../../mol-plugin-state/transforms';
+import { CreateVolumeStreamingInfo, InitVolumeStreaming } from '../../mol-plugin/behavior/dynamic/volume-streaming/transformers';
+import { PluginCommands } from '../../mol-plugin/commands';
+import { PluginContext } from '../../mol-plugin/context';
+import { PluginState } from '../../mol-plugin/state';
+import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
+import { StateBuilder, StateObject, StateSelection } from '../../mol-state';
 import { Asset } from '../../mol-util/assets';
+import { Color } from '../../mol-util/color';
+import { ColorNames } from '../../mol-util/color/names';
+import { getFormattedTime } from '../../mol-util/date';
+import { download } from '../../mol-util/download';
+import { RxEventHelper } from '../../mol-util/rx-event-helper';
+import { EvolutionaryConservation } from './annotation';
+import { createProteopediaCustomTheme } from './coloring';
+import { LoadParams, ModelInfo, RepresentationStyle, StateElements, SupportedFormats } from './helpers';
+import './index.html';
+import { volumeStreamingControls } from './ui/controls';
 require('../../mol-plugin-ui/skin/light.scss');
 
 class MolStarProteopediaWrapper {
@@ -233,7 +232,6 @@ class MolStarProteopediaWrapper {
         await this.updateStyle(representationStyle);
 
         this.loadedParams = { url, format, assemblyId };
-        Scheduler.setImmediate(() => PluginCommands.Camera.Reset(this.plugin, { }));
     }
 
     async updateStyle(style?: RepresentationStyle, partial?: boolean) {

src/extensions/cellpack/model.ts

@@ -27,61 +27,73 @@ 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 { readFromFile } from '../../mol-util/data-source';
+import { objectForEach } from '../../mol-util/object';
 
 function getCellPackModelUrl(fileName: string, baseUrl: string) {
     return `${baseUrl}/results/${fileName}`;
 }
 
-async function getModel(plugin: PluginContext, id: string, ingredient: Ingredient, baseUrl: string, file?: Asset.File) {
+class TrajectoryCache {
+    private map = new Map<string, Model.Trajectory>();
+    set(id: string, trajectory: Model.Trajectory) { this.map.set(id, trajectory); }
+    get(id: string) { return this.map.get(id); }
+}
+
+async function getModel(plugin: PluginContext, id: string, ingredient: Ingredient, baseUrl: string, trajCache: TrajectoryCache, file?: Asset.File) {
     const assetManager = plugin.managers.asset;
-    const model_id = (ingredient.source.model) ? parseInt(ingredient.source.model) : 0;
+    const modelIndex = (ingredient.source.model) ? parseInt(ingredient.source.model) : 0;
     const surface = (ingredient.ingtype) ? (ingredient.ingtype === 'transmembrane') : false;
-    let model: Model;
+    let trajectory = trajCache.get(id);
     let assets: Asset.Wrapper[] = [];
-    if (file) {
-        if (file.name.endsWith('.cif')) {
-            const text = await plugin.runTask(assetManager.resolve(file, 'string'));
-            assets.push(text);
-            const cif = (await parseCif(plugin, text.data)).blocks[0];
-            model = (await plugin.runTask(trajectoryFromMmCIF(cif)))[model_id];
-        } else if (file.name.endsWith('.bcif')) {
-            const binary = await plugin.runTask(assetManager.resolve(file, 'binary'));
-            assets.push(binary);
-            const cif = (await parseCif(plugin, binary.data)).blocks[0];
-            model = (await plugin.runTask(trajectoryFromMmCIF(cif)))[model_id];
-        } else if (file.name.endsWith('.pdb')) {
-            const text = await plugin.runTask(assetManager.resolve(file, 'string'));
-            assets.push(text);
-            const pdb = await parsePDBfile(plugin, text.data, id);
-            model = (await plugin.runTask(trajectoryFromPDB(pdb)))[model_id];
-        } else {
-            throw new Error(`unsupported file type '${file.name}'`);
-        }
-    } else if (id.match(/^[1-9][a-zA-Z0-9]{3,3}$/i)) {
-        if (surface){
-            const data = await getFromOPM(plugin, id, assetManager);
-            if (data.asset){
-                assets.push(data.asset);
-                model = (await plugin.runTask(trajectoryFromPDB(data.pdb)))[model_id];
+    if (!trajectory) {
+        if (file) {
+            if (file.name.endsWith('.cif')) {
+                const text = await plugin.runTask(assetManager.resolve(file, 'string'));
+                assets.push(text);
+                const cif = (await parseCif(plugin, text.data)).blocks[0];
+                trajectory = await plugin.runTask(trajectoryFromMmCIF(cif));
+            } else if (file.name.endsWith('.bcif')) {
+                const binary = await plugin.runTask(assetManager.resolve(file, 'binary'));
+                assets.push(binary);
+                const cif = (await parseCif(plugin, binary.data)).blocks[0];
+                trajectory = await plugin.runTask(trajectoryFromMmCIF(cif));
+            } else if (file.name.endsWith('.pdb')) {
+                const text = await plugin.runTask(assetManager.resolve(file, 'string'));
+                assets.push(text);
+                const pdb = await parsePDBfile(plugin, text.data, id);
+                trajectory = await plugin.runTask(trajectoryFromPDB(pdb));
+            } else {
+                throw new Error(`unsupported file type '${file.name}'`);
+            }
+        } else if (id.match(/^[1-9][a-zA-Z0-9]{3,3}$/i)) {
+            if (surface){
+                const data = await getFromOPM(plugin, id, assetManager);
+                if (data.asset){
+                    assets.push(data.asset);
+                    trajectory = await plugin.runTask(trajectoryFromPDB(data.pdb));
+                } else {
+                    const { mmcif, asset } = await getFromPdb(plugin, id, assetManager);
+                    assets.push(asset);
+                    trajectory = await plugin.runTask(trajectoryFromMmCIF(mmcif));
+                }
             } else {
                 const { mmcif, asset } = await getFromPdb(plugin, id, assetManager);
                 assets.push(asset);
-                model = (await plugin.runTask(trajectoryFromMmCIF(mmcif)))[model_id];
+                trajectory = await plugin.runTask(trajectoryFromMmCIF(mmcif));
             }
         } else {
-            const { mmcif, asset } = await getFromPdb(plugin, id, assetManager);
-            assets.push(asset);
-            model = (await plugin.runTask(trajectoryFromMmCIF(mmcif)))[model_id];
-        }
-    } else {
-        const data = await getFromCellPackDB(plugin, id, baseUrl, assetManager);
-        assets.push(data.asset);
-        if ('pdb' in data) {
-            model = (await plugin.runTask(trajectoryFromPDB(data.pdb)))[model_id];
-        } else {
-            model = (await plugin.runTask(trajectoryFromMmCIF(data.mmcif)))[model_id];
+            const data = await getFromCellPackDB(plugin, id, baseUrl, assetManager);
+            assets.push(data.asset);
+            if ('pdb' in data) {
+                trajectory = await plugin.runTask(trajectoryFromPDB(data.pdb));
+            } else {
+                trajectory = await plugin.runTask(trajectoryFromMmCIF(data.mmcif));
+            }
         }
+        trajCache.set(id, trajectory);
     }
+    const model = trajectory[modelIndex];
     return { model, assets };
 }
 
@@ -133,7 +145,6 @@ function getTransform(trans: Vec3, rot: Quat) {
     return m;
 }
 
-
 function getResultTransforms(results: Ingredient['results'], legacy: boolean) {
     if (legacy) return results.map((r: Ingredient['results'][0]) => getTransformLegacy(r[0], r[1]));
     else return results.map((r: Ingredient['results'][0]) => getTransform(r[0], r[1]));
@@ -288,7 +299,7 @@ async function getCurve(plugin: PluginContext, name: string, ingredient: Ingredi
     return getStructure(plugin, curveModel, ingredient.source);
 }
 
-async function getIngredientStructure(plugin: PluginContext, ingredient: Ingredient, baseUrl: string, ingredientFiles: IngredientFiles) {
+async function getIngredientStructure(plugin: PluginContext, ingredient: Ingredient, baseUrl: string, ingredientFiles: IngredientFiles, trajCache: TrajectoryCache) {
     const { name, source, results, nbCurve } = ingredient;
     if (source.pdb === 'None') return;
 
@@ -303,7 +314,7 @@ async function getIngredientStructure(plugin: PluginContext, ingredient: Ingredi
     }
 
     // model id in case structure is NMR
-    const { model, assets } = await getModel(plugin, source.pdb || name, ingredient, baseUrl, file);
+    const { model, assets } = await getModel(plugin, source.pdb || name, ingredient, baseUrl, trajCache, file);
     if (!model) return;
 
     let structure: Structure;
@@ -354,10 +365,11 @@ export function createStructureFromCellPack(plugin: PluginContext, packing: Cell
     return Task.create('Create Packing Structure', async ctx => {
         const { ingredients, name } = packing;
         const assets: Asset.Wrapper[] = [];
+        const trajCache = new TrajectoryCache();
         const structures: Structure[] = [];
         for (const iName in ingredients) {
             if (ctx.shouldUpdate) await ctx.update(iName);
-            const ingredientStructure = await getIngredientStructure(plugin, ingredients[iName], baseUrl, ingredientFiles);
+            const ingredientStructure = await getIngredientStructure(plugin, ingredients[iName], baseUrl, ingredientFiles, trajCache);
             if (ingredientStructure) {
                 structures.push(ingredientStructure.structure);
                 assets.push(...ingredientStructure.assets);
@@ -444,6 +456,8 @@ async function loadMembrane(plugin: PluginContext, name: string, state: State, p
 }
 
 async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, state: State, params: LoadCellPackModelParams) {
+    const ingredientFiles = params.ingredients.files || [];
+
     let cellPackJson: StateBuilder.To<PSO.Format.Json, StateTransformer<PSO.Data.String, PSO.Format.Json>>;
     if (params.source.name === 'id') {
         const url = Asset.getUrlAsset(plugin.managers.asset, getCellPackModelUrl(params.source.params, params.baseUrl));
@@ -451,12 +465,25 @@ async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, stat
             .apply(StateTransforms.Data.Download, { url, isBinary: false, label: params.source.params }, { state: { isGhost: true } });
     } else {
         const file = params.source.params;
-        if (file === null) {
+        if (!file?.file) {
             plugin.log.error('No file selected');
             return;
         }
+
+        let jsonFile: Asset.File;
+        if (file.name.toLowerCase().endsWith('.zip')) {
+            const data = await readFromFile(file.file, 'zip').runInContext(runtime);
+            jsonFile = Asset.File(new File([data['model.json']], 'model.json'));
+            objectForEach(data, (v, k) => {
+                if (k === 'model.json') return;
+                ingredientFiles.push(Asset.File(new File([v], k)));
+            });
+        } else {
+            jsonFile = file;
+        }
+
         cellPackJson = state.build().toRoot()
-            .apply(StateTransforms.Data.ReadFile, { file, isBinary: false, label: file.name }, { state: { isGhost: true } });
+            .apply(StateTransforms.Data.ReadFile, { file: jsonFile, isBinary: false, label: jsonFile.name }, { state: { isGhost: true } });
     }
 
     const cellPackBuilder = cellPackJson
@@ -469,7 +496,7 @@ async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, stat
     await handleHivRna(plugin, packings, params.baseUrl);
 
     for (let i = 0, il = packings.length; i < il; ++i) {
-        const p = { packing: i, baseUrl: params.baseUrl, ingredientFiles: params.ingredients.files };
+        const p = { packing: i, baseUrl: params.baseUrl, ingredientFiles };
 
         const packing = await state.build()
             .to(cellPackBuilder.ref)
@@ -497,8 +524,8 @@ const LoadCellPackModelParams = {
             ['influenza_model1.json', 'influenza_model1'],
             ['ExosomeModel.json', 'ExosomeModel'],
             ['Mycoplasma1.5_mixed_pdb_fixed.cpr', 'Mycoplasma1.5_mixed_pdb_fixed'],
-        ] as const),
-        'file': PD.File({ accept: 'id' }),
+        ] 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),
     ingredients : PD.Group({

src/mol-model/volume/volume.ts

@@ -7,7 +7,7 @@
 import { VolumeData, VolumeIsoValue } from './data';
 import { OrderedSet } from '../../mol-data/int';
 import { Sphere3D } from '../../mol-math/geometry';
-import { Vec3 } from '../../mol-math/linear-algebra';
+import { Vec3, Mat4 } from '../../mol-math/linear-algebra';
 import { BoundaryHelper } from '../../mol-math/geometry/boundary-helper';
 
 export namespace Volume {
@@ -86,7 +86,8 @@ export namespace Volume {
                 boundaryHelper.radiusPosition(tmpBoundaryPos);
             }
 
-            return boundaryHelper.getSphere(boundingSphere);
+            const bs = boundaryHelper.getSphere(boundingSphere);
+            return Sphere3D.expand(bs, bs, Mat4.getMaxScaleOnAxis(transform) * 10);
         }
     }
 }

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

@@ -237,7 +237,13 @@ const atomicDetail = StructureRepresentationPresetProvider({
 
         const components = {
             all: await presetStaticComponent(plugin, structureCell, 'all'),
+            branched: undefined
         };
+        if (params.showCarbohydrateSymbol) {
+            Object.assign(components, {
+                branched: await presetStaticComponent(plugin, structureCell, 'branched', { label: 'Carbohydrate' }),
+            });
+        }
 
         const { update, builder, typeParams, color } = reprBuilder(plugin, params);
         const representations = {
@@ -245,7 +251,7 @@ const atomicDetail = StructureRepresentationPresetProvider({
         };
         if (params.showCarbohydrateSymbol) {
             Object.assign(representations, {
-                snfg3d: builder.buildRepresentation(update, components.all, { type: 'carbohydrate', typeParams: { ...typeParams, alpha: 0.4, visuals: ['carbohydrate-symbol'] }, color }, { tag: 'snfg-3d' }),
+                snfg3d: builder.buildRepresentation(update, components.branched, { type: 'carbohydrate', typeParams: { ...typeParams, alpha: 0.4, visuals: ['carbohydrate-symbol'] }, color }, { tag: 'snfg-3d' }),
             });
         }
 

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

@@ -114,10 +114,10 @@ export const Provider3dg: TrajectoryFormatProvider = {
 };
 
 export const MolProvider: TrajectoryFormatProvider = {
-    label: 'MOL',
-    description: 'MOL',
+    label: 'MOL/SDF',
+    description: 'MOL/SDF',
     category: Category,
-    stringExtensions: ['mol', 'sdf'],
+    stringExtensions: ['mol', 'sdf', 'sd'],
     parse: directTrajectory(StateTransforms.Model.TrajectoryFromMOL),
     visuals: defaultVisuals
 };

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

@@ -394,63 +394,68 @@ const wholeResidues = StructureSelectionQuery('Whole Residues of Selection', MS.
 });
 
 const StandardAminoAcids = [
-    [['HIS'], 'HISTIDINE'],
-    [['ARG'], 'ARGININE'],
-    [['LYS'], 'LYSINE'],
-    [['ILE'], 'ISOLEUCINE'],
-    [['PHE'], 'PHENYLALANINE'],
-    [['LEU'], 'LEUCINE'],
-    [['TRP'], 'TRYPTOPHAN'],
-    [['ALA'], 'ALANINE'],
-    [['MET'], 'METHIONINE'],
-    [['PRO'], 'PROLINE'],
-    [['CYS'], 'CYSTEINE'],
-    [['ASN'], 'ASPARAGINE'],
-    [['VAL'], 'VALINE'],
-    [['GLY'], 'GLYCINE'],
-    [['SER'], 'SERINE'],
-    [['GLN'], 'GLUTAMINE'],
-    [['TYR'], 'TYROSINE'],
-    [['ASP'], 'ASPARTIC ACID'],
-    [['GLU'], 'GLUTAMIC ACID'],
-    [['THR'], 'THREONINE'],
-    [['SEC'], 'SELENOCYSTEINE'],
-    [['PYL'], 'PYRROLYSINE'],
-    [['UNK'], 'UNKNOWN'],
+    [['HIS'], 'Histidine'],
+    [['ARG'], 'Arginine'],
+    [['LYS'], 'Lysine'],
+    [['ILE'], 'Isoleucine'],
+    [['PHE'], 'Phenylalanine'],
+    [['LEU'], 'Leucine'],
+    [['TRP'], 'Tryptophan'],
+    [['ALA'], 'Alanine'],
+    [['MET'], 'Methionine'],
+    [['PRO'], 'Proline'],
+    [['CYS'], 'Cysteine'],
+    [['ASN'], 'Asparagine'],
+    [['VAL'], 'Valine'],
+    [['GLY'], 'Glycine'],
+    [['SER'], 'Serine'],
+    [['GLN'], 'Glutamine'],
+    [['TYR'], 'Tyrosine'],
+    [['ASP'], 'Aspartic Acid'],
+    [['GLU'], 'Glutamic Acid'],
+    [['THR'], 'Threonine'],
+    [['SEC'], 'Selenocysteine'],
+    [['PYL'], 'Pyrrolysine'],
+    [['UNK'], 'Unknown'],
 ].sort((a, b) => a[1] < b[1] ? -1 : a[1] > b[1] ? 1 : 0) as [string[], string][];
 
 const StandardNucleicBases = [
-    [['A', 'DA'], 'ADENOSINE'],
-    [['C', 'DC'], 'CYTIDINE'],
-    [['T', 'DT'], 'THYMIDINE'],
-    [['G', 'DG'], 'GUANOSINE'],
-    [['I', 'DI'], 'INOSINE'],
-    [['U', 'DU'], 'URIDINE'],
-    [['N', 'DN'], 'UNKNOWN'],
+    [['A', 'DA'], 'Adenosine'],
+    [['C', 'DC'], 'Cytidine'],
+    [['T', 'DT'], 'Thymidine'],
+    [['G', 'DG'], 'Guanosine'],
+    [['I', 'DI'], 'Inosine'],
+    [['U', 'DU'], 'Uridine'],
+    [['N', 'DN'], 'Unknown'],
 ].sort((a, b) => a[1] < b[1] ? -1 : a[1] > b[1] ? 1 : 0) as [string[], string][];
 
 export function ResidueQuery([names, label]: [string[], string], category: string, priority = 0) {
-    return StructureSelectionQuery(`${label} (${names.join(', ')})`, MS.struct.modifier.union([
+    const description = names.length === 1 && !StandardResidues.has(names[0])
+        ? `[${names[0]}] ${label}`
+        : `${label} (${names.join(', ')})`;
+    return StructureSelectionQuery(description, MS.struct.modifier.union([
         MS.struct.generator.atomGroups({
             'residue-test': MS.core.set.has([MS.set(...names), MS.ammp('auth_comp_id')])
         })
-    ]), { category, priority, description: label });
+    ]), { category, priority, description });
 }
 
 export function ElementSymbolQuery([names, label]: [string[], string], category: string, priority: number) {
-    return StructureSelectionQuery(`${label} (${names.join(', ')})`, MS.struct.modifier.union([
+    const description = `${label} (${names.join(', ')})`;
+    return StructureSelectionQuery(description, MS.struct.modifier.union([
         MS.struct.generator.atomGroups({
             'atom-test': MS.core.set.has([MS.set(...names), MS.acp('elementSymbol')])
         })
-    ]), { category, priority });
+    ]), { category, priority, description });
 }
 
-export function EntityDescriptionQuery([description, label]: [string[], string], category: string, priority: number) {
+export function EntityDescriptionQuery([names, label]: [string[], string], category: string, priority: number) {
+    const description = `${label}`;
     return StructureSelectionQuery(`${label}`, MS.struct.modifier.union([
         MS.struct.generator.atomGroups({
-            'entity-test': MS.core.list.equal([MS.list(...description), MS.ammp('entityDescription')])
+            'entity-test': MS.core.list.equal([MS.list(...names), MS.ammp('entityDescription')])
         })
-    ]), { category, priority, description: description.join(', ') });
+    ]), { category, priority, description });
 }
 
 const StandardResidues = SetUtils.unionMany(

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

@@ -88,21 +88,18 @@
     outline: none;
 }
 
-// .msp-btn-icon, .msp-btn-icon-small {
-//     svg {
-//         display: inline-flex;
-//         vertical-align: middle;
-//         font-size: 1rem;
-//         margin-bottom: 3px;
-//     }
-// }
-
 .msp-material-icon {
     svg {
         display: inline-flex;
         vertical-align: middle;
-        font-size: 1rem;
+        font-size: 1.2em;
         margin-bottom: 3px;
+
+        fill: currentColor;
+        width: 1em;
+        height: 1em;
+        flex-shrink: 0;
+        user-select: none;
     }
 }
 
@@ -270,7 +267,7 @@ select[multiple],
 select[size] {
     height: auto;
 }
-  
+
 // Reset height for `textarea`s
 textarea.msp-form-control {
     height: auto;

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

@@ -173,10 +173,10 @@ export class StructureSelectionActionsControls extends PluginUIComponent<{}, Str
         return <>
             <div className='msp-flex-row' style={{ background: 'none' }}>
                 <PureSelectControl title={`Picking Level for selecting and highlighting`} param={StructureSelectionParams.granularity} name='granularity' value={granularity} onChange={this.setGranuality} isDisabled={this.isDisabled} />
-                <ToggleButton icon={Union} title={ActionHeader.get('add')} toggle={this.toggleAdd} isSelected={this.state.action === 'add'} disabled={this.isDisabled} />
-                <ToggleButton icon={Subtract} title={ActionHeader.get('remove')} toggle={this.toggleRemove} isSelected={this.state.action === 'remove'} disabled={this.isDisabled} />
-                <ToggleButton icon={Intersect} title={ActionHeader.get('intersect')} toggle={this.toggleIntersect} isSelected={this.state.action === 'intersect'} disabled={this.isDisabled} />
-                <ToggleButton icon={SetSvg} title={ActionHeader.get('set')} toggle={this.toggleSet} isSelected={this.state.action === 'set'} disabled={this.isDisabled} />
+                <ToggleButton icon={Union} title={`${ActionHeader.get('add')}. Hold shift key to keep menu open.`} toggle={this.toggleAdd} isSelected={this.state.action === 'add'} disabled={this.isDisabled} />
+                <ToggleButton icon={Subtract} title={`${ActionHeader.get('remove')}. Hold shift key to keep menu open.`} toggle={this.toggleRemove} isSelected={this.state.action === 'remove'} disabled={this.isDisabled} />
+                <ToggleButton icon={Intersect} title={`${ActionHeader.get('intersect')}. Hold shift key to keep menu open.`} toggle={this.toggleIntersect} isSelected={this.state.action === 'intersect'} disabled={this.isDisabled} />
+                <ToggleButton icon={SetSvg} title={`${ActionHeader.get('set')}. Hold shift key to keep menu open.`} toggle={this.toggleSet} isSelected={this.state.action === 'set'} disabled={this.isDisabled} />
 
                 <ToggleButton icon={Brush} title='Color Selection' toggle={this.toggleColor} isSelected={this.state.action === 'color'} disabled={this.isDisabled} style={{ marginLeft: '10px' }}  />
                 <ToggleButton icon={CubeSvg} title='Create Representation of Selection' toggle={this.toggleAddRepr} isSelected={this.state.action === 'add-repr'} disabled={this.isDisabled} />

src/mol-repr/structure/visual/label-text.ts

@@ -148,7 +148,7 @@ function createElementText(ctx: VisualContext, structure: Structure, theme: Them
     const { label_atom_id, label_alt_id } = StructureProperties.atom;
     const { cumulativeUnitElementCount } = serialMapping;
 
-    const sizeTheme = PhysicalSizeTheme({}, {});
+    const sizeTheme = PhysicalSizeTheme({}, { scale: 1 });
 
     const count = structure.elementCount;
     const { elementScale } = props;

src/mol-repr/structure/visual/util/common.ts

@@ -175,7 +175,7 @@ export function getUnitConformationAndRadius(structure: Structure, unit: Unit, p
     const boundary = unit === rootUnit ? unit.boundary : getBoundary(position);
 
     const l = StructureElement.Location.create(structure, rootUnit);
-    const sizeTheme = PhysicalSizeTheme({}, {});
+    const sizeTheme = PhysicalSizeTheme({}, { scale: 1 });
     const radius = (index: number) => {
         l.element = index as ElementIndex;
         return sizeTheme.size(l);
@@ -186,7 +186,7 @@ export function getUnitConformationAndRadius(structure: Structure, unit: Unit, p
 
 export function getStructureConformationAndRadius(structure: Structure, ignoreHydrogens: boolean, traceOnly: boolean) {
     const l = StructureElement.Location.create(structure);
-    const sizeTheme = PhysicalSizeTheme({}, {});
+    const sizeTheme = PhysicalSizeTheme({}, { scale: 1 });
 
     let xs: ArrayLike<number>;
     let ys: ArrayLike<number>;

src/mol-theme/label.ts

@@ -173,7 +173,7 @@ export function _bundleLabel(bundle: Loci.Bundle<any>, options: LabelOptions) {
         }
 
         let offset = 0;
-        for (let i = 0, il = Math.min(...labels.map(l => l.length)); i < il; ++i) {
+        for (let i = 0, il = Math.min(...labels.map(l => l.length)) - 1; i < il; ++i) {
             let areIdentical = true;
             for (let j = 1, jl = labels.length; j < jl; ++j) {
                 if (labels[0][i] !== labels[j][i]) {

src/mol-theme/size/physical.ts

@@ -14,7 +14,9 @@ import { ThemeDataContext } from '../../mol-theme/theme';
 const DefaultSize = 1;
 const Description = 'Assigns a physical size, i.e. vdW radius for atoms or given radius for coarse spheres.';
 
-export const PhysicalSizeThemeParams = {};
+export const PhysicalSizeThemeParams = {
+    scale: PD.Numeric(1, { min: 0.1, max: 5, step: 0.1 })
+};
 export type PhysicalSizeThemeParams = typeof PhysicalSizeThemeParams
 export function getPhysicalSizeThemeParams(ctx: ThemeDataContext) {
     return PhysicalSizeThemeParams; // TODO return copy
@@ -35,14 +37,16 @@ export function getPhysicalRadius(unit: Unit, element: ElementIndex): number {
  * i.e. vdw for atoms and radius for coarse spheres
  */
 export function PhysicalSizeTheme(ctx: ThemeDataContext, props: PD.Values<PhysicalSizeThemeParams>): SizeTheme<PhysicalSizeThemeParams> {
+    const scale = props.scale === void 0 ? 1 : props.scale;
+
     function size(location: Location): number {
         let size: number;
         if (StructureElement.Location.is(location)) {
-            size = getPhysicalRadius(location.unit, location.element);
+            size = scale * getPhysicalRadius(location.unit, location.element);
         } else if (Bond.isLocation(location)) {
-            size = getPhysicalRadius(location.aUnit, location.aUnit.elements[location.aIndex]);
+            size = scale * getPhysicalRadius(location.aUnit, location.aUnit.elements[location.aIndex]);
         } else {
-            size = DefaultSize;
+            size = scale * DefaultSize;
         }
         return size;
     }

src/mol-util/param-definition.ts

@@ -271,7 +271,7 @@ export namespace ParamDefinition {
         getLabel(t: T): string
     }
     export function ObjectList<T>(element: For<T>, getLabel: (e: T) => string, info?: Info & { defaultValue?: T[], ctor?: () => T }): ObjectList<Normalize<T>> {
-        return setInfo<ObjectList<Normalize<T>>>({ type: 'object-list', element: element as any as Params, getLabel, ctor: _defaultObjectListCtor, defaultValue: (info?.defaultValue) || []  }, info);
+        return setInfo<ObjectList<Normalize<T>>>({ type: 'object-list', element: element as any as Params, getLabel, ctor: _defaultObjectListCtor, defaultValue: (info?.defaultValue) || [] }, info);
     }
     function _defaultObjectListCtor(this: ObjectList) { return getDefaultValues(this.element) as any; }
 
@@ -316,7 +316,7 @@ export namespace ParamDefinition {
     export type ValuesFor<T extends For<any>> = Normalize<{ [k in keyof T]: T[k]['defaultValue'] }>
 
     type Optionals<P> = { [K in keyof P]-?: undefined extends P[K] ? K : never }[keyof P]
-    type NonOptionals<P> = { [K in keyof P]-?: undefined extends P[K] ? never: K }[keyof P]
+    type NonOptionals<P> = { [K in keyof P]-?: undefined extends P[K] ? never : K }[keyof P]
     export type Normalize<P> = Pick<P, NonOptionals<P>> & Partial<Pick<P, Optionals<P>>>
     export type For<P> = { [K in keyof P]-?: Base<P[K]> }
     export type Def<P> = { [K in keyof P]: Any }
@@ -435,8 +435,8 @@ export namespace ParamDefinition {
     }
 
     export function mergeParam(p: Any, a: any, b: any): any {
-        if (a === undefined) return typeof b === 'object' ? { ...b } : b;
-        if (b === undefined) return typeof a === 'object' ? { ...a } : a;
+        if (a === undefined) return typeof b === 'object' && !Array.isArray(b) ? { ...b } : b;
+        if (b === undefined) return typeof a === 'object' && !Array.isArray(a) ? { ...a } : a;
 
         if (p.type === 'group') {
             return merge(p.params, a, b);
@@ -448,7 +448,12 @@ export namespace ParamDefinition {
                 name: v.name,
                 params: mergeParam(map, u.params, v.params)
             };
+        } else if (p.type === 'value') {
+            return b;
         } else if (typeof a === 'object' && typeof b === 'object') {
+            if (Array.isArray(b)) {
+                return b;
+            }
             return { ...a, ...b };
         } else {
             return b;