3.2.0

Add TraceOnly option for Structure Superposition

CHANGELOG.md

@@ -6,6 +6,45 @@ Note that since we don't clearly distinguish between a public and private interf
 
 ## [Unreleased]
 
+## [v3.2.0] - 2022-02-17
+
+- Rename "best database mapping" to "SIFTS Mapping"
+- Add schema and export support for ``atom_site.pdbx_sifts_xref_*`` fields
+- Add schema export support for ``atom_site.pdbx_label_index`` field
+- Add `traceOnly` parameter to chain/UniProt-based structure alignment
+- Store ``IndexPairBonds`` as a dynamic property.
+
+## [v3.1.0] - 2022-02-06
+
+- Fix ``xrayShaded`` & ``ignoreLight`` params not working at the same time
+- Add ``ignoreLight`` to component params
+- Tweaks for cleaner default representation style
+    - Cartoon: use ``nucleotide-ring`` instead of ``nucleotide-block``
+    - Focus: use ``xrayShaded`` instead of opacity; adjust target size; don't show non-covalent interactions twice
+- Fix representation preset side effects (changing post-processing parameters, see #363)
+- Add Quick Styles panel (default, illustrative, stylized)
+- Fix exported structure missing secondary-structure categories (#364)
+- Fix volume streaming error message: distinguish between missing data and server error (#364)
+
+## [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"

data/cif-field-names/mmcif-field-names.csv

@@ -24,6 +24,11 @@ atom_site.auth_asym_id
 atom_site.auth_seq_id
 atom_site.pdbx_PDB_model_num
 atom_site.ihm_model_id
+atom_site.pdbx_label_index
+atom_site.pdbx_sifts_xref_db_name
+atom_site.pdbx_sifts_xref_db_acc
+atom_site.pdbx_sifts_xref_db_num
+atom_site.pdbx_sifts_xref_db_res
 
 atom_site_anisotrop.id
 atom_site_anisotrop.U

package.json

@@ -1,6 +1,6 @@
 {
   "name": "molstar",
-  "version": "3.0.0",
+  "version": "3.2.0",
   "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",
@@ -92,50 +92,50 @@
   "license": "MIT",
   "devDependencies": {
     "@graphql-codegen/add": "^3.1.1",
-    "@graphql-codegen/cli": "^2.4.0",
+    "@graphql-codegen/cli": "^2.5.0",
     "@graphql-codegen/time": "^3.1.1",
-    "@graphql-codegen/typescript": "^2.4.2",
+    "@graphql-codegen/typescript": "^2.4.3",
     "@graphql-codegen/typescript-graphql-files-modules": "^2.1.1",
-    "@graphql-codegen/typescript-graphql-request": "^4.3.3",
-    "@graphql-codegen/typescript-operations": "^2.2.2",
+    "@graphql-codegen/typescript-graphql-request": "^4.3.4",
+    "@graphql-codegen/typescript-operations": "^2.2.4",
     "@types/cors": "^2.8.12",
     "@types/gl": "^4.1.0",
     "@types/jest": "^27.4.0",
-    "@typescript-eslint/eslint-plugin": "^5.10.0",
-    "@typescript-eslint/parser": "^5.10.0",
+    "@typescript-eslint/eslint-plugin": "^5.10.2",
+    "@typescript-eslint/parser": "^5.10.2",
     "benchmark": "^2.1.4",
     "concurrently": "^7.0.0",
     "cpx2": "^4.1.2",
     "crypto-browserify": "^3.12.0",
-    "css-loader": "^6.5.1",
-    "eslint": "^8.7.0",
+    "css-loader": "^6.6.0",
+    "eslint": "^8.8.0",
     "extra-watch-webpack-plugin": "^1.0.3",
     "file-loader": "^6.2.0",
     "fs-extra": "^10.0.0",
-    "graphql": "^16.2.0",
+    "graphql": "^16.3.0",
     "http-server": "^14.1.0",
-    "jest": "^27.4.7",
-    "mini-css-extract-plugin": "^2.5.2",
+    "jest": "^27.5.0",
+    "mini-css-extract-plugin": "^2.5.3",
     "path-browserify": "^1.0.1",
     "raw-loader": "^4.0.2",
-    "sass": "^1.49.0",
+    "sass": "^1.49.7",
     "sass-loader": "^12.4.0",
-    "simple-git": "^2.48.0",
+    "simple-git": "^3.1.1",
     "stream-browserify": "^3.0.0",
     "style-loader": "^3.3.1",
     "ts-jest": "^27.1.3",
     "typescript": "^4.5.5",
-    "webpack": "^5.67.0",
-    "webpack-cli": "^4.9.1"
+    "webpack": "^5.68.0",
+    "webpack-cli": "^4.9.2"
   },
   "dependencies": {
     "@types/argparse": "^2.0.10",
     "@types/benchmark": "^2.1.1",
     "@types/compression": "1.7.2",
     "@types/express": "^4.17.13",
-    "@types/node": "^16.11.21",
+    "@types/node": "^16.11.22",
     "@types/node-fetch": "^2.5.12",
-    "@types/react": "^17.0.38",
+    "@types/react": "^17.0.39",
     "@types/react-dom": "^17.0.11",
     "@types/swagger-ui-dist": "3.30.1",
     "argparse": "^2.0.1",
@@ -148,7 +148,7 @@
     "immutable": "^4.0.0",
     "node-fetch": "^2.6.7",
     "rxjs": "^7.5.2",
-    "swagger-ui-dist": "^4.2.1",
+    "swagger-ui-dist": "^4.5.0",
     "tslib": "^2.3.1",
     "util.promisify": "^1.1.1",
     "xhr2": "^0.2.1"
@@ -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/extensions/rcsb/graphql/types.ts

@@ -4,7 +4,7 @@ export type InputMaybe<T> = Maybe<T>;
 export type Exact<T extends { [key: string]: unknown }> = { [K in keyof T]: T[K] };
 export type MakeOptional<T, K extends keyof T> = Omit<T, K> & { [SubKey in K]?: Maybe<T[SubKey]> };
 export type MakeMaybe<T, K extends keyof T> = Omit<T, K> & { [SubKey in K]: Maybe<T[SubKey]> };
-// Generated on 2022-01-15T19:52:34-08:00
+// Generated on 2022-02-06T15:40:15-08:00
 
 /** All built-in and custom scalars, mapped to their actual values */
 export type Scalars = {
@@ -13145,4 +13145,4 @@ export type AssemblySymmetryQueryVariables = Exact<{
 }>;
 
 
-export type AssemblySymmetryQuery = { readonly assembly?: { readonly rcsb_struct_symmetry?: ReadonlyArray<{ readonly kind: string, readonly oligomeric_state: string, readonly stoichiometry: ReadonlyArray<string | null | undefined>, readonly symbol: string, readonly type: string, readonly clusters: ReadonlyArray<{ readonly avg_rmsd?: number | null | undefined, readonly members: ReadonlyArray<{ readonly asym_id: string, readonly pdbx_struct_oper_list_ids?: ReadonlyArray<string | null | undefined> | null | undefined } | null | undefined> } | null | undefined>, readonly rotation_axes?: ReadonlyArray<{ readonly order?: number | null | undefined, readonly start: ReadonlyArray<number | null | undefined>, readonly end: ReadonlyArray<number | null | undefined> } | null | undefined> | null | undefined } | null | undefined> | null | undefined } | null | undefined };
+export type AssemblySymmetryQuery = { readonly assembly?: { readonly rcsb_struct_symmetry?: ReadonlyArray<{ readonly kind: string, readonly oligomeric_state: string, readonly stoichiometry: ReadonlyArray<string | null>, readonly symbol: string, readonly type: string, readonly clusters: ReadonlyArray<{ readonly avg_rmsd?: number | null, readonly members: ReadonlyArray<{ readonly asym_id: string, readonly pdbx_struct_oper_list_ids?: ReadonlyArray<string | null> | null } | null> } | null>, readonly rotation_axes?: ReadonlyArray<{ readonly order?: number | null, readonly start: ReadonlyArray<number | null>, readonly end: ReadonlyArray<number | null> } | null> | null } | null> | null } | null };

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-gl/shader/chunks/apply-light-color.glsl.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 Alexander Rose <alexander.rose@weirdbyte.de>
  *
@@ -8,61 +8,65 @@
  */
 
 export const apply_light_color = `
-#ifdef bumpEnabled
-    if (uBumpFrequency > 0.0 && uBumpAmplitude > 0.0) {
-        vec3 bumpNormal = perturbNormal(-vViewPosition, normal, fbm(vModelPosition * uBumpFrequency), (uBumpAmplitude * bumpiness) / uBumpFrequency);
-        #ifdef enabledFragDepth
-            if (!isNaN(bumpNormal.x) && !isNaN(bumpNormal.y) && !isNaN(bumpNormal.z)) {
-                normal = bumpNormal;
-            }
-        #else
-            normal = bumpNormal;
-        #endif
-    }
-#endif
-
-vec4 color = material;
-
-ReflectedLight reflectedLight = ReflectedLight(vec3(0.0), vec3(0.0), vec3(0.0), vec3(0.0));
-
-PhysicalMaterial physicalMaterial;
-physicalMaterial.diffuseColor = color.rgb * (1.0 - metalness);
-#ifdef enabledFragDepth
-    physicalMaterial.roughness = min(max(roughness, 0.0525), 1.0);
+#ifdef dIgnoreLight
+    gl_FragColor = material;
 #else
-    vec3 dxy = max(abs(dFdx(normal)), abs(dFdy(normal)));
-    float geometryRoughness = max(max(dxy.x, dxy.y), dxy.z);
-    physicalMaterial.roughness = min(max(roughness, 0.0525) + geometryRoughness, 1.0);
+    #ifdef bumpEnabled
+        if (uBumpFrequency > 0.0 && uBumpAmplitude > 0.0) {
+            vec3 bumpNormal = perturbNormal(-vViewPosition, normal, fbm(vModelPosition * uBumpFrequency), (uBumpAmplitude * bumpiness) / uBumpFrequency);
+            #ifdef enabledFragDepth
+                if (!isNaN(bumpNormal.x) && !isNaN(bumpNormal.y) && !isNaN(bumpNormal.z)) {
+                    normal = bumpNormal;
+                }
+            #else
+                normal = bumpNormal;
+            #endif
+        }
+    #endif
+
+    vec4 color = material;
+
+    ReflectedLight reflectedLight = ReflectedLight(vec3(0.0), vec3(0.0), vec3(0.0), vec3(0.0));
+
+    PhysicalMaterial physicalMaterial;
+    physicalMaterial.diffuseColor = color.rgb * (1.0 - metalness);
+    #ifdef enabledFragDepth
+        physicalMaterial.roughness = min(max(roughness, 0.0525), 1.0);
+    #else
+        vec3 dxy = max(abs(dFdx(normal)), abs(dFdy(normal)));
+        float geometryRoughness = max(max(dxy.x, dxy.y), dxy.z);
+        physicalMaterial.roughness = min(max(roughness, 0.0525) + geometryRoughness, 1.0);
+    #endif
+    physicalMaterial.specularColor = mix(vec3(0.04), color.rgb, metalness);
+    physicalMaterial.specularF90 = 1.0;
+
+    GeometricContext geometry;
+    geometry.position = -vViewPosition;
+    geometry.normal = normal;
+    geometry.viewDir = normalize(vViewPosition);
+
+    IncidentLight directLight;
+    #pragma unroll_loop_start
+    for (int i = 0; i < dLightCount; ++i) {
+        directLight.direction = uLightDirection[i];
+        directLight.color = uLightColor[i] * PI; // * PI for punctual light
+        RE_Direct_Physical(directLight, geometry, physicalMaterial, reflectedLight);
+    }
+    #pragma unroll_loop_end
+
+    vec3 irradiance = uAmbientColor * PI; // * PI for punctual light
+    RE_IndirectDiffuse_Physical(irradiance, geometry, physicalMaterial, reflectedLight);
+
+    // indirect specular only metals
+    vec3 radiance = uAmbientColor * metalness;
+    vec3 iblIrradiance = uAmbientColor * metalness;
+    vec3 clearcoatRadiance = vec3(0.0);
+    RE_IndirectSpecular_Physical(radiance, iblIrradiance, clearcoatRadiance, geometry, physicalMaterial, reflectedLight);
+
+    vec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + reflectedLight.directSpecular + reflectedLight.indirectSpecular;
+
+    gl_FragColor = vec4(outgoingLight, color.a);
 #endif
-physicalMaterial.specularColor = mix(vec3(0.04), color.rgb, metalness);
-physicalMaterial.specularF90 = 1.0;
-
-GeometricContext geometry;
-geometry.position = -vViewPosition;
-geometry.normal = normal;
-geometry.viewDir = normalize(vViewPosition);
-
-IncidentLight directLight;
-#pragma unroll_loop_start
-for (int i = 0; i < dLightCount; ++i) {
-    directLight.direction = uLightDirection[i];
-    directLight.color = uLightColor[i] * PI; // * PI for punctual light
-    RE_Direct_Physical(directLight, geometry, physicalMaterial, reflectedLight);
-}
-#pragma unroll_loop_end
-
-vec3 irradiance = uAmbientColor * PI; // * PI for punctual light
-RE_IndirectDiffuse_Physical(irradiance, geometry, physicalMaterial, reflectedLight);
-
-// indirect specular only metals
-vec3 radiance = uAmbientColor * metalness;
-vec3 iblIrradiance = uAmbientColor * metalness;
-vec3 clearcoatRadiance = vec3(0.0);
-RE_IndirectSpecular_Physical(radiance, iblIrradiance, clearcoatRadiance, geometry, physicalMaterial, reflectedLight);
-
-vec3 outgoingLight = reflectedLight.directDiffuse + reflectedLight.indirectDiffuse + reflectedLight.directSpecular + reflectedLight.indirectSpecular;
-
-gl_FragColor = vec4(outgoingLight, color.a);
 
 #ifdef dXrayShaded
     gl_FragColor.a *= 1.0 - pow(abs(dot(normal, vec3(0.0, 0.0, 1.0))), uXrayEdgeFalloff);

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

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2021 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>
  */
@@ -127,13 +127,9 @@ void main() {
     #elif defined(dRenderVariant_marking)
         gl_FragColor = material;
     #elif defined(dRenderVariant_color)
-        #ifdef dIgnoreLight
-            gl_FragColor = material;
-        #else
-            mat3 normalMatrix = transpose3(inverse3(mat3(uView)));
-            vec3 normal = normalize(normalMatrix * -normalize(intersection.yzw));
-            #include apply_light_color
-        #endif
+        mat3 normalMatrix = transpose3(inverse3(mat3(uView)));
+        vec3 normal = normalize(normalMatrix * -normalize(intersection.yzw));
+        #include apply_light_color
 
         #include apply_interior_color
         #include apply_marker_color

src/mol-gl/shader/direct-volume.frag.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 Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Michael Krone <michael.krone@uni-tuebingen.de>
@@ -166,9 +166,7 @@ vec3 v3m4(vec3 p, mat4 m) {
 float preFogAlphaBlended = 0.0;
 
 vec4 raymarch(vec3 startLoc, vec3 step, vec3 rayDir) {
-    #if !defined(dIgnoreLight)
-        mat3 normalMatrix = transpose3(inverse3(mat3(uModelView * vTransform)));
-    #endif
+    mat3 normalMatrix = transpose3(inverse3(mat3(uModelView * vTransform)));
     mat4 cartnToUnit = uCartnToUnit * inverse4(vTransform);
     #if defined(dClipVariant_pixel) && dClipObjectCount != 0
         mat4 modelTransform = uModel * vTransform * uTransform;
@@ -296,24 +294,20 @@ vec4 raymarch(vec3 startLoc, vec3 step, vec3 rayDir) {
             material.rgb = mix(material.rgb, overpaint.rgb, overpaint.a);
         #endif
 
-        #ifdef dIgnoreLight
+        if (material.a >= 0.01) {
+            #ifdef dPackedGroup
+                // compute gradient by central differences
+                gradient.x = textureVal(unitPos - dx).a - textureVal(unitPos + dx).a;
+                gradient.y = textureVal(unitPos - dy).a - textureVal(unitPos + dy).a;
+                gradient.z = textureVal(unitPos - dz).a - textureVal(unitPos + dz).a;
+            #else
+                gradient = cell.xyz * 2.0 - 1.0;
+            #endif
+            vec3 normal = -normalize(normalMatrix * normalize(gradient));
+            #include apply_light_color
+        } else {
             gl_FragColor.rgb = material.rgb;
-        #else
-            if (material.a >= 0.01) {
-                #ifdef dPackedGroup
-                    // compute gradient by central differences
-                    gradient.x = textureVal(unitPos - dx).a - textureVal(unitPos + dx).a;
-                    gradient.y = textureVal(unitPos - dy).a - textureVal(unitPos + dy).a;
-                    gradient.z = textureVal(unitPos - dz).a - textureVal(unitPos + dz).a;
-                #else
-                    gradient = cell.xyz * 2.0 - 1.0;
-                #endif
-                vec3 normal = -normalize(normalMatrix * normalize(gradient));
-                #include apply_light_color
-            } else {
-                gl_FragColor.rgb = material.rgb;
-            }
-        #endif
+        }
 
         gl_FragColor.a = material.a * uAlpha * uTransferScale;
 

src/mol-gl/shader/mesh.frag.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>
  */
@@ -43,17 +43,13 @@ void main() {
     #elif defined(dRenderVariant_marking)
         gl_FragColor = material;
     #elif defined(dRenderVariant_color)
-        #ifdef dIgnoreLight
-            gl_FragColor = material;
+        #if defined(dFlatShaded)
+            vec3 normal = -faceNormal;
         #else
-            #if defined(dFlatShaded)
-                vec3 normal = -faceNormal;
-            #else
-                vec3 normal = -normalize(vNormal);
-                if (uDoubleSided) normal *= float(frontFacing) * 2.0 - 1.0;
-            #endif
-            #include apply_light_color
+            vec3 normal = -normalize(vNormal);
+            if (uDoubleSided) normal *= float(frontFacing) * 2.0 - 1.0;
         #endif
+        #include apply_light_color
 
         #include apply_interior_color
         #include apply_marker_color

src/mol-gl/shader/spheres.frag.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>
  */
@@ -92,12 +92,8 @@ void main(void){
     #elif defined(dRenderVariant_marking)
         gl_FragColor = material;
     #elif defined(dRenderVariant_color)
-        #ifdef dIgnoreLight
-            gl_FragColor = material;
-        #else
-            vec3 normal = -cameraNormal;
-            #include apply_light_color
-        #endif
+        vec3 normal = -cameraNormal;
+        #include apply_light_color
 
         #include apply_interior_color
         #include apply_marker_color

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.355, IHM 1.17, MA 1.3.4.
  *
  * @author molstar/ciftools package
  */

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.355, IHM 1.17, MA 1.3.4.
  *
  * @author molstar/ciftools package
  */

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.354, IHM 1.17, MA 1.3.3.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.355, IHM 1.17, MA 1.3.4.
  *
  * @author molstar/ciftools package
  */
@@ -215,6 +215,28 @@ export const mmCIF_Schema = {
          * formal charge assignment normally found in chemical diagrams.
          */
         pdbx_formal_charge: int,
+        /**
+         * This data item is an ordinal which identifies distinct chemical components in the atom_site category, both
+         * polymeric and non-polymeric.
+         */
+        pdbx_label_index: int,
+        /**
+         * The name of additional external databases with residue level mapping.
+         */
+        pdbx_sifts_xref_db_name: str,
+        /**
+         * The accession code related to the additional external database entry.
+         */
+        pdbx_sifts_xref_db_acc: str,
+        /**
+         * The sequence position of the external database entry that corresponds
+         * to the residue mapping defined by the SIFTS process.
+         */
+        pdbx_sifts_xref_db_num: str,
+        /**
+         * Describes the residue type of the given UniProt match
+         */
+        pdbx_sifts_xref_db_res: str,
         /**
          * The model id corresponding to the atom site.
          * This data item is a pointer to _ihm_model_list.model_id
@@ -682,7 +704,7 @@ export const mmCIF_Schema = {
         /**
          * An abbreviation that identifies the database.
          */
-        database_id: Aliased<'AFDB' | 'CAS' | 'CSD' | 'EMDB' | 'ICSD' | 'MA' | 'MDF' | 'MODBASE' | 'NDB' | 'NBS' | 'PDB' | 'PDF' | 'RCSB' | 'SMR' | 'EBI' | 'PDBE' | 'BMRB' | 'WWPDB' | 'PDB_ACC'>(str),
+        database_id: Aliased<'AlphaFoldDB' | 'CAS' | 'CSD' | 'EMDB' | 'ICSD' | 'ModelArchive' | 'MDF' | 'MODBASE' | 'NDB' | 'NBS' | 'PDB' | 'PDF' | 'RCSB' | 'SWISS-MODEL_REPOSITORY' | 'EBI' | 'PDBE' | 'BMRB' | 'WWPDB' | 'PDB_ACC'>(str),
         /**
          * The code assigned by the database identified in
          * _database_2.database_id.

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-formats/structure/common/property.ts

@@ -1,7 +1,8 @@
 /**
- * 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>
  */
 
 import { Model } from '../../../mol-model/structure';
@@ -44,7 +45,7 @@ interface FormatPropertyProvider<T> {
 }
 
 namespace FormatPropertyProvider {
-    export function create<T>(descriptor: CustomPropertyDescriptor): FormatPropertyProvider<T> {
+    export function create<T>(descriptor: CustomPropertyDescriptor, options?: { asDynamic?: boolean }): FormatPropertyProvider<T> {
         const { name } = descriptor;
         const formatRegistry = new FormatRegistry<T>();
 
@@ -55,21 +56,31 @@ namespace FormatPropertyProvider {
                 return formatRegistry.isApplicable(model);
             },
             get(model: Model): T | undefined {
-                if (model._staticPropertyData[name]) return model._staticPropertyData[name];
+                const store = options?.asDynamic ? model._dynamicPropertyData : model._staticPropertyData;
+
+                if (store[name]) return store[name];
                 if (model.customProperties.has(descriptor)) return;
 
                 const obtain = formatRegistry.get(model.sourceData.kind);
                 if (!obtain) return;
 
-                model._staticPropertyData[name] = obtain(model);
+                store[name] = obtain(model);
                 model.customProperties.add(descriptor);
-                return model._staticPropertyData[name];
+                return store[name];
             },
             set(model: Model, value: T) {
-                model._staticPropertyData[name] = value;
+                if (options?.asDynamic) {
+                    model._dynamicPropertyData[name] = value;
+                } else {
+                    model._staticPropertyData[name] = value;
+                }
             },
             delete(model: Model) {
-                delete model._staticPropertyData[name];
+                if (options?.asDynamic) {
+                    delete model._dynamicPropertyData[name];
+                } else {
+                    delete model._staticPropertyData[name];
+                }
             }
         };
     }

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

@@ -2,6 +2,7 @@
  * Copyright (c) 2019-2022 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>
  */
 
 import { CustomPropertyDescriptor } from '../../../../mol-model/custom-property';
@@ -42,7 +43,7 @@ export namespace IndexPairBonds {
         name: 'index_pair_bonds',
     };
 
-    export const Provider = FormatPropertyProvider.create<IndexPairBonds>(Descriptor);
+    export const Provider = FormatPropertyProvider.create<IndexPairBonds>(Descriptor, { asDynamic: true });
 
     export type Data = {
         pairs: {

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-props/sequence/sifts-mapping.ts

@@ -11,30 +11,43 @@ import { Model } from '../../mol-model/structure';
 import { StructureElement } from '../../mol-model/structure/structure';
 import { CustomModelProperty } from '../common/custom-model-property';
 
-export { BestDatabaseSequenceMapping };
+export { SIFTSMapping as SIFTSMapping };
 
-interface BestDatabaseSequenceMapping {
+interface SIFTSMappingMapping {
     readonly dbName: string[],
     readonly accession: string[],
-    readonly num: number[],
+    readonly num: string[],
     readonly residue: string[]
 }
 
-namespace BestDatabaseSequenceMapping {
-    export const Provider: CustomModelProperty.Provider<{}, BestDatabaseSequenceMapping> = CustomModelProperty.createProvider({
-        label: 'Best Database Sequence Mapping',
+namespace SIFTSMapping {
+    export const Provider: CustomModelProperty.Provider<{}, SIFTSMappingMapping> = CustomModelProperty.createProvider({
+        label: 'SIFTS Mapping',
         descriptor: CustomPropertyDescriptor({
-            name: 'molstar_best_database_sequence_mapping'
+            name: 'sifts_sequence_mapping'
         }),
         type: 'static',
         defaultParams: {},
         getParams: () => ({}),
-        isApplicable: (data: Model) => MmcifFormat.is(data.sourceData) && data.sourceData.data.frame.categories?.atom_site?.fieldNames.indexOf('pdbx_sifts_xref_db_name') >= 0,
+        isApplicable: (data: Model) => isAvailable(data),
         obtain: async (ctx, data) => {
             return { value: fromCif(data) };
         }
     });
 
+    export function isAvailable(model: Model) {
+        if (!MmcifFormat.is(model.sourceData)) return false;
+
+        const {
+            pdbx_sifts_xref_db_name: db_name,
+            pdbx_sifts_xref_db_acc: db_acc,
+            pdbx_sifts_xref_db_num: db_num,
+            pdbx_sifts_xref_db_res: db_res
+        } = model.sourceData.data.db.atom_site;
+
+        return db_name.isDefined && db_acc.isDefined && db_num.isDefined && db_res.isDefined;
+    }
+
     export function getKey(loc: StructureElement.Location) {
         const model = loc.unit.model;
         const data = Provider.get(model).value;
@@ -55,22 +68,23 @@ namespace BestDatabaseSequenceMapping {
         return `${dbName} ${data.accession[rI]} ${data.num[rI]} ${data.residue[rI]}`;
     }
 
-    function fromCif(model: Model): BestDatabaseSequenceMapping | undefined {
+    function fromCif(model: Model): SIFTSMappingMapping | undefined {
         if (!MmcifFormat.is(model.sourceData)) return;
 
-        const { atom_site } = model.sourceData.data.frame.categories;
-        const db_name = atom_site.getField('pdbx_sifts_xref_db_name');
-        const db_acc = atom_site.getField('pdbx_sifts_xref_db_acc');
-        const db_num = atom_site.getField('pdbx_sifts_xref_db_num');
-        const db_res = atom_site.getField('pdbx_sifts_xref_db_res');
+        const {
+            pdbx_sifts_xref_db_name: db_name,
+            pdbx_sifts_xref_db_acc: db_acc,
+            pdbx_sifts_xref_db_num: db_num,
+            pdbx_sifts_xref_db_res: db_res
+        } = model.sourceData.data.db.atom_site;
 
-        if (!db_name || !db_acc || !db_num || !db_res) return;
+        if (!db_name.isDefined || !db_acc.isDefined || !db_num.isDefined || !db_res.isDefined) return;
 
         const { atomSourceIndex } = model.atomicHierarchy;
         const { count, offsets: residueOffsets } = model.atomicHierarchy.residueAtomSegments;
         const dbName = new Array<string>(count);
         const accession = new Array<string>(count);
-        const num = new Array<number>(count);
+        const num = new Array<string>(count);
         const residue = new Array<string>(count);
 
         for (let i = 0; i < count; i++) {
@@ -79,15 +93,15 @@ namespace BestDatabaseSequenceMapping {
             if (db_name.valueKind(row) !== Column.ValueKind.Present) {
                 dbName[i] = '';
                 accession[i] = '';
-                num[i] = 0;
+                num[i] = '';
                 residue[i] = '';
                 continue;
             }
 
-            dbName[i] = db_name.str(row);
-            accession[i] = db_acc.str(row);
-            num[i] = db_num.int(row);
-            residue[i] = db_res.str(row);
+            dbName[i] = db_name.value(row);
+            accession[i] = db_acc.value(row);
+            num[i] = db_num.value(row);
+            residue[i] = db_res.value(row);
         }
 
         return { dbName, accession, num, residue };

src/mol-model-props/sequence/themes/sifts-mapping.ts

@@ -12,27 +12,27 @@ import { Color } from '../../../mol-util/color';
 import { getPalette, getPaletteParams } from '../../../mol-util/color/palette';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { CustomProperty } from '../../common/custom-property';
-import { BestDatabaseSequenceMapping } from '../best-database-mapping';
+import { SIFTSMapping } from '../sifts-mapping';
 
 const DefaultColor = Color(0xFAFAFA);
-const Description = 'Assigns a color based on best dababase sequence mapping.';
+const Description = 'Assigns a color based on SIFTS mapping.';
 
 // same colors for same accessions
 const globalAccessionMap = new Map<string, number>();
 
-export const BestDatabaseSequenceMappingColorThemeParams = {
+export const SIFTSMappingColorThemeParams = {
     ...getPaletteParams({ type: 'colors', colorList: 'set-1' }),
 };
-export type BestDatabaseSequenceMappingColorThemeParams = typeof BestDatabaseSequenceMappingColorThemeParams
-export function getBestDatabaseSequenceMappingColorThemeParams(ctx: ThemeDataContext) {
-    return BestDatabaseSequenceMappingColorThemeParams; // TODO return copy
+export type SIFTSMappingColorThemeParams = typeof SIFTSMappingColorThemeParams
+export function getSIFTSMappingColorThemeParams(ctx: ThemeDataContext) {
+    return SIFTSMappingColorThemeParams; // TODO return copy
 }
-export function BestDatabaseSequenceMappingColorTheme(ctx: ThemeDataContext, props: PD.Values<BestDatabaseSequenceMappingColorThemeParams>): ColorTheme<BestDatabaseSequenceMappingColorThemeParams> {
+export function SIFTSMappingColorTheme(ctx: ThemeDataContext, props: PD.Values<SIFTSMappingColorThemeParams>): ColorTheme<SIFTSMappingColorThemeParams> {
     let color: LocationColor;
 
     if (ctx.structure) {
         for (const m of ctx.structure.models) {
-            const mapping = BestDatabaseSequenceMapping.Provider.get(m).value;
+            const mapping = SIFTSMapping.Provider.get(m).value;
             if (!mapping) continue;
             for (const acc of mapping.accession) {
                 if (!acc || globalAccessionMap.has(acc)) continue;
@@ -45,7 +45,7 @@ export function BestDatabaseSequenceMappingColorTheme(ctx: ThemeDataContext, pro
         const colorMap = new Map<string, Color>();
 
         const getColor = (location: StructureElement.Location) => {
-            const key = BestDatabaseSequenceMapping.getKey(location);
+            const key = SIFTSMapping.getKey(location);
             if (!key) return DefaultColor;
 
             if (colorMap.has(key)) return colorMap.get(key)!;
@@ -70,7 +70,7 @@ export function BestDatabaseSequenceMappingColorTheme(ctx: ThemeDataContext, pro
     }
 
     return {
-        factory: BestDatabaseSequenceMappingColorTheme,
+        factory: SIFTSMappingColorTheme,
         granularity: 'group',
         preferSmoothing: true,
         color,
@@ -79,26 +79,26 @@ export function BestDatabaseSequenceMappingColorTheme(ctx: ThemeDataContext, pro
     };
 }
 
-export const BestDatabaseSequenceMappingColorThemeProvider: ColorTheme.Provider<BestDatabaseSequenceMappingColorThemeParams, 'best-sequence-database-mapping'> = {
-    name: 'best-sequence-database-mapping',
-    label: 'Best Database Sequence Mapping',
+export const SIFTSMappingColorThemeProvider: ColorTheme.Provider<SIFTSMappingColorThemeParams, 'sifts-mapping'> = {
+    name: 'sifts-mapping',
+    label: 'SIFTS Mapping',
     category: ColorTheme.Category.Residue,
-    factory: BestDatabaseSequenceMappingColorTheme,
-    getParams: getBestDatabaseSequenceMappingColorThemeParams,
-    defaultValues: PD.getDefaultValues(BestDatabaseSequenceMappingColorThemeParams),
-    isApplicable: (ctx: ThemeDataContext) => !!ctx.structure?.models.some(m => BestDatabaseSequenceMapping.Provider.isApplicable(m)),
+    factory: SIFTSMappingColorTheme,
+    getParams: getSIFTSMappingColorThemeParams,
+    defaultValues: PD.getDefaultValues(SIFTSMappingColorThemeParams),
+    isApplicable: (ctx: ThemeDataContext) => !!ctx.structure?.models.some(m => SIFTSMapping.Provider.isApplicable(m)),
     ensureCustomProperties: {
         attach: async (ctx: CustomProperty.Context, data: ThemeDataContext) => {
             if (!data.structure) return;
 
             for (const m of data.structure.models) {
-                await BestDatabaseSequenceMapping.Provider.attach(ctx, m, void 0, true);
+                await SIFTSMapping.Provider.attach(ctx, m, void 0, true);
             }
         },
         detach: (data) => {
             if (!data.structure) return;
             for (const m of data.structure.models) {
-                BestDatabaseSequenceMapping.Provider.ref(m, false);
+                SIFTSMapping.Provider.ref(m, false);
             }
         }
     }

src/mol-model/structure/export/categories/atom_site.ts

@@ -5,7 +5,11 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 
+import { Column } from '../../../../mol-data/db';
+import { mmCIF_Database } from '../../../../mol-io/reader/cif/schema/mmcif';
 import { CifWriter } from '../../../../mol-io/writer/cif';
+import { MmcifFormat } from '../../../../mol-model-formats/structure/mmcif';
+import { SIFTSMapping } from '../../../../mol-model-props/sequence/sifts-mapping';
 import { StructureElement, Structure, StructureProperties as P } from '../../structure';
 import { CifExportContext } from '../mmcif';
 import CifField = CifWriter.Field
@@ -26,7 +30,64 @@ function atom_site_auth_asym_id(e: StructureElement.Location) {
     return l + suffix;
 }
 
-const atom_site_fields = () => CifWriter.fields<StructureElement.Location, Structure>()
+
+const atom_site_pdbx_label_index = {
+    shouldInclude(s: AtomSiteData) {
+        return !!s.atom_site?.pdbx_label_index.isDefined;
+    },
+    value(e: StructureElement.Location, d: AtomSiteData) {
+        const srcIndex = d.sourceIndex.value(e.element);
+        return d.atom_site!.pdbx_label_index.value(srcIndex);
+    },
+};
+
+const SIFTS = {
+    shouldInclude(s: AtomSiteData) {
+        return SIFTSMapping.isAvailable(s.structure.models[0]);
+    },
+    pdbx_sifts_xref_db_name: {
+        value(e: StructureElement.Location, d: AtomSiteData) {
+            const srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site!.pdbx_sifts_xref_db_name.value(srcIndex);
+        },
+        valueKind(e: StructureElement.Location, d: any) {
+            const srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site!.pdbx_sifts_xref_db_name.valueKind(srcIndex);
+        },
+    },
+    pdbx_sifts_xref_db_acc: {
+        value(e: StructureElement.Location, d: AtomSiteData) {
+            const srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site!.pdbx_sifts_xref_db_acc.value(srcIndex);
+        },
+        valueKind(e: StructureElement.Location, d: any) {
+            const srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site!.pdbx_sifts_xref_db_acc.valueKind(srcIndex);
+        },
+    },
+    pdbx_sifts_xref_db_num: {
+        value(e: StructureElement.Location, d: AtomSiteData) {
+            const srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site!.pdbx_sifts_xref_db_num.value(srcIndex);
+        },
+        valueKind(e: StructureElement.Location, d: any) {
+            const srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site!.pdbx_sifts_xref_db_num.valueKind(srcIndex);
+        },
+    },
+    pdbx_sifts_xref_db_res: {
+        value(e: StructureElement.Location, d: AtomSiteData) {
+            const srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site!.pdbx_sifts_xref_db_res.value(srcIndex);
+        },
+        valueKind(e: StructureElement.Location, d: any) {
+            const srcIndex = d.sourceIndex.value(e.element);
+            return d.atom_site!.pdbx_sifts_xref_db_res.valueKind(srcIndex);
+        },
+    }
+};
+
+const atom_site_fields = () => CifWriter.fields<StructureElement.Location, AtomSiteData>()
     .str('group_PDB', P.residue.group_PDB)
     .index('id')
     .str('type_symbol', P.atom.type_symbol as any)
@@ -62,18 +123,37 @@ const atom_site_fields = () => CifWriter.fields<StructureElement.Location, Struc
     .str('auth_asym_id', atom_site_auth_asym_id)
 
     .int('pdbx_PDB_model_num', P.unit.model_num, { encoder: E.deltaRLE })
+
+    .int('pdbx_label_index', atom_site_pdbx_label_index.value, { shouldInclude: atom_site_pdbx_label_index.shouldInclude })
+
+    // SIFTS
+    .str('pdbx_sifts_xref_db_name', SIFTS.pdbx_sifts_xref_db_name.value, { shouldInclude: SIFTS.shouldInclude, valueKind: SIFTS.pdbx_sifts_xref_db_name.valueKind })
+    .str('pdbx_sifts_xref_db_acc', SIFTS.pdbx_sifts_xref_db_acc.value, { shouldInclude: SIFTS.shouldInclude, valueKind: SIFTS.pdbx_sifts_xref_db_acc.valueKind })
+    .str('pdbx_sifts_xref_db_num', SIFTS.pdbx_sifts_xref_db_num.value, { shouldInclude: SIFTS.shouldInclude, valueKind: SIFTS.pdbx_sifts_xref_db_num.valueKind })
+    .str('pdbx_sifts_xref_db_res', SIFTS.pdbx_sifts_xref_db_res.value, { shouldInclude: SIFTS.shouldInclude, valueKind: SIFTS.pdbx_sifts_xref_db_res.valueKind })
+
     // .str('operator_name', P.unit.operator_name, {
     //     shouldInclude: structure => structure.units.some(u => !u.conformation.operator.isIdentity)
     // })
     .getFields();
 
+interface AtomSiteData {
+    structure: Structure,
+    sourceIndex: Column<number>,
+    atom_site?: mmCIF_Database['atom_site']
+}
+
 export const _atom_site: CifCategory<CifExportContext> = {
     name: 'atom_site',
     instance({ structures }: CifExportContext) {
         return {
             fields: atom_site_fields(),
             source: structures.map(s => ({
-                data: s,
+                data: {
+                    structure: s,
+                    sourceIndex: s.model.atomicHierarchy.atomSourceIndex,
+                    atom_site: MmcifFormat.is(s.model.sourceData) ? s.model.sourceData.data.db.atom_site : void 0
+                } as AtomSiteData,
                 rowCount: s.elementCount,
                 keys: () => s.elementLocations()
             }))

src/mol-model/structure/export/categories/secondary-structure.ts

@@ -78,12 +78,12 @@ function findElements<T extends SecondaryStructure.Element>(ctx: CifExportContex
     const ssElements: SSElement<any>[] = [];
 
     const structure = ctx.structures[0];
-    for (const unit of structure.units) {
-        // currently can only support this for "identity" operators.
-        if (!Unit.isAtomic(unit) || !unit.conformation.operator.isIdentity) continue;
+    for (const { units } of structure.unitSymmetryGroups) {
+        const u = units[0];
+        if (!Unit.isAtomic(u)) continue;
 
-        const segs = unit.model.atomicHierarchy.residueAtomSegments;
-        const residues = Segmentation.transientSegments(segs, unit.elements);
+        const segs = u.model.atomicHierarchy.residueAtomSegments;
+        const residues = Segmentation.transientSegments(segs, u.elements);
 
         let current: Segmentation.Segment, move = true;
         while (residues.hasNext) {
@@ -104,8 +104,8 @@ function findElements<T extends SecondaryStructure.Element>(ctx: CifExportContex
                 if (startIdx !== key[current.index]) {
                     move = false;
                     ssElements[ssElements.length] = {
-                        start: StructureElement.Location.create(structure, unit, segs.offsets[start]),
-                        end: StructureElement.Location.create(structure, unit, segs.offsets[prev]),
+                        start: StructureElement.Location.create(structure, u, segs.offsets[start]),
+                        end: StructureElement.Location.create(structure, u, segs.offsets[prev]),
                         length: prev - start + 1,
                         element
                     };

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/structure/structure/util/superposition-sifts-mapping.ts

@@ -1,28 +1,34 @@
 /**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
  */
 
 import { Segmentation } from '../../../../mol-data/int';
-import { Mat4 } from '../../../../mol-math/linear-algebra';
 import { MinimizeRmsd } from '../../../../mol-math/linear-algebra/3d/minimize-rmsd';
-import { BestDatabaseSequenceMapping } from '../../../../mol-model-props/sequence/best-database-mapping';
+import { SIFTSMapping } from '../../../../mol-model-props/sequence/sifts-mapping';
 import { ElementIndex } from '../../model/indexing';
 import { Structure } from '../structure';
 import { Unit } from '../unit';
 
-export interface AlignmentResult {
+export interface AlignmentResultEntry {
     transform: MinimizeRmsd.Result,
     pivot: number,
     other: number
 }
 
-export function alignAndSuperposeWithBestDatabaseMapping(structures: Structure[]): AlignmentResult[] {
+export interface AlignmentResult {
+    entries: AlignmentResultEntry[],
+    zeroOverlapPairs: [number, number][],
+    failedPairs: [number, number][]
+}
+
+export function alignAndSuperposeWithSIFTSMapping(structures: Structure[], options?: { traceOnly?: boolean }): AlignmentResult {
     const indexMap = new Map<string, IndexEntry>();
 
     for (let i = 0; i < structures.length; i++) {
-        buildIndex(structures[i], indexMap, i);
+        buildIndex(structures[i], indexMap, i, options?.traceOnly ?? true);
     }
 
     const index = Array.from(indexMap.values());
@@ -30,15 +36,26 @@ export function alignAndSuperposeWithBestDatabaseMapping(structures: Structure[]
     // TODO: support non-first structure pivots
     const pairs = findPairs(structures.length, index);
 
-    const ret: AlignmentResult[] = [];
+    const zeroOverlapPairs: AlignmentResult['zeroOverlapPairs'] = [];
+    const failedPairs: AlignmentResult['failedPairs'] = [];
+
+
+    const entries: AlignmentResultEntry[] = [];
     for (const p of pairs) {
-        const [a, b] = getPositionTables(index, p.i, p.j, p.count);
-        const transform = MinimizeRmsd.compute({ a, b });
-        console.log(Mat4.makeTable(transform.bTransform), transform.rmsd);
-        ret.push({ transform, pivot: p.i, other: p.j });
+        if (p.count === 0) {
+            zeroOverlapPairs.push([p.i, p.j]);
+        } else {
+            const [a, b] = getPositionTables(index, p.i, p.j, p.count);
+            const transform = MinimizeRmsd.compute({ a, b });
+            if (Number.isNaN(transform.rmsd)) {
+                failedPairs.push([p.i, p.j]);
+            } else {
+                entries.push({ transform, pivot: p.i, other: p.j });
+            }
+        }
     }
 
-    return ret;
+    return { entries, zeroOverlapPairs, failedPairs };
 }
 
 function getPositionTables(index: IndexEntry[], pivot: number, other: number, N: number) {
@@ -53,7 +70,6 @@ function getPositionTables(index: IndexEntry[], pivot: number, other: number, N:
 
         const l = Math.min(a[2] - a[1], b[2] - b[1]);
 
-        // TODO: allow to use just backbone atoms?
         // TODO: check if residue types match?
         for (let i = 0; i < l; i++) {
             let eI = (a[1] + i) as ElementIndex;
@@ -121,19 +137,20 @@ interface IndexEntry {
     pivots: { [i: number]: [unit: Unit.Atomic, start: ElementIndex, end: ElementIndex] | undefined }
 }
 
-function buildIndex(structure: Structure, index: Map<string, IndexEntry>, sI: number) {
+function buildIndex(structure: Structure, index: Map<string, IndexEntry>, sI: number, traceOnly: boolean) {
     for (const unit of structure.units) {
         if (unit.kind !== Unit.Kind.Atomic) continue;
 
         const { elements, model } = unit;
 
-        const map = BestDatabaseSequenceMapping.Provider.get(model).value;
+        const map = SIFTSMapping.Provider.get(model).value;
         if (!map) return;
 
         const { dbName, accession, num } = map;
 
         const chainsIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
         const residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
+        const traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex;
 
         while (chainsIt.hasNext) {
             const chainSegment = chainsIt.move();
@@ -144,8 +161,15 @@ function buildIndex(structure: Structure, index: Map<string, IndexEntry>, sI: nu
 
                 if (!dbName[rI]) continue;
 
-                const start = elements[residueSegment.start];
-                const end = elements[residueSegment.end - 1] + 1 as ElementIndex;
+                let start, end;
+                if (traceOnly) {
+                    start = traceElementIndex[rI];
+                    if (start === -1) continue;
+                    end = start + 1 as ElementIndex;
+                } else {
+                    start = elements[residueSegment.start];
+                    end = elements[residueSegment.end - 1] + 1 as ElementIndex;
+                }
 
                 const key = `${dbName[rI]}-${accession[rI]}-${num[rI]}`;
 
@@ -161,6 +185,4 @@ function buildIndex(structure: Structure, index: Map<string, IndexEntry>, sI: nu
             }
         }
     }
-
-    console.log(index);
 }

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/builder/structure/representation-preset.ts

@@ -24,8 +24,6 @@ import { IndexPairBonds } from '../../../mol-model-formats/structure/property/bo
 import { StructConn } from '../../../mol-model-formats/structure/property/bonds/struct_conn';
 import { StructureRepresentationRegistry } from '../../../mol-repr/structure/registry';
 import { assertUnreachable } from '../../../mol-util/type-helpers';
-import { Color } from '../../../mol-util/color';
-import { PostprocessingParams } from '../../../mol-canvas3d/passes/postprocessing';
 
 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; }
@@ -39,6 +37,7 @@ export namespace StructureRepresentationPresetProvider {
 
     export const CommonParams = {
         ignoreHydrogens: PD.Optional(PD.Boolean(false)),
+        ignoreLight: PD.Optional(PD.Boolean(false)),
         quality: PD.Optional(PD.Select<VisualQuality>('auto', VisualQualityOptions)),
         theme: PD.Optional(PD.Group({
             globalName: PD.Optional(PD.Text<ColorTheme.BuiltIn>('')),
@@ -70,9 +69,11 @@ export namespace StructureRepresentationPresetProvider {
         const typeParams = {
             quality: plugin.managers.structure.component.state.options.visualQuality,
             ignoreHydrogens: !plugin.managers.structure.component.state.options.showHydrogens,
+            ignoreLight: plugin.managers.structure.component.state.options.ignoreLight,
         };
         if (params.quality && params.quality !== 'auto') typeParams.quality = params.quality;
         if (params.ignoreHydrogens !== void 0) typeParams.ignoreHydrogens = !!params.ignoreHydrogens;
+        if (params.ignoreLight !== void 0) typeParams.ignoreLight = !!params.ignoreLight;
         const color: ColorTheme.BuiltIn | undefined = params.theme?.globalName ? params.theme?.globalName : void 0;
         const ballAndStickColor: ColorTheme.BuiltInParams<'element-symbol'> = params.theme?.carbonColor !== undefined
             ? { carbonColor: getCarbonColorParams(params.theme?.carbonColor) }
@@ -100,15 +101,6 @@ type CommonParams = StructureRepresentationPresetProvider.CommonParams
 const reprBuilder = StructureRepresentationPresetProvider.reprBuilder;
 const updateFocusRepr = StructureRepresentationPresetProvider.updateFocusRepr;
 
-function resetPostprocessingProps(plugin: PluginContext) {
-    if (plugin.canvas3d) {
-        const p = PD.getDefaultValues(PostprocessingParams);
-        plugin.canvas3d.setProps({
-            postprocessing: { outline: p.outline, occlusion: p.occlusion }
-        });
-    }
-}
-
 const auto = StructureRepresentationPresetProvider({
     id: 'preset-structure-representation-auto',
     display: {
@@ -148,7 +140,6 @@ const empty = StructureRepresentationPresetProvider({
     id: 'preset-structure-representation-empty',
     display: { name: 'Empty', description: 'Removes all existing representations.' },
     async apply(ref, params, plugin) {
-        resetPostprocessingProps(plugin);
         return { };
     }
 });
@@ -203,8 +194,6 @@ const polymerAndLigand = StructureRepresentationPresetProvider({
         await update.commit({ revertOnError: false });
         await updateFocusRepr(plugin, structure, params.theme?.focus?.name, params.theme?.focus?.params);
 
-        resetPostprocessingProps(plugin);
-
         return { components, representations };
     }
 });
@@ -244,8 +233,6 @@ const proteinAndNucleic = StructureRepresentationPresetProvider({
         await update.commit({ revertOnError: true });
         await updateFocusRepr(plugin, structure, params.theme?.focus?.name, params.theme?.focus?.params);
 
-        resetPostprocessingProps(plugin);
-
         return { components, representations };
     }
 });
@@ -298,8 +285,6 @@ const coarseSurface = StructureRepresentationPresetProvider({
         await update.commit({ revertOnError: true });
         await updateFocusRepr(plugin, structure, params.theme?.focus?.name, params.theme?.focus?.params);
 
-        resetPostprocessingProps(plugin);
-
         return { components, representations };
     }
 });
@@ -333,8 +318,6 @@ const polymerCartoon = StructureRepresentationPresetProvider({
         await update.commit({ revertOnError: true });
         await updateFocusRepr(plugin, structure, params.theme?.focus?.name, params.theme?.focus?.params);
 
-        resetPostprocessingProps(plugin);
-
         return { components, representations };
     }
 });
@@ -401,8 +384,6 @@ const atomicDetail = StructureRepresentationPresetProvider({
         await update.commit({ revertOnError: true });
         await updateFocusRepr(plugin, structure, params.theme?.focus?.name ?? color, params.theme?.focus?.params ?? colorParams);
 
-        resetPostprocessingProps(plugin);
-
         return { components, representations };
     }
 });
@@ -436,21 +417,6 @@ const illustrative = StructureRepresentationPresetProvider({
         await update.commit({ revertOnError: true });
         await updateFocusRepr(plugin, structure, params.theme?.focus?.name ?? color, params.theme?.focus?.params);
 
-        if (plugin.canvas3d) {
-            plugin.canvas3d.setProps({
-                postprocessing: {
-                    outline: {
-                        name: 'on',
-                        params: { scale: 1, color: Color(0x000000), threshold: 0.25 }
-                    },
-                    occlusion: {
-                        name: 'on',
-                        params: { bias: 0.9, blurKernelSize: 15, radius: 5, samples: 32 }
-                    },
-                }
-            });
-        }
-
         return { components, representations };
     }
 });
@@ -471,6 +437,6 @@ export const PresetStructureRepresentations = {
     'polymer-and-ligand': polymerAndLigand,
     'protein-and-nucleic': proteinAndNucleic,
     'coarse-surface': coarseSurface,
-    'illustrative': illustrative,
+    illustrative,
 };
 export type PresetStructureRepresentations = typeof PresetStructureRepresentations;

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

@@ -29,7 +29,7 @@ export class StructureRepresentationBuilder {
 
     readonly defaultProvider = PresetStructureRepresentations.auto;
 
-    private resolveProvider(ref: StructureRepresentationPresetProviderRef) {
+    resolveProvider(ref: StructureRepresentationPresetProviderRef) {
         return typeof ref === 'string'
             ? PresetStructureRepresentations[ref as keyof PresetStructureRepresentations] ?? arrayFind(this._providers, p => p.id === ref)
             : ref;

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-state/manager/structure/component.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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -71,6 +71,7 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
             await update.commit();
             await this.plugin.state.updateBehavior(StructureFocusRepresentation, p => {
                 p.ignoreHydrogens = !options.showHydrogens;
+                p.ignoreLight = options.ignoreLight;
                 p.material = options.materialStyle;
                 p.clip = options.clipObjects;
             });
@@ -79,16 +80,17 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
     }
 
     private updateReprParams(update: StateBuilder.Root, component: StructureComponentRef) {
-        const { showHydrogens, visualQuality: quality, materialStyle: material, clipObjects: clip } = this.state.options;
+        const { showHydrogens, visualQuality: quality, ignoreLight, materialStyle: material, clipObjects: clip } = this.state.options;
         const ignoreHydrogens = !showHydrogens;
         for (const r of component.representations) {
             if (r.cell.transform.transformer !== StructureRepresentation3D) continue;
 
             const params = r.cell.transform.params as StateTransformer.Params<StructureRepresentation3D>;
-            if (!!params.type.params.ignoreHydrogens !== ignoreHydrogens || params.type.params.quality !== quality || !shallowEqual(params.type.params.material, material) || !PD.areEqual(Clip.Params, params.type.params.clip, clip)) {
+            if (!!params.type.params.ignoreHydrogens !== ignoreHydrogens || params.type.params.quality !== quality || params.type.params.ignoreLight !== ignoreLight || !shallowEqual(params.type.params.material, material) || !PD.areEqual(Clip.Params, params.type.params.clip, clip)) {
                 update.to(r.cell).update(old => {
                     old.type.params.ignoreHydrogens = ignoreHydrogens;
                     old.type.params.quality = quality;
+                    old.type.params.ignoreLight = ignoreLight;
                     old.type.params.material = material;
                     old.type.params.clip = clip;
                 });
@@ -309,9 +311,9 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
     addRepresentation(components: ReadonlyArray<StructureComponentRef>, type: string) {
         if (components.length === 0) return;
 
-        const { showHydrogens, visualQuality: quality, materialStyle: material, clipObjects: clip } = this.state.options;
+        const { showHydrogens, visualQuality: quality, ignoreLight, materialStyle: material, clipObjects: clip } = this.state.options;
         const ignoreHydrogens = !showHydrogens;
-        const typeParams = { ignoreHydrogens, quality, material, clip };
+        const typeParams = { ignoreHydrogens, quality, ignoreLight, material, clip };
 
         return this.plugin.dataTransaction(async () => {
             for (const component of components) {
@@ -346,9 +348,9 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
             const xs = structures || this.currentStructures;
             if (xs.length === 0) return;
 
-            const { showHydrogens, visualQuality: quality, materialStyle: material, clipObjects: clip } = this.state.options;
+            const { showHydrogens, visualQuality: quality, ignoreLight, materialStyle: material, clipObjects: clip } = this.state.options;
             const ignoreHydrogens = !showHydrogens;
-            const typeParams = { ignoreHydrogens, quality, material, clip };
+            const typeParams = { ignoreHydrogens, quality, ignoreLight, material, clip };
 
             const componentKey = UUID.create22();
             for (const s of xs) {
@@ -458,6 +460,7 @@ namespace StructureComponentManager {
     export const OptionsParams = {
         showHydrogens: PD.Boolean(true, { description: 'Toggle display of hydrogen atoms in representations' }),
         visualQuality: PD.Select('auto', VisualQualityOptions, { description: 'Control the visual/rendering quality of representations' }),
+        ignoreLight: PD.Boolean(false, { description: 'Ignore light for stylized rendering of representtions' }),
         materialStyle: Material.getParam(),
         clipObjects: PD.Group(Clip.Params),
         interactions: PD.Group(InteractionsProvider.defaultParams, { label: 'Non-covalent Interactions' }),

src/mol-plugin-ui/controls.tsx

@@ -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>
@@ -24,6 +24,7 @@ import { StructureSourceControls } from './structure/source';
 import { VolumeStreamingControls, VolumeSourceControls } from './structure/volume';
 import { PluginConfig } from '../mol-plugin/config';
 import { StructureSuperpositionControls } from './structure/superposition';
+import { StructureQuickStylesControls } from './structure/quick-styles';
 
 export class TrajectoryViewportControls extends PluginUIComponent<{}, { show: boolean, label: string }> {
     state = { show: false, label: '' };
@@ -292,6 +293,7 @@ export class DefaultStructureTools extends PluginUIComponent {
             <StructureSourceControls />
             <StructureMeasurementsControls />
             <StructureSuperpositionControls />
+            <StructureQuickStylesControls />
             <StructureComponentControls />
             {this.plugin.config.get(PluginConfig.VolumeStreaming.Enabled) && <VolumeStreamingControls />}
             <VolumeSourceControls />

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

@@ -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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -38,10 +38,10 @@ export function MoleculeSvg() { return _Molecule; }
 // The following icons are adapted from https://materialdesignicons.com/ and
 // licensed with https://github.com/Templarian/MaterialDesign/blob/master/LICENSE
 
-const _CubeOutline = <svg width='24px' height='24px' viewBox='0 0 24 24' strokeWidth='0.1px'><path d="M21,16.5C21,16.88 20.79,17.21 20.47,17.38L12.57,21.82C12.41,21.94 12.21,22 12,22C11.79,22 11.59,21.94 11.43,21.82L3.53,17.38C3.21,17.21 3,16.88 3,16.5V7.5C3,7.12 3.21,6.79 3.53,6.62L11.43,2.18C11.59,2.06 11.79,2 12,2C12.21,2 12.41,2.06 12.57,2.18L20.47,6.62C20.79,6.79 21,7.12 21,7.5V16.5M12,4.15L6.04,7.5L12,10.85L17.96,7.5L12,4.15M5,15.91L11,19.29V12.58L5,9.21V15.91M19,15.91V9.21L13,12.58V19.29L19,15.91Z" /></svg>;
+const _CubeOutline = <svg width='24px' height='24px' viewBox='0 0 24 24' strokeWidth='0.1px'><path d='M21,16.5C21,16.88 20.79,17.21 20.47,17.38L12.57,21.82C12.41,21.94 12.21,22 12,22C11.79,22 11.59,21.94 11.43,21.82L3.53,17.38C3.21,17.21 3,16.88 3,16.5V7.5C3,7.12 3.21,6.79 3.53,6.62L11.43,2.18C11.59,2.06 11.79,2 12,2C12.21,2 12.41,2.06 12.57,2.18L20.47,6.62C20.79,6.79 21,7.12 21,7.5V16.5M12,4.15L6.04,7.5L12,10.85L17.96,7.5L12,4.15M5,15.91L11,19.29V12.58L5,9.21V15.91M19,15.91V9.21L13,12.58V19.29L19,15.91Z' /></svg>;
 export function CubeOutlineSvg() { return _CubeOutline; }
 
-const _CubeScan = <svg width='24px' height='24px' viewBox='0 0 24 24' strokeWidth='0.1px'><path d="M17,22V20H20V17H22V20.5C22,20.89 21.84,21.24 21.54,21.54C21.24,21.84 20.89,22 20.5,22H17M7,22H3.5C3.11,22 2.76,21.84 2.46,21.54C2.16,21.24 2,20.89 2,20.5V17H4V20H7V22M17,2H20.5C20.89,2 21.24,2.16 21.54,2.46C21.84,2.76 22,3.11 22,3.5V7H20V4H17V2M7,2V4H4V7H2V3.5C2,3.11 2.16,2.76 2.46,2.46C2.76,2.16 3.11,2 3.5,2H7M13,17.25L17,14.95V10.36L13,12.66V17.25M12,10.92L16,8.63L12,6.28L8,8.63L12,10.92M7,14.95L11,17.25V12.66L7,10.36V14.95M18.23,7.59C18.73,7.91 19,8.34 19,8.91V15.23C19,15.8 18.73,16.23 18.23,16.55L12.75,19.73C12.25,20.05 11.75,20.05 11.25,19.73L5.77,16.55C5.27,16.23 5,15.8 5,15.23V8.91C5,8.34 5.27,7.91 5.77,7.59L11.25,4.41C11.5,4.28 11.75,4.22 12,4.22C12.25,4.22 12.5,4.28 12.75,4.41L18.23,7.59Z" /></svg>;
+const _CubeScan = <svg width='24px' height='24px' viewBox='0 0 24 24' strokeWidth='0.1px'><path d='M17,22V20H20V17H22V20.5C22,20.89 21.84,21.24 21.54,21.54C21.24,21.84 20.89,22 20.5,22H17M7,22H3.5C3.11,22 2.76,21.84 2.46,21.54C2.16,21.24 2,20.89 2,20.5V17H4V20H7V22M17,2H20.5C20.89,2 21.24,2.16 21.54,2.46C21.84,2.76 22,3.11 22,3.5V7H20V4H17V2M7,2V4H4V7H2V3.5C2,3.11 2.16,2.76 2.46,2.46C2.76,2.16 3.11,2 3.5,2H7M13,17.25L17,14.95V10.36L13,12.66V17.25M12,10.92L16,8.63L12,6.28L8,8.63L12,10.92M7,14.95L11,17.25V12.66L7,10.36V14.95M18.23,7.59C18.73,7.91 19,8.34 19,8.91V15.23C19,15.8 18.73,16.23 18.23,16.55L12.75,19.73C12.25,20.05 11.75,20.05 11.25,19.73L5.77,16.55C5.27,16.23 5,15.8 5,15.23V8.91C5,8.34 5.27,7.91 5.77,7.59L11.25,4.41C11.5,4.28 11.75,4.22 12,4.22C12.25,4.22 12.5,4.28 12.75,4.41L18.23,7.59Z' /></svg>;
 export function CubeScanSvg() { return _CubeScan; }
 
 const _CubeSend = <svg width='24px' height='24px' viewBox='0 0 24 24' strokeWidth='0.1px'><path d="M16,4L9,8.04V15.96L16,20L23,15.96V8.04M16,6.31L19.8,8.5L16,10.69L12.21,8.5M0,7V9H7V7M11,10.11L15,12.42V17.11L11,14.81M21,10.11V14.81L17,17.11V12.42M2,11V13H7V11M4,15V17H7V15" /></svg>;
@@ -53,9 +53,12 @@ export function CursorDefaultOutlineSvg() { return _CursorDefaultOutline; }
 const _FileOutline = <svg width='24px' height='24px' viewBox='0 0 24 24' strokeWidth='0.1px'><path fill='currentColor' d='M14,2H6A2,2 0 0,0 4,4V20A2,2 0 0,0 6,22H18A2,2 0 0,0 20,20V8L14,2M18,20H6V4H13V9H18V20Z' /></svg>;
 export function FileOutlineSvg() { return _FileOutline; }
 
-const _PencilRuler = <svg width='24px' height='24px' viewBox='0 0 24 24' strokeWidth='0.1px'><path d="M3 17.25V21H6.75L17.81 9.93L14.06 6.18L3 17.25M22.61 18.36L18.36 22.61L13.16 17.41L14.93 15.64L15.93 16.64L18.4 14.16L19.82 15.58L18.36 17L19.42 18L20.84 16.6L22.61 18.36M6.61 10.83L1.39 5.64L5.64 1.39L7.4 3.16L4.93 5.64L6 6.7L8.46 4.22L9.88 5.64L8.46 7.05L9.46 8.05L6.61 10.83M20.71 7C21.1 6.61 21.1 6 20.71 5.59L18.37 3.29C18 2.9 17.35 2.9 16.96 3.29L15.12 5.12L18.87 8.87L20.71 7Z" /></svg>;
+const _PencilRuler = <svg width='24px' height='24px' viewBox='0 0 24 24' strokeWidth='0.1px'><path d='M3 17.25V21H6.75L17.81 9.93L14.06 6.18L3 17.25M22.61 18.36L18.36 22.61L13.16 17.41L14.93 15.64L15.93 16.64L18.4 14.16L19.82 15.58L18.36 17L19.42 18L20.84 16.6L22.61 18.36M6.61 10.83L1.39 5.64L5.64 1.39L7.4 3.16L4.93 5.64L6 6.7L8.46 4.22L9.88 5.64L8.46 7.05L9.46 8.05L6.61 10.83M20.71 7C21.1 6.61 21.1 6 20.71 5.59L18.37 3.29C18 2.9 17.35 2.9 16.96 3.29L15.12 5.12L18.87 8.87L20.71 7Z' /></svg>;
 export function PencilRulerSvg() { return _PencilRuler; }
 
+const _MagicWand = <svg width='24px' height='24px' viewBox='0 0 24 24'><path fill='currentColor' d='M7.5,5.6L5,7L6.4,4.5L5,2L7.5,3.4L10,2L8.6,4.5L10,7L7.5,5.6M19.5,15.4L22,14L20.6,16.5L22,19L19.5,17.6L17,19L18.4,16.5L17,14L19.5,15.4M22,2L20.6,4.5L22,7L19.5,5.6L17,7L18.4,4.5L17,2L19.5,3.4L22,2M13.34,12.78L15.78,10.34L13.66,8.22L11.22,10.66L13.34,12.78M14.37,7.29L16.71,9.63C17.1,10 17.1,10.65 16.71,11.04L5.04,22.71C4.65,23.1 4,23.1 3.63,22.71L1.29,20.37C0.9,20 0.9,19.35 1.29,18.96L12.96,7.29C13.35,6.9 14,6.9 14.37,7.29Z' /></svg>;
+export function MagicWandSvg() { return _MagicWand; }
+
 // The following icons are adapted from https://material-ui.com/components/material-icons/ and
 // licensed with https://github.com/mui-org/material-ui/blob/master/LICENSE
 

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

@@ -0,0 +1,107 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { PresetStructureRepresentations } from '../../mol-plugin-state/builder/structure/representation-preset';
+import { Color } from '../../mol-util/color';
+import { CollapsableControls, PurePluginUIComponent } from '../base';
+import { Button } from '../controls/common';
+import { MagicWandSvg } from '../controls/icons';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { PostprocessingParams } from '../../mol-canvas3d/passes/postprocessing';
+import { PluginConfig } from '../../mol-plugin/config';
+import { StructureComponentManager } from '../../mol-plugin-state/manager/structure/component';
+
+export class StructureQuickStylesControls extends CollapsableControls {
+    defaultState() {
+        return {
+            isCollapsed: false,
+            header: 'Quick Styles',
+            brand: { accent: 'gray' as const, svg: MagicWandSvg }
+        };
+    }
+
+    renderControls() {
+        return <>
+            <QuickStyles />
+        </>;
+    }
+}
+
+export class QuickStyles extends PurePluginUIComponent {
+    async default() {
+        const { structures } = this.plugin.managers.structure.hierarchy.selection;
+        const preset = this.plugin.config.get(PluginConfig.Structure.DefaultRepresentationPreset) || PresetStructureRepresentations.auto.id;
+        const provider = this.plugin.builders.structure.representation.resolveProvider(preset);
+        await this.plugin.managers.structure.component.applyPreset(structures, provider);
+
+        this.plugin.managers.structure.component.setOptions(PD.getDefaultValues(StructureComponentManager.OptionsParams));
+
+        if (this.plugin.canvas3d) {
+            const p = PD.getDefaultValues(PostprocessingParams);
+            this.plugin.canvas3d.setProps({
+                postprocessing: { outline: p.outline, occlusion: p.occlusion }
+            });
+        }
+    }
+
+    async illustrative() {
+        const { structures } = this.plugin.managers.structure.hierarchy.selection;
+        await this.plugin.managers.structure.component.applyPreset(structures, PresetStructureRepresentations.illustrative);
+
+        if (this.plugin.canvas3d) {
+            this.plugin.canvas3d.setProps({
+                postprocessing: {
+                    outline: {
+                        name: 'on',
+                        params: { scale: 1, color: Color(0x000000), threshold: 0.25 }
+                    },
+                    occlusion: {
+                        name: 'on',
+                        params: { bias: 0.9, blurKernelSize: 15, radius: 5, samples: 32 }
+                    },
+                }
+            });
+        }
+    }
+
+    async stylized() {
+        this.plugin.managers.structure.component.setOptions({ ...this.plugin.managers.structure.component.state.options, ignoreLight: true });
+
+        if (this.plugin.canvas3d) {
+            const pp = this.plugin.canvas3d.props.postprocessing;
+            this.plugin.canvas3d.setProps({
+                postprocessing: {
+                    outline: {
+                        name: 'on',
+                        params: pp.outline.name === 'on'
+                            ? pp.outline.params
+                            : { scale: 1, color: Color(0x000000), threshold: 0.33 }
+                    },
+                    occlusion: {
+                        name: 'on',
+                        params: pp.occlusion.name === 'on'
+                            ? pp.occlusion.params
+                            : { bias: 0.9, blurKernelSize: 15, radius: 5, samples: 32 }
+                    },
+                }
+            });
+        }
+    }
+
+    render() {
+        return <div className='msp-flex-row'>
+            <Button noOverflow title='Applies default representation preset. Set outline and occlusion effects to defaults.' onClick={() => this.default()} style={{ width: 'auto' }}>
+                Default
+            </Button>
+            <Button noOverflow title='Applies no representation preset. Enables outline and occlusion effects. Enables ignore-light representation parameter.' onClick={() => this.stylized()} style={{ width: 'auto' }}>
+                Stylized
+            </Button>
+            <Button noOverflow title='Applies illustrative representation preset. Enables outline and occlusion effects. Enables ignore-light parameter.' onClick={() => this.illustrative()} style={{ width: 'auto' }}>
+                Illustrative
+            </Button>
+        </div>;
+    }
+}

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

@@ -1,7 +1,8 @@
 /**
- * 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 Sebastian Bittrich <sebastian.bittrich@rcsb.org>
  */
 
 import { CollapsableControls, PurePluginUIComponent } from '../base';
@@ -20,9 +21,9 @@ import { ParameterControls } from '../controls/parameters';
 import { stripTags } from '../../mol-util/string';
 import { StructureSelectionHistoryEntry } from '../../mol-plugin-state/manager/structure/selection';
 import { ToggleSelectionModeButton } from './selection';
-import { alignAndSuperposeWithBestDatabaseMapping } from '../../mol-model/structure/structure/util/superposition-db-mapping';
+import { alignAndSuperposeWithSIFTSMapping } from '../../mol-model/structure/structure/util/superposition-sifts-mapping';
 import { PluginCommands } from '../../mol-plugin/commands';
-import { BestDatabaseSequenceMapping } from '../../mol-model-props/sequence/best-database-mapping';
+import { SIFTSMapping } from '../../mol-model-props/sequence/sifts-mapping';
 
 export class StructureSuperpositionControls extends CollapsableControls {
     defaultState() {
@@ -48,7 +49,8 @@ export class StructureSuperpositionControls extends CollapsableControls {
 }
 
 export const StructureSuperpositionParams = {
-    alignSequences: PD.Boolean(true, { isEssential: true, description: 'Perform a sequence alignment and use the aligned residue pairs to guide the 3D superposition.' }),
+    alignSequences: PD.Boolean(true, { isEssential: true, description: 'For Chain-based 3D superposition, perform a sequence alignment and use the aligned residue pairs to guide the 3D superposition.' }),
+    traceOnly: PD.Boolean(true, { description: 'For Chain- and Uniprot-based 3D superposition, base superposition only on CA (and equivalent) atoms.' })
 };
 const DefaultStructureSuperpositionOptions = PD.getDefaultValues(StructureSuperpositionParams);
 export type StructureSuperpositionOptions = PD.ValuesFor<typeof StructureSuperpositionParams>
@@ -94,7 +96,7 @@ export class SuperpositionControls extends PurePluginUIComponent<{ }, Superposit
         });
 
         this.subscribe(this.plugin.managers.structure.hierarchy.behaviors.selection, sel => {
-            this.setState({ canUseDb: sel.structures.every(s => !!s.cell.obj?.data && s.cell.obj.data.models.some(m => BestDatabaseSequenceMapping.Provider.isApplicable(m))) });
+            this.setState({ canUseDb: sel.structures.every(s => !!s.cell.obj?.data && s.cell.obj.data.models.some(m => SIFTSMapping.Provider.isApplicable(m))) });
         });
     }
 
@@ -123,10 +125,10 @@ export class SuperpositionControls extends PurePluginUIComponent<{ }, Superposit
     }
 
     superposeChains = async () => {
-        const { query } = StructureSelectionQueries.trace;
+        const { query } = this.state.options.traceOnly ? StructureSelectionQueries.trace : StructureSelectionQueries.polymer;
         const entries = this.chainEntries;
 
-        const traceLocis = entries.map((e, i) => {
+        const locis = entries.map((e, i) => {
             const s = StructureElement.Loci.toStructure(e.loci);
             const loci = StructureSelection.toLociWithSourceUnits(query(new QueryContext(s)));
             return StructureElement.Loci.remap(loci, i === 0
@@ -136,11 +138,11 @@ export class SuperpositionControls extends PurePluginUIComponent<{ }, Superposit
         });
 
         const transforms = this.state.options.alignSequences
-            ? alignAndSuperpose(traceLocis)
-            : superpose(traceLocis);
+            ? alignAndSuperpose(locis)
+            : superpose(locis);
 
         const eA = entries[0];
-        for (let i = 1, il = traceLocis.length; i < il; ++i) {
+        for (let i = 1, il = locis.length; i < il; ++i) {
             const eB = entries[i];
             const { bTransform, rmsd } = transforms[i - 1];
             await this.transform(eB.cell, bTransform);
@@ -148,6 +150,7 @@ export class SuperpositionControls extends PurePluginUIComponent<{ }, Superposit
             const labelB = stripTags(eB.label);
             this.plugin.log.info(`Superposed [${labelA}] and [${labelB}] with RMSD ${rmsd.toFixed(2)}.`);
         }
+        await this.cameraReset();
     };
 
     superposeAtoms = async () => {
@@ -171,26 +174,47 @@ export class SuperpositionControls extends PurePluginUIComponent<{ }, Superposit
             const count = entries[i].atoms.length;
             this.plugin.log.info(`Superposed ${count} ${count === 1 ? 'atom' : 'atoms'} of [${labelA}] and [${labelB}] with RMSD ${rmsd.toFixed(2)}.`);
         }
+        await this.cameraReset();
     };
 
     superposeDb = async () => {
         const input = this.plugin.managers.structure.hierarchy.behaviors.selection.value.structures;
+        const traceOnly = this.state.options.traceOnly;
 
-        const transforms = alignAndSuperposeWithBestDatabaseMapping(input.map(s => s.cell.obj?.data!));
+        const structures = input.map(s => s.cell.obj?.data!);
+        const { entries, failedPairs, zeroOverlapPairs } = alignAndSuperposeWithSIFTSMapping(structures, { traceOnly });
 
         let rmsd = 0;
 
-        for (const xform of transforms) {
+        for (const xform of entries) {
             await this.transform(input[xform.other].cell, xform.transform.bTransform);
             rmsd += xform.transform.rmsd;
         }
 
-        rmsd /= Math.max(transforms.length - 1, 1);
+        rmsd /= Math.max(entries.length - 1, 1);
 
-        this.plugin.log.info(`Superposed ${input.length} structures with avg. RMSD ${rmsd.toFixed(2)} Å.`);
+        const formatPairs = (pairs: [number, number][]) => {
+            return `[${pairs.map(([i, j]) => `(${structures[i].models[0].entryId}, ${structures[j].models[0].entryId})`).join(', ')}]`;
+        };
+
+        if (zeroOverlapPairs.length) {
+            this.plugin.log.warn(`Superposition: No UNIPROT mapping overlap between structures ${formatPairs(zeroOverlapPairs)}.`);
+        }
+
+        if (failedPairs.length) {
+            this.plugin.log.error(`Superposition: Failed to superpose structures ${formatPairs(failedPairs)}.`);
+        }
+
+        if (entries.length) {
+            this.plugin.log.info(`Superposed ${entries.length + 1} structures with avg. RMSD ${rmsd.toFixed(2)} Å.`);
+            await this.cameraReset();
+        }
+    };
+
+    async cameraReset() {
         await new Promise(res => requestAnimationFrame(res));
         PluginCommands.Camera.Reset(this.plugin);
-    };
+    }
 
     toggleByChains = () => this.setState({ action: this.state.action === 'byChains' ? void 0 : 'byChains' });
     toggleByAtoms = () => this.setState({ action: this.state.action === 'byAtoms' ? void 0 : 'byAtoms' });
@@ -323,8 +347,8 @@ export class SuperpositionControls extends PurePluginUIComponent<{ }, Superposit
 
     superposeByDbMapping() {
         return <>
-            <Button icon={SuperposeChainsSvg} title='Superpose structures using database mapping.' className='msp-btn msp-btn-block' onClick={this.superposeDb} style={{ marginTop: '1px' }} disabled={this.state.isBusy}>
-                DB
+            <Button icon={SuperposeChainsSvg} title='Superpose structures using intersection of residues from SIFTS UNIPROT mapping.' className='msp-btn msp-btn-block' onClick={this.superposeDb} style={{ marginTop: '1px' }} disabled={this.state.isBusy}>
+                Uniprot
             </Button>
         </>;
     }

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

@@ -77,9 +77,9 @@ export class VolumeStreamingControls extends CollapsableControls<{}, VolumeStrea
         const rootCell = root && pivot.cell.parent.cells.get(root);
 
         const simpleApply = rootCell && rootCell.status === 'error'
-            ? { header: 'Error enabling', icon: ErrorSvg, title: rootCell.errorText }
+            ? { header: !!rootCell.errorText && rootCell.errorText?.includes('404') ? 'No Density Data Available' : 'Error Enabling', icon: ErrorSvg, title: rootCell.errorText }
             : rootCell && rootCell.obj?.data.entries.length === 0
-                ? { header: 'Error enabling', icon: ErrorSvg, title: 'No entry for streaming found' }
+                ? { header: 'Error Enabling', icon: ErrorSvg, title: 'No Entry for Streaming Found' }
                 : { header: 'Enable', icon: CheckSvg, title: 'Enable' };
 
         return <ApplyActionControl state={pivot.cell.parent} action={InitVolumeStreaming} initiallyCollapsed={true} nodeRef={pivot.cell.transform.ref} simpleApply={simpleApply} />;

src/mol-plugin/behavior/dynamic/custom-props.ts

@@ -11,6 +11,6 @@ export { AccessibleSurfaceArea } from './custom-props/computed/accessible-surfac
 export { Interactions } from './custom-props/computed/interactions';
 export { SecondaryStructure } from './custom-props/computed/secondary-structure';
 export { ValenceModel } from './custom-props/computed/valence-model';
-export { BestDatabaseSequenceMapping } from './custom-props/sequence/best-database-mapping';
+export { SIFTSMapping as BestDatabaseSequenceMapping } from './custom-props/sequence/sifts-mapping';
 
 export { CrossLinkRestraint } from './custom-props/integrative/cross-link-restraint';

src/mol-plugin/behavior/dynamic/custom-props/sequence/sifts-mapping.ts

@@ -5,17 +5,17 @@
  */
 
 import { OrderedSet } from '../../../../../mol-data/int';
-import { BestDatabaseSequenceMapping as BestDatabaseSequenceMappingProp } from '../../../../../mol-model-props/sequence/best-database-mapping';
-import { BestDatabaseSequenceMappingColorThemeProvider } from '../../../../../mol-model-props/sequence/themes/best-database-mapping';
+import { SIFTSMapping as BestDatabaseSequenceMappingProp } from '../../../../../mol-model-props/sequence/sifts-mapping';
+import { SIFTSMappingColorThemeProvider } from '../../../../../mol-model-props/sequence/themes/sifts-mapping';
 import { Loci } from '../../../../../mol-model/loci';
 import { StructureElement } from '../../../../../mol-model/structure';
 import { ParamDefinition as PD } from '../../../../../mol-util/param-definition';
 import { PluginBehavior } from '../../../behavior';
 
-export const BestDatabaseSequenceMapping = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
-    name: 'best-sequence-database-mapping-prop',
+export const SIFTSMapping = PluginBehavior.create<{ autoAttach: boolean, showTooltip: boolean }>({
+    name: 'sifts-mapping-prop',
     category: 'custom-props',
-    display: { name: 'Best Database Sequence Mapping' },
+    display: { name: 'SIFTS Mapping' },
     ctor: class extends PluginBehavior.Handler<{ autoAttach: boolean, showTooltip: boolean }> {
         private provider = BestDatabaseSequenceMappingProp.Provider;
 
@@ -39,13 +39,13 @@ export const BestDatabaseSequenceMapping = PluginBehavior.create<{ autoAttach: b
 
         register(): void {
             this.ctx.customModelProperties.register(this.provider, this.params.autoAttach);
-            this.ctx.representation.structure.themes.colorThemeRegistry.add(BestDatabaseSequenceMappingColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.add(SIFTSMappingColorThemeProvider);
             this.ctx.managers.lociLabels.addProvider(this.labelProvider);
         }
 
         unregister() {
             this.ctx.customModelProperties.unregister(this.provider.descriptor.name);
-            this.ctx.representation.structure.themes.colorThemeRegistry.remove(BestDatabaseSequenceMappingColorThemeProvider);
+            this.ctx.representation.structure.themes.colorThemeRegistry.remove(SIFTSMappingColorThemeProvider);
             this.ctx.managers.lociLabels.removeProvider(this.labelProvider);
         }
     },

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/dynamic/selection/structure-focus-representation.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 David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -27,11 +27,19 @@ const StructureFocusRepresentationParams = (plugin: PluginContext) => {
         expandRadius: PD.Numeric(5, { min: 1, max: 10, step: 1 }),
         targetParams: PD.Group(reprParams, {
             label: 'Target',
-            customDefault: createStructureRepresentationParams(plugin, void 0, { type: 'ball-and-stick', size: 'physical', typeParams: { sizeFactor: 0.26, alpha: 0.51, adjustCylinderLength: true } })
+            customDefault: createStructureRepresentationParams(plugin, void 0, {
+                type: 'ball-and-stick',
+                size: 'physical',
+                typeParams: { sizeFactor: 0.22, sizeAspectRatio: 0.73, adjustCylinderLength: true, xrayShaded: true, aromaticBonds: false, multipleBonds: 'off', excludeTypes: ['hydrogen-bond', 'metal-coordination'] },
+            })
         }),
         surroundingsParams: PD.Group(reprParams, {
             label: 'Surroundings',
-            customDefault: createStructureRepresentationParams(plugin, void 0, { type: 'ball-and-stick', size: 'physical', typeParams: { sizeFactor: 0.16 } })
+            customDefault: createStructureRepresentationParams(plugin, void 0, {
+                type: 'ball-and-stick',
+                size: 'physical',
+                typeParams: { sizeFactor: 0.16, excludeTypes: ['hydrogen-bond', 'metal-coordination'] }
+            })
         }),
         nciParams: PD.Group(reprParams, {
             label: 'Non-covalent Int.',
@@ -44,6 +52,7 @@ const StructureFocusRepresentationParams = (plugin: PluginContext) => {
         components: PD.MultiSelect(FocusComponents, PD.arrayToOptions(FocusComponents)),
         excludeTargetFromSurroundings: PD.Boolean(false, { label: 'Exclude Target', description: 'Exclude the focus "target" from the surroudings component.' }),
         ignoreHydrogens: PD.Boolean(false),
+        ignoreLight: PD.Boolean(false),
         material: Material.getParam(),
         clip: PD.Group(Clip.Params),
     };
@@ -68,10 +77,10 @@ class StructureFocusRepresentationBehavior extends PluginBehavior.WithSubscriber
 
     private getReprParams(reprParams: PD.Values<PD.Params>) {
         return {
-            ...this.params.targetParams,
+            ...reprParams,
             type: {
                 name: reprParams.type.name,
-                params: { ...reprParams.type.params, ignoreHydrogens: this.params.ignoreHydrogens, material: this.params.material, clip: this.params.clip }
+                params: { ...reprParams.type.params, ignoreHydrogens: this.params.ignoreHydrogens, ignoreLight: this.params.ignoreLight, material: this.params.material, clip: this.params.clip }
             }
         };
     }
@@ -114,7 +123,7 @@ class StructureFocusRepresentationBehavior extends PluginBehavior.WithSubscriber
         if (components.indexOf('interactions') >= 0 && !refs[StructureFocusRepresentationTags.SurrNciRepr] && cell.obj && InteractionsRepresentationProvider.isApplicable(cell.obj?.data)) {
             refs[StructureFocusRepresentationTags.SurrNciRepr] = builder
                 .to(refs[StructureFocusRepresentationTags.SurrSel]!)
-                .apply(StateTransforms.Representation.StructureRepresentation3D, this.params.nciParams, { tags: StructureFocusRepresentationTags.SurrNciRepr }).ref;
+                .apply(StateTransforms.Representation.StructureRepresentation3D, this.getReprParams(this.params.nciParams), { tags: StructureFocusRepresentationTags.SurrNciRepr }).ref;
         }
 
         return { state, builder, refs };
@@ -216,7 +225,7 @@ class StructureFocusRepresentationBehavior extends PluginBehavior.WithSubscriber
         hasComponent = components.indexOf('interactions') >= 0;
         for (const repr of state.select(all.withTag(StructureFocusRepresentationTags.SurrNciRepr))) {
             if (!hasComponent) builder.delete(repr.transform.ref);
-            else builder.to(repr).update(this.params.nciParams);
+            else builder.to(repr).update(this.getReprParams(this.params.nciParams));
         }
 
         await PluginCommands.State.Update(this.plugin, { state, tree: builder, options: { doNotLogTiming: true, doNotUpdateCurrent: true } });

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/representation/cartoon.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>
  */
@@ -35,7 +35,7 @@ export const CartoonParams = {
     ...NucleotideRingParams,
     ...PolymerDirectionParams,
     sizeFactor: PD.Numeric(0.2, { min: 0, max: 10, step: 0.01 }),
-    visuals: PD.MultiSelect(['polymer-trace', 'polymer-gap', 'nucleotide-block'], PD.objectToOptions(CartoonVisuals)),
+    visuals: PD.MultiSelect(['polymer-trace', 'polymer-gap', 'nucleotide-ring'], PD.objectToOptions(CartoonVisuals)),
     bumpFrequency: PD.Numeric(2, { min: 0, max: 10, step: 0.1 }, BaseGeometry.ShadingCategory),
 };
 
@@ -49,7 +49,7 @@ export function getCartoonParams(ctx: ThemeRegistryContext, structure: Structure
         if (!hasGaps && u.gapElements.length) hasGaps = true;
     });
     params.visuals.defaultValue = ['polymer-trace'];
-    if (hasNucleotides) params.visuals.defaultValue.push('nucleotide-block');
+    if (hasNucleotides) params.visuals.defaultValue.push('nucleotide-ring');
     if (hasGaps) params.visuals.defaultValue.push('polymer-gap');
     return params;
 }

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`,