3.0.2

Fix visual visibility edge case

CHANGELOG.md

@@ -6,6 +6,25 @@ Note that since we don't clearly distinguish between a public and private interf
 
 ## [Unreleased]
 
+## [v3.0.2] - 2022-01-30
+
+- Fix color smoothing of elongated structures (by fixing ``Sphere.expand`` for spheres with highly directional extrema)
+- Fix entity label not displayed when multiple instances of the same entity are highlighted
+- Fix empty elements created in ``StructureElement.Loci.extendToAllInstances``
+- Measurement options tweaks (allow larger ``textSize``; make ``customText`` essential)
+- Fix visual visibility sync edge case when changing state snapshots
+
+## [v3.0.1] - 2022-01-27
+
+- Fix marking pass not working with ``transparentBackground``
+- Fix pdbe xray maps url not https
+- Fix entity-id color theme broken for non-IHM models
+- Improve/fix marking of ``InteractionsInterUnitVisual`` (mark when all contact-feature members are given)
+- Add missing "entity-id" and "enity-source" options for carbon coloring to "element-symbol" color theme
+- Fix VolumeServer/query CLI
+- Support automatic iso-value adjustment for VolumeServer data in ``Viewer.loadVolumeFromUrl``
+- Emit drag event whenever started within viewport (not only for non-empty loci)
+
 ## [v3.0.0] - 2022-01-23
 
 - Assembly handling tweaks:

CITATION.cff

@@ -0,0 +1,72 @@
+cff-version: 1.2.0
+title: >-
+  Mol* library
+message: >-
+  Please cite this software using the metadata from
+  'preferred-citation'.
+authors:
+  - given-names: Alexander S
+    family-names: Rose
+    orcid: 'https://orcid.org/0000-0002-0893-5551'
+  - given-names: David
+    family-names: Sehnal
+    orcid: 'https://orcid.org/0000-0002-0682-3089'
+  - given-names: Sebastian
+    family-names: Bittrich
+    orcid: 'https://orcid.org/0000-0003-3576-0387'
+  - given-names: Áron Samuel
+    family-names: Kovács
+  - given-names: Ludovic
+    family-names: Autin
+    orcid: 'https://orcid.org/0000-0002-2197-191X'
+  - given-names: Michal
+    family-names: Malý
+  - given-names: Jiří
+    family-names: Černý
+  - given-names: Panagiotis
+    family-names: Tourlas
+type: software
+doi: 10.5281/zenodo.3947306
+preferred-citation:
+  authors:
+    - given-names: David
+      family-names: Sehnal
+      orcid: 'https://orcid.org/0000-0002-0682-3089'
+    - given-names: Sebastian
+      family-names: Bittrich
+      orcid: 'https://orcid.org/0000-0003-3576-0387'
+    - given-names: Mandar
+      family-names: Deshpande
+      orcid: 'https://orcid.org/0000-0002-9043-7665'
+    - given-names: Radka
+      family-names: Svobodová
+      orcid: 'https://orcid.org/0000-0002-3840-8760'
+    - given-names: Karel
+      family-names: Berka
+      orcid: 'https://orcid.org/0000-0001-9472-2589'
+    - given-names: Václav
+      family-names: Bazgier
+      orcid: 'https://orcid.org/0000-0003-3393-3010'
+    - given-names: Sameer
+      family-names: Velankar
+      orcid: 'https://orcid.org/0000-0002-8439-5964'
+    - given-names: Stephen K
+      family-names: Burley
+      orcid: 'https://orcid.org/0000-0002-2487-9713'
+    - given-names: Jaroslav
+      family-names: Koča
+      orcid: 'https://orcid.org/0000-0002-2780-4901'
+    - given-names: Alexander S
+      family-names: Rose
+      orcid: 'https://orcid.org/0000-0002-0893-5551'
+  title: >-
+    Mol* Viewer: modern web app for 3D visualization
+    and analysis of large biomolecular structures
+  type: article
+  doi: 10.1093/nar/gkab314
+  journal: "Nucleic Acids Research"
+  issue: W1
+  volume: 49
+  year: 2021
+  month: 7
+  pages: "W431–W437"

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "3.0.0",
+  "version": "3.0.2",
   "description": "A comprehensive macromolecular library.",
   "homepage": "https://github.com/molstar/molstar#readme",
   "repository": {
@@ -13,7 +13,7 @@
   "scripts": {
     "lint": "eslint .",
     "lint-fix": "eslint . --fix",
-    "test": "npm run lint && jest",
+    "test": "npm install --no-save \"gl@^5.0.0\" && npm run lint && jest",
     "jest": "jest",
     "build": "npm run build-tsc && npm run build-extra && npm run build-webpack",
     "clean": "node ./scripts/clean.js",
@@ -156,8 +156,5 @@
   "peerDependencies": {
     "react": "^17.0.2",
     "react-dom": "^17.0.2"
-  },
-  "optionalDependencies": {
-    "gl": "^5.0.0"
   }
 }

src/apps/viewer/app.ts

@@ -17,6 +17,7 @@ import { ModelExport } from '../../extensions/model-export';
 import { Mp4Export } from '../../extensions/mp4-export';
 import { PDBeStructureQualityReport } from '../../extensions/pdbe';
 import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
+import { Volume } from '../../mol-model/volume';
 import { DownloadStructure, PdbDownloadProvider } from '../../mol-plugin-state/actions/structure';
 import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
 import { PresetTrajectoryHierarchy } from '../../mol-plugin-state/builder/structure/hierarchy-preset';
@@ -366,11 +367,13 @@ export class Viewer {
 
             const repr = plugin.build();
             for (const iso of isovalues) {
+                const volume: StateObjectSelector<PluginStateObject.Volume.Data> = parsed.volumes?.[iso.volumeIndex ?? 0] ?? parsed.volume;
+                const volumeData = volume.cell!.obj!.data;
                 repr
-                    .to(parsed.volumes?.[iso.volumeIndex ?? 0] ?? parsed.volume)
+                    .to(volume)
                     .apply(StateTransforms.Representation.VolumeRepresentation3D, createVolumeRepresentationParams(this.plugin, firstVolume.data!, {
                         type: 'isosurface',
-                        typeParams: { alpha: iso.alpha ?? 1, isoValue: iso.type === 'absolute' ? { kind: 'absolute', absoluteValue: iso.value } : { kind: 'relative', relativeValue: iso.value } },
+                        typeParams: { alpha: iso.alpha ?? 1, isoValue: Volume.adjustedIsoValue(volumeData, iso.value, iso.type) },
                         color: 'uniform',
                         colorParams: { value: iso.color }
                     }));

src/mol-canvas3d/helper/interaction-events.ts

@@ -71,7 +71,7 @@ export class Canvas3dInteractionHelper {
         const xyChanged = this.startX !== this.endX || this.startY !== this.endY;
 
         if (e === InputEvent.Drag) {
-            if (xyChanged && !Representation.Loci.isEmpty(this.prevLoci)) {
+            if (xyChanged && !this.outsideViewport(this.startX, this.startY)) {
                 this.events.drag.next({ current: this.prevLoci, buttons: this.buttons, button: this.button, modifiers: this.modifiers, pageStart: Vec2.create(this.startX, this.startY), pageEnd: Vec2.create(this.endX, this.endY) });
 
                 this.startX = this.endX;

src/mol-canvas3d/passes/draw.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Áron Samuel Kovács <aron.kovacs@mail.muni.cz>
@@ -310,12 +310,12 @@ export class DrawPass {
             const markingDepthTest = props.marking.ghostEdgeStrength < 1;
             if (markingDepthTest) {
                 this.marking.depthTarget.bind();
-                renderer.clear(false);
+                renderer.clear(false, true);
                 renderer.renderMarkingDepth(scene.primitives, camera, null);
             }
 
             this.marking.maskTarget.bind();
-            renderer.clear(false);
+            renderer.clear(false, true);
             renderer.renderMarkingMask(scene.primitives, camera, markingDepthTest ? this.marking.depthTarget.texture : null);
 
             this.marking.update(props.marking);

src/mol-gl/renderer.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -53,7 +53,7 @@ interface Renderer {
     readonly stats: RendererStats
     readonly props: Readonly<RendererProps>
 
-    clear: (toBackgroundColor: boolean) => void
+    clear: (toBackgroundColor: boolean, ignoreTransparentBackground?: boolean) => void
     clearDepth: () => void
     update: (camera: ICamera) => void
 
@@ -523,13 +523,13 @@ namespace Renderer {
         };
 
         return {
-            clear: (toBackgroundColor: boolean) => {
+            clear: (toBackgroundColor: boolean, ignoreTransparentBackground?: boolean) => {
                 state.enable(gl.SCISSOR_TEST);
                 state.enable(gl.DEPTH_TEST);
                 state.colorMask(true, true, true, true);
                 state.depthMask(true);
 
-                if (transparentBackground) {
+                if (transparentBackground && !ignoreTransparentBackground) {
                     state.clearColor(0, 0, 0, 0);
                 } else if (toBackgroundColor) {
                     state.clearColor(bgColor[0], bgColor[1], bgColor[2], 1);

src/mol-math/geometry/primitives/sphere3d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -11,6 +11,7 @@ import { OrderedSet } from '../../../mol-data/int';
 import { NumberArray, PickRequired } from '../../../mol-util/type-helpers';
 import { Box3D } from './box3d';
 import { Axes3D } from './axes3d';
+import { PrincipalAxes } from '../../linear-algebra/matrix/principal-axes';
 
 interface Sphere3D {
     center: Vec3,
@@ -202,11 +203,28 @@ namespace Sphere3D {
             return out;
         }
         if (hasExtrema(sphere)) {
+            const positions = new Float32Array(sphere.extrema.length * 3);
+            for (let i = 0; i < sphere.extrema.length; i++) {
+                Vec3.toArray(sphere.extrema[i], positions, i * 3);
+            }
+
+            const axes = PrincipalAxes.calculateMomentsAxes(positions);
+            Axes3D.scale(axes, Axes3D.normalize(axes, axes), delta);
+
             setExtrema(out, sphere.extrema.map(e => {
                 Vec3.sub(tmpDir, e, sphere.center);
-                const dist = Vec3.distance(sphere.center, e);
-                Vec3.normalize(tmpDir, tmpDir);
-                return Vec3.scaleAndAdd(Vec3(), sphere.center, tmpDir, dist + delta);
+                const out = Vec3.clone(e);
+
+                const sA = Vec3.dot(tmpDir, axes.dirA) < 0 ? -1 : 1;
+                Vec3.scaleAndAdd(out, out, axes.dirA, sA);
+
+                const sB = Vec3.dot(tmpDir, axes.dirB) < 0 ? -1 : 1;
+                Vec3.scaleAndAdd(out, out, axes.dirB, sB);
+
+                const sC = Vec3.dot(tmpDir, axes.dirC) < 0 ? -1 : 1;
+                Vec3.scaleAndAdd(out, out, axes.dirC, sC);
+
+                return out;
             }));
         }
         return out;

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -98,29 +98,20 @@ class InteractionsInterContacts extends InterUnitGraph<number, Features.FeatureI
     constructor(map: Map<number, InterUnitGraph.UnitPairEdges<number, Features.FeatureIndex, InteractionsInterContacts.Props>[]>, unitsFeatures: IntMap<Features>) {
         super(map);
 
-        let count = 0;
-        const elementKeyIndex = new Map<string, number[]>();
-
-        const add = (index: StructureElement.UnitIndex, unitId: number) => {
-            const vertexKey = this.getElementKey(index, unitId);
-            const e = elementKeyIndex.get(vertexKey);
-            if (e === undefined) elementKeyIndex.set(vertexKey, [count]);
-            else e.push(count);
-        };
-
-        this.map.forEach(pairEdgesArray => {
-            pairEdgesArray.forEach(({ unitA, connectedIndices }) => {
-                connectedIndices.forEach(indexA => {
-                    const { offsets: offsetsA, members: membersA } = unitsFeatures.get(unitA);
-                    for (let j = offsetsA[indexA], jl = offsetsA[indexA + 1]; j < jl; ++j) {
-                        add(membersA[j], unitA);
-                    }
-                    count += 1;
-                });
-            });
-        });
-
-        this.elementKeyIndex = elementKeyIndex;
+        this.elementKeyIndex = new Map<string, number[]>();
+        for (let i = 0, il = this.edges.length; i < il; ++i) {
+            const { unitA, indexA } = this.edges[i];
+            const { offsets, members } = unitsFeatures.get(unitA);
+            for (let j = offsets[indexA], jl = offsets[indexA + 1]; j < jl; ++j) {
+                const vertexKey = this.getElementKey(members[j], unitA);
+                const e = this.elementKeyIndex.get(vertexKey);
+                if (e === undefined) {
+                    this.elementKeyIndex.set(vertexKey, [i]);
+                } else {
+                    e.push(i);
+                }
+            }
+        }
     }
 }
 namespace InteractionsInterContacts {

src/mol-model-props/computed/representations/interactions-inter-unit-cylinder.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -74,10 +74,11 @@ function createInterUnitInteractionCylinderMesh(ctx: VisualContext, structure: S
                 if (!childUnitA) return true;
 
                 const unitA = structure.unitMap.get(b.unitA);
-                const fA = unitsFeatures.get(b.unitA);
-                // TODO: check all members
-                const eA = unitA.elements[fA.members[fA.offsets[b.indexA]]];
-                if (!SortedArray.has(childUnitA.elements, eA)) return true;
+                const { offsets, members } = unitsFeatures.get(b.unitA);
+                for (let i = offsets[b.indexA], il = offsets[b.indexA + 1]; i < il; ++i) {
+                    const eA = unitA.elements[members[i]];
+                    if (!SortedArray.has(childUnitA.elements, eA)) return true;
+                }
             }
 
             return false;
@@ -144,6 +145,9 @@ function getInteractionLoci(pickingId: PickingId, structure: Structure, id: numb
     return EmptyLoci;
 }
 
+const __unitMap = new Map<number, OrderedSet<StructureElement.UnitIndex>>();
+const __contactIndicesSet = new Set<number>();
+
 function eachInteraction(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean, isMarking: boolean) {
     let changed = false;
     if (Interactions.isLoci(loci)) {
@@ -162,21 +166,48 @@ function eachInteraction(loci: Loci, structure: Structure, apply: (interval: Int
         if (!Structure.areEquivalent(loci.structure, structure)) return false;
         if (isMarking && loci.elements.length === 1) return false; // only a single unit
 
-        const contacts = InteractionsProvider.get(structure).value?.contacts;
-        if (!contacts) return false;
+        const interactions = InteractionsProvider.get(structure).value;
+        if (!interactions) return false;
+
+        const { contacts, unitsFeatures } = interactions;
+
+        for (const e of loci.elements) __unitMap.set(e.unit.id, e.indices);
 
-        // TODO when isMarking, all elements of contact features need to be in the loci
         for (const e of loci.elements) {
             const { unit } = e;
             if (!Unit.isAtomic(unit)) continue;
-            if (isMarking && OrderedSet.size(e.indices) === 1) continue;
 
             OrderedSet.forEach(e.indices, v => {
                 for (const idx of contacts.getContactIndicesForElement(v, unit)) {
-                    if (apply(Interval.ofSingleton(idx))) changed = true;
+                    __contactIndicesSet.add(idx);
                 }
             });
         }
+
+        __contactIndicesSet.forEach(i => {
+            if (isMarking) {
+                const { indexA, unitA, indexB, unitB } = contacts.edges[i];
+
+                const indicesA = __unitMap.get(unitA);
+                const indicesB = __unitMap.get(unitB);
+                if (!indicesA || !indicesB) return;
+
+                const { offsets: offsetsA, members: membersA } = unitsFeatures.get(unitA);
+                for (let j = offsetsA[indexA], jl = offsetsA[indexA + 1]; j < jl; ++j) {
+                    if (!OrderedSet.has(indicesA, membersA[j])) return;
+                }
+
+                const { offsets: offsetsB, members: membersB } = unitsFeatures.get(unitB);
+                for (let j = offsetsB[indexB], jl = offsetsB[indexB + 1]; j < jl; ++j) {
+                    if (!OrderedSet.has(indicesB, membersB[j])) return;
+                }
+            }
+
+            if (apply(Interval.ofSingleton(i))) changed = true;
+        });
+
+        __unitMap.clear();
+        __contactIndicesSet.clear();
     }
     return changed;
 }

src/mol-model-props/computed/representations/interactions-intra-unit-cylinder.ts

@@ -56,11 +56,19 @@ async function createIntraUnitInteractionsCylinderMesh(ctx: VisualContext, unit:
             const sizeB = theme.size.size(location);
             return Math.min(sizeA, sizeB) * sizeFactor;
         },
-        ignore: (edgeIndex: number) => (
-            flag[edgeIndex] === InteractionFlag.Filtered ||
-            // TODO: check all members
-            (!!childUnit && !SortedArray.has(childUnit.elements, unit.elements[members[offsets[a[edgeIndex]]]]))
-        )
+        ignore: (edgeIndex: number) => {
+            if (flag[edgeIndex] === InteractionFlag.Filtered) return true;
+
+            if (childUnit) {
+                const f = a[edgeIndex];
+                for (let i = offsets[f], jl = offsets[f + 1]; i < jl; ++i) {
+                    const e = unit.elements[members[offsets[i]]];
+                    if (!SortedArray.has(childUnit.elements, e)) return true;
+                }
+            }
+
+            return false;
+        }
     };
 
     const m = createLinkCylinderMesh(ctx, builderProps, props, mesh);
@@ -164,7 +172,6 @@ function eachInteraction(loci: Loci, structureGroup: StructureGroup, apply: (int
             const unitIdx = group.unitIndexMap.get(e.unit.id);
             if (unitIdx === undefined) continue;
 
-            __contactIndicesSet.clear();
             OrderedSet.forEach(e.indices, v => {
                 for (let i = fOffsets[v], il = fOffsets[v + 1]; i < il; ++i) {
                     const fI = fIndices[i];
@@ -188,6 +195,8 @@ function eachInteraction(loci: Loci, structureGroup: StructureGroup, apply: (int
 
                 if (apply(Interval.ofSingleton(unitIdx * groupCount + i))) changed = true;
             });
+
+            __contactIndicesSet.clear();
         }
     }
     return changed;

src/mol-model/structure/model/properties/coarse/hierarchy.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -63,6 +63,28 @@ export interface CoarseHierarchy {
     gaussians: CoarseElements
 }
 
+const EmptyCoarseElements: CoarseElements = {
+    chainKey: [],
+    entityKey: [],
+    findSequenceKey: () => -1 as ElementIndex,
+    findChainKey: () => -1 as ChainIndex,
+    getEntityFromChain: () => -1 as EntityIndex,
+
+    count: 0,
+    entity_id: Column.Undefined(0, Column.Schema.str),
+    asym_id: Column.Undefined(0, Column.Schema.str),
+    seq_id_begin: Column.Undefined(0, Column.Schema.int),
+    seq_id_end: Column.Undefined(0, Column.Schema.int),
+    chainElementSegments: Segmentation.create([]),
+
+    polymerRanges: SortedRanges.ofSortedRanges([]),
+    gapRanges: SortedRanges.ofSortedRanges([]),
+};
+
 export namespace CoarseHierarchy {
-    export const Empty: CoarseHierarchy = { isDefined: false } as any;
+    export const Empty: CoarseHierarchy = {
+        isDefined: false,
+        spheres: EmptyCoarseElements,
+        gaussians: EmptyCoarseElements
+    };
 }

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -497,7 +497,9 @@ export namespace Loci {
             if (!elementIndices) continue;
 
             const indices = getUnitIndices(unit.elements, elementIndices);
-            elements[elements.length] = { unit, indices };
+            if (OrderedSet.size(indices)) {
+                elements[elements.length] = { unit, indices };
+            }
         }
 
         return Loci(loci.structure, elements);

src/mol-model/volume/volume.ts

@@ -15,6 +15,7 @@ import { ModelFormat } from '../../mol-model-formats/format';
 import { CustomProperties } from '../custom-property';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { toPrecision } from '../../mol-util/number';
+import { DscifFormat } from '../../mol-model-formats/volume/density-server';
 
 export interface Volume {
     readonly label?: string
@@ -84,6 +85,23 @@ export namespace Volume {
         }
     }
 
+    // Converts iso value to relative if using downsample VolumeServer data
+    export function adjustedIsoValue(volume: Volume, value: number, kind: 'absolute' | 'relative') {
+        if (kind === 'relative') return IsoValue.relative(value);
+
+        const absolute = IsoValue.absolute(value);
+        if (DscifFormat.is(volume.sourceData)) {
+            const stats = {
+                min: volume.sourceData.data.volume_data_3d_info.min_source.value(0),
+                max: volume.sourceData.data.volume_data_3d_info.max_source.value(0),
+                mean: volume.sourceData.data.volume_data_3d_info.mean_source.value(0),
+                sigma: volume.sourceData.data.volume_data_3d_info.sigma_source.value(0),
+            };
+            return Volume.IsoValue.toRelative(absolute, stats);
+        }
+        return absolute;
+    }
+
     const defaultStats: Grid['stats'] = { min: -1, max: 1, mean: 0, sigma: 0.1 };
     export function createIsoValueParam(defaultValue: Volume.IsoValue, stats?: Grid['stats']) {
         const sts = stats || defaultStats;

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -75,8 +75,8 @@ const DownloadDensity = StateAction.build({
         case 'pdb-xray':
             downloadParams = src.params.provider.server === 'pdbe' ? {
                 url: Asset.Url(src.params.type === '2fofc'
-                    ? `http://www.ebi.ac.uk/pdbe/coordinates/files/${src.params.provider.id.toLowerCase()}.ccp4`
-                    : `http://www.ebi.ac.uk/pdbe/coordinates/files/${src.params.provider.id.toLowerCase()}_diff.ccp4`),
+                    ? `https://www.ebi.ac.uk/pdbe/coordinates/files/${src.params.provider.id.toLowerCase()}.ccp4`
+                    : `https://www.ebi.ac.uk/pdbe/coordinates/files/${src.params.provider.id.toLowerCase()}_diff.ccp4`),
                 isBinary: true,
                 label: `PDBe X-ray map: ${src.params.provider.id}`
             } : {

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

@@ -18,7 +18,6 @@ import { objectForEach } from '../../mol-util/object';
 import { RecommendedIsoValue } from '../../mol-model-formats/volume/property';
 import { getContourLevelEmdb } from '../../mol-plugin/behavior/dynamic/volume-streaming/util';
 import { Task } from '../../mol-task';
-import { DscifFormat } from '../../mol-model-formats/volume/density-server';
 
 export const VolumeFormatCategory = 'Volume';
 type Params = { entryId?: string };
@@ -42,19 +41,9 @@ async function tryObtainRecommendedIsoValue(plugin: PluginContext, volume?: Volu
 function tryGetRecomendedIsoValue(volume: Volume) {
     const recommendedIsoValue = RecommendedIsoValue.Provider.get(volume);
     if (!recommendedIsoValue) return;
-
     if (recommendedIsoValue.kind === 'relative') return recommendedIsoValue;
 
-    let stats = volume.grid.stats;
-    if (DscifFormat.is(volume.sourceData)) {
-        stats = {
-            min: volume.sourceData.data.volume_data_3d_info.min_source.value(0),
-            max: volume.sourceData.data.volume_data_3d_info.max_source.value(0),
-            mean: volume.sourceData.data.volume_data_3d_info.mean_source.value(0),
-            sigma: volume.sourceData.data.volume_data_3d_info.sigma_source.value(0),
-        };
-    }
-    return Volume.IsoValue.toRelative(recommendedIsoValue, stats);
+    return Volume.adjustedIsoValue(volume, recommendedIsoValue.absoluteValue, 'absolute');
 }
 
 async function defaultVisuals(plugin: PluginContext, data: { volume: StateObjectSelector<PluginStateObject.Volume.Data> }) {

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -212,11 +212,14 @@ export const DefaultLociLabelProvider = PluginBehavior.create({
         private f = {
             label: (loci: Loci) => {
                 const label: string[] = [];
-                if (StructureElement.Loci.is(loci) && loci.elements.length === 1) {
-                    const { unit: u } = loci.elements[0];
-                    const l = StructureElement.Location.create(loci.structure, u, u.elements[0]);
-                    const name = StructureProperties.entity.pdbx_description(l).join(', ');
-                    label.push(name);
+                if (StructureElement.Loci.is(loci)) {
+                    const entityNames = new Set<string>();
+                    for (const { unit: u } of loci.elements) {
+                        const l = StructureElement.Location.create(loci.structure, u, u.elements[0]);
+                        const name = StructureProperties.entity.pdbx_description(l).join(', ');
+                        entityNames.add(name);
+                    }
+                    if (entityNames.size === 1) entityNames.forEach(name => label.push(name));
                 }
                 label.push(lociLabel(loci));
                 return label.filter(l => !!l).join('</br>');

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

@@ -84,7 +84,7 @@ export function UpdateRepresentationVisibility(ctx: PluginContext) {
 }
 
 function updateVisibility(cell: StateObjectCell, r: Representation<any>) {
-    if (r.state.visible === cell.state.isHidden) {
+    if (r.state.visible === !!cell.state.isHidden) {
         r.setState({ visible: !cell.state.isHidden });
         return true;
     } else {

src/mol-repr/shape/loci/common.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
@@ -10,9 +10,9 @@ import { ColorNames } from '../../../mol-util/color/names';
 import { Text } from '../../../mol-geo/geometry/text/text';
 
 export const MeasurementRepresentationCommonTextParams = {
-    customText: PD.Text('', { label: 'Text', description: 'Override the label with custom value.' }),
+    customText: PD.Text('', { label: 'Text', description: 'Override the label with custom value.', isEssential: true }),
     textColor: PD.Color(ColorNames.black, { isEssential: true }),
-    textSize: PD.Numeric(0.5, { min: 0.1, max: 5, step: 0.1 }, { isEssential: true }),
+    textSize: PD.Numeric(0.5, { min: 0.1, max: 10, step: 0.1 }, { isEssential: true }),
 };
 
 export const LociLabelTextParams = {

src/mol-repr/structure/visual/molecular-surface-mesh.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -57,7 +57,7 @@ async function createMolecularSurfaceMesh(ctx: VisualContext, unit: Unit, struct
     Mesh.transform(surface, transform);
     if (ctx.webgl && !ctx.webgl.isWebGL2) Mesh.uniformTriangleGroup(surface);
 
-    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, props.probeRadius + getUnitExtraRadius(unit));
+    const sphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, getUnitExtraRadius(unit));
     surface.setBoundingSphere(sphere);
     (surface.meta as MolecularSurfaceMeta).resolution = resolution;
 

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -224,6 +224,8 @@ export function getInterBondLoci(pickingId: PickingId, structure: Structure, id:
     return EmptyLoci;
 }
 
+const __unitMap = new Map<number, OrderedSet<StructureElement.UnitIndex>>();
+
 export function eachInterBond(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean, isMarking: boolean) {
     let changed = false;
     if (Bond.isLoci(loci)) {
@@ -238,14 +240,13 @@ export function eachInterBond(loci: Loci, structure: Structure, apply: (interval
         if (!Structure.areEquivalent(loci.structure, structure)) return false;
         if (isMarking && loci.elements.length === 1) return false; // only a single unit
 
-        const map = new Map<number, OrderedSet<StructureElement.UnitIndex>>();
-        for (const e of loci.elements) map.set(e.unit.id, e.indices);
+        for (const e of loci.elements) __unitMap.set(e.unit.id, e.indices);
 
         for (const e of loci.elements) {
             const { unit } = e;
             if (!Unit.isAtomic(unit)) continue;
             structure.interUnitBonds.getConnectedUnits(unit.id).forEach(b => {
-                const otherLociIndices = map.get(b.unitB);
+                const otherLociIndices = __unitMap.get(b.unitB);
                 if (!isMarking || otherLociIndices) {
                     OrderedSet.forEach(e.indices, v => {
                         if (!b.connectedIndices.includes(v)) return;
@@ -259,6 +260,8 @@ export function eachInterBond(loci: Loci, structure: Structure, apply: (interval
                 }
             });
         }
+
+        __unitMap.clear();
     }
     return changed;
 }

src/mol-state/transform.ts

@@ -76,14 +76,23 @@ namespace Transform {
             const s = (b as any)[k], t = (a as any)[k];
             if (!!s === !!t) continue;
             changed = true;
-            (a as any)[k] = s;
+            if (s !== void 0) {
+                (a as any)[k] = s;
+            } else {
+                delete (a as any)[k];
+            }
         }
         for (const k of Object.keys(a)) {
             const s = (b as any)[k], t = (a as any)[k];
             if (!!s === !!t) continue;
             changed = true;
-            (a as any)[k] = s;
+            if (s !== void 0) {
+                (a as any)[k] = s;
+            } else {
+                delete (a as any)[k];
+            }
         }
+
         return changed;
     }
 

src/mol-theme/color/element-symbol.ts

@@ -16,6 +16,9 @@ import { getAdjustedColorMap } from '../../mol-util/color/color';
 import { getColorMapParams } from '../../mol-util/color/params';
 import { ChainIdColorTheme, ChainIdColorThemeParams } from './chain-id';
 import { OperatorNameColorThemeParams, OperatorNameColorTheme } from './operator-name';
+import { EntityIdColorTheme, EntityIdColorThemeParams } from './entity-id';
+import { assertUnreachable } from '../../mol-util/type-helpers';
+import { EntitySourceColorTheme, EntitySourceColorThemeParams } from './entity-source';
 
 // from Jmol http://jmol.sourceforge.net/jscolors/ (or 0xFFFFFF)
 export const ElementSymbolColors = ColorMap({
@@ -26,13 +29,13 @@ export type ElementSymbolColors = typeof ElementSymbolColors
 const DefaultElementSymbolColor = Color(0xFFFFFF);
 const Description = 'Assigns a color to every atom according to its chemical element.';
 
-// TODO generalise `carbonColor` param to all themes?
-
 export const ElementSymbolColorThemeParams = {
     carbonColor: PD.MappedStatic('chain-id', {
-        'chain-id': PD.Group({ ...ChainIdColorThemeParams }),
-        'operator-name': PD.Group({ ...OperatorNameColorThemeParams }),
-        'element-symbol': PD.Group({})
+        'chain-id': PD.Group(ChainIdColorThemeParams),
+        'entity-id': PD.Group(EntityIdColorThemeParams),
+        'entity-source': PD.Group(EntitySourceColorThemeParams),
+        'operator-name': PD.Group(OperatorNameColorThemeParams),
+        'element-symbol': PD.EmptyGroup()
     }, { description: 'Use chain-id coloring for carbon atoms.' }),
     saturation: PD.Numeric(0, { min: -6, max: 6, step: 0.1 }),
     lightness: PD.Numeric(0.2, { min: -6, max: 6, step: 0.1 }),
@@ -54,11 +57,14 @@ export function elementSymbolColor(colorMap: ElementSymbolColors, element: Eleme
 export function ElementSymbolColorTheme(ctx: ThemeDataContext, props: PD.Values<ElementSymbolColorThemeParams>): ColorTheme<ElementSymbolColorThemeParams> {
     const colorMap = getAdjustedColorMap(props.colors.name === 'default' ? ElementSymbolColors : props.colors.params, props.saturation, props.lightness);
 
-    const carbonColor = props.carbonColor.name === 'chain-id'
-        ? ChainIdColorTheme(ctx, props.carbonColor.params).color
-        : props.carbonColor.name === 'operator-name'
-            ? OperatorNameColorTheme(ctx, props.carbonColor.params).color
-            : undefined;
+    const pcc = props.carbonColor;
+    const carbonColor =
+        pcc.name === 'chain-id' ? ChainIdColorTheme(ctx, pcc.params).color :
+            pcc.name === 'entity-id' ? EntityIdColorTheme(ctx, pcc.params).color :
+                pcc.name === 'entity-source' ? EntitySourceColorTheme(ctx, pcc.params).color :
+                    pcc.name === 'operator-name' ? OperatorNameColorTheme(ctx, pcc.params).color :
+                        pcc.name === 'element-symbol' ? undefined :
+                            assertUnreachable(pcc);
 
     function elementColor(element: ElementSymbol, location: Location) {
         return (carbonColor && element === 'C')

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

@@ -38,15 +38,18 @@ function getEntityIdSerialMap(structure: Structure) {
             const k = key(label_entity_id.value(j), i);
             if (!map.has(k)) map.set(k, map.size);
         }
-        const { entity_id: spheres_entity_id } = structure.models[i].coarseHierarchy.spheres;
-        for (let j = 0, jl = spheres_entity_id.rowCount; j < jl; ++j) {
-            const k = key(spheres_entity_id.value(j), i);
-            if (!map.has(k)) map.set(k, map.size);
-        }
-        const { entity_id: gaussians_entity_id } = structure.models[i].coarseHierarchy.gaussians;
-        for (let j = 0, jl = gaussians_entity_id.rowCount; j < jl; ++j) {
-            const k = key(gaussians_entity_id.value(j), i);
-            if (!map.has(k)) map.set(k, map.size);
+        const { coarseHierarchy } = structure.models[i];
+        if (coarseHierarchy.isDefined) {
+            const { entity_id: spheres_entity_id } = coarseHierarchy.spheres;
+            for (let j = 0, jl = spheres_entity_id.rowCount; j < jl; ++j) {
+                const k = key(spheres_entity_id.value(j), i);
+                if (!map.has(k)) map.set(k, map.size);
+            }
+            const { entity_id: gaussians_entity_id } = coarseHierarchy.gaussians;
+            for (let j = 0, jl = gaussians_entity_id.rowCount; j < jl; ++j) {
+                const k = key(gaussians_entity_id.value(j), i);
+                if (!map.has(k)) map.set(k, map.size);
+            }
         }
     }
     return map;

src/servers/volume/config.ts

@@ -197,13 +197,13 @@ export function configureLocal() {
         description: VOLUME_SERVER_HEADER
     });
     parser.add_argument('--jobs', { help: `Path to a JSON file with job specification.`, required: false });
-    parser.add_argument('--jobsTemplate', { help: 'Print example template for jobs.json and exit.', required: false, nargs: 0 });
+    parser.add_argument('--jobsTemplate', { help: 'Print example template for jobs.json and exit.', required: false, action: 'store_true' });
     addJsonConfigArgs(parser);
     addLimitsArgs(parser);
 
     const config = parser.parse_args() as LimitsConfig & ServerJsonConfig;
 
-    if (config.cfgTemplate !== null) {
+    if (config.cfgTemplate) {
         console.log(JSON.stringify(DefaultLimitsConfig, null, 2));
         process.exit(0);
     }
@@ -216,7 +216,7 @@ export function configureLocal() {
             setLimitsConfig(cfg);
         }
 
-        if (config.printCfg !== null) {
+        if (config.printCfg) {
             console.log(JSON.stringify(LimitsConfig, null, 2));
             process.exit(0);
         }

src/servers/volume/query.ts

@@ -14,7 +14,7 @@ import * as LocalApi from './server/local-api';
 
 const config = configureLocal();
 
-if (config.jobsTemplate !== null) {
+if (config.jobsTemplate) {
     const exampleJobs: LocalApi.JobEntry[] = [{
         source: {
             filename: `g:/test/mdb/xray-1tqn.mdb`,