wip, prototype for mesh clipping

spelling
3.3.1
2026-06-06 14:44:22 +08:00 · 2022-03-02 19:51:34 -08:00 · 2022-03-02 19:50:30 -08:00 · 2022-02-27 18:45:45 -08:00 · 2022-02-27 18:40:48 -08:00 · 2022-02-27 18:40:27 -08:00
128 changed files with 4828 additions and 5363 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,88 @@ Note that since we don't clearly distinguish between a public and private interf

 ## [Unreleased]

+## [v3.3.1] - 2022-02-27
+
+- Fix issue with unit boundary reuse (do at visual level instead)
+- Add option to ignore ions for inter-unit bond computation
+
+## [v3.3.0] - 2022-02-27
+
+- Fix parsing contour-level from emdb v3 header files
+- Fix invalid CSS (#376)
+- Fix "texture not renderable" & "texture not bound" warnings (#319)
+- Fix visual for bonds between two aromatic rings
+- Fix visual for delocalized bonds (parsed from mmcif and mol2)
+- Fix ring computation algorithm
+- Add ``UnitResonance`` property with info about delocalized triplets
+- Resolve marking in main renderer loop to improve overall performance
+- Use ``throttleTime`` instead of ``debounceTime`` in sequence viewer for better responsiveness
+- Change line geometry default ``scaleFactor`` to 2 (3 is too big after fixing line rendering)
+- Trajectory animation performance improvements
+    - Reuse ``Model.CoarseGrained`` for coordinate trajectories
+    - Avoid calculating ``InterUnitBonds`` when ``Structure.parent`` ones are empty
+    - Reuse unit boundary if sphere has not changed too much
+    - Don't show 'inter-bond' and 'element-cross' visuals in line representations of polymerAndLigand preset
+- Fix additional mononucleotides detected as polymer components
+- Fix and improve ``canRemap`` handling in ``IntraUnitBonds``
+- Reuse occlusion for secondary passes during multi-sampling
+- Check if marking passes are needed before doing them
+- Add ``resolutionScale`` parameter to allow trading quality of occlusion for performance
+
+## [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:
+    - Do not include suffix for "identity assembly operators"
+    - Do not include assembly-related categories to export if the structure was composed from an assembly
+    - Special case for ``structAsymMap`` if Mol* asym id operator mapping is present
+- Support for opening ZIP files with multiple entries
+- Add Model Export extension
+- Bugfix: Automatically treat empty string as "non-present" value in BinaryCIF writer.
+- Fix coarse model support in entity-id color theme
+- Fix marking of carbohydrate visuals (whole chain could get marked instead of single residue)
+- Add custom colors to "element-symbol", "molecule-type", "residue-name", and "secondary-structure" themes
+- Support/bugfixes for ``atom_site.pdbx_sifts_xref`` categories
+- Improve/fix marking of ``InteractionsIntraUnitVisual`` (mark when all contact-feature members are given)
+
 ## [v3.0.0-dev.10] - 2022-01-17

 - Fix ``getOperatorsForIndex``
@@ -19,7 +101,7 @@ Note that since we don't clearly distinguish between a public and private interf
 - Add "camera rock" state animation
 - Add support for custom colors to "molecule-type" theme
 - [Breaking] Add style parameter to "illustrative" color theme
-    - Defaults to "entity-id" style instad of "chain-id"
+    - Defaults to "entity-id" style instead of "chain-id"
 - Add "illustrative" representation preset

 ## [v3.0.0-dev.9] - 2022-01-09
--- a/CITATION.cff
+++ b/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"
--- a/data/cif-field-names/mmcif-field-names.csv
+++ b/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
--- a/docs/interesting-pdb-entries.md
+++ b/docs/interesting-pdb-entries.md
@@ -34,6 +34,14 @@
    * ACE (many, e.g. 5AGU, 1E1X)
    * ACY in 7ABY
    * NH2 (many, e.g. 6Y13)
+* Ligands with many rings
+    * STU (e.g. 1U59) - many fused rings
+    * HT (e.g. 127D) - rings connected by a single bond
+    * J2C (e.g. 7EFJ) - rings connected by a single atom
+    * RBF (e.g. 7QF2) - three linearly fused rings
+    * TA1 (e.g. 1JFF) - many fused rings (incl. a 8-member rings)
+    * BPA (e.g. 1JDG) - many fused rings
+    * CLR (e.g. 3GKI) - four fused rings

 Assembly symmetries
 * 5M30 (Assembly 1, C3 local and pseudo)
--- a/package-lock.json
+++ b/package-lock.json
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
  "name": "molstar",
-  "version": "3.0.0-dev.10",
+  "version": "3.3.1",
  "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",
@@ -92,72 +92,69 @@
  "license": "MIT",
  "devDependencies": {
    "@graphql-codegen/add": "^3.1.1",
-    "@graphql-codegen/cli": "^2.3.1",
+    "@graphql-codegen/cli": "^2.6.2",
    "@graphql-codegen/time": "^3.1.1",
-    "@graphql-codegen/typescript": "^2.4.2",
+    "@graphql-codegen/typescript": "^2.4.5",
    "@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": "^4.3.7",
+    "@graphql-codegen/typescript-operations": "^2.3.2",
    "@types/cors": "^2.8.12",
    "@types/gl": "^4.1.0",
-    "@types/jest": "^27.4.0",
-    "@typescript-eslint/eslint-plugin": "^5.9.1",
-    "@typescript-eslint/parser": "^5.9.1",
+    "@types/jest": "^27.4.1",
+    "@typescript-eslint/eslint-plugin": "^5.12.1",
+    "@typescript-eslint/parser": "^5.12.1",
    "benchmark": "^2.1.4",
    "concurrently": "^7.0.0",
-    "cpx2": "^4.1.2",
+    "cpx2": "^4.2.0",
    "crypto-browserify": "^3.12.0",
-    "css-loader": "^6.5.1",
-    "eslint": "^8.7.0",
+    "css-loader": "^6.6.0",
+    "eslint": "^8.10.0",
    "extra-watch-webpack-plugin": "^1.0.3",
    "file-loader": "^6.2.0",
-    "fs-extra": "^10.0.0",
-    "graphql": "^16.2.0",
+    "fs-extra": "^10.0.1",
+    "graphql": "^16.3.0",
    "http-server": "^14.1.0",
-    "jest": "^27.4.7",
-    "mini-css-extract-plugin": "~2.4.7",
+    "jest": "^27.5.1",
+    "mini-css-extract-plugin": "^2.5.3",
    "path-browserify": "^1.0.1",
    "raw-loader": "^4.0.2",
-    "sass": "^1.48.0",
-    "sass-loader": "^12.4.0",
-    "simple-git": "^2.48.0",
+    "sass": "^1.49.9",
+    "sass-loader": "^12.6.0",
+    "simple-git": "^3.2.6",
    "stream-browserify": "^3.0.0",
    "style-loader": "^3.3.1",
    "ts-jest": "^27.1.3",
-    "typescript": "^4.5.4",
-    "webpack": "^5.66.0",
-    "webpack-cli": "^4.9.1"
+    "typescript": "^4.5.5",
+    "webpack": "^5.69.1",
+    "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": "^16.11.19",
-    "@types/node-fetch": "^2.5.12",
-    "@types/react": "^17.0.38",
+    "@types/node": "^16.11.26",
+    "@types/node-fetch": "^2.6.1",
+    "@types/react": "^17.0.39",
    "@types/react-dom": "^17.0.11",
    "@types/swagger-ui-dist": "3.30.1",
    "argparse": "^2.0.1",
-    "body-parser": "^1.19.1",
+    "body-parser": "^1.19.2",
    "compression": "^1.7.4",
    "cors": "^2.8.5",
-    "express": "^4.17.2",
+    "express": "^4.17.3",
    "h264-mp4-encoder": "^1.0.12",
    "immer": "^9.0.12",
    "immutable": "^4.0.0",
-    "node-fetch": "^2.6.2",
-    "rxjs": "^7.5.2",
-    "swagger-ui-dist": "^4.1.3",
+    "node-fetch": "^2.6.7",
+    "rxjs": "^7.5.4",
+    "swagger-ui-dist": "^4.5.2",
    "tslib": "^2.3.1",
    "util.promisify": "^1.1.1",
    "xhr2": "^0.2.1"
  },
  "peerDependencies": {
-    "react": "^17.0.2",
-    "react-dom": "^17.0.2"
-  },
-  "optionalDependencies": {
-    "gl": "^5.0.0"
+    "react": "^17.0.2 || ^16.14.0",
+    "react-dom": "^17.0.2 || ^16.14.0"
  }
 }
--- a/src/apps/docking-viewer/viewport.tsx
+++ b/src/apps/docking-viewer/viewport.tsx
@@ -44,10 +44,11 @@ function occlusionStyle(plugin: PluginContext) {
        postprocessing: {
            ...plugin.canvas3d!.props.postprocessing,
            occlusion: { name: 'on', params: {
-                samples: 64,
-                radius: 8,
-                bias: 1.0,
-                blurKernelSize: 13
+                bias: 0.8,
+                blurKernelSize: 15,
+                radius: 5,
+                samples: 32,
+                resolutionScale: 1
            } },
            outline: { name: 'on', params: {
                scale: 1.0,
--- a/src/apps/viewer/app.ts
+++ b/src/apps/viewer/app.ts
@@ -13,9 +13,11 @@ import { GeometryExport } from '../../extensions/geo-export';
 import { MAQualityAssessment } from '../../extensions/model-archive/quality-assessment/behavior';
 import { QualityAssessmentPLDDTPreset, QualityAssessmentQmeanPreset } from '../../extensions/model-archive/quality-assessment/behavior';
 import { QualityAssessment } from '../../extensions/model-archive/quality-assessment/prop';
+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';
@@ -57,6 +59,7 @@ const Extensions = {
    'rcsb-validation-report': PluginSpec.Behavior(RCSBValidationReport),
    'anvil-membrane-orientation': PluginSpec.Behavior(ANVILMembraneOrientation),
    'g3d': PluginSpec.Behavior(G3DFormat),
+    'model-export': PluginSpec.Behavior(ModelExport),
    'mp4-export': PluginSpec.Behavior(Mp4Export),
    'geo-export': PluginSpec.Behavior(GeometryExport),
    'ma-quality-assessment': PluginSpec.Behavior(MAQualityAssessment),
@@ -99,7 +102,14 @@ export class Viewer {
    }

    static async create(elementOrId: string | HTMLElement, options: Partial<ViewerOptions> = {}) {
-        const o = { ...DefaultViewerOptions, ...options };
+        const definedOptions = {} as any;
+        // filter for defined properies only so the default values
+        // are property applied
+        for (const p of Object.keys(options) as (keyof ViewerOptions)[]) {
+            if (options[p] !== void 0) definedOptions[p] = options[p];
+        }
+
+        const o: ViewerOptions = { ...DefaultViewerOptions, ...definedOptions };
        const defaultSpec = DefaultPluginUISpec();

        const spec: PluginUISpec = {
@@ -357,11 +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 }
                    }));
--- a/src/apps/viewer/index.html
+++ b/src/apps/viewer/index.html
@@ -57,7 +57,7 @@
            var pickScale = getParam('pick-scale', '[^&]+').trim();
            var pickPadding = getParam('pick-padding', '[^&]+').trim();
            var disableWboit = getParam('disable-wboit', '[^&]+').trim() === '1';
-            var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1';
+            var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;

            molstar.Viewer.create('app', {
                layoutShowControls: !hideControls,
@@ -71,7 +71,7 @@
                pixelScale: parseFloat(pixelScale) || 1,
                pickScale: parseFloat(pickScale) || 0.25,
                pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
-                enableWboit: !disableWboit,
+                enableWboit: disableWboit ? true : void 0, // use default value if disable-wboit is not set
                preferWebgl1: preferWebgl1,
            }).then(viewer => {
                var snapshotId = getParam('snapshot-id', '[^&]+').trim();
--- a/src/apps/viewer/index.ts
+++ b/src/apps/viewer/index.ts
@@ -9,4 +9,4 @@ import './embedded.html';
 import './favicon.ico';
 import './index.html';
 require('mol-plugin-ui/skin/light.scss');
-export * from './app';
+export * from './app';
--- a/src/examples/lighting/index.ts
+++ b/src/examples/lighting/index.ts
@@ -24,7 +24,7 @@ const Canvas3DPresets = {
    illustrative: {
        canvas3d: <Preset>{
            postprocessing: {
-                occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15 } },
+                occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15, resolutionScale: 1 } },
                outline: { name: 'on', params: { scale: 1, threshold: 0.33, color: Color(0x000000) } }
            },
            renderer: {
@@ -36,7 +36,7 @@ const Canvas3DPresets = {
    occlusion: {
        canvas3d: <Preset>{
            postprocessing: {
-                occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15 } },
+                occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15, resolutionScale: 1 } },
                outline: { name: 'off', params: {} }
            },
            renderer: {
--- a/src/extensions/model-export/export.ts
+++ b/src/extensions/model-export/export.ts
@@ -0,0 +1,87 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { utf8ByteCount, utf8Write } from '../../mol-io/common/utf8';
+import { to_mmCIF, Unit } from '../../mol-model/structure';
+import { PluginContext } from '../../mol-plugin/context';
+import { Task } from '../../mol-task';
+import { getFormattedTime } from '../../mol-util/date';
+import { download } from '../../mol-util/download';
+import { zip } from '../../mol-util/zip/zip';
+
+export async function exportHierarchy(plugin: PluginContext, options?: { format?: 'cif' | 'bcif' }) {
+    try {
+        await plugin.runTask(_exportHierarchy(plugin, options), { useOverlay: true });
+    } catch (e) {
+        console.error(e);
+        plugin.log.error(`Model export failed. See console for details.`);
+    }
+}
+
+function _exportHierarchy(plugin: PluginContext, options?: { format?: 'cif' | 'bcif' }) {
+    return Task.create('Export', async ctx => {
+        await ctx.update({ message: 'Exporting...', isIndeterminate: true, canAbort: false });
+
+        const format = options?.format ?? 'cif';
+        const { structures } = plugin.managers.structure.hierarchy.current;
+
+        const files: [name: string, data: string | Uint8Array][] = [];
+        const entryMap = new Map<string, number>();
+
+        for (const _s of structures) {
+            const s = _s.transform?.cell.obj?.data ?? _s.cell.obj?.data;
+            if (!s) continue;
+            if (s.models.length > 1) {
+                plugin.log.warn(`[Export] Skipping ${_s.cell.obj?.label}: Multimodel exports not supported.`);
+                continue;
+            }
+            if (s.units.some(u => !Unit.isAtomic(u))) {
+                plugin.log.warn(`[Export] Skipping ${_s.cell.obj?.label}: Non-atomic model exports not supported.`);
+                continue;
+            }
+
+            const name = entryMap.has(s.model.entryId)
+                ? `${s.model.entryId}_${entryMap.get(s.model.entryId)! + 1}.${format}`
+                : `${s.model.entryId}.${format}`;
+            entryMap.set(s.model.entryId, (entryMap.get(s.model.entryId) ?? 0) + 1);
+
+            await ctx.update({ message: `Exporting ${s.model.entryId}...`, isIndeterminate: true, canAbort: false });
+            if (s.elementCount > 100000) {
+                // Give UI chance to update, only needed for larger structures.
+                await new Promise(res => setTimeout(res, 50));
+            }
+
+            try {
+                files.push([name, to_mmCIF(s.model.entryId, s, format === 'bcif', { copyAllCategories: true })]);
+            } catch (e) {
+                if (format === 'cif' && s.elementCount > 2000000) {
+                    plugin.log.warn(`[Export] The structure might be too big to be exported as Text CIF, consider using the BinaryCIF format instead.`);
+                }
+                throw e;
+            }
+        }
+
+        if (files.length === 1) {
+            download(new Blob([files[0][1]]), files[0][0]);
+        } else if (files.length > 1) {
+            const zipData: Record<string, Uint8Array> = {};
+            for (const [fn, data] of files) {
+                if (data instanceof Uint8Array) {
+                    zipData[fn] = data;
+                } else {
+                    const bytes = new Uint8Array(utf8ByteCount(data));
+                    utf8Write(bytes, 0, data);
+                    zipData[fn] = bytes;
+                }
+            }
+            await ctx.update({ message: `Compressing Data...`, isIndeterminate: true, canAbort: false });
+            const buffer = await zip(ctx, zipData);
+            download(new Blob([new Uint8Array(buffer, 0, buffer.byteLength)]), `structures_${getFormattedTime()}.zip`);
+        }
+
+        plugin.log.info(`[Export] Done.`);
+    });
+}
--- a/src/extensions/model-export/index.ts
+++ b/src/extensions/model-export/index.ts
@@ -0,0 +1,30 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
+import { ModelExportUI } from './ui';
+
+export const ModelExport = PluginBehavior.create<{}>({
+    name: 'extension-model-export',
+    category: 'misc',
+    display: {
+        name: 'Model Export'
+    },
+    ctor: class extends PluginBehavior.Handler<{}> {
+        register(): void {
+            this.ctx.customStructureControls.set('model-export', ModelExportUI as any);
+        }
+
+        update() {
+            return false;
+        }
+
+        unregister() {
+            this.ctx.customStructureControls.delete('model-export');
+        }
+    },
+    params: () => ({})
+});
--- a/src/extensions/model-export/ui.tsx
+++ b/src/extensions/model-export/ui.tsx
@@ -0,0 +1,69 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { useState } from 'react';
+import { CollapsableControls, CollapsableState } from '../../mol-plugin-ui/base';
+import { Button } from '../../mol-plugin-ui/controls/common';
+import { GetAppSvg } from '../../mol-plugin-ui/controls/icons';
+import { ParameterControls } from '../../mol-plugin-ui/controls/parameters';
+import { useBehavior } from '../../mol-plugin-ui/hooks/use-behavior';
+import { PluginContext } from '../../mol-plugin/context';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { exportHierarchy } from './export';
+
+export class ModelExportUI extends CollapsableControls<{}, {}> {
+    protected defaultState(): CollapsableState {
+        return {
+            header: 'Export Models',
+            isCollapsed: true,
+            brand: { accent: 'cyan', svg: GetAppSvg }
+        };
+    }
+    protected renderControls(): JSX.Element | null {
+        return <ExportControls plugin={this.plugin} />;
+    }
+}
+
+const Params = {
+    format: PD.Select<'cif' | 'bcif'>('cif', [['cif', 'mmCIF'], ['bcif', 'Binary mmCIF']])
+};
+const DefaultParams = PD.getDefaultValues(Params);
+
+function ExportControls({ plugin }: { plugin: PluginContext }) {
+    const [params, setParams] = useState(DefaultParams);
+    const [exporting, setExporting] = useState(false);
+    useBehavior(plugin.managers.structure.hierarchy.behaviors.selection); // triggers UI update
+    const isBusy = useBehavior(plugin.behaviors.state.isBusy);
+    const hierarchy = plugin.managers.structure.hierarchy.current;
+
+    let label: string = 'Nothing to Export';
+    if (hierarchy.structures.length === 1) {
+        label = 'Export';
+    } if (hierarchy.structures.length > 1) {
+        label = 'Export (as ZIP)';
+    }
+
+    const onExport = async () => {
+        setExporting(true);
+        try {
+            await exportHierarchy(plugin, { format: params.format });
+        } finally {
+            setExporting(false);
+        }
+    };
+
+    return <>
+        <ParameterControls params={Params} values={params} onChangeValues={setParams} isDisabled={isBusy || exporting} />
+        <Button
+            onClick={onExport}
+            style={{ marginTop: 1 }}
+            disabled={isBusy || hierarchy.structures.length === 0 || exporting}
+            commit={hierarchy.structures.length ? 'on' : 'off'}
+        >
+            {label}
+        </Button>
+    </>;
+}
--- a/src/extensions/rcsb/graphql/types.ts
+++ b/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 2022-02-27T12:49:36-08:00

 /** All built-in and custom scalars, mapped to their actual values */
 export type Scalars = {
@@ -477,6 +477,8 @@ export type ClustersMembers = {
 export type CoreAssembly = {
  /** Get PDB entry that includes this assembly. */
  readonly entry?: Maybe<CoreEntry>;
+  /** Get all pairwise polymer interfaces for this PDB assembly. */
+  readonly interfaces?: Maybe<ReadonlyArray<Maybe<CoreInterface>>>;
  readonly pdbx_struct_assembly?: Maybe<PdbxStructAssembly>;
  readonly pdbx_struct_assembly_auth_evidence?: Maybe<ReadonlyArray<Maybe<PdbxStructAssemblyAuthEvidence>>>;
  readonly pdbx_struct_assembly_gen?: Maybe<ReadonlyArray<Maybe<PdbxStructAssemblyGen>>>;
@@ -724,6 +726,16 @@ export type CoreEntry = {
  readonly symmetry?: Maybe<Symmetry>;
 };

+export type CoreInterface = {
+  readonly rcsb_id: Scalars['String'];
+  readonly rcsb_interface_container_identifiers: RcsbInterfaceContainerIdentifiers;
+  readonly rcsb_interface_info?: Maybe<RcsbInterfaceInfo>;
+  /** List of operations for each interface partner. */
+  readonly rcsb_interface_operator: ReadonlyArray<Maybe<ReadonlyArray<Maybe<ReadonlyArray<Maybe<Scalars['String']>>>>>>;
+  readonly rcsb_interface_partner: ReadonlyArray<Maybe<RcsbInterfacePartner>>;
+  readonly rcsb_latest_revision?: Maybe<RcsbLatestRevision>;
+};
+
 export type CoreNonpolymerEntity = {
  /** Get PDB entry that contains this non-polymer entity. */
  readonly entry?: Maybe<CoreEntry>;
@@ -3186,6 +3198,28 @@ export type GeneName = {
  readonly value?: Maybe<Scalars['String']>;
 };

+export type InterfacePartnerFeatureAdditionalProperties = {
+  /**
+   * The additional property name.
+   *
+   * Allowable values:
+   * TO_BE_DEFINED
+   *
+   */
+  readonly name?: Maybe<Scalars['String']>;
+  /** The value(s) of the additional property. */
+  readonly values?: Maybe<ReadonlyArray<Maybe<Scalars['ObjectScalar']>>>;
+};
+
+export type InterfacePartnerFeatureFeaturePositions = {
+  /** An identifier for the monomer at which this segment of the feature begins. */
+  readonly beg_seq_id: Scalars['Int'];
+  /** An identifier for the monomer at which this segment of the feature ends. */
+  readonly end_seq_id?: Maybe<Scalars['Int']>;
+  /** The value(s) of the feature over the monomer segment. */
+  readonly values?: Maybe<ReadonlyArray<Maybe<Scalars['Float']>>>;
+};
+
 export type PdbxAuditRevisionCategory = {
  /**
   * The category updated in the pdbx_audit_revision_category record.
@@ -6745,6 +6779,10 @@ export type Query = {
  readonly entries?: Maybe<ReadonlyArray<Maybe<CoreEntry>>>;
  /** Get PDB entry given the PDB id. */
  readonly entry?: Maybe<CoreEntry>;
+  /** Get a pairwise polymeric interface given the PDB ID, ASSEMBLY ID and INTERFACE ID. */
+  readonly interface?: Maybe<CoreInterface>;
+  /** Get a list of pairwise polymeric interfaces given a list of INTERFACE IDs. Here INTERFACE ID is a compound identifier that includes entry_id, assembly_id and interface_id e.g. 1XXX-1.1. */
+  readonly interfaces?: Maybe<ReadonlyArray<Maybe<CoreInterface>>>;
  /** Get a list of PDB non-polymer entities given a list of ENTITY IDs. Here ENTITY ID is a compound identifier that includes entry_id and entity_id separated by '_', e.g. 1XXX_1. */
  readonly nonpolymer_entities?: Maybe<ReadonlyArray<Maybe<CoreNonpolymerEntity>>>;
  /** Get a PDB non-polymer entity, given the PDB ID and ENTITY ID. Here ENTITY ID is a '1', '2', '3', etc. */
@@ -6831,6 +6869,20 @@ export type QueryEntryArgs = {
 };


+/** Query root */
+export type QueryInterfaceArgs = {
+  assembly_id: Scalars['String'];
+  entry_id: Scalars['String'];
+  interface_id: Scalars['String'];
+};
+
+
+/** Query root */
+export type QueryInterfacesArgs = {
+  interface_ids: ReadonlyArray<Scalars['String']>;
+};
+
+
 /** Query root */
 export type QueryNonpolymer_EntitiesArgs = {
  entity_ids: ReadonlyArray<Scalars['String']>;
@@ -6952,6 +7004,8 @@ export type RcsbAssemblyContainerIdentifiers = {
  readonly assembly_id: Scalars['String'];
  /** Entry identifier for the container. */
  readonly entry_id: Scalars['String'];
+  /** List of binary interface Ids within the assembly (it points to interface id collection). */
+  readonly interface_ids?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
  /**
   * A unique identifier for each object in this assembly container formed by
   *  a dash separated concatenation of entry and assembly identifiers.
@@ -7010,6 +7064,24 @@ export type RcsbAssemblyInfo = {
   *  This is the total count of non-polymer entity instances generated in the assembly coordinate data.
   */
  readonly nonpolymer_entity_instance_count?: Maybe<Scalars['Int']>;
+  /** Number of heterologous (both binding sites are different) interface entities */
+  readonly num_heterologous_interface_entities?: Maybe<Scalars['Int']>;
+  /** Number of heteromeric (both partners are different polymeric entities) interface entities */
+  readonly num_heteromeric_interface_entities?: Maybe<Scalars['Int']>;
+  /** Number of homomeric (both partners are the same polymeric entity) interface entities */
+  readonly num_homomeric_interface_entities?: Maybe<Scalars['Int']>;
+  /** Number of polymer-polymer interface entities, grouping equivalent interfaces at the entity level (i.e. same entity_ids on either side, with similar but not identical binding sites) */
+  readonly num_interface_entities?: Maybe<Scalars['Int']>;
+  /** Number of geometrically equivalent (i.e. same asym_ids on either side) polymer-polymer interfaces in the assembly */
+  readonly num_interfaces?: Maybe<Scalars['Int']>;
+  /** Number of isologous (both binding sites are same, i.e. interface is symmetric) interface entities */
+  readonly num_isologous_interface_entities?: Maybe<Scalars['Int']>;
+  /** Number of nucleic acid-nucleic acid interface entities */
+  readonly num_na_interface_entities?: Maybe<Scalars['Int']>;
+  /** Number of protein-nucleic acid interface entities */
+  readonly num_prot_na_interface_entities?: Maybe<Scalars['Int']>;
+  /** Number of protein-protein interface entities */
+  readonly num_protein_interface_entities?: Maybe<Scalars['Int']>;
  /** The assembly non-hydrogen polymer entity atomic coordinate count. */
  readonly polymer_atom_count?: Maybe<Scalars['Int']>;
  /**
@@ -7085,6 +7157,10 @@ export type RcsbAssemblyInfo = {
   *  This is the total count of solvent entity instances generated in the assembly coordinate data.
   */
  readonly solvent_entity_instance_count?: Maybe<Scalars['Int']>;
+  /** Total buried surface area calculated as the sum of buried surface areas over all interfaces */
+  readonly total_assembly_buried_surface_area?: Maybe<Scalars['Float']>;
+  /** Total number of interfacing residues in the assembly, calculated as the sum of interfacing residues over all interfaces */
+  readonly total_number_interface_residues?: Maybe<Scalars['Int']>;
  /**
   * The number of unmodeled polymer monomers in the assembly coordinate data. This is
   *  the total count of monomers with unreported coordinate data for all polymer
@@ -8817,6 +8893,99 @@ export type RcsbGenomicLineage = {
  readonly name?: Maybe<Scalars['String']>;
 };

+export type RcsbInterfaceContainerIdentifiers = {
+  /** This item references an assembly in pdbx_struct_assembly */
+  readonly assembly_id: Scalars['String'];
+  /** Entry identifier for the container. */
+  readonly entry_id: Scalars['String'];
+  /**
+   * Identifier for NCS-equivalent interfaces within the assembly (same entity_ids on both sides)
+   *
+   * Examples:
+   * 1, 2
+   *
+   */
+  readonly interface_entity_id?: Maybe<Scalars['String']>;
+  /**
+   * Identifier for the geometrically equivalent (same asym_ids on either side) interfaces within the assembly
+   *
+   * Examples:
+   * 1, 2
+   *
+   */
+  readonly interface_id: Scalars['String'];
+  /**
+   * Unique identifier for the document
+   *
+   * Examples:
+   * 2UZI-1.A.B?1
+   *
+   */
+  readonly rcsb_id: Scalars['String'];
+};
+
+export type RcsbInterfaceInfo = {
+  /** Total interface buried surface area */
+  readonly interface_area?: Maybe<Scalars['Float']>;
+  /** Allowable values: homo, hetero. */
+  readonly interface_character?: Maybe<Scalars['String']>;
+  /** Number of core interface residues, defined as those that bury >90% accessible surface area with respect to the unbound state */
+  readonly num_core_interface_residues?: Maybe<Scalars['Int']>;
+  /** Number of interface residues, defined as those with burial fraction > 0 */
+  readonly num_interface_residues?: Maybe<Scalars['Int']>;
+  /** Allowable values: Nucleic acid (only), Protein (only), Protein/NA. */
+  readonly polymer_composition?: Maybe<Scalars['String']>;
+  /** The Jaccard score (intersection over union) of interface contacts in homomeric interfaces, comparing contact sets left-right vs right-left. High values indicate isologous (symmetric) interfaces, with value=1 if perfectly symmetric (e.g. crystallographic symmetry) */
+  readonly self_jaccard_contact_score?: Maybe<Scalars['Float']>;
+};
+
+export type RcsbInterfacePartner = {
+  readonly interface_partner_feature?: Maybe<ReadonlyArray<Maybe<RcsbInterfacePartnerInterfacePartnerFeature>>>;
+  readonly interface_partner_identifier?: Maybe<RcsbInterfacePartnerInterfacePartnerIdentifier>;
+};
+
+export type RcsbInterfacePartnerInterfacePartnerFeature = {
+  readonly additional_properties?: Maybe<ReadonlyArray<Maybe<InterfacePartnerFeatureAdditionalProperties>>>;
+  /**
+   * Identifies the version of the feature assignment.
+   *
+   * Examples:
+   * V4_0_2
+   *
+   */
+  readonly assignment_version?: Maybe<Scalars['String']>;
+  /** A description for the feature. */
+  readonly description?: Maybe<Scalars['String']>;
+  /** An identifier for the feature. */
+  readonly feature_id?: Maybe<Scalars['String']>;
+  readonly feature_positions?: Maybe<ReadonlyArray<Maybe<InterfacePartnerFeatureFeaturePositions>>>;
+  /** A name for the feature. */
+  readonly name?: Maybe<Scalars['String']>;
+  /**
+   * Code identifying the individual, organization or program that assigned the feature.
+   *
+   * Examples:
+   * NACCESS
+   *
+   */
+  readonly provenance_source?: Maybe<Scalars['String']>;
+  /**
+   * A type or category of the feature.
+   *
+   * Allowable values:
+   * ASA_UNBOUND, ASA_BOUND
+   *
+   */
+  readonly type?: Maybe<Scalars['String']>;
+};
+
+export type RcsbInterfacePartnerInterfacePartnerIdentifier = {
+  /** Instance identifier for this container. */
+  readonly asym_id: Scalars['String'];
+  /** Polymer entity identifier for the container. */
+  readonly entity_id: Scalars['String'];
+};
+
 export type RcsbLatestRevision = {
  /** The major version number of the latest revision. */
  readonly major_revision?: Maybe<Scalars['Int']>;
@@ -10263,7 +10432,7 @@ export type RcsbPolymerInstanceFeature = {
   * A type or category of the feature.
   *
   * Allowable values:
-   * ANGLE_OUTLIER, BINDING_SITE, BOND_OUTLIER, C-MANNOSYLATION_SITE, CATH, CIS-PEPTIDE, ECOD, HELIX_P, MEMBRANE_SEGMENT, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, N-GLYCOSYLATION_SITE, O-GLYCOSYLATION_SITE, RAMACHANDRAN_OUTLIER, ROTAMER_OUTLIER, RSCC_OUTLIER, RSRZ_OUTLIER, S-GLYCOSYLATION_SITE, SABDAB_ANTIBODY_HEAVY_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_TYPE, SCOP, SCOP2B_SUPERFAMILY, SCOP2_FAMILY, SCOP2_SUPERFAMILY, SHEET, STEREO_OUTLIER, UNASSIGNED_SEC_STRUCT, UNOBSERVED_ATOM_XYZ, UNOBSERVED_RESIDUE_XYZ, ZERO_OCCUPANCY_ATOM_XYZ, ZERO_OCCUPANCY_RESIDUE_XYZ
+   * ANGLE_OUTLIER, BINDING_SITE, BOND_OUTLIER, C-MANNOSYLATION_SITE, CATH, CIS-PEPTIDE, ECOD, HELIX_P, MEMBRANE_SEGMENT, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, N-GLYCOSYLATION_SITE, O-GLYCOSYLATION_SITE, RAMACHANDRAN_OUTLIER, ROTAMER_OUTLIER, RSCC_OUTLIER, RSRZ_OUTLIER, S-GLYCOSYLATION_SITE, SABDAB_ANTIBODY_HEAVY_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_TYPE, SCOP, SCOP2B_SUPERFAMILY, SCOP2_FAMILY, SCOP2_SUPERFAMILY, SHEET, STEREO_OUTLIER, UNASSIGNED_SEC_STRUCT, UNOBSERVED_ATOM_XYZ, UNOBSERVED_RESIDUE_XYZ, ZERO_OCCUPANCY_ATOM_XYZ, ZERO_OCCUPANCY_RESIDUE_XYZ, ASA
   *
   */
  readonly type?: Maybe<Scalars['String']>;
@@ -13145,4 +13314,4 @@ 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 };
--- a/src/extensions/rcsb/validation-report/representation.ts
+++ b/src/extensions/rcsb/validation-report/representation.ts
@@ -55,7 +55,16 @@ function createIntraUnitClashCylinderMesh(ctx: VisualContext, unit: Unit, struct
        radius: (edgeIndex: number) => magnitude[edgeIndex] * sizeFactor,
    };

-    return createLinkCylinderMesh(ctx, builderProps, props, mesh);
+    const { mesh: m, boundingSphere } = createLinkCylinderMesh(ctx, builderProps, props, mesh);
+
+    if (boundingSphere) {
+        m.setBoundingSphere(boundingSphere);
+    } else if (m.triangleCount > 0) {
+        const sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, 1 * sizeFactor);
+        m.setBoundingSphere(sphere);
+    }
+
+    return m;
 }

 export const IntraUnitClashParams = {
@@ -169,7 +178,16 @@ function createInterUnitClashCylinderMesh(ctx: VisualContext, structure: Structu
        radius: (edgeIndex: number) => edges[edgeIndex].props.magnitude * sizeFactor
    };

-    return createLinkCylinderMesh(ctx, builderProps, props, mesh);
+    const { mesh: m, boundingSphere } = createLinkCylinderMesh(ctx, builderProps, props, mesh);
+
+    if (boundingSphere) {
+        m.setBoundingSphere(boundingSphere);
+    } else {
+        const sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, 1 * sizeFactor);
+        m.setBoundingSphere(sphere);
+    }
+
+    return m;
 }

 export const InterUnitClashParams = {
--- a/src/mol-canvas3d/canvas3d.ts
+++ b/src/mol-canvas3d/canvas3d.ts
@@ -236,7 +236,7 @@ interface Canvas3D {
    /** Sets drawPaused = false without starting the built in animation loop */
    resume(): void
    identify(x: number, y: number): PickData | undefined
-    mark(loci: Representation.Loci, action: MarkerAction, noDraw?: boolean): void
+    mark(loci: Representation.Loci, action: MarkerAction): void
    getLoci(pickingId: PickingId | undefined): Representation.Loci

    notifyDidDraw: boolean,
@@ -345,7 +345,30 @@ namespace Canvas3D {
            return { loci, repr };
        }

-        function mark(reprLoci: Representation.Loci, action: MarkerAction, noDraw = false) {
+        let markBuffer: [reprLoci: Representation.Loci, action: MarkerAction][] = [];
+
+        function mark(reprLoci: Representation.Loci, action: MarkerAction) {
+            // NOTE: might try to optimize a case with opposite actions for the
+            //       same loci. Tho this might end up being more expensive (and error prone)
+            //       then just applying everything "naively".
+            markBuffer.push([reprLoci, action]);
+        }
+
+        function resolveMarking() {
+            let changed = false;
+            for (const [r, l] of markBuffer) {
+                changed = applyMark(r, l) || changed;
+            }
+            markBuffer = [];
+            if (changed) {
+                scene.update(void 0, true);
+                helper.handle.scene.update(void 0, true);
+                helper.camera.scene.update(void 0, true);
+            }
+            return changed;
+        }
+
+        function applyMark(reprLoci: Representation.Loci, action: MarkerAction) {
            const { repr, loci } = reprLoci;
            let changed = false;
            if (repr) {
@@ -355,24 +378,10 @@ namespace Canvas3D {
                changed = helper.camera.mark(loci, action) || changed;
                reprRenderObjects.forEach((_, _repr) => { changed = _repr.mark(loci, action) || changed; });
            }
-            if (changed) {
-                if (noDraw) {
-                    // Even with `noDraw` make sure changes will be rendered.
-                    // Note that with this calling mark (with or without `noDraw`) multiple times
-                    // during a JS event loop iteration will only result in a single render call.
-                    forceNextRender = true;
-                } else {
-                    scene.update(void 0, true);
-                    helper.handle.scene.update(void 0, true);
-                    helper.camera.scene.update(void 0, true);
-                    const prevPickDirty = pickHelper.dirty;
-                    draw({ force: true, allowMulti: true });
-                    pickHelper.dirty = prevPickDirty; // marking does not change picking buffers
-                }
-            }
+            return changed;
        }

-        function render(force: boolean, allowMulti: boolean) {
+        function render(force: boolean) {
            if (webgl.isContextLost) return false;

            let resized = false;
@@ -386,6 +395,8 @@ namespace Canvas3D {
                y > gl.drawingBufferHeight || y + height < 0
            ) return false;

+            const markingUpdated = resolveMarking();
+
            let didRender = false;
            controls.update(currentTime);
            const cameraChanged = camera.update();
@@ -393,9 +404,9 @@ namespace Canvas3D {
            const shouldRender = force || cameraChanged || resized || forceNextRender;
            forceNextRender = false;

-            const multiSampleChanged = multiSampleHelper.update(shouldRender, p.multiSample);
+            const multiSampleChanged = multiSampleHelper.update(markingUpdated || shouldRender, p.multiSample);

-            if (shouldRender || multiSampleChanged) {
+            if (shouldRender || multiSampleChanged || markingUpdated) {
                let cam: Camera | StereoCamera = camera;
                if (p.camera.stereo.name === 'on') {
                    stereoCamera.update();
@@ -404,12 +415,13 @@ namespace Canvas3D {

                const ctx = { renderer, camera: cam, scene, helper };
                if (MultiSamplePass.isEnabled(p.multiSample)) {
-                    const forceOn = !cameraChanged && allowMulti && !controls.isAnimating;
+                    const forceOn = !cameraChanged && markingUpdated && !controls.isAnimating;
                    multiSampleHelper.render(ctx, p, true, forceOn);
                } else {
                    passes.draw.render(ctx, p, true);
                }
-                pickHelper.dirty = true;
+                // if only marking has updated, do not set the flag to dirty
+                pickHelper.dirty = pickHelper.dirty || shouldRender;
                didRender = true;
            }

@@ -421,9 +433,9 @@ namespace Canvas3D {
        let currentTime = 0;
        let drawPaused = false;

-        function draw(options?: { force?: boolean, allowMulti?: boolean }) {
+        function draw(options?: { force?: boolean }) {
            if (drawPaused) return;
-            if (render(!!options?.force, !!options?.allowMulti) && notifyDidDraw) {
+            if (render(!!options?.force) && notifyDidDraw) {
                didDraw.next(now() - startTime as now.Timestamp);
            }
        }
@@ -831,6 +843,8 @@ namespace Canvas3D {
            dispose: () => {
                contextRestoredSub.unsubscribe();

+                markBuffer = [];
+
                scene.clear();
                helper.debug.clear();
                controls.dispose();
--- a/src/mol-canvas3d/helper/interaction-events.ts
+++ b/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;
--- a/src/mol-canvas3d/passes/draw.ts
+++ b/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>
@@ -307,19 +307,22 @@ export class DrawPass {
        }

        if (markingEnabled) {
-            const markingDepthTest = props.marking.ghostEdgeStrength < 1;
-            if (markingDepthTest) {
-                this.marking.depthTarget.bind();
-                renderer.clear(false);
-                renderer.renderMarkingDepth(scene.primitives, camera, null);
+            const markerAverage = scene.getMarkerAverage();
+            if (markerAverage > 0) {
+                const markingDepthTest = props.marking.ghostEdgeStrength < 1;
+                if (markingDepthTest && markerAverage !== 1) {
+                    this.marking.depthTarget.bind();
+                    renderer.clear(false, true);
+                    renderer.renderMarkingDepth(scene.primitives, camera, null);
+                }
+
+                this.marking.maskTarget.bind();
+                renderer.clear(false, true);
+                renderer.renderMarkingMask(scene.primitives, camera, markingDepthTest ? this.marking.depthTarget.texture : null);
+
+                this.marking.update(props.marking);
+                this.marking.render(camera.viewport, postprocessingEnabled ? this.postprocessing.target : this.colorTarget);
            }
-
-            this.marking.maskTarget.bind();
-            renderer.clear(false);
-            renderer.renderMarkingMask(scene.primitives, camera, markingDepthTest ? this.marking.depthTarget.texture : null);
-
-            this.marking.update(props.marking);
-            this.marking.render(camera.viewport, postprocessingEnabled ? this.postprocessing.target : this.colorTarget);
        }

        if (helper.debug.isEnabled) {
--- a/src/mol-canvas3d/passes/multi-sample.ts
+++ b/src/mol-canvas3d/passes/multi-sample.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>
 */
@@ -157,6 +157,14 @@ export class MultiSamplePass {
            ValueCell.update(compose.values.uWeight, sampleWeight);

            // render scene
+            if (i === 0) {
+                drawPass.postprocessing.setOcclusionOffset(0, 0);
+            } else {
+                drawPass.postprocessing.setOcclusionOffset(
+                    offset[0] / width,
+                    offset[1] / height
+                );
+            }
            drawPass.render(ctx, props, false);

            // compose rendered scene with compose target
@@ -175,6 +183,8 @@ export class MultiSamplePass {
            compose.render();
        }

+        drawPass.postprocessing.setOcclusionOffset(0, 0);
+
        ValueCell.update(compose.values.uWeight, 1.0);
        ValueCell.update(compose.values.tColor, composeTarget.texture);
        compose.update();
@@ -236,6 +246,14 @@ export class MultiSamplePass {
                camera.update();

                // render scene
+                if (sampleIndex === 0) {
+                    drawPass.postprocessing.setOcclusionOffset(0, 0);
+                } else {
+                    drawPass.postprocessing.setOcclusionOffset(
+                        offset[0] / width,
+                        offset[1] / height
+                    );
+                }
                drawPass.render(ctx, props, false);

                // compose rendered scene with compose target
@@ -258,6 +276,8 @@ export class MultiSamplePass {
            }
        }

+        drawPass.postprocessing.setOcclusionOffset(0, 0);
+
        this.bindOutputTarget(toDrawingBuffer);
        gl.viewport(x, y, width, height);
        gl.scissor(x, y, width, height);
@@ -291,23 +311,23 @@ const JitterVectors = [
        [0, 0]
    ],
    [
-        [4, 4], [-4, -4]
+        [0, 0], [-4, -4]
    ],
    [
-        [-2, -6], [6, -2], [-6, 2], [2, 6]
+        [0, 0], [6, -2], [-6, 2], [2, 6]
    ],
    [
-        [1, -3], [-1, 3], [5, 1], [-3, -5],
+        [0, 0], [-1, 3], [5, 1], [-3, -5],
        [-5, 5], [-7, -1], [3, 7], [7, -7]
    ],
    [
-        [1, 1], [-1, -3], [-3, 2], [4, -1],
+        [0, 0], [-1, -3], [-3, 2], [4, -1],
        [-5, -2], [2, 5], [5, 3], [3, -5],
        [-2, 6], [0, -7], [-4, -6], [-6, 4],
        [-8, 0], [7, -4], [6, 7], [-7, -8]
    ],
    [
-        [-4, -7], [-7, -5], [-3, -5], [-5, -4],
+        [0, 0], [-7, -5], [-3, -5], [-5, -4],
        [-1, -4], [-2, -2], [-6, -1], [-4, 0],
        [-7, 1], [-1, 2], [-6, 3], [-3, 3],
        [-7, 6], [-3, 6], [-5, 7], [-1, 7],
--- a/src/mol-canvas3d/passes/postprocessing.ts
+++ b/src/mol-canvas3d/passes/postprocessing.ts
@@ -1,11 +1,11 @@
 /**
- * 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>
 */

-import { QuadSchema, QuadValues } from '../../mol-gl/compute/util';
+import { CopyRenderable, createCopyRenderable, QuadSchema, QuadValues } from '../../mol-gl/compute/util';
 import { TextureSpec, Values, UniformSpec, DefineSpec } from '../../mol-gl/renderable/schema';
 import { ShaderCode } from '../../mol-gl/shader-code';
 import { WebGLContext } from '../../mol-gl/webgl/context';
@@ -199,6 +199,7 @@ const PostprocessingSchema = {
    uMaxPossibleViewZDiff: UniformSpec('f'),

    dOcclusionEnable: DefineSpec('boolean'),
+    uOcclusionOffset: UniformSpec('v2'),

    dOutlineEnable: DefineSpec('boolean'),
    dOutlineScale: DefineSpec('number'),
@@ -227,6 +228,7 @@ function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, d
        uMaxPossibleViewZDiff: ValueCell.create(0.5),

        dOcclusionEnable: ValueCell.create(true),
+        uOcclusionOffset: ValueCell.create(Vec2.create(0, 0)),

        dOutlineEnable: ValueCell.create(false),
        dOutlineScale: ValueCell.create(1),
@@ -244,9 +246,10 @@ export const PostprocessingParams = {
    occlusion: PD.MappedStatic('on', {
        on: PD.Group({
            samples: PD.Numeric(32, { min: 1, max: 256, step: 1 }),
-            radius: PD.Numeric(5, { min: 0, max: 10, step: 0.1 }, { description: 'Final radius is 2^x.' }),
+            radius: PD.Numeric(5, { min: 0, max: 10, step: 0.1 }, { description: 'Final occlusion radius is 2^x' }),
            bias: PD.Numeric(0.8, { min: 0, max: 3, step: 0.1 }),
            blurKernelSize: PD.Numeric(15, { min: 1, max: 25, step: 2 }),
+            resolutionScale: PD.Numeric(1, { min: 0.1, max: 1, step: 0.05 }, { description: 'Adjust resolution of occlusion calculation' }),
        }),
        off: PD.Group({})
    }, { cycle: true, description: 'Darken occluded crevices with the ambient occlusion effect' }),
@@ -281,6 +284,9 @@ export class PostprocessingPass {
    private readonly ssaoBlurFirstPassFramebuffer: Framebuffer;
    private readonly ssaoBlurSecondPassFramebuffer: Framebuffer;

+    private readonly downsampledDepthTarget: RenderTarget;
+    private readonly downsampleDepthRenderable: CopyRenderable;
+
    private readonly ssaoDepthTexture: Texture;
    private readonly ssaoDepthBlurProxyTexture: Texture;

@@ -290,24 +296,25 @@ export class PostprocessingPass {

    private nSamples: number;
    private blurKernelSize: number;
+    private downsampleFactor: number;

    private readonly renderable: PostprocessingRenderable;

    private ssaoScale: number;
    private calcSsaoScale() {
        // downscale ssao for high pixel-ratios
-        return Math.min(1, 1 / this.webgl.pixelRatio);
+        return Math.min(1, 1 / this.webgl.pixelRatio) * this.downsampleFactor;
    }

-    constructor(private webgl: WebGLContext, drawPass: DrawPass) {
-        this.ssaoScale = this.calcSsaoScale();
-
+    constructor(private webgl: WebGLContext, private drawPass: DrawPass) {
        const { colorTarget, depthTexture } = drawPass;
        const width = colorTarget.getWidth();
        const height = colorTarget.getHeight();

        this.nSamples = 1;
        this.blurKernelSize = 1;
+        this.downsampleFactor = 1;
+        this.ssaoScale = this.calcSsaoScale();

        // needs to be linear for anti-aliasing pass
        this.target = webgl.createRenderTarget(width, height, false, 'uint8', 'linear');
@@ -332,17 +339,20 @@ export class PostprocessingPass {
        const sw = Math.floor(width * this.ssaoScale);
        const sh = Math.floor(height * this.ssaoScale);

-        this.ssaoDepthTexture = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'nearest');
+        this.downsampledDepthTarget = webgl.createRenderTarget(sw, sh, false, 'uint8', 'linear');
+        this.downsampleDepthRenderable = createCopyRenderable(webgl, depthTexture);
+
+        this.ssaoDepthTexture = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'linear');
        this.ssaoDepthTexture.define(sw, sh);
        this.ssaoDepthTexture.attachFramebuffer(this.ssaoFramebuffer, 'color0');

-        this.ssaoDepthBlurProxyTexture = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'nearest');
+        this.ssaoDepthBlurProxyTexture = webgl.resources.texture('image-uint8', 'rgba', 'ubyte', 'linear');
        this.ssaoDepthBlurProxyTexture.define(sw, sh);
        this.ssaoDepthBlurProxyTexture.attachFramebuffer(this.ssaoBlurFirstPassFramebuffer, 'color0');

        this.ssaoDepthTexture.attachFramebuffer(this.ssaoBlurSecondPassFramebuffer, 'color0');

-        this.ssaoRenderable = getSsaoRenderable(webgl, depthTexture);
+        this.ssaoRenderable = getSsaoRenderable(webgl, this.downsampleFactor === 1 ? depthTexture : this.downsampledDepthTarget.texture);
        this.ssaoBlurFirstPassRenderable = getSsaoBlurRenderable(webgl, this.ssaoDepthTexture, 'horizontal');
        this.ssaoBlurSecondPassRenderable = getSsaoBlurRenderable(webgl, this.ssaoDepthBlurProxyTexture, 'vertical');
        this.renderable = getPostprocessingRenderable(webgl, colorTarget.texture, depthTexture, this.outlinesTarget.texture, this.ssaoDepthTexture);
@@ -359,11 +369,13 @@ export class PostprocessingPass {
            const sh = Math.floor(height * this.ssaoScale);
            this.target.setSize(width, height);
            this.outlinesTarget.setSize(width, height);
+            this.downsampledDepthTarget.setSize(sw, sh);
            this.ssaoDepthTexture.define(sw, sh);
            this.ssaoDepthBlurProxyTexture.define(sw, sh);

            ValueCell.update(this.renderable.values.uTexSize, Vec2.set(this.renderable.values.uTexSize.ref.value, width, height));
            ValueCell.update(this.outlinesRenderable.values.uTexSize, Vec2.set(this.outlinesRenderable.values.uTexSize.ref.value, width, height));
+            ValueCell.update(this.downsampleDepthRenderable.values.uTexSize, Vec2.set(this.downsampleDepthRenderable.values.uTexSize.ref.value, sw, sh));
            ValueCell.update(this.ssaoRenderable.values.uTexSize, Vec2.set(this.ssaoRenderable.values.uTexSize.ref.value, sw, sh));
            ValueCell.update(this.ssaoBlurFirstPassRenderable.values.uTexSize, Vec2.set(this.ssaoBlurFirstPassRenderable.values.uTexSize.ref.value, sw, sh));
            ValueCell.update(this.ssaoBlurSecondPassRenderable.values.uTexSize, Vec2.set(this.ssaoBlurSecondPassRenderable.values.uTexSize.ref.value, sw, sh));
@@ -434,6 +446,30 @@ export class PostprocessingPass {
                ValueCell.updateIfChanged(this.ssaoBlurSecondPassRenderable.values.dOcclusionKernelSize, this.blurKernelSize);
            }

+            if (this.downsampleFactor !== props.occlusion.params.resolutionScale) {
+                needsUpdateSsao = true;
+
+                this.downsampleFactor = props.occlusion.params.resolutionScale;
+                this.ssaoScale = this.calcSsaoScale();
+
+                const sw = Math.floor(w * this.ssaoScale);
+                const sh = Math.floor(h * this.ssaoScale);
+
+                this.downsampledDepthTarget.setSize(sw, sh);
+                this.ssaoDepthTexture.define(sw, sh);
+                this.ssaoDepthBlurProxyTexture.define(sw, sh);
+
+                if (this.ssaoScale === 1) {
+                    ValueCell.update(this.ssaoRenderable.values.tDepth, this.drawPass.depthTexture);
+                } else {
+                    ValueCell.update(this.ssaoRenderable.values.tDepth, this.downsampledDepthTarget.texture);
+                }
+
+                ValueCell.update(this.downsampleDepthRenderable.values.uTexSize, Vec2.set(this.downsampleDepthRenderable.values.uTexSize.ref.value, sw, sh));
+                ValueCell.update(this.ssaoRenderable.values.uTexSize, Vec2.set(this.ssaoRenderable.values.uTexSize.ref.value, sw, sh));
+                ValueCell.update(this.ssaoBlurFirstPassRenderable.values.uTexSize, Vec2.set(this.ssaoBlurFirstPassRenderable.values.uTexSize.ref.value, sw, sh));
+                ValueCell.update(this.ssaoBlurSecondPassRenderable.values.uTexSize, Vec2.set(this.ssaoBlurSecondPassRenderable.values.uTexSize.ref.value, sw, sh));
+            }
        }

        if (props.outline.name === 'on') {
@@ -494,6 +530,13 @@ export class PostprocessingPass {
        gl.scissor(x, y, width, height);
    }

+    private occlusionOffset: [x: number, y: number] = [0, 0];
+    setOcclusionOffset(x: number, y: number) {
+        this.occlusionOffset[0] = x;
+        this.occlusionOffset[1] = y;
+        ValueCell.update(this.renderable.values.uOcclusionOffset, Vec2.set(this.renderable.values.uOcclusionOffset.ref.value, x, y));
+    }
+
    render(camera: ICamera, toDrawingBuffer: boolean, transparentBackground: boolean, backgroundColor: Color, props: PostprocessingProps) {
        this.updateState(camera, transparentBackground, backgroundColor, props);

@@ -502,14 +545,13 @@ export class PostprocessingPass {
            this.outlinesRenderable.render();
        }

-        if (props.occlusion.name === 'on') {
-            const { x, y, width, height } = camera.viewport;
-            const sx = Math.floor(x * this.ssaoScale);
-            const sy = Math.floor(y * this.ssaoScale);
-            const sw = Math.ceil(width * this.ssaoScale);
-            const sh = Math.ceil(height * this.ssaoScale);
-            this.webgl.gl.viewport(sx, sy, sw, sh);
-            this.webgl.gl.scissor(sx, sy, sw, sh);
+        // don't render occlusion if offset is given,
+        // which will reuse the existing occlusion
+        if (props.occlusion.name === 'on' && this.occlusionOffset[0] === 0 && this.occlusionOffset[1] === 0) {
+            if (this.ssaoScale < 1) {
+                this.downsampledDepthTarget.bind();
+                this.downsampleDepthRenderable.render();
+            }

            this.ssaoFramebuffer.bind();
            this.ssaoRenderable.render();
@@ -519,9 +561,6 @@ export class PostprocessingPass {

            this.ssaoBlurSecondPassFramebuffer.bind();
            this.ssaoBlurSecondPassRenderable.render();
-
-            this.webgl.gl.viewport(x, y, width, height);
-            this.webgl.gl.scissor(x, y, width, height);
        }

        if (toDrawingBuffer) {
--- a/src/mol-geo/geometry/lines/lines.ts
+++ b/src/mol-geo/geometry/lines/lines.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 Alexander Rose <alexander.rose@weirdbyte.de>
 */
@@ -165,7 +165,7 @@ export namespace Lines {

    export const Params = {
        ...BaseGeometry.Params,
-        sizeFactor: PD.Numeric(3, { min: 0, max: 10, step: 0.1 }),
+        sizeFactor: PD.Numeric(2, { min: 0, max: 10, step: 0.1 }),
        lineSizeAttenuation: PD.Boolean(false),
    };
    export type Params = typeof Params
--- a/src/mol-geo/geometry/mesh/object-clipping.ts
+++ b/src/mol-geo/geometry/mesh/object-clipping.ts
@@ -0,0 +1,215 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { ChunkedArray } from '../../../mol-data/util';
+import { MeshValues } from '../../../mol-gl/renderable/mesh';
+import { Sphere3D } from '../../../mol-math/geometry';
+import { sphereIntersect } from '../../../mol-math/intersect';
+import { Vec3 } from '../../../mol-math/linear-algebra';
+import { ValueCell } from '../../../mol-util';
+import { Clip } from '../../../mol-util/clip';
+
+interface ObjectClippingInput {
+    drawCount: number
+    vertexCount: number
+    instanceCount: number
+    groupCount: number
+    transformBuffer: Float32Array
+    instanceBuffer: Float32Array
+    positionBuffer: Float32Array
+    indexBuffer: Uint32Array
+    normalBuffer: Float32Array
+    groupBuffer: Float32Array
+    // colorData: TextureImage<Uint8Array>
+    // colorType: 'group' | 'groupInstance'
+    boundingSphere: Sphere3D
+    invariantBoundingSphere: Sphere3D
+
+    objectCount: number
+    objectType: number[]
+    objectPosition: number[]
+    objectScale: number[]
+    objectInvert: boolean[]
+}
+
+export function calcMeshObjectClipping(input: ObjectClippingInput) {
+    console.log('calcMeshObjectClipping', input);
+    const { drawCount, vertexCount, indexBuffer, positionBuffer, normalBuffer, objectCount, groupBuffer, objectPosition, objectScale, objectType, objectInvert } = input;
+    const triangleCount = drawCount / 3;
+
+    if (objectCount === 0) {
+        return {
+            indexBuffer,
+            positionBuffer,
+            normalBuffer,
+            groupBuffer,
+            drawCount,
+            vertexCount
+        };
+    }
+
+    const tests: ((p: Vec3) => boolean)[] = [];
+    for (let i = 0; i < objectCount; ++i) {
+        if (objectType[i] === Clip.Type.sphere) {
+            const c = Vec3.fromArray(Vec3(), objectPosition, i * 3);
+            const r = objectScale[i * 3] / 2;
+            if (objectInvert[i]) {
+                tests.push((p: Vec3) => Vec3.distance(p, c) <= r);
+            } else {
+                tests.push((p: Vec3) => Vec3.distance(p, c) >= r);
+            }
+        }
+    }
+
+    const invert = objectInvert[0];
+    const center = Vec3.fromArray(Vec3(), objectPosition, 0);
+    const radius = objectScale[0] / 2;
+
+    // new
+    const index = ChunkedArray.create(Uint32Array, 3, 1024, triangleCount);
+
+    // re-use
+    const vertex = ChunkedArray.create(Float32Array, 3, 1024, positionBuffer);
+    vertex.currentIndex = vertexCount * 3;
+    vertex.elementCount = vertexCount;
+    const normal = ChunkedArray.create(Float32Array, 3, 1024, normalBuffer);
+    normal.currentIndex = vertexCount * 3;
+    normal.elementCount = vertexCount;
+    const group = ChunkedArray.create(Float32Array, 1, 1024, groupBuffer);
+    group.currentIndex = vertexCount;
+    group.elementCount = vertexCount;
+
+    const vA = Vec3();
+    const vB = Vec3();
+    const vC = Vec3();
+
+    const xA = Vec3();
+    const xB = Vec3();
+
+    const nA = Vec3();
+    const nB = Vec3();
+
+    function add(a: number, b: number, p: Vec3) {
+        Vec3.fromArray(nA, normalBuffer, a * 3);
+        Vec3.fromArray(nB, normalBuffer, b * 3);
+        Vec3.scale(nA, Vec3.add(nA, nA, nB), 0.5);
+        ChunkedArray.add3(vertex, p[0], p[1], p[2]);
+        ChunkedArray.add3(normal, nA[0], nA[1], nA[2]);
+        ChunkedArray.add(group, groupBuffer[a]);
+    }
+
+    function split(tip: Vec3, sideA: Vec3, sideB: Vec3, tipIdx: number, sideIdxA: number, sideIdxB: number, reverse: boolean) {
+        if (reverse) {
+            sphereIntersect(xA, sideA, tip, center, radius, invert);
+            sphereIntersect(xB, sideB, tip, center, radius, invert);
+        } else {
+            sphereIntersect(xA, tip, sideA, center, radius, invert);
+            sphereIntersect(xB, tip, sideB, center, radius, invert);
+        }
+        add(tipIdx, sideIdxA, xA);
+        add(tipIdx, sideIdxB, xB);
+        if (reverse) {
+            ChunkedArray.add3(index, tipIdx, newVertexCount + 1, newVertexCount);
+            newTriangleCount += 1;
+        } else {
+            ChunkedArray.add3(index, newVertexCount, newVertexCount + 1, sideIdxA);
+            ChunkedArray.add3(index, newVertexCount + 1, sideIdxB, sideIdxA);
+            newTriangleCount += 2;
+        }
+        newVertexCount += 2;
+    }
+
+    let newVertexCount = vertexCount;
+    let newTriangleCount = 0;
+
+    for (let i = 0; i < triangleCount; ++i) {
+        const iA = indexBuffer[i * 3];
+        const iB = indexBuffer[i * 3 + 1];
+        const iC = indexBuffer[i * 3 + 2];
+
+        Vec3.fromArray(vA, positionBuffer, iA * 3);
+        Vec3.fromArray(vB, positionBuffer, iB * 3);
+        Vec3.fromArray(vC, positionBuffer, iC * 3);
+
+        let tA = true;
+        let tB = true;
+        let tC = true;
+        for (const t of tests) {
+            if (!t(vA)) { tA = false; }
+            if (!t(vB)) { tB = false; }
+            if (!t(vC)) { tC = false; }
+        }
+
+        if (!tA && !tB && !tC) continue;
+
+        if (tA && tB && tC) {
+            ChunkedArray.add3(index, iA, iB, iC);
+            newTriangleCount += 1;
+        } else if (tA && tB && !tC) {
+            split(vC, vA, vB, iC, iA, iB, false);
+        } else if (!tA && !tB && tC) {
+            split(vC, vA, vB, iC, iA, iB, true);
+        } else if (tA && tC && !tB) {
+            split(vB, vA, vC, iB, iA, iC, false);
+        } else if (!tA && !tC && tB) {
+            split(vB, vA, vC, iB, iA, iC, true);
+        } else if (tB && tC && !tA) {
+            split(vA, vC, vB, iA, iC, iB, false);
+        } else if (!tB && !tC && tA) {
+            split(vA, vC, vB, iA, iC, iB, true);
+        } else {
+            console.log('what');
+        }
+    }
+
+    console.log({ vertexCount, newVertexCount, triangleCount, newTriangleCount });
+
+    return {
+        indexBuffer: ChunkedArray.compact(index),
+        positionBuffer: ChunkedArray.compact(vertex),
+        normalBuffer: ChunkedArray.compact(normal),
+        groupBuffer: ChunkedArray.compact(group),
+        drawCount: newTriangleCount * 3,
+        vertexCount: newVertexCount
+    };
+}
+
+//
+
+export function applyMeshObjectClipping(values: MeshValues) {
+    console.log('applyMeshObjectClipping');
+    const clippingData = calcMeshObjectClipping({
+        drawCount: values.drawCount.ref.value,
+        vertexCount: values.uVertexCount.ref.value,
+        instanceCount: values.instanceCount.ref.value,
+        groupCount: values.uGroupCount.ref.value,
+        transformBuffer: values.transform.ref.value,
+        instanceBuffer: values.aInstance.ref.value,
+        positionBuffer: values.aPosition.ref.value,
+        indexBuffer: values.elements.ref.value,
+        normalBuffer: values.aNormal.ref.value,
+        groupBuffer: values.aGroup.ref.value,
+        // colorData: TextureImage<Uint8Array>
+        // colorType: 'group' | 'groupInstance'
+        boundingSphere: values.boundingSphere.ref.value,
+        invariantBoundingSphere: values.invariantBoundingSphere.ref.value,
+
+        objectCount: values.dClipObjectCount.ref.value,
+        objectType: values.uClipObjectType.ref.value,
+        objectPosition: values.uClipObjectPosition.ref.value,
+        objectScale: values.uClipObjectScale.ref.value,
+        objectInvert: values.uClipObjectInvert.ref.value,
+    });
+    console.log(values.dClipObjectCount.ref.value, values.drawCount.ref.value, clippingData);
+
+    ValueCell.updateIfChanged(values.dClipObjectCount, 0);
+    ValueCell.update(values.elements, clippingData.indexBuffer);
+    ValueCell.update(values.aPosition, clippingData.positionBuffer);
+    ValueCell.update(values.aNormal, clippingData.normalBuffer);
+    ValueCell.update(values.aGroup, clippingData.groupBuffer);
+    ValueCell.updateIfChanged(values.drawCount, clippingData.drawCount);
+    ValueCell.updateIfChanged(values.uVertexCount, clippingData.vertexCount);
+}
--- a/src/mol-gl/_spec/renderer.spec.ts
+++ b/src/mol-gl/_spec/renderer.spec.ts
@@ -31,7 +31,7 @@ describe('renderer', () => {
        expect(ctx.gl.drawingBufferHeight).toBe(32);

        expect(ctx.stats.resourceCounts.attribute).toBe(0);
-        expect(ctx.stats.resourceCounts.texture).toBe(0);
+        expect(ctx.stats.resourceCounts.texture).toBe(1);
        expect(ctx.stats.resourceCounts.vertexArray).toBe(0);
        expect(ctx.stats.resourceCounts.program).toBe(0);
        expect(ctx.stats.resourceCounts.shader).toBe(0);
@@ -52,7 +52,7 @@ describe('renderer', () => {
        scene.add(points);
        scene.commit();
        expect(ctx.stats.resourceCounts.attribute).toBe(ctx.isWebGL2 ? 4 : 5);
-        expect(ctx.stats.resourceCounts.texture).toBe(8);
+        expect(ctx.stats.resourceCounts.texture).toBe(9);
        expect(ctx.stats.resourceCounts.vertexArray).toBe(ctx.extensions.vertexArrayObject ? 5 : 0);
        expect(ctx.stats.resourceCounts.program).toBe(5);
        expect(ctx.stats.resourceCounts.shader).toBe(10);
@@ -60,7 +60,7 @@ describe('renderer', () => {
        scene.remove(points);
        scene.commit();
        expect(ctx.stats.resourceCounts.attribute).toBe(0);
-        expect(ctx.stats.resourceCounts.texture).toBe(0);
+        expect(ctx.stats.resourceCounts.texture).toBe(1);
        expect(ctx.stats.resourceCounts.vertexArray).toBe(0);
        expect(ctx.stats.resourceCounts.program).toBe(5);
        expect(ctx.stats.resourceCounts.shader).toBe(10);
--- a/src/mol-gl/renderer.ts
+++ b/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>
 */
@@ -16,7 +16,7 @@ import { GlobalUniformValues } from './renderable/schema';
 import { GraphicsRenderVariant } from './webgl/render-item';
 import { ParamDefinition as PD } from '../mol-util/param-definition';
 import { degToRad } from '../mol-math/misc';
-import { createNullTexture, Texture, Textures } from './webgl/texture';
+import { Texture, Textures } from './webgl/texture';
 import { arrayMapUpsert } from '../mol-util/array';
 import { clamp } from '../mol-math/interpolate';

@@ -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

@@ -146,9 +146,9 @@ namespace Renderer {

        let transparentBackground = false;

-        const nullDepthTexture = createNullTexture(gl);
+        const emptyDepthTexture = ctx.resources.texture('image-depth', 'depth', 'ushort', 'nearest');
        const sharedTexturesList: Textures = [
-            ['tDepth', nullDepthTexture]
+            ['tDepth', emptyDepthTexture]
        ];

        const view = Mat4();
@@ -309,7 +309,7 @@ namespace Renderer {
        };

        const updateInternal = (group: Scene.Group, camera: ICamera, depthTexture: Texture | null, renderWboit: boolean, markingDepthTest: boolean) => {
-            arrayMapUpsert(sharedTexturesList, 'tDepth', depthTexture || nullDepthTexture);
+            arrayMapUpsert(sharedTexturesList, 'tDepth', depthTexture || emptyDepthTexture);

            ValueCell.update(globalUniforms.uModel, group.view);
            ValueCell.update(globalUniforms.uModelView, Mat4.mul(modelView, group.view, camera.view));
@@ -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);
--- a/src/mol-gl/scene.ts
+++ b/src/mol-gl/scene.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>
 * @author David Sehnal <david.sehnal@gmail.com>
@@ -79,6 +79,7 @@ interface Scene extends Object3D {
    has: (o: GraphicsRenderObject) => boolean
    clear: () => void
    forEach: (callbackFn: (value: GraphicsRenderable, key: GraphicsRenderObject) => void) => void
+    getMarkerAverage: () => number
 }

 namespace Scene {
@@ -243,7 +244,18 @@ namespace Scene {
                    visibleHash = computeVisibleHash();
                }
                return boundingSphereVisible;
-            }
+            },
+            getMarkerAverage() {
+                if (primitives.length === 0 && volumes.length === 0) return 0;
+                let markerAverage = 0;
+                for (let i = 0, il = primitives.length; i < il; ++i) {
+                    markerAverage += primitives[i].values.markerAverage.ref.value;
+                }
+                for (let i = 0, il = volumes.length; i < il; ++i) {
+                    markerAverage += volumes[i].values.markerAverage.ref.value;
+                }
+                return markerAverage / (primitives.length + volumes.length);
+            },
        };
    }
 }
--- a/src/mol-gl/shader/chunks/apply-light-color.glsl.ts
+++ b/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);
--- a/src/mol-gl/shader/chunks/clip-pixel.glsl.ts
+++ b/src/mol-gl/shader/chunks/clip-pixel.glsl.ts
@@ -6,7 +6,8 @@ export const clip_pixel = `
        int clippingFlag = 0;
    #endif

-    if (clipTest(vec4(vModelPosition, 0.0), clippingFlag))
-        discard;
+    // TODO: disabled for testing
+    // if (clipTest(vec4(vModelPosition, 0.0), clippingFlag))
+    //     discard;
 #endif
 `;
--- a/src/mol-gl/shader/cylinders.frag.ts
+++ b/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
--- a/src/mol-gl/shader/direct-volume.frag.ts
+++ b/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;

--- a/src/mol-gl/shader/mesh.frag.ts
+++ b/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
--- a/src/mol-gl/shader/postprocessing.frag.ts
+++ b/src/mol-gl/shader/postprocessing.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>
 * @author Áron Samuel Kovács <aron.kovacs@mail.muni.cz>
@@ -24,8 +24,7 @@ uniform vec3 uFogColor;
 uniform vec3 uOutlineColor;
 uniform bool uTransparentBackground;

-uniform float uOcclusionBias;
-uniform float uOcclusionRadius;
+uniform vec2 uOcclusionOffset;

 uniform float uMaxPossibleViewZDiff;

@@ -102,7 +101,7 @@ void main(void) {
        if (!isBackground(depth)) {
            viewDist = abs(getViewZ(depth));
            fogFactor = smoothstep(uFogNear, uFogFar, viewDist);
-            float occlusionFactor = getSsao(coords);
+            float occlusionFactor = getSsao(coords + uOcclusionOffset);
            if (!uTransparentBackground) {
                color.rgb = mix(mix(occlusionColor, uFogColor, fogFactor), color.rgb, occlusionFactor);
            } else {
--- a/src/mol-gl/shader/spheres.frag.ts
+++ b/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
--- a/src/mol-gl/webgl/buffer.ts
+++ b/src/mol-gl/webgl/buffer.ts
@@ -67,7 +67,7 @@ function dataTypeFromArray(gl: GLRenderingContext, array: ArrayType) {
    } else if (array instanceof Float32Array) {
        return gl.FLOAT;
    } else {
-        throw new Error('Should nevver happen');
+        throw new Error('Should never happen');
    }
 }

--- a/src/mol-gl/webgl/texture.ts
+++ b/src/mol-gl/webgl/texture.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>
 */
@@ -176,7 +176,7 @@ function isTexture2d(x: TextureImage<any> | TextureVolume<any>, target: number,
    return target === gl.TEXTURE_2D;
 }

-function isTexture3d(x: TextureImage<any> | TextureVolume<any>, target: number, gl: WebGL2RenderingContext): x is TextureImage<any> {
+function isTexture3d(x: TextureImage<any> | TextureVolume<any>, target: number, gl: WebGL2RenderingContext): x is TextureVolume<any> {
    return target === gl.TEXTURE_3D;
 }

@@ -260,6 +260,10 @@ export function createTexture(gl: GLRenderingContext, extensions: WebGLExtension
    let destroyed = false;

    function define(_width: number, _height: number, _depth?: number) {
+        if (_width === 0 || _height === 0 || (isWebGL2(gl) && target === gl.TEXTURE_3D && _depth === 0)) {
+            throw new Error('empty textures are not allowed');
+        }
+
        if (width === _width && height === _height && depth === (_depth || 0)) return;

        width = _width, height = _height, depth = _depth || 0;
@@ -272,14 +276,20 @@ export function createTexture(gl: GLRenderingContext, extensions: WebGLExtension
            throw new Error('unknown texture target');
        }
    }
+    define(1, 1, isWebGL2(gl) && target === gl.TEXTURE_3D ? 1 : 0);

    function load(data: TextureImage<any> | TextureVolume<any> | HTMLImageElement, sub = false) {
+        if (data.width === 0 || data.height === 0 || (!isImage(data) && isWebGL2(gl) && isTexture3d(data, target, gl) && data.depth === 0)) {
+            throw new Error('empty textures are not allowed');
+        }
+
        gl.bindTexture(target, texture);
        // unpack alignment of 1 since we use textures only for data
        gl.pixelStorei(gl.UNPACK_ALIGNMENT, 1);
        gl.pixelStorei(gl.UNPACK_COLORSPACE_CONVERSION_WEBGL, gl.NONE);
        gl.pixelStorei(gl.UNPACK_PREMULTIPLY_ALPHA_WEBGL, 0);
        if (isImage(data)) {
+            width = data.width, height = data.height;
            gl.pixelStorei(gl.UNPACK_FLIP_Y_WEBGL, false);
            gl.bindTexture(gl.TEXTURE_2D, texture);
            gl.texImage2D(gl.TEXTURE_2D, 0, internalFormat, format, type, data);
--- a/src/mol-io/common/_spec/encoder.spec.ts
+++ b/src/mol-io/common/_spec/encoder.spec.ts
@@ -0,0 +1,28 @@
+import { ArrayEncoding } from '../binary-cif/array-encoder';
+import { decode } from '../binary-cif/decoder';
+
+const E = ArrayEncoding;
+
+test('fixedPoint2', async () => {
+    const fixedPoint2 = E.by(E.fixedPoint(100)).and(E.delta).and(E.integerPacking);
+
+    const x = [1.092, 1.960, 0.666, 0.480, 1.267];
+    const y = [7.428, 7.026, 6.851, 7.524, 8.333];
+    const z = [26.270, 26.561, 25.573, 27.055, 25.881];
+
+    const xEnc = fixedPoint2.encode(new Float32Array(x));
+    const yEnc = fixedPoint2.encode(new Float32Array(y));
+    const zEnc = fixedPoint2.encode(new Float32Array(z));
+
+    expect(xEnc.data.length).toEqual(6);
+    expect(yEnc.data.length).toEqual(5);
+    expect(zEnc.data.length).toEqual(6);
+
+    const xDec = decode(xEnc);
+    const yDec = decode(yEnc);
+    const zDec = decode(zEnc);
+
+    x.forEach((a, i) => expect(xDec[i]).toBeCloseTo(a, 2));
+    y.forEach((a, i) => expect(yDec[i]).toBeCloseTo(a, 2));
+    z.forEach((a, i) => expect(zDec[i]).toBeCloseTo(a, 2));
+});
--- a/src/mol-io/reader/cif/schema/bird.ts
+++ b/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 5.356, IHM 1.17, MA 1.3.5.
 *
 * @author molstar/ciftools package
 */
--- a/src/mol-io/reader/cif/schema/ccd.ts
+++ b/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 5.356, IHM 1.17, MA 1.3.5.
 *
 * @author molstar/ciftools package
 */
--- a/src/mol-io/reader/cif/schema/mmcif.ts
+++ b/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 5.356, IHM 1.17, MA 1.3.5.
 *
 * @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.
@@ -2211,6 +2233,10 @@ export const mmCIF_Schema = {
        oligomeric_count: int,
        /**
         * A description of special aspects of the macromolecular assembly.
+         *
+         * In the PDB, 'representative helical assembly', 'complete point assembly',
+         * 'complete icosahedral assembly', 'software_defined_assembly', 'author_defined_assembly',
+         * and 'author_and_software_defined_assembly' are considered "biologically relevant assemblies.
         */
        details: str,
        /**
--- a/src/mol-io/writer/cif/encoder/binary.ts
+++ b/src/mol-io/writer/cif/encoder/binary.ts
@@ -191,8 +191,14 @@ function getFieldData(field: Field<any, any>, arrayCtor: ArrayCtor<string | numb
                    array[offset] = '';
                allPresent = false;
            } else {
-                mask[offset] = Column.ValueKind.Present;
-                array[offset] = getter(key, d, offset);
+                const value = getter(key, d, offset);
+                if (typeof value === 'string' && !value) {
+                    mask[offset] = Column.ValueKind.NotPresent;
+                    allPresent = false;
+                } else {
+                    mask[offset] = Column.ValueKind.Present;
+                }
+                array[offset] = value;
            }
            offset++;
        }
--- a/src/mol-math/geometry/primitives/sphere3d.ts
+++ b/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;
--- a/src/mol-math/geometry/symmetry-operator.ts
+++ b/src/mol-math/geometry/symmetry-operator.ts
@@ -52,24 +52,30 @@ namespace SymmetryOperator {
    export const RotationTranslationEpsilon = 0.005;

    export type CreateInfo = { assembly?: SymmetryOperator['assembly'], ncsId?: number, hkl?: Vec3, spgrOp?: number }
-    export function create(name: string, matrix: Mat4, info?: CreateInfo): SymmetryOperator {
+    export function create(name: string, matrix: Mat4, info?: CreateInfo | SymmetryOperator): SymmetryOperator {
        let { assembly, ncsId, hkl, spgrOp } = info || { };
        const _hkl = hkl ? Vec3.clone(hkl) : Vec3();
        spgrOp = defaults(spgrOp, -1);
        ncsId = ncsId || -1;
-        const suffix = getSuffix(info);
-        if (Mat4.isIdentity(matrix)) return { name, assembly, matrix, inverse: Mat4.identity(), isIdentity: true, hkl: _hkl, spgrOp, ncsId, suffix };
+        const isIdentity = Mat4.isIdentity(matrix);
+        const suffix = getSuffix(info, isIdentity);
+        if (isIdentity) return { name, assembly, matrix, inverse: Mat4.identity(), isIdentity: true, hkl: _hkl, spgrOp, ncsId, suffix };
        if (!Mat4.isRotationAndTranslation(matrix, RotationTranslationEpsilon)) {
            console.warn(`Symmetry operator (${name}) should be a composition of rotation and translation.`);
        }
        return { name, assembly, matrix, inverse: Mat4.invert(Mat4(), matrix), isIdentity: false, hkl: _hkl, spgrOp, ncsId, suffix };
    }

-    function getSuffix(info?: CreateInfo) {
+    function isSymmetryOperator(x: any): x is SymmetryOperator {
+        return !!x && !!x.matrix && !!x.inverse && typeof x.name === 'string';
+    }
+
+    function getSuffix(info?: CreateInfo | SymmetryOperator, isIdentity?: boolean) {
        if (!info) return '';

        if (info.assembly) {
-            return `_${info.assembly.operId}`;
+            if (isSymmetryOperator(info)) return info.suffix;
+            return isIdentity ? '' : `_${info.assembly.operId}`;
        }

        if (typeof info.spgrOp !== 'undefined' && typeof info.hkl !== 'undefined' && info.spgrOp !== -1) {
--- a/src/mol-math/intersect.ts
+++ b/src/mol-math/intersect.ts
@@ -0,0 +1,80 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Vec2, Vec3 } from './linear-algebra';
+
+const tmpT = Vec2();
+const tmpOrigin = Vec3();
+const tmpDir = Vec3();
+
+export function sphereIntersect(result: Vec3, p0: Vec3, p1: Vec3, center: Vec3, radius: number, invert: boolean) {
+    Vec3.copy(tmpOrigin, p0);
+    Vec3.sub(tmpDir, p1, p0);
+
+    const maxT = Vec3.magnitude(tmpDir);
+    Vec3.normalize(tmpDir, tmpDir);
+
+    const ts = raySphere(tmpT, tmpOrigin, tmpDir, center, radius);
+    if (ts === undefined || ts[1] < 0.0 || ts[0] > maxT) {
+        return undefined;
+    }
+
+    const t = invert ? Math.max(ts[0], 0.0) : Math.min(ts[1], maxT);
+
+    Vec3.scaleAndAdd(result, tmpOrigin, tmpDir, t);
+    return result;
+};
+
+function solveQuadratic(result: Vec2, a: number, b: number, c: number) {
+    const det = b * b - 4.0 * a * c;
+    if (det < 0.0) {
+        return undefined;
+    } else if (det > 0.0) {
+        const denom = 1.0 / (2.0 * a);
+        const disc = Math.sqrt(det);
+        const root0 = (-b + disc) * denom;
+        const root1 = (-b - disc) * denom;
+
+        if (root0 < root1) {
+            result[0] = root0;
+            result[1] = root1;
+        } else {
+            result[0] = root1;
+            result[1] = root0;
+        }
+
+        return result;
+    }
+
+    const root = -b / (2.0 * a);
+    if (root === 0.0) {
+        return undefined;
+    }
+
+    result[0] = result[1] = root;
+    return result;
+}
+
+const tmpRaySphereRoots = Vec2();
+const tmpDiff = Vec3();
+
+function raySphere(result: Vec2, origin: Vec3, direction: Vec3, center: Vec3, radius: number) {
+    const radiusSquared = radius * radius;
+
+    Vec3.sub(tmpDiff, origin, center);
+
+    const a = Vec3.dot(direction, direction);
+    const b = 2.0 * Vec3.dot(direction, tmpDiff);
+    const c = Vec3.squaredMagnitude(tmpDiff) - radiusSquared;
+
+    const roots = solveQuadratic(tmpRaySphereRoots, a, b, c);
+    if (roots === undefined) {
+        return undefined;
+    }
+
+    Vec2.copy(result, roots);
+    return result;
+}
--- a/src/mol-model-formats/structure/basic/atomic.ts
+++ b/src/mol-model-formats/structure/basic/atomic.ts
@@ -7,21 +7,21 @@

 import { Column, Table } from '../../../mol-data/db';
 import { Interval, Segmentation } from '../../../mol-data/int';
-import { UUID } from '../../../mol-util/uuid';
-import { ElementIndex, ChainIndex } from '../../../mol-model/structure';
+import { toDatabase } from '../../../mol-io/reader/cif/schema';
+import { SymmetryOperator } from '../../../mol-math/geometry';
+import { Mat4, Vec3 } from '../../../mol-math/linear-algebra';
+import { ChainIndex, ElementIndex } from '../../../mol-model/structure';
+import { AtomSiteOperatorMappingSchema } from '../../../mol-model/structure/export/categories/atom_site_operator_mapping';
 import { Model } from '../../../mol-model/structure/model/model';
 import { AtomicConformation, AtomicData, AtomicHierarchy, AtomicSegments, AtomsSchema, ChainsSchema, ResiduesSchema } from '../../../mol-model/structure/model/properties/atomic';
-import { getAtomicIndex } from '../../../mol-model/structure/model/properties/utils/atomic-index';
-import { ElementSymbol } from '../../../mol-model/structure/model/types';
 import { Entities } from '../../../mol-model/structure/model/properties/common';
 import { getAtomicDerivedData } from '../../../mol-model/structure/model/properties/utils/atomic-derived';
-import { AtomSite } from './schema';
+import { getAtomicIndex } from '../../../mol-model/structure/model/properties/utils/atomic-index';
+import { ElementSymbol } from '../../../mol-model/structure/model/types';
+import { UUID } from '../../../mol-util/uuid';
 import { ModelFormat } from '../../format';
-import { SymmetryOperator } from '../../../mol-math/geometry';
 import { MmcifFormat } from '../mmcif';
-import { AtomSiteOperatorMappingSchema } from '../../../mol-model/structure/export/categories/atom_site_operator_mapping';
-import { toDatabase } from '../../../mol-io/reader/cif/schema';
-import { Mat4, Vec3 } from '../../../mol-math/linear-algebra';
+import { AtomSite } from './schema';

 function findHierarchyOffsets(atom_site: AtomSite) {
    if (atom_site._rowCount === 0) return { residues: [], chains: [] };
--- a/src/mol-model-formats/structure/basic/coarse.ts
+++ b/src/mol-model-formats/structure/basic/coarse.ts
@@ -30,7 +30,7 @@ export interface CoarseData {

 export const EmptyCoarse = { hierarchy: CoarseHierarchy.Empty, conformation: void 0 as any };

-export function getCoarse(data: CoarseData, properties: Model['properties']): { hierarchy: CoarseHierarchy, conformation: CoarseConformation } {
+export function getCoarse(data: CoarseData, chemicalComponentMap: Model['properties']['chemicalComponentMap']): { hierarchy: CoarseHierarchy, conformation: CoarseConformation } {
    const { ihm_sphere_obj_site, ihm_gaussian_obj_site } = data;

    if (ihm_sphere_obj_site._rowCount === 0 && ihm_gaussian_obj_site._rowCount === 0) return EmptyCoarse;
@@ -38,12 +38,12 @@ export function getCoarse(data: CoarseData, properties: Model['properties']): {
    const sphereData = getData(ihm_sphere_obj_site);
    const sphereConformation = getSphereConformation(ihm_sphere_obj_site);
    const sphereKeys = getCoarseKeys(sphereData, data.entities);
-    const sphereRanges = getCoarseRanges(sphereData, properties.chemicalComponentMap);
+    const sphereRanges = getCoarseRanges(sphereData, chemicalComponentMap);

    const gaussianData = getData(ihm_gaussian_obj_site);
    const gaussianConformation = getGaussianConformation(ihm_gaussian_obj_site);
    const gaussianKeys = getCoarseKeys(gaussianData, data.entities);
-    const gaussianRanges = getCoarseRanges(gaussianData, properties.chemicalComponentMap);
+    const gaussianRanges = getCoarseRanges(gaussianData, chemicalComponentMap);

    return {
        hierarchy: {
--- a/src/mol-model-formats/structure/basic/entities.ts
+++ b/src/mol-model-formats/structure/basic/entities.ts
@@ -11,7 +11,7 @@ import { getEntityType, getEntitySubtype } from '../../../mol-model/structure/mo
 import { ElementIndex, EntityIndex, Model } from '../../../mol-model/structure/model';
 import { BasicData, BasicSchema, Entity } from './schema';

-export function getEntities(data: BasicData, properties: Model['properties']): Entities {
+export function getEntityData(data: BasicData): Entities {
    let entityData: Entity;

    if (!data.entity.id.isDefined) {
@@ -121,28 +121,32 @@ export function getEntities(data: BasicData, properties: Model['properties']): E

    const subtypeColumn = Column.ofArray({ array: subtypes, schema: EntitySubtype });

-    //
-
-    const prdIds: string[] = new Array(entityData._rowCount);
-    prdIds.fill('');
-
-    if (data.pdbx_molecule && data.pdbx_molecule.prd_id.isDefined) {
-        const { asym_id, prd_id, _rowCount } = data.pdbx_molecule;
-        for (let i = 0; i < _rowCount; ++i) {
-            const asymId = asym_id.value(i);
-            const entityId = properties.structAsymMap.get(asymId)?.entity_id;
-            if (entityId !== undefined) {
-                prdIds[getEntityIndex(entityId)] = prd_id.value(i);
-            }
-        }
-    }
-
-    const prdIdColumn = Column.ofArray({ array: prdIds, schema: Column.Schema.str });
-
    return {
        data: entityData,
        subtype: subtypeColumn,
-        prd_id: prdIdColumn,
        getEntityIndex
    };
+}
+
+export function getEntitiesWithPRD(data: BasicData, entities: Entities, structAsymMap: Model['properties']['structAsymMap']): Entities {
+    if (!data.pdbx_molecule || !data.pdbx_molecule.prd_id.isDefined) {
+        return entities;
+    }
+
+    const prdIds: string[] = new Array(entities.data._rowCount);
+    prdIds.fill('');
+    const { asym_id, prd_id, _rowCount } = data.pdbx_molecule;
+    for (let i = 0; i < _rowCount; ++i) {
+        const asymId = asym_id.value(i);
+        const entityId = structAsymMap.get(asymId)?.entity_id;
+        if (entityId !== undefined) {
+            prdIds[entities.getEntityIndex(entityId)] = prd_id.value(i);
+        }
+    }
+    const prdIdColumn = Column.ofArray({ array: prdIds, schema: Column.Schema.str });
+
+    return {
+        ...entities,
+        prd_id: prdIdColumn
+    };
 }
--- a/src/mol-model-formats/structure/basic/parser.ts
+++ b/src/mol-model-formats/structure/basic/parser.ts
@@ -18,13 +18,13 @@ import { sortAtomSite } from './sort';
 import { ModelFormat } from '../../format';
 import { getAtomicRanges } from '../../../mol-model/structure/model/properties/utils/atomic-ranges';
 import { AtomSite, BasicData } from './schema';
-import { getProperties } from './properties';
-import { getEntities } from './entities';
+import { getChemicalComponentMap, getMissingResidues, getSaccharideComponentMap, getStructAsymMap } from './properties';
+import { getEntitiesWithPRD, getEntityData } from './entities';
 import { getModelGroupName } from './util';
 import { ArrayTrajectory } from '../../../mol-model/structure/trajectory';

 export async function createModels(data: BasicData, format: ModelFormat, ctx: RuntimeContext) {
-    const properties = getProperties(data);
+    const properties = getCommonProperties(data, format);
    const models = data.ihm_model_list._rowCount > 0
        ? await readIntegrative(ctx, data, properties, format)
        : await readStandard(ctx, data, properties, format);
@@ -36,9 +36,18 @@ export async function createModels(data: BasicData, format: ModelFormat, ctx: Ru
    return new ArrayTrajectory(models);
 }

-/** Standard atomic model */
-function createStandardModel(data: BasicData, atom_site: AtomSite, sourceIndex: Column<number>, entities: Entities, properties: Model['properties'], format: ModelFormat, previous?: Model): Model {
+type CommonProperties = Omit<Model['properties'], 'structAsymMap'>

+function getCommonProperties(data: BasicData, format: ModelFormat): CommonProperties {
+    return {
+        missingResidues: getMissingResidues(data),
+        chemicalComponentMap: getChemicalComponentMap(data),
+        saccharideComponentMap: getSaccharideComponentMap(data)
+    };
+}
+
+/** Standard atomic model */
+function createStandardModel(data: BasicData, atom_site: AtomSite, sourceIndex: Column<number>, entities: Entities, properties: CommonProperties, format: ModelFormat, previous?: Model): Model {
    const atomic = getAtomicHierarchyAndConformation(atom_site, sourceIndex, entities, properties.chemicalComponentMap, format, previous);
    const modelNum = atom_site.pdbx_PDB_model_num.value(0);
    if (previous && atomic.sameAsPrevious) {
@@ -54,6 +63,7 @@ function createStandardModel(data: BasicData, atom_site: AtomSite, sourceIndex:
    const coarse = EmptyCoarse;
    const sequence = getSequence(data, entities, atomic.hierarchy, coarse.hierarchy);
    const atomicRanges = getAtomicRanges(atomic.hierarchy, entities, atomic.conformation, sequence);
+    const structAsymMap = getStructAsymMap(atomic.hierarchy);

    const entry = data.entry.id.valueKind(0) === Column.ValueKind.Present
        ? data.entry.id.value(0) : format.name;
@@ -70,7 +80,7 @@ function createStandardModel(data: BasicData, atom_site: AtomSite, sourceIndex:
        sourceData: format,
        modelNum,
        parent: undefined,
-        entities,
+        entities: getEntitiesWithPRD(data, entities, structAsymMap),
        sequence,
        atomicHierarchy: atomic.hierarchy,
        atomicConformation: atomic.conformation,
@@ -78,7 +88,10 @@ function createStandardModel(data: BasicData, atom_site: AtomSite, sourceIndex:
        atomicChainOperatorMappinng: atomic.chainOperatorMapping,
        coarseHierarchy: coarse.hierarchy,
        coarseConformation: coarse.conformation,
-        properties,
+        properties: {
+            ...properties,
+            structAsymMap
+        },
        customProperties: new CustomProperties(),
        _staticPropertyData: Object.create(null),
        _dynamicPropertyData: Object.create(null)
@@ -86,9 +99,9 @@ function createStandardModel(data: BasicData, atom_site: AtomSite, sourceIndex:
 }

 /** Integrative model with atomic/coarse parts */
-function createIntegrativeModel(data: BasicData, ihm: CoarseData, properties: Model['properties'], format: ModelFormat): Model {
+function createIntegrativeModel(data: BasicData, ihm: CoarseData, properties: CommonProperties, format: ModelFormat): Model {
    const atomic = getAtomicHierarchyAndConformation(ihm.atom_site, ihm.atom_site_sourceIndex, ihm.entities, properties.chemicalComponentMap, format);
-    const coarse = getCoarse(ihm, properties);
+    const coarse = getCoarse(ihm, properties.chemicalComponentMap);
    const sequence = getSequence(data, ihm.entities, atomic.hierarchy, coarse.hierarchy);
    const atomicRanges = getAtomicRanges(atomic.hierarchy, ihm.entities, atomic.conformation, sequence);

@@ -101,6 +114,8 @@ function createIntegrativeModel(data: BasicData, ihm: CoarseData, properties: Mo
    if (ihm.model_name) label.push(ihm.model_name);
    if (ihm.model_group_name) label.push(ihm.model_group_name);

+    const structAsymMap = getStructAsymMap(atomic.hierarchy, data);
+
    return {
        id: UUID.create22(),
        entryId: entry,
@@ -109,7 +124,7 @@ function createIntegrativeModel(data: BasicData, ihm: CoarseData, properties: Mo
        sourceData: format,
        modelNum: ihm.model_id,
        parent: undefined,
-        entities: ihm.entities,
+        entities: getEntitiesWithPRD(data, ihm.entities, structAsymMap),
        sequence,
        atomicHierarchy: atomic.hierarchy,
        atomicConformation: atomic.conformation,
@@ -117,7 +132,10 @@ function createIntegrativeModel(data: BasicData, ihm: CoarseData, properties: Mo
        atomicChainOperatorMappinng: atomic.chainOperatorMapping,
        coarseHierarchy: coarse.hierarchy,
        coarseConformation: coarse.conformation,
-        properties,
+        properties: {
+            ...properties,
+            structAsymMap
+        },
        customProperties: new CustomProperties(),
        _staticPropertyData: Object.create(null),
        _dynamicPropertyData: Object.create(null)
@@ -132,12 +150,12 @@ function findModelEnd(num: Column<number>, startIndex: number) {
    return endIndex;
 }

-async function readStandard(ctx: RuntimeContext, data: BasicData, properties: Model['properties'], format: ModelFormat) {
+async function readStandard(ctx: RuntimeContext, data: BasicData, properties: CommonProperties, format: ModelFormat) {
    const models: Model[] = [];

    if (data.atom_site) {
        const atomCount = data.atom_site.id.rowCount;
-        const entities = getEntities(data, properties);
+        const entities = getEntityData(data);

        let modelStart = 0;
        while (modelStart < atomCount) {
@@ -170,8 +188,8 @@ function splitTable<T extends Table<any>>(table: T, col: Column<number>) {



-async function readIntegrative(ctx: RuntimeContext, data: BasicData, properties: Model['properties'], format: ModelFormat) {
-    const entities = getEntities(data, properties);
+async function readIntegrative(ctx: RuntimeContext, data: BasicData, properties: CommonProperties, format: ModelFormat) {
+    const entities = getEntityData(data);
    // when `atom_site.ihm_model_id` is undefined fall back to `atom_site.pdbx_PDB_model_num`
    const atom_sites_modelColumn = data.atom_site.ihm_model_id.isDefined
        ? data.atom_site.ihm_model_id : data.atom_site.pdbx_PDB_model_num;
@@ -206,7 +224,7 @@ async function readIntegrative(ctx: RuntimeContext, data: BasicData, properties:
                model_id: id,
                model_name: model_name.value(i),
                model_group_name: getModelGroupName(id, data),
-                entities: entities,
+                entities,
                atom_site,
                atom_site_sourceIndex,
                ihm_sphere_obj_site: sphere_sites.has(id) ? sphere_sites.get(id)!.table : Table.window(data.ihm_sphere_obj_site, data.ihm_sphere_obj_site._schema, 0, 0),
--- a/src/mol-model-formats/structure/basic/properties.ts
+++ b/src/mol-model-formats/structure/basic/properties.ts
@@ -5,15 +5,16 @@
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */

+import { Table } from '../../../mol-data/db';
 import { Model } from '../../../mol-model/structure/model/model';
+import { AtomicHierarchy } from '../../../mol-model/structure/model/properties/atomic';
 import { ChemicalComponent, MissingResidue, StructAsym } from '../../../mol-model/structure/model/properties/common';
-import { getMoleculeType, MoleculeType, getDefaultChemicalComponent } from '../../../mol-model/structure/model/types';
-import { SaccharideComponentMap, SaccharideComponent, SaccharidesSnfgMap, SaccharideCompIdMap, UnknownSaccharideComponent } from '../../../mol-model/structure/structure/carbohydrates/constants';
+import { getDefaultChemicalComponent, getMoleculeType, MoleculeType } from '../../../mol-model/structure/model/types';
+import { SaccharideCompIdMap, SaccharideComponent, SaccharideComponentMap, SaccharidesSnfgMap, UnknownSaccharideComponent } from '../../../mol-model/structure/structure/carbohydrates/constants';
 import { memoize1 } from '../../../mol-util/memoize';
 import { BasicData } from './schema';
-import { Table } from '../../../mol-data/db';

-function getMissingResidues(data: BasicData): Model['properties']['missingResidues'] {
+export function getMissingResidues(data: BasicData): Model['properties']['missingResidues'] {
    const map = new Map<string, MissingResidue>();
    const getKey = (model_num: number, asym_id: string, seq_id: number) => {
        return `${model_num}|${asym_id}|${seq_id}`;
@@ -36,7 +37,7 @@ function getMissingResidues(data: BasicData): Model['properties']['missingResidu
    };
 }

-function getChemicalComponentMap(data: BasicData): Model['properties']['chemicalComponentMap'] {
+export function getChemicalComponentMap(data: BasicData): Model['properties']['chemicalComponentMap'] {
    const map = new Map<string, ChemicalComponent>();

    if (data.chem_comp._rowCount > 0) {
@@ -53,7 +54,7 @@ function getChemicalComponentMap(data: BasicData): Model['properties']['chemical
    return map;
 }

-function getSaccharideComponentMap(data: BasicData): SaccharideComponentMap {
+export function getSaccharideComponentMap(data: BasicData): SaccharideComponentMap {
    const map = new Map<string, SaccharideComponent>();

    if (data.pdbx_chem_comp_identifier._rowCount > 0) {
@@ -108,22 +109,18 @@ const getUniqueComponentNames = memoize1((data: BasicData) => {
 });


-function getStructAsymMap(data: BasicData): Model['properties']['structAsymMap'] {
+export function getStructAsymMap(atomic: AtomicHierarchy, data?: BasicData): Model['properties']['structAsymMap'] {
    const map = new Map<string, StructAsym>();

-    const { label_asym_id, auth_asym_id, label_entity_id } = data.atom_site;
-    for (let i = 0, il = label_asym_id.rowCount; i < il; ++i) {
+    const { auth_asym_id, label_asym_id, label_entity_id } = atomic.chains;
+
+    for (let i = 0, _i = atomic.chains._rowCount; i < _i; i ++) {
        const id = label_asym_id.value(i);
-        if (!map.has(id)) {
-            map.set(id, {
-                id,
-                auth_id: auth_asym_id.value(i),
-                entity_id: label_entity_id.value(i)
-            });
-        }
+        map.set(id, { id, auth_id: auth_asym_id.value(i), entity_id: label_entity_id.value(i) });
    }

-    if (data.struct_asym._rowCount > 0) {
+    // to get asym mapping for coarse/ihm data
+    if (data?.struct_asym._rowCount) {
        const { id, entity_id } = data.struct_asym;
        for (let i = 0, il = id.rowCount; i < il; ++i) {
            const _id = id.value(i);
@@ -136,14 +133,6 @@ function getStructAsymMap(data: BasicData): Model['properties']['structAsymMap']
            }
        }
    }
-    return map;
-}

-export function getProperties(data: BasicData): Model['properties'] {
-    return {
-        missingResidues: getMissingResidues(data),
-        chemicalComponentMap: getChemicalComponentMap(data),
-        saccharideComponentMap: getSaccharideComponentMap(data),
-        structAsymMap: getStructAsymMap(data)
-    };
+    return map;
 }
--- a/src/mol-model-formats/structure/common/component.ts
+++ b/src/mol-model-formats/structure/common/component.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>
 */
@@ -30,7 +30,7 @@ const DnaAtomIdsList = [

 /** Used to reduce false positives for atom name-based type guessing */
 const NonPolymerNames = new Set([
-    'FMN', 'NCN', 'FNS', 'FMA' // Mononucleotides
+    'FMN', 'NCN', 'FNS', 'FMA', 'ATP', 'ADP', 'AMP', 'GTP', 'GDP', 'GMP' // Mononucleotides
 ]);

 const StandardComponents = (function () {
@@ -156,7 +156,7 @@ export class ComponentBuilder {
                this.set(StandardComponents.get(compId)!);
            } else if (WaterNames.has(compId)) {
                this.set({ id: compId, name: 'WATER', type: 'non-polymer' });
-            } else if (NonPolymerNames.has(compId)) {
+            } else if (NonPolymerNames.has(compId.toUpperCase())) {
                this.set({ id: compId, name: this.namesMap.get(compId) || compId, type: 'non-polymer' });
            } else {
                const atomIds = this.getAtomIds(index);
--- a/src/mol-model-formats/structure/common/property.ts
+++ b/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];
+                }
            }
        };
    }
--- a/src/mol-model-formats/structure/mol2.ts
+++ b/src/mol-model-formats/structure/mol2.ts
@@ -103,11 +103,11 @@ async function getModels(mol2: Mol2File, ctx: RuntimeContext) {
            const flag = Column.ofIntArray(Column.mapToArray(bonds.bond_type, x => {
                switch (x) {
                    case 'ar': // aromatic
+                    case 'am': // amide
                        return BondType.Flag.Aromatic | BondType.Flag.Covalent;
                    case 'du': // dummy
                    case 'nc': // not connected
                        return BondType.Flag.None;
-                    case 'am': // amide
                    case 'un': // unknown
                    default:
                        return BondType.Flag.Covalent;
--- a/src/mol-model-formats/structure/property/bonds/chem_comp.ts
+++ b/src/mol-model-formats/structure/property/bonds/chem_comp.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 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>
@@ -56,10 +56,10 @@ export namespace ComponentBond {
        const entries: Map<string, Entry> = new Map();

        function addEntry(id: string) {
-            // weird behavior when 'PRO' is requested - will report a single bond between N and H because a later operation would override real content
-            if (entries.has(id)) {
-                return entries.get(id)!;
-            }
+            // weird behavior when 'PRO' is requested - will report a single bond
+            // between N and H because a later operation would override real content
+            if (entries.has(id)) return entries.get(id)!;
+
            const e = new Entry(id);
            entries.set(id, e);
            return e;
@@ -83,10 +83,8 @@ export namespace ComponentBond {
            let ord = 1;
            if (aromatic) flags |= BondType.Flag.Aromatic;
            switch (order.toLowerCase()) {
-                case 'doub':
-                case 'delo':
-                    ord = 2;
-                    break;
+                case 'delo': flags |= BondType.Flag.Aromatic; break;
+                case 'doub': ord = 2; break;
                case 'trip': ord = 3; break;
                case 'quad': ord = 4; break;
            }
--- a/src/mol-model-formats/structure/property/bonds/index-pair.ts
+++ b/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: {
--- a/src/mol-model-props/computed/interactions/common.ts
+++ b/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 {
--- a/src/mol-model-props/computed/representations/interactions-inter-unit-cylinder.ts
+++ b/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>
 */
@@ -74,20 +74,26 @@ 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;
        }
    };

-    const m = createLinkCylinderMesh(ctx, builderProps, props, mesh);
+    const { mesh: m, boundingSphere } = createLinkCylinderMesh(ctx, builderProps, props, mesh);

-    const sphere = Sphere3D.expand(Sphere3D(), (child ?? structure).boundary.sphere, 1 * sizeFactor);
-    m.setBoundingSphere(sphere);
+    if (boundingSphere) {
+        m.setBoundingSphere(boundingSphere);
+    } else if (m.triangleCount > 0) {
+        const { child } = structure;
+        const sphere = Sphere3D.expand(Sphere3D(), (child ?? structure).boundary.sphere, 1 * sizeFactor);
+        m.setBoundingSphere(sphere);
+    }

    return m;
 }
@@ -144,6 +150,9 @@ 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 +171,48 @@ 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;
 }
--- a/src/mol-model-props/computed/representations/interactions-intra-unit-cylinder.ts
+++ b/src/mol-model-props/computed/representations/interactions-intra-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>
 */
@@ -56,17 +56,29 @@ 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);
+    const { mesh: m, boundingSphere } = createLinkCylinderMesh(ctx, builderProps, props, mesh);

-    const sphere = Sphere3D.expand(Sphere3D(), (childUnit ?? unit).boundary.sphere, 1 * sizeFactor);
-    m.setBoundingSphere(sphere);
+    if (boundingSphere) {
+        m.setBoundingSphere(boundingSphere);
+    } else if (m.triangleCount > 0) {
+        const sphere = Sphere3D.expand(Sphere3D(), (childUnit ?? unit).boundary.sphere, 1 * sizeFactor);
+        m.setBoundingSphere(sphere);
+    }

    return m;
 }
@@ -123,6 +135,8 @@ function getInteractionLoci(pickingId: PickingId, structureGroup: StructureGroup
    return EmptyLoci;
 }

+const __contactIndicesSet = new Set<number>();
+
 function eachInteraction(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean, isMarking: boolean) {
    let changed = false;
    if (Interactions.isLoci(loci)) {
@@ -156,21 +170,37 @@ function eachInteraction(loci: Loci, structureGroup: StructureGroup, apply: (int

        const { offset } = contacts;
        const { offsets: fOffsets, indices: fIndices } = features.elementsIndex;
+        const { members, offsets } = features;

-        // TODO: when isMarking, all elements of contact features need to be in the loci
        for (const e of loci.elements) {
            const unitIdx = group.unitIndexMap.get(e.unit.id);
-            if (unitIdx !== undefined) continue;
-            if (isMarking && OrderedSet.size(e.indices) === 1) continue;
+            if (unitIdx === undefined) continue;

            OrderedSet.forEach(e.indices, v => {
                for (let i = fOffsets[v], il = fOffsets[v + 1]; i < il; ++i) {
                    const fI = fIndices[i];
                    for (let j = offset[fI], jl = offset[fI + 1]; j < jl; ++j) {
-                        if (apply(Interval.ofSingleton(unitIdx * groupCount + j))) changed = true;
+                        __contactIndicesSet.add(j);
                    }
                }
            });
+
+            __contactIndicesSet.forEach(i => {
+                if (isMarking) {
+                    const fA = contacts.a[i];
+                    for (let j = offsets[fA], jl = offsets[fA + 1]; j < jl; ++j) {
+                        if (!OrderedSet.has(e.indices, members[j])) return;
+                    }
+                    const fB = contacts.b[i];
+                    for (let j = offsets[fB], jl = offsets[fB + 1]; j < jl; ++j) {
+                        if (!OrderedSet.has(e.indices, members[j])) return;
+                    }
+                }
+
+                if (apply(Interval.ofSingleton(unitIdx * groupCount + i))) changed = true;
+            });
+
+            __contactIndicesSet.clear();
        }
    }
    return changed;
--- a/src/mol-model-props/integrative/cross-link-restraint/representation.ts
+++ b/src/mol-model-props/integrative/cross-link-restraint/representation.ts
@@ -22,6 +22,7 @@ import { VisualUpdateState } from '../../../mol-repr/util';
 import { ComplexRepresentation, StructureRepresentation, StructureRepresentationStateBuilder, StructureRepresentationProvider } from '../../../mol-repr/structure/representation';
 import { CustomProperty } from '../../common/custom-property';
 import { CrossLinkRestraintProvider, CrossLinkRestraint } from './property';
+import { Sphere3D } from '../../../mol-math/geometry';

 function createCrossLinkRestraintCylinderMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: PD.Values<CrossLinkRestraintCylinderParams>, mesh?: Mesh) {

@@ -47,7 +48,16 @@ function createCrossLinkRestraintCylinderMesh(ctx: VisualContext, structure: Str
        },
    };

-    return createLinkCylinderMesh(ctx, builderProps, props, mesh);
+    const { mesh: m, boundingSphere } = createLinkCylinderMesh(ctx, builderProps, props, mesh);
+
+    if (boundingSphere) {
+        m.setBoundingSphere(boundingSphere);
+    } else if (m.triangleCount > 0) {
+        const sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, 1 * sizeFactor);
+        m.setBoundingSphere(sphere);
+    }
+
+    return m;
 }

 export const CrossLinkRestraintCylinderParams = {
--- a/src/mol-model-props/sequence/best-database-mapping.ts
+++ b/src/mol-model-props/sequence/best-database-mapping.ts
@@ -11,36 +11,49 @@ 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('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;
        if (!data) return '';
        const eI = loc.unit.elements[loc.element];
-        const rI = model.atomicHierarchy.residueAtomSegments.offsets[eI];
+        const rI = model.atomicHierarchy.residueAtomSegments.index[eI];
        return data.accession[rI];
    }

@@ -49,45 +62,46 @@ namespace BestDatabaseSequenceMapping {
        const data = Provider.get(model).value;
        if (!data) return;
        const eI = loc.unit.elements[loc.element];
-        const rI = model.atomicHierarchy.residueAtomSegments.offsets[eI];
+        const rI = model.atomicHierarchy.residueAtomSegments.index[eI];
        const dbName = data.dbName[rI];
        if (!dbName) return;
        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('db_name');
-        const db_acc = atom_site.getField('db_acc');
-        const db_num = atom_site.getField('db_num');
-        const db_res = atom_site.getField('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++) {
            const row = atomSourceIndex.value(residueOffsets[i]);

            if (db_name.valueKind(row) !== Column.ValueKind.Present) {
-                dbName[row] = '';
-                accession[row] = '';
-                num[row] = 0;
-                residue[row] = '';
+                dbName[i] = '';
+                accession[i] = '';
+                num[i] = '';
+                residue[i] = '';
                continue;
            }

-            dbName[row] = db_name.str(row);
-            accession[row] = db_acc.str(row);
-            num[row] = db_num.int(row);
-            residue[row] = 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 };
--- a/src/mol-model-props/sequence/themes/best-database-mapping.ts
+++ b/src/mol-model-props/sequence/themes/best-database-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);
            }
        }
    }
--- a/src/mol-model/structure/export/categories/atom_site.ts
+++ b/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()
            }))
--- a/src/mol-model/structure/export/categories/secondary-structure.ts
+++ b/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
                    };
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -52,6 +52,10 @@ function isWithoutSymmetry(structure: Structure) {
    return structure.units.every(u => u.conformation.operator.isIdentity);
 }

+function isWithoutOperator(structure: Structure) {
+    return isWithoutSymmetry(structure) && structure.units.every(u => !u.conformation.operator.assembly && !u.conformation.operator.suffix);
+}
+
 const Categories = [
    // Basics
    copy_mmCif_category('entry'),
@@ -63,9 +67,9 @@ const Categories = [
    copy_mmCif_category('symmetry', isWithoutSymmetry),

    // Assemblies
-    copy_mmCif_category('pdbx_struct_assembly', isWithoutSymmetry),
-    copy_mmCif_category('pdbx_struct_assembly_gen', isWithoutSymmetry),
-    copy_mmCif_category('pdbx_struct_oper_list', isWithoutSymmetry),
+    copy_mmCif_category('pdbx_struct_assembly', isWithoutOperator),
+    copy_mmCif_category('pdbx_struct_assembly_gen', isWithoutOperator),
+    copy_mmCif_category('pdbx_struct_oper_list', isWithoutOperator),

    // Secondary structure
    _struct_conf,
@@ -250,10 +254,10 @@ function encode_mmCIF_categories_copyAll(encoder: CifWriter.Encoder, ctx: CifExp
 }


-function to_mmCIF(name: string, structure: Structure, asBinary = false) {
+function to_mmCIF(name: string, structure: Structure, asBinary = false, params?: encode_mmCIF_categories_Params) {
    const enc = CifWriter.createEncoder({ binary: asBinary });
    enc.startDataBlock(name);
-    encode_mmCIF_categories(enc, structure);
+    encode_mmCIF_categories(enc, structure, params);
    return enc.getData();
 }

--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.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>
@@ -98,6 +98,7 @@ export namespace Model {
        const srcIndex = model.atomicHierarchy.atomSourceIndex;
        const isIdentity = Column.isIdentity(srcIndex);
        const srcIndexArray = isIdentity ? void 0 : srcIndex.toArray({ array: Int32Array });
+        const coarseGrained = isCoarseGrained(model);

        for (let i = 0, il = frames.length; i < il; ++i) {
            const f = frames[i];
@@ -119,6 +120,7 @@ export namespace Model {
            }

            TrajectoryInfo.set(m, { index: i, size: frames.length });
+            CoarseGrained.set(m, coarseGrained);

            trajectory.push(m);
        }
@@ -138,11 +140,13 @@ export namespace Model {

            const bondData = { pairs: topology.bonds, count: model.atomicHierarchy.atoms._rowCount };
            const indexPairBonds = IndexPairBonds.fromData(bondData);
+            const coarseGrained = isCoarseGrained(model);

            let index = 0;
            for (const m of trajectory) {
                IndexPairBonds.Provider.set(m, indexPairBonds);
                TrajectoryInfo.set(m, { index: index++, size: trajectory.length });
+                CoarseGrained.set(m, coarseGrained);
            }
            return new ArrayTrajectory(trajectory);
        });
@@ -225,35 +229,44 @@ export namespace Model {
    };

    const CoarseGrainedProp = '__CoarseGrained__';
+    export const CoarseGrained = {
+        get(model: Model): boolean | undefined {
+            return model._staticPropertyData[CoarseGrainedProp];
+        },
+        set(model: Model, coarseGrained: boolean) {
+            return model._staticPropertyData[CoarseGrainedProp] = coarseGrained;
+        }
+    };
    /**
     * Has typical coarse grained atom names (BB, SC1) or less than three times as many
     * atoms as polymer residues (C-alpha only models).
     */
    export function isCoarseGrained(model: Model): boolean {
-        if (model._staticPropertyData[CoarseGrainedProp] !== undefined) return model._staticPropertyData[CoarseGrainedProp];
+        let coarseGrained = CoarseGrained.get(model);
+        if (coarseGrained === undefined) {
+            let polymerResidueCount = 0;
+            const { polymerType } = model.atomicHierarchy.derived.residue;
+            for (let i = 0; i < polymerType.length; ++i) {
+                if (polymerType[i] !== PolymerType.NA) polymerResidueCount += 1;
+            }

-        let polymerResidueCount = 0;
-        const { polymerType } = model.atomicHierarchy.derived.residue;
-        for (let i = 0; i < polymerType.length; ++i) {
-            if (polymerType[i] !== PolymerType.NA) polymerResidueCount += 1;
+            // check for coarse grained atom names
+            let hasBB = false, hasSC1 = false;
+            const { label_atom_id, _rowCount: atomCount } = model.atomicHierarchy.atoms;
+            for (let i = 0; i < atomCount; ++i) {
+                const atomName = label_atom_id.value(i);
+                if (!hasBB && atomName === 'BB') hasBB = true;
+                if (!hasSC1 && atomName === 'SC1') hasSC1 = true;
+                if (hasBB && hasSC1) break;
+            }
+
+            coarseGrained = (hasBB && hasSC1) || (
+                polymerResidueCount && atomCount
+                    ? atomCount / polymerResidueCount < 3
+                    : false
+            );
+            CoarseGrained.set(model, coarseGrained);
        }
-
-        // check for coarse grained atom names
-        let hasBB = false, hasSC1 = false;
-        const { label_atom_id, _rowCount: atomCount } = model.atomicHierarchy.atoms;
-        for (let i = 0; i < atomCount; ++i) {
-            const atomName = label_atom_id.value(i);
-            if (!hasBB && atomName === 'BB') hasBB = true;
-            if (!hasSC1 && atomName === 'SC1') hasSC1 = true;
-            if (hasBB && hasSC1) break;
-        }
-
-        const coarseGrained = (hasBB && hasSC1) || (
-            polymerResidueCount && atomCount
-                ? atomCount / polymerResidueCount < 3
-                : false
-        );
-        model._staticPropertyData[CoarseGrainedProp] = coarseGrained;
        return coarseGrained;
    }

--- a/src/mol-model/structure/model/properties/coarse/hierarchy.ts
+++ b/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
+    };
 }
--- a/src/mol-model/structure/model/properties/common.ts
+++ b/src/mol-model/structure/model/properties/common.ts
@@ -22,7 +22,7 @@ export const EntitySubtype = Column.Schema.Aliased<EntitySubtype>(Column.Schema.
 export interface Entities {
    data: mmCIF_Database['entity'],
    subtype: Column<EntitySubtype>,
-    prd_id: Column<string>,
+    prd_id?: Column<string>,
    getEntityIndex(id: string): EntityIndex
 }

--- a/src/mol-model/structure/structure/element/loci.ts
+++ b/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);
--- a/src/mol-model/structure/structure/properties.ts
+++ b/src/mol-model/structure/structure/properties.ts
@@ -126,6 +126,7 @@ const coarse = {
    z: atom.z,

    asym_id: p(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.asym_id.value(l.element)),
+    entity_id: p(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.entity_id.value(l.element)),
    seq_id_begin: p(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.seq_id_begin.value(l.element)),
    seq_id_end: p(l => !Unit.isCoarse(l.unit) ? notCoarse() : l.unit.coarseElements.seq_id_end.value(l.element)),

@@ -162,7 +163,7 @@ const entity = {
    pdbx_ec: p(l => l.unit.model.entities.data.pdbx_ec.value(eK(l))),

    subtype: p(l => l.unit.model.entities.subtype.value(eK(l))),
-    prd_id: p(l => l.unit.model.entities.prd_id.value(eK(l))),
+    prd_id: p(l => l.unit.model.entities.prd_id?.value(eK(l)) ?? ''),
 };

 const _emptyList: any[] = [];
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.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>
@@ -232,7 +232,17 @@ class Structure {

    get interUnitBonds() {
        if (this.state.interUnitBonds) return this.state.interUnitBonds;
-        this.state.interUnitBonds = computeInterUnitBonds(this, { ignoreWater: !this.dynamicBonds });
+        if (this.parent && this.state.dynamicBonds === this.parent.state.dynamicBonds &&
+            this.parent.state.interUnitBonds && this.parent.state.interUnitBonds.edgeCount === 0
+        ) {
+            // no need to compute InterUnitBonds if parent's ones are empty
+            this.state.interUnitBonds = new InterUnitBonds(new Map());
+        } else {
+            this.state.interUnitBonds = computeInterUnitBonds(this, {
+                ignoreWater: !this.dynamicBonds,
+                ignoreIon: !this.dynamicBonds,
+            });
+        }
        return this.state.interUnitBonds;
    }

--- a/src/mol-model/structure/structure/unit.ts
+++ b/src/mol-model/structure/structure/unit.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>
@@ -25,6 +25,7 @@ import { Mat4, Vec3 } from '../../../mol-math/linear-algebra';
 import { IndexPairBonds } from '../../../mol-model-formats/structure/property/bonds/index-pair';
 import { ElementSetIntraBondCache } from './unit/bonds/element-set-intra-bond-cache';
 import { ModelSymmetry } from '../../../mol-model-formats/structure/property/symmetry';
+import { getResonance, UnitResonance } from './unit/resonance';

 /**
 * A building block of a structure that corresponds to an atomic or
@@ -220,7 +221,12 @@ namespace Unit {

        remapModel(model: Model, dynamicBonds: boolean, props?: AtomicProperties) {
            if (!props) {
-                props = { ...this.props, bonds: dynamicBonds ? undefined : tryRemapBonds(this, this.props.bonds, model) };
+                props = {
+                    ...this.props,
+                    bonds: dynamicBonds && !this.props.bonds?.props?.canRemap
+                        ? undefined
+                        : tryRemapBonds(this, this.props.bonds, model, dynamicBonds)
+                };
                if (!Unit.isSameConformation(this, model)) {
                    props.boundary = undefined;
                    props.lookup3d = undefined;
@@ -282,6 +288,12 @@ namespace Unit {
            return this.props.rings;
        }

+        get resonance() {
+            if (this.props.resonance) return this.props.resonance;
+            this.props.resonance = getResonance(this);
+            return this.props.resonance;
+        }
+
        get polymerElements() {
            if (this.props.polymerElements) return this.props.polymerElements;
            this.props.polymerElements = getAtomicPolymerElements(this);
@@ -342,6 +354,7 @@ namespace Unit {
    interface AtomicProperties extends BaseProperties {
        bonds?: IntraUnitBonds
        rings?: UnitRings
+        resonance?: UnitResonance
        nucleotideElements?: SortedArray<ElementIndex>
        proteinElements?: SortedArray<ElementIndex>
        residueCount?: number
@@ -481,7 +494,7 @@ namespace Unit {
        return isSameConformation(a, b.model);
    }

-    function tryRemapBonds(a: Atomic, old: IntraUnitBonds | undefined, model: Model) {
+    function tryRemapBonds(a: Atomic, old: IntraUnitBonds | undefined, model: Model, dynamicBonds: boolean) {
        // TODO: should include additional checks?

        if (!old) return void 0;
@@ -495,7 +508,7 @@ namespace Unit {
            return void 0;
        }

-        if (old.props?.canRemap) {
+        if (old.props?.canRemap || !dynamicBonds) {
            return old;
        }
        return isSameConformation(a, model) ? old : void 0;
--- a/src/mol-model/structure/structure/unit/bonds/data.ts
+++ b/src/mol-model/structure/structure/unit/bonds/data.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 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>
@@ -12,7 +12,13 @@ import { StructureElement } from '../../element';
 import { Bond } from '../bonds';
 import { InterUnitGraph } from '../../../../../mol-math/graph/inter-unit-graph';

-type IntraUnitBonds = IntAdjacencyGraph<StructureElement.UnitIndex, { readonly order: ArrayLike<number>, readonly flags: ArrayLike<BondType.Flag> }, { readonly canRemap?: boolean }>
+type IntraUnitBonds = IntAdjacencyGraph<StructureElement.UnitIndex, {
+    readonly order: ArrayLike<number>,
+    readonly flags: ArrayLike<BondType.Flag>
+}, {
+    /** can remap even with dynamicBonds on, e.g., for water molecules */
+    readonly canRemap?: boolean
+}>

 namespace IntraUnitBonds {
    export const Empty: IntraUnitBonds = IntAdjacencyGraph.create([], [], [], 0, { flags: [], order: [] });
--- a/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
@@ -193,11 +193,13 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
 export interface InterBondComputationProps extends BondComputationProps {
    validUnitPair: (structure: Structure, unitA: Unit, unitB: Unit) => boolean
    ignoreWater: boolean
+    ignoreIon: boolean
 }

 const DefaultInterBondComputationProps = {
    ...DefaultBondComputationProps,
-    ignoreWater: true
+    ignoreWater: true,
+    ignoreIon: true,
 };

 function findBonds(structure: Structure, props: InterBondComputationProps) {
@@ -233,7 +235,11 @@ function computeInterUnitBonds(structure: Structure, props?: Partial<InterBondCo
                (!Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== MoleculeType.Water) &&
                (!Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== MoleculeType.Water)
            );
-            return Structure.validUnitPair(s, a, b) && (notWater || !p.ignoreWater);
+            const notIon = (
+                (!Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== MoleculeType.Ion) &&
+                (!Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== MoleculeType.Ion)
+            );
+            return Structure.validUnitPair(s, a, b) && (notWater || !p.ignoreWater) && (notIon || !p.ignoreIon);
        }),
    });
 }
--- a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
@@ -141,7 +141,7 @@ function findBonds(unit: Unit.Atomic, props: BondComputationProps): IntraUnitBon
        const aI = atoms[_aI];

        const elemA = type_symbol.value(aI);
-        if (isWatery && (elemA !== 'H' || elemA !== 'O')) isWatery = false;
+        if (isWatery && (elemA !== 'H' && elemA !== 'O')) isWatery = false;

        const structConnEntries = props.forceCompute ? void 0 : structConn && structConn.byAtomIndex.get(aI);
        let hasStructConn = false;
--- a/src/mol-model/structure/structure/unit/resonance.ts
+++ b/src/mol-model/structure/structure/unit/resonance.ts
@@ -0,0 +1,83 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { SortedArray } from '../../../../mol-data/int/sorted-array';
+import { sortedCantorPairing } from '../../../../mol-data/util';
+import { BondType } from '../../model/types';
+import { StructureElement } from '../element';
+import { Unit } from '../unit';
+
+export type UnitResonance = {
+    /**
+     * Lookup for triplets of atoms in delocalized bonds.
+     *
+     * Does not include triplets that are part of aromatic rings.
+     */
+    readonly delocalizedTriplets: {
+        /** Return 3rd element in triplet or undefined if `a` and `b` are not part of a triplet */
+        readonly getThirdElement: (a: StructureElement.UnitIndex, b: StructureElement.UnitIndex) => StructureElement.UnitIndex | undefined
+        /** Return index into `triplets` or undefined if `a` is not part of any triplet */
+        readonly getTripletIndices: (a: StructureElement.UnitIndex) => number[] | undefined
+        readonly triplets: SortedArray<StructureElement.UnitIndex>[]
+    }
+}
+
+export function getResonance(unit: Unit.Atomic): UnitResonance {
+    return {
+        delocalizedTriplets: getDelocalizedTriplets(unit)
+    };
+}
+
+function getDelocalizedTriplets(unit: Unit.Atomic) {
+    const bonds = unit.bonds;
+    const { b, edgeProps, offset } = bonds;
+    const { order: _order, flags: _flags } = edgeProps;
+    const { elementAromaticRingIndices } = unit.rings;
+
+    const triplets: SortedArray<StructureElement.UnitIndex>[] = [];
+    const thirdElementMap = new Map<number, StructureElement.UnitIndex>();
+    const indicesMap = new Map<number, number[]>();
+
+    const add = (a: StructureElement.UnitIndex, b: StructureElement.UnitIndex, c: StructureElement.UnitIndex) => {
+        const index = triplets.length;
+        triplets.push(SortedArray.ofUnsortedArray([a, b, c]));
+        thirdElementMap.set(sortedCantorPairing(a, b), c);
+        if (indicesMap.has(a)) indicesMap.get(a)!.push(index);
+        else indicesMap.set(a, [index]);
+    };
+
+    for (let i = 0 as StructureElement.UnitIndex; i < unit.elements.length; i++) {
+        if (elementAromaticRingIndices.has(i)) continue;
+
+        const count = offset[i + 1] - offset[i] + 1;
+        if (count < 2) continue;
+
+        const deloBonds: StructureElement.UnitIndex[] = [];
+        for (let t = offset[i], _t = offset[i + 1]; t < _t; t++) {
+            const f = _flags[t];
+            if (!BondType.is(f, BondType.Flag.Aromatic)) continue;
+
+            deloBonds.push(b[t]);
+        }
+
+        if (deloBonds.length >= 2) {
+            add(i, deloBonds[0], deloBonds[1]);
+            for (let j = 1, jl = deloBonds.length; j < jl; j++) {
+                add(i, deloBonds[j], deloBonds[0]);
+            }
+        }
+    }
+
+    return {
+        getThirdElement: (a: StructureElement.UnitIndex, b: StructureElement.UnitIndex) => {
+            return thirdElementMap.get(sortedCantorPairing(a, b));
+        },
+        getTripletIndices: (a: StructureElement.UnitIndex) => {
+            return indicesMap.get(a);
+        },
+        triplets,
+    };
+}
--- a/src/mol-model/structure/structure/unit/rings/compute.ts
+++ b/src/mol-model/structure/structure/unit/rings/compute.ts
@@ -28,17 +28,19 @@ export function computeRings(unit: Unit.Atomic) {
 }

 const enum Constants {
-    MaxDepth = 4
+    MaxDepth = 5
 }

 interface State {
    startVertex: number,
    endVertex: number,
    count: number,
-    visited: Int32Array,
+    isRingAtom: Int32Array,
+    marked: Int32Array,
    queue: Int32Array,
    color: Int32Array,
    pred: Int32Array,
+    depth: Int32Array,

    left: Int32Array,
    right: Int32Array,
@@ -59,9 +61,11 @@ function State(unit: Unit.Atomic, capacity: number): State {
        startVertex: 0,
        endVertex: 0,
        count: 0,
-        visited: new Int32Array(capacity),
+        isRingAtom: new Int32Array(capacity),
+        marked: new Int32Array(capacity),
        queue: new Int32Array(capacity),
        pred: new Int32Array(capacity),
+        depth: new Int32Array(capacity),
        left: new Int32Array(Constants.MaxDepth),
        right: new Int32Array(Constants.MaxDepth),
        color: new Int32Array(capacity),
@@ -78,17 +82,26 @@ function State(unit: Unit.Atomic, capacity: number): State {

 function resetState(state: State) {
    state.count = state.endVertex - state.startVertex;
-    const { visited, pred, color } = state;
+    const { isRingAtom, pred, color, depth, marked } = state;
    for (let i = 0; i < state.count; i++) {
-        visited[i] = -1;
+        isRingAtom[i] = 0;
        pred[i] = -1;
+        marked[i] = -1;
        color[i] = 0;
+        depth[i] = 0;
    }
    state.currentColor = 0;
    state.currentAltLoc = '';
    state.hasAltLoc = false;
 }

+function resetDepth(state: State) {
+    const { depth } = state;
+    for (let i = 0; i < state.count; i++) {
+        depth[i] = state.count + 1;
+    }
+}
+
 function largestResidue(unit: Unit.Atomic) {
    const residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, unit.elements);
    let size = 0;
@@ -99,8 +112,16 @@ function largestResidue(unit: Unit.Atomic) {
    return size;
 }

+function isStartIndex(state: State, i: number) {
+    const bondOffset = state.bonds.offset;
+    const a = state.startVertex + i;
+    const bStart = bondOffset[a], bEnd = bondOffset[a + 1];
+    const bondCount = bEnd - bStart;
+    if (bondCount <= 1 || (state.isRingAtom[i] && bondCount === 2)) return false;
+    return true;
+}
+
 function processResidue(state: State, start: number, end: number) {
-    const { visited } = state;
    state.startVertex = start;
    state.endVertex = end;

@@ -117,11 +138,13 @@ function processResidue(state: State, start: number, end: number) {
    }
    arraySetRemove(altLocs, '');

+    let mark = 1;
    if (altLocs.length === 0) {
        resetState(state);
        for (let i = 0; i < state.count; i++) {
-            if (visited[i] >= 0) continue;
-            findRings(state, i);
+            if (!isStartIndex(state, i)) continue;
+            resetDepth(state);
+            mark = findRings(state, i, mark);
        }
    } else {
        for (let aI = 0; aI < altLocs.length; aI++) {
@@ -129,12 +152,13 @@ function processResidue(state: State, start: number, end: number) {
            state.hasAltLoc = true;
            state.currentAltLoc = altLocs[aI];
            for (let i = 0; i < state.count; i++) {
-                if (visited[i] >= 0) continue;
+                if (!isStartIndex(state, i)) continue;
                const altLoc = state.altLoc.value(elements[state.startVertex + i]);
                if (altLoc && altLoc !== state.currentAltLoc) {
                    continue;
                }
-                findRings(state, i);
+                resetDepth(state);
+                mark = findRings(state, i, mark);
            }
        }
    }
@@ -144,10 +168,10 @@ function processResidue(state: State, start: number, end: number) {
    }
 }

-function addRing(state: State, a: number, b: number) {
+function addRing(state: State, a: number, b: number, isRingAtom: Int32Array) {
    // only "monotonous" rings
    if (b < a) {
-        return;
+        return false;
    }

    const { pred, color, left, right } = state;
@@ -176,7 +200,7 @@ function addRing(state: State, a: number, b: number) {
        if (current < 0) break;
    }
    if (!found) {
-        return;
+        return false;
    }

    current = a;
@@ -190,50 +214,50 @@ function addRing(state: State, a: number, b: number) {
    const len = leftOffset + rightOffset;
    // rings must have at least three elements
    if (len < 3) {
-        return;
+        return false;
    }

    const ring = new Int32Array(len);
    let ringOffset = 0;
-    for (let t = 0; t < leftOffset; t++) ring[ringOffset++] = state.startVertex + left[t];
-    for (let t = rightOffset - 1; t >= 0; t--) ring[ringOffset++] = state.startVertex + right[t];
+    for (let t = 0; t < leftOffset; t++) {
+        ring[ringOffset++] = state.startVertex + left[t];
+        isRingAtom[left[t]] = 1;
+    }
+    for (let t = rightOffset - 1; t >= 0; t--) {
+        ring[ringOffset++] = state.startVertex + right[t];
+        isRingAtom[right[t]] = 1;
+    }

    sortArray(ring);

-    if (state.hasAltLoc) {
-        // we need to check if the ring was already added because alt locs are present.
+    // Check if the ring is unique and another one is not it's subset
+    for (let rI = 0, _rI = state.currentRings.length; rI < _rI; rI++) {
+        const r = state.currentRings[rI];

-        for (let rI = 0, _rI = state.currentRings.length; rI < _rI; rI++) {
-            const r = state.currentRings[rI];
-            if (ring[0] !== r[0]) continue;
-            if (ring.length !== r.length) continue;
-
-            let areSame = true;
-            for (let aI = 0, _aI = ring.length; aI < _aI; aI++) {
-                if (ring[aI] !== r[aI]) {
-                    areSame = false;
-                    break;
-                }
-            }
-            if (areSame) {
-                return;
-            }
+        if (ring.length === r.length) {
+            if (SortedArray.areEqual(ring as any, r)) return false;
+        } else if (ring.length > r.length) {
+            if (SortedArray.isSubset(ring as any, r)) return false;
        }
    }

    state.currentRings.push(SortedArray.ofSortedArray(ring));
+
+    return true;
 }

-function findRings(state: State, from: number) {
-    const { bonds, startVertex, endVertex, visited, queue, pred } = state;
+function findRings(state: State, from: number, mark: number) {
+    const { bonds, startVertex, endVertex, isRingAtom, marked, queue, pred, depth } = state;
    const { elements } = state.unit;
    const { b: neighbor, edgeProps: { flags: bondFlags }, offset } = bonds;
-    visited[from] = 1;
+    marked[from] = mark;
+    depth[from] = 0;
    queue[0] = from;
    let head = 0, size = 1;

    while (head < size) {
        const top = queue[head++];
+        const d = depth[top];
        const a = startVertex + top;
        const start = offset[a], end = offset[a + 1];

@@ -250,18 +274,25 @@ function findRings(state: State, from: number) {

            const other = b - startVertex;

-            if (visited[other] > 0) {
+            if (marked[other] === mark) {
                if (pred[other] !== top && pred[top] !== other) {
-                    addRing(state, top, other);
+                    if (addRing(state, top, other, isRingAtom)) {
+                        return mark + 1;
+                    }
                }
                continue;
            }

-            visited[other] = 1;
+            const newDepth = Math.min(depth[other], d + 1);
+            if (newDepth > Constants.MaxDepth) continue;
+
+            depth[other] = newDepth;
+            marked[other] = mark;
            queue[size++] = other;
            pred[other] = top;
        }
    }
+    return mark + 1;
 }

 export function getFingerprint(elements: string[]) {
--- a/src/mol-model/structure/structure/util/superposition-sifts-mapping.ts
+++ b/src/mol-model/structure/structure/util/superposition-sifts-mapping.ts
@@ -1,27 +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 { 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());
@@ -29,14 +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 });
-        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) {
@@ -51,6 +70,7 @@ function getPositionTables(index: IndexEntry[], pivot: number, other: number, N:

        const l = Math.min(a[2] - a[1], b[2] - b[1]);

+        // TODO: check if residue types match?
        for (let i = 0; i < l; i++) {
            let eI = (a[1] + i) as ElementIndex;
            xs.x[o] = a[0].conformation.x(eI);
@@ -117,40 +137,49 @@ 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 { offsets: residueOffset } = model.atomicHierarchy.residueAtomSegments;

-        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();
            residuesIt.setSegment(chainSegment);
            while (residuesIt.hasNext) {
                const residueSegment = residuesIt.move();
-                const eI = elements[residueSegment.start];
-                const rI = residueOffset[eI];
+                const rI = residueSegment.index;

                if (!dbName[rI]) continue;

+                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]}`;

                if (!index.has(key)) {
-                    index.set(key, { key, pivots: { [sI]: [unit, eI, elements[residueSegment.end]] } });
+                    index.set(key, { key, pivots: { [sI]: [unit, start, end] } });
                } else {
                    const entry = index.get(key)!;

                    if (!entry.pivots[sI]) {
-                        entry.pivots[sI] = [unit, eI, elements[residueSegment.end]];
+                        entry.pivots[sI] = [unit, start, end];
                    }
                }
            }
--- a/src/mol-model/volume/volume.ts
+++ b/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;
--- a/src/mol-plugin-state/actions/file.ts
+++ b/src/mol-plugin-state/actions/file.ts
@@ -7,8 +7,10 @@
 import { PluginContext } from '../../mol-plugin/context';
 import { StateAction } from '../../mol-state';
 import { Task } from '../../mol-task';
+import { Asset } from '../../mol-util/assets';
 import { getFileInfo } from '../../mol-util/file-info';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { unzip } from '../../mol-util/zip/zip';
 import { PluginStateObject } from '../objects';

 export const OpenFiles = StateAction.build({
@@ -33,24 +35,37 @@ export const OpenFiles = StateAction.build({
            plugin.log.error('No file(s) selected');
            return;
        }
+
+        const processFile = async (file: Asset.File) => {
+            const info = getFileInfo(file.file!);
+            const isBinary = plugin.dataFormats.binaryExtensions.has(info.ext);
+            const { data } = await plugin.builders.data.readFile({ file, isBinary });
+            const provider = params.format.name === 'auto'
+                ? plugin.dataFormats.auto(info, data.cell?.obj!)
+                : plugin.dataFormats.get(params.format.params);
+
+            if (!provider) {
+                plugin.log.warn(`OpenFiles: could not find data provider for '${info.name}.${info.ext}'`);
+                return;
+            }
+
+            // need to await so that the enclosing Task finishes after the update is done.
+            const parsed = await provider.parse(plugin, data);
+            if (params.visuals) {
+                await provider.visuals?.(plugin, parsed);
+            }
+        };
+
        for (const file of params.files) {
            try {
-                const info = getFileInfo(file.file!);
-                const isBinary = plugin.dataFormats.binaryExtensions.has(info.ext);
-                const { data } = await plugin.builders.data.readFile({ file, isBinary });
-                const provider = params.format.name === 'auto'
-                    ? plugin.dataFormats.auto(info, data.cell?.obj!)
-                    : plugin.dataFormats.get(params.format.params);
-
-                if (!provider) {
-                    plugin.log.warn(`OpenFiles: could not find data provider for '${info.name}.${info.ext}'`);
-                    continue;
-                }
-
-                // need to await so that the enclosing Task finishes after the update is done.
-                const parsed = await provider.parse(plugin, data);
-                if (params.visuals) {
-                    await provider.visuals?.(plugin, parsed);
+                if (file.file && file.name.toLowerCase().endsWith('.zip')) {
+                    const zippedFiles = await unzip(taskCtx, await file.file.arrayBuffer());
+                    for (const [fn, filedata] of Object.entries(zippedFiles)) {
+                        const asset = Asset.File(new File([filedata as Uint8Array], fn));
+                        await processFile(asset);
+                    }
+                } else {
+                    await processFile(file);
                }
            } catch (e) {
                console.error(e);
--- a/src/mol-plugin-state/actions/volume.ts
+++ b/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}`
            } : {
--- a/src/mol-plugin-state/builder/structure/representation-preset.ts
+++ b/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 { };
    }
 });
@@ -194,17 +185,15 @@ const polymerAndLigand = StructureRepresentationPresetProvider({
            nonStandard: builder.buildRepresentation(update, components.nonStandard, { type: 'ball-and-stick', typeParams, color, colorParams: ballAndStickColor }, { tag: 'non-standard' }),
            branchedBallAndStick: builder.buildRepresentation(update, components.branched, { type: 'ball-and-stick', typeParams: { ...typeParams, alpha: 0.3 }, color, colorParams: ballAndStickColor }, { tag: 'branched-ball-and-stick' }),
            branchedSnfg3d: builder.buildRepresentation(update, components.branched, { type: 'carbohydrate', typeParams, color }, { tag: 'branched-snfg-3d' }),
-            water: builder.buildRepresentation(update, components.water, { type: waterType, typeParams: { ...typeParams, alpha: 0.6 }, color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'water' }),
+            water: builder.buildRepresentation(update, components.water, { type: waterType, typeParams: { ...typeParams, alpha: 0.6, visuals: waterType === 'line' ? ['intra-bond', 'element-point'] : undefined }, color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'water' }),
            ion: builder.buildRepresentation(update, components.ion, { type: 'ball-and-stick', typeParams, color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'ion' }),
-            lipid: builder.buildRepresentation(update, components.lipid, { type: lipidType, typeParams: { ...typeParams, alpha: 0.6 }, color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'lipid' }),
+            lipid: builder.buildRepresentation(update, components.lipid, { type: lipidType, typeParams: { ...typeParams, alpha: 0.6, visuals: lipidType === 'line' ? ['intra-bond'] : undefined }, color, colorParams: { carbonColor: { name: 'element-symbol', params: {} } } }, { tag: 'lipid' }),
            coarse: builder.buildRepresentation(update, components.coarse, { type: 'spacefill', typeParams, color: color || 'chain-id' }, { tag: 'coarse' })
        };

        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;
--- a/src/mol-plugin-state/builder/structure/representation.ts
+++ b/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;
--- a/src/mol-plugin-state/formats/volume.ts
+++ b/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> }) {
--- a/src/mol-plugin-state/helpers/root-structure.ts
+++ b/src/mol-plugin-state/helpers/root-structure.ts
@@ -17,7 +17,7 @@ import { PluginStateObject as SO } from '../objects';
 import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';

 const CommonStructureParams = {
-    dynamicBonds: PD.Optional(PD.Boolean(false, { description: 'Ensure bonds are recalculated upon model changes. Also enables calculation of inter-unit bonds in water molecules.' })),
+    dynamicBonds: PD.Optional(PD.Boolean(false, { description: 'Ensure bonds are recalculated upon model changes. Also enables calculation of inter-unit bonds in water molecules and ions.' })),
 };
 type CommonStructureProps = PD.ValuesFor<typeof CommonStructureParams>

--- a/src/mol-plugin-state/manager/interactivity.ts
+++ b/src/mol-plugin-state/manager/interactivity.ts
@@ -76,9 +76,11 @@ namespace InteractivityManager {

    /**
     * The `noRender` argument indicates that the action should only update the internal
-     * data structure but not render anything user visible. For example 1) no drawing of
-     * the canvas3d scene or 2) no ui update of loci labels. This is useful because some
-     * actions require clearing any markings before they can be applied.
+     * data structure but not render anything user visible. For example, no ui update of
+     * loci labels.
+     *
+     * This is useful because some actions require clearing any markings before
+     * they can be applied.
     */
    export type LociMarkProvider = (loci: Representation.Loci, action: MarkerAction, /* test */ noRender?: boolean) => void

--- a/src/mol-plugin-state/manager/structure/component.ts
+++ b/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' }),
--- a/src/mol-plugin-ui/controls.tsx
+++ b/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 />
--- a/src/mol-plugin-ui/controls/icons.tsx
+++ b/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

--- a/src/mol-plugin-ui/sequence/sequence.tsx
+++ b/src/mol-plugin-ui/sequence/sequence.tsx
@@ -6,15 +6,15 @@
 */

 import * as React from 'react';
-import { PluginUIComponent } from '../base';
-import { MarkerAction } from '../../mol-util/marker-action';
-import { ButtonsType, ModifiersKeys, getButtons, getModifiers, getButton } from '../../mol-util/input/input-observer';
-import { SequenceWrapper } from './wrapper';
-import { StructureElement, StructureProperties, Unit } from '../../mol-model/structure';
 import { Subject } from 'rxjs';
-import { debounceTime } from 'rxjs/operators';
+import { throttleTime } from 'rxjs/operators';
 import { OrderedSet } from '../../mol-data/int';
+import { StructureElement, StructureProperties, Unit } from '../../mol-model/structure';
 import { Representation } from '../../mol-repr/representation';
+import { ButtonsType, getButton, getButtons, getModifiers, ModifiersKeys } from '../../mol-util/input/input-observer';
+import { MarkerAction } from '../../mol-util/marker-action';
+import { PluginUIComponent } from '../base';
+import { SequenceWrapper } from './wrapper';

 type SequenceProps = {
    sequenceWrapper: SequenceWrapper.Any,
@@ -55,12 +55,10 @@ export class Sequence<P extends SequenceProps> extends PluginUIComponent<P> {
        this.plugin.managers.interactivity.lociHighlights.addProvider(this.lociHighlightProvider);
        this.plugin.managers.interactivity.lociSelects.addProvider(this.lociSelectionProvider);

-        this.subscribe(debounceTime<{ seqIdx: number, buttons: number, button: number, modifiers: ModifiersKeys }>(15)(this.highlightQueue), (e) => {
+        this.subscribe(this.highlightQueue.pipe(throttleTime(3 * 16.666, void 0, { leading: true, trailing: true })), (e) => {
            const loci = this.getLoci(e.seqIdx < 0 ? void 0 : e.seqIdx);
            this.hover(loci, e.buttons, e.button, e.modifiers);
        });
-
-        // this.updateMarker()
    }

    componentWillUnmount() {
--- a/src/mol-plugin-ui/skin/base/components/misc.scss
+++ b/src/mol-plugin-ui/skin/base/components/misc.scss
@@ -490,7 +490,7 @@
    }
 }

-.msp-action-menu-options {   
+.msp-action-menu-options {
    &-no-header, .msp-control-group-children {
        max-height: 300px;
        overflow: hidden;
@@ -602,10 +602,10 @@
    }

    .msp-slider {
-        > div:first-child() {
+        > div:first-child {
            right: 42px;
        }
-        > div:last-child() {
+        > div:last-child {
            width: 30px;
        }
    }
--- a/src/mol-plugin-ui/skin/base/components/viewport.scss
+++ b/src/mol-plugin-ui/skin/base/components/viewport.scss
@@ -24,6 +24,7 @@
    right: 0;
    bottom: 0;
    -webkit-user-select: none;
+    user-select: none;
    -webkit-tap-highlight-color: rgba(0,0,0,0);
    -webkit-touch-callout: none;
    touch-action: manipulation;
@@ -71,7 +72,7 @@
    }
 }

-.msp-semi-transparent-background {    
+.msp-semi-transparent-background {
    background: $default-background;
    opacity: 0.5;
    position: absolute;
@@ -94,7 +95,7 @@

    .msp-viewport-controls-panel-controls {
        overflow-y: auto;
-        max-height: 400px;    
+        max-height: 400px;
    }
 }

--- a/src/mol-plugin-ui/structure/quick-styles.tsx
+++ b/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: 0.8, blurKernelSize: 15, radius: 5, samples: 32, resolutionScale: 1 }
+                    },
+                }
+            });
+        }
+    }
+
+    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: 0.8, blurKernelSize: 15, radius: 5, samples: 32, resolutionScale: 1 }
+                    },
+                }
+            });
+        }
+    }
+
+    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>;
+    }
+}
--- a/src/mol-plugin-ui/structure/superposition.tsx
+++ b/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 /= transforms.length - 1;
+        rmsd /= Math.max(entries.length - 1, 1);

-        this.plugin.log.info(`Superposed ${input.length} structures with avg. RMSD ${rmsd.toFixed(2)}.`);
+        const formatPairs = (pairs: [number, number][]) => {
+            return `[${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>
        </>;
    }
--- a/src/mol-plugin-ui/structure/volume.tsx
+++ b/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} />;
--- a/src/mol-plugin/behavior/dynamic/custom-props.ts
+++ b/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';
--- a/src/mol-plugin/behavior/dynamic/custom-props/sequence/best-database-mapping.ts
+++ b/src/mol-plugin/behavior/dynamic/custom-props/sequence/best-database-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);
        }
    },
--- a/src/mol-plugin/behavior/dynamic/representation.ts
+++ b/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>
@@ -43,9 +43,9 @@ export const HighlightLoci = PluginBehavior.create({
    name: 'representation-highlight-loci',
    category: 'interaction',
    ctor: class extends PluginBehavior.Handler<HighlightLociProps> {
-        private lociMarkProvider = (interactionLoci: Representation.Loci, action: MarkerAction, noRender?: boolean) => {
+        private lociMarkProvider = (interactionLoci: Representation.Loci, action: MarkerAction) => {
            if (!this.ctx.canvas3d || !this.params.mark) return;
-            this.ctx.canvas3d.mark(interactionLoci, action, noRender);
+            this.ctx.canvas3d.mark(interactionLoci, action);
        };
        private getLoci(loci: Loci) {
            return this.params.preferAtoms && Bond.isLoci(loci) && loci.bonds.length === 2
@@ -113,9 +113,9 @@ export const SelectLoci = PluginBehavior.create({
    category: 'interaction',
    ctor: class extends PluginBehavior.Handler<SelectLociProps> {
        private spine: StateTreeSpine.Impl;
-        private lociMarkProvider = (reprLoci: Representation.Loci, action: MarkerAction, noRender?: boolean) => {
+        private lociMarkProvider = (reprLoci: Representation.Loci, action: MarkerAction) => {
            if (!this.ctx.canvas3d || !this.params.mark) return;
-            this.ctx.canvas3d.mark({ loci: reprLoci.loci }, action, noRender);
+            this.ctx.canvas3d.mark({ loci: reprLoci.loci }, action);
        };
        private getLoci(loci: Loci) {
            return this.params.preferAtoms && Bond.isLoci(loci) && loci.bonds.length === 2
@@ -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>');
--- a/src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts
+++ b/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 } });
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/util.ts
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/util.ts
@@ -69,8 +69,16 @@ export async function getContourLevel(provider: 'emdb' | 'pdbe', plugin: PluginC
 export async function getContourLevelEmdb(plugin: PluginContext, taskCtx: RuntimeContext, emdbId: string) {
    const emdbHeaderServer = plugin.config.get(PluginConfig.VolumeStreaming.EmdbHeaderServer);
    const header = await plugin.fetch({ url: `${emdbHeaderServer}/${emdbId.toUpperCase()}/header/${emdbId.toLowerCase()}.xml`, type: 'xml' }).runInContext(taskCtx);
-    const map = header.getElementsByTagName('map')[0];
-    const contourLevel = parseFloat(map.getElementsByTagName('contourLevel')[0].textContent!);
+    const contours = header.getElementsByTagName('contour');
+
+    let primaryContour = contours[0];
+    for (let i = 1; i < contours.length; i++) {
+        if (contours[i].getAttribute('primary') === 'true') {
+            primaryContour = contours[i];
+            break;
+        }
+    }
+    const contourLevel = parseFloat(primaryContour.getElementsByTagName('level')[0].textContent!);

    return contourLevel;
 }
--- a/src/mol-plugin/behavior/static/representation.ts
+++ b/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 {
--- a/src/mol-plugin/util/viewport-screenshot.ts
+++ b/src/mol-plugin/util/viewport-screenshot.ts
@@ -119,7 +119,7 @@ class ViewportScreenshotHelper extends PluginComponent {
            postprocessing: {
                ...c.props.postprocessing,
                occlusion: aoProps.name === 'on'
-                    ? { name: 'on', params: { ...aoProps.params, samples: 128 } }
+                    ? { name: 'on', params: { ...aoProps.params, samples: 128, resolutionScale: 1 } }
                    : aoProps
            },
            marking: { ...c.props.marking }
@@ -143,7 +143,7 @@ class ViewportScreenshotHelper extends PluginComponent {
                postprocessing: {
                    ...c.props.postprocessing,
                    occlusion: aoProps.name === 'on'
-                        ? { name: 'on', params: { ...aoProps.params, samples: 128 } }
+                        ? { name: 'on', params: { ...aoProps.params, samples: 128, resolutionScale: 1 } }
                        : aoProps
                },
                marking: { ...c.props.marking }
--- a/src/mol-repr/shape/loci/common.ts
+++ b/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 = {
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
Alexander Rose	c2b652d5ab	wip, prototype for mesh clipping	2022-03-02 19:51:34 -08:00
Alexander Rose	c3afabb4b1	spelling	2022-03-02 19:50:30 -08:00
Alexander Rose	d5ed3aa674	3.3.1	2022-02-27 18:45:45 -08:00
Alexander Rose	cfb9c9acfe	changelog	2022-02-27 18:40:48 -08:00
Alexander Rose	67feef0b1d	add option to ignore ions for inter-unit bonds	2022-02-27 18:40:27 -08:00
Alexander Rose	e0192ab5aa	fix issue with unit boundary reuse - do at visual level instead	2022-02-27 18:03:41 -08:00
Alexander Rose	eae7c11c55	3.3.0	2022-02-27 13:03:01 -08:00
Alexander Rose	b8251e1ade	changelog	2022-02-27 12:57:51 -08:00
Alexander Rose	2ff2b9f348	schema updates	2022-02-27 12:50:48 -08:00
Alexander Rose	164e3f3343	package updates	2022-02-27 12:47:45 -08:00
Alexander Rose	4901a1bd87	rename occlusion scaleFactor to resolutionScale	2022-02-27 12:16:37 -08:00
Alexander Rose	cd194cca65	Merge pull request #385 from molstar/traj-anim Coordinate trajectory related improvements	2022-02-27 12:04:28 -08:00
Alexander Rose	1748efbc18	Merge branch 'master' of https://github.com/molstar/molstar into traj-anim	2022-02-27 12:03:54 -08:00
Alexander Rose	4d60b40403	fix interUnitBonds parent check	2022-02-27 12:02:36 -08:00
Alexander Rose	6e5a41879f	Merge pull request #386 from molstar/improve-ao Improve AO performance	2022-02-27 11:58:50 -08:00
Alexander Rose	c5f9eb54da	set default occlusion scaleFactor to 1	2022-02-26 23:51:21 -08:00
Alexander Rose	aebbfeb061	add support for lower resolution AO - downsample depth for AO - add scaleFactor param - full res for image/video	2022-02-26 22:23:52 -08:00
Alexander Rose	a0a5a6b578	add encoder spec - mostly as example	2022-02-26 17:43:37 -08:00
Alexander Rose	6bdafb85d7	Check if marking passes are needed - add Scene.getMarkerAverage	2022-02-26 13:30:05 -08:00
Alexander Rose	0dd7debf5d	reuse occlusion in multi-sample pass	2022-02-26 13:02:53 -08:00
Alexander Rose	962b9ee7af	Merge pull request #378 from molstar/ar-bonds fix visuals for aromatic/delocalized bonds	2022-02-26 11:34:42 -08:00
Alexander Rose	15bcc5df88	Merge branch 'master' into ar-bonds	2022-02-26 11:26:29 -08:00
Alexander Rose	8495d834c8	add getTripletIndices & triplets to UnitResonance	2022-02-26 11:25:35 -08:00
Alexander Rose	7282399709	fix/improve canRemap handling in IntraUnitBonds	2022-02-26 10:56:32 -08:00
Alexander Rose	780bdd6e7e	don't compute InterUnitBonds when parent ones empty	2022-02-26 10:53:54 -08:00
Alexander Rose	ad08e7c67f	reuse unit boundary if it has not changed too much	2022-02-26 10:52:26 -08:00
Alexander Rose	ff089964ca	improve line visuals in polymerAndLigand preset	2022-02-26 10:50:02 -08:00
Alexander Rose	990191529a	reuse Model.CoarseGrained for coordinate trajectories	2022-02-26 10:48:05 -08:00
Alexander Rose	ce1bec12b4	fix mononucleotides detected as polymer components	2022-02-26 10:46:51 -08:00
Alexander Rose	703ea9af53	change line geometry default scaleFactor to 2 - 3 is too big after fixing line rendering	2022-02-26 10:45:51 -08:00
David Sehnal	df0227ae1e	Merge pull request #383 from molstar/batch-highlights Resolve marking in main render loop	2022-02-24 07:46:44 +01:00
dsehnal	486d12b6ac	Fix multisample pass "forceOn"	2022-02-24 07:20:03 +01:00
dsehnal	9c18375ab4	typo	2022-02-23 23:34:09 +01:00
dsehnal	e1708aed68	dispose mark buffer	2022-02-23 19:09:40 +01:00
dsehnal	a42d778b84	changelog	2022-02-23 12:04:38 +01:00
dsehnal	7692b59c7c	resolve marking in main render loop insread of eagerly	2022-02-23 11:59:29 +01:00
dsehnal	82de9b36b3	addRing check tweak	2022-02-22 16:02:11 +01:00
dsehnal	49b3c8f65f	ring computation algorithm fixes	2022-02-22 13:16:32 +01:00
Alexander Rose	90ad32d936	add ring example PDB IDs	2022-02-21 13:48:43 -08:00
David Sehnal	2509e91f1a	Merge pull request #381 from russellp17/disable-ts-config-for-sourceMappingURL Disable ts config that leads to sourceMappingURL comment	2022-02-21 15:20:00 +01:00
David Sehnal	80dc2219e4	Merge pull request #380 from russellp17/allow-react-16-in-peer-dependency Allow React ^16.14.0 as peer dependency	2022-02-21 15:10:33 +01:00
Russell Parker	931cb0fa7d	Disable ts config that leads to sourceMappingURL comment in transpilation	2022-02-21 08:24:09 -05:00
Russell Parker	4383f2ea90	Allow React ^16.14.0 as peer dependency	2022-02-21 08:20:55 -05:00
dsehnal	add79dc242	ring computation algorithm fix	2022-02-21 14:15:13 +01:00
Alexander Rose	b6e142f04c	move delocalizedTriplets code to unit.resonance	2022-02-20 16:28:42 -08:00
Alexander Rose	105f6c3041	fix visuals for aromatic/delocalized bonds	2022-02-20 12:50:44 -08:00
Alexander Rose	4babbb65c1	fix spec	2022-02-19 17:22:25 -08:00
Alexander Rose	878159f7ed	fix texture warnings (#319 ) - bind real texture to tDepth in renderer - ensure textures are not empty; init as 1x1(x1)	2022-02-19 16:59:03 -08:00
Alexander Rose	c320386019	changelog	2022-02-19 14:23:37 -08:00
Alexander Rose	1e7a0159f0	Merge pull request #377 from JonStargaryen/master parse contour-level from emdb v3 header files	2022-02-19 14:20:48 -08:00
JonStargaryen	bbf4f1d1d3	break early	2022-02-19 11:02:30 -08:00
Alexander Rose	8cd1c69c76	css tweaks, fixes #376	2022-02-19 10:46:06 -08:00
JonStargaryen	2372a878ac	parse contour-level from emdb v3 header files	2022-02-19 09:12:20 -08:00
dsehnal	9bec644997	3.2.0	2022-02-17 19:24:55 +01:00
dsehnal	650d38dff8	Store IndexPairBonds as a dynamic property	2022-02-17 19:21:49 +01:00
David Sehnal	097277e397	Merge pull request #373 from JonStargaryen/master Add TraceOnly option for Structure Superposition	2022-02-14 19:53:51 +01:00
Sebastian Bittrich	82a4d5eedf	cleanup	2022-02-14 10:46:03 -08:00
Sebastian Bittrich	2a00248812	determine trace during buildIndex	2022-02-14 10:41:10 -08:00
Sebastian Bittrich	9841c773cb	reset camera after all alignments	2022-02-10 13:55:09 -08:00
Sebastian Bittrich	b21a78ad14	support shuffled atoms when aligning SIFTS trace	2022-02-10 13:49:37 -08:00
Sebastian Bittrich	7329fa597d	options obj for alignAndSuperposeWithSIFTSMapping	2022-02-10 11:36:50 -08:00
Sebastian Bittrich	f1d8f0ecb4	auth	2022-02-10 11:32:21 -08:00
Sebastian Bittrich	1d127f2364	changelog	2022-02-10 11:30:55 -08:00
Sebastian Bittrich	b244405cc3	polymer-based query	2022-02-10 10:39:22 -08:00
Sebastian Bittrich	38adfe0ca6	cleanup	2022-02-10 10:29:34 -08:00
Sebastian Bittrich	6f0d798847	optional filtering for trace during alignment	2022-02-10 10:23:31 -08:00
Sebastian Bittrich	6e58bfd2b0	traceOnly param for superpos	2022-02-08 16:03:05 -08:00
David Sehnal	bc2e8d8ac4	Merge pull request #369 from molstar/pdbx_sifts-export Better support for atom_site.pdbx_sifts_xref	2022-02-08 10:19:02 +01:00
dsehnal	7be654d47f	tweak labels	2022-02-08 10:18:01 +01:00
dsehnal	bfe46e3604	pdbx_sifts_xref PR feedback	2022-02-08 10:12:21 +01:00
dsehnal	008b597fc5	changelog	2022-02-07 17:51:13 +01:00
dsehnal	c4b4f2e3b1	rename BestDatabaseSequenceMapping -> SIFTSMapping	2022-02-07 17:49:10 +01:00
dsehnal	76ee97301b	atom_site.pdbx_label_index support	2022-02-07 17:44:03 +01:00
dsehnal	289dc09eae	add support for atom_site.pdbx_sifts_xref export	2022-02-07 17:33:11 +01:00
Alexander Rose	f23f84f0f3	3.1.0	2022-02-06 15:56:41 -08:00
Alexander Rose	62259f3295	changelog	2022-02-06 15:51:40 -08:00
Alexander Rose	854a430a12	tweak quick-styles order	2022-02-06 15:46:40 -08:00
Alexander Rose	d27cdb5637	schema updates	2022-02-06 15:41:09 -08:00
Alexander Rose	7d12d9ee90	package udpdates	2022-02-06 15:38:09 -08:00
Alexander Rose	d70a4ff347	Merge pull request #366 from molstar/repr-defaults-tweaks cleaner default representation style	2022-02-06 15:24:27 -08:00
Alexander Rose	49541558d1	Merge branch 'master' into repr-defaults-tweaks	2022-02-06 15:24:16 -08:00
Alexander Rose	7b00a1227c	changelog	2022-02-06 15:22:50 -08:00
Alexander Rose	7800603c81	Merge pull request #367 from molstar/quick-styles Quick styles	2022-02-06 15:16:43 -08:00
Alexander Rose	fca00c8116	variable naming	2022-02-06 15:15:55 -08:00
Alexander Rose	00fa549e44	Merge pull request #368 from JonStargaryen/master iterate over `structure.unitSymmetryGroups`, fixes #364	2022-02-06 15:13:57 -08:00
Alexander Rose	36181b6b87	tweak quick style names	2022-02-06 15:13:15 -08:00
JonStargaryen	88a95162e9	iterate over `structure.unitSymmetryGroups`, fixes #364	2022-02-06 10:47:40 -08:00
Alexander Rose	9c1d59a2c8	add Quick Styles panel	2022-02-05 12:58:32 -08:00
Alexander Rose	fdd894956a	fix representation preset side effects	2022-02-05 12:56:55 -08:00
Alexander Rose	eb6dc0859d	cleaner default representation style	2022-02-05 12:23:28 -08:00
Alexander Rose	b99026bba2	add ignoreLight to component params	2022-02-05 12:10:56 -08:00
Alexander Rose	6fa50eb8d5	fix xrayShader & ignoreLight not working together	2022-02-05 11:57:39 -08:00
David Sehnal	e5046f15a9	Merge pull request #365 from JonStargaryen/master Volume Streaming Error Message	2022-02-04 17:11:31 +01:00
JonStargaryen	09f1c066a0	logic	2022-02-03 17:11:50 -08:00
Sebastian Bittrich	ed2f0b34c9	volume streaming err msg	2022-02-03 16:11:10 -08:00
Alexander Rose	c7f75861de	3.0.2	2022-01-30 12:24:48 -08:00
Alexander Rose	ccd04dbc9d	changelog	2022-01-30 12:19:49 -08:00
Alexander Rose	e71f8d2c10	Merge pull request #360 from molstar/fix/visual-visibility Fix visual visibility edge case	2022-01-30 12:17:12 -08:00
dsehnal	d9b4c60239	Fix visual visibility edge case	2022-01-30 15:02:46 +01:00
Alexander Rose	103c1fca21	measurement options tweaks - allow larger text size - make customText essential	2022-01-29 19:30:03 -08:00
Alexander Rose	49559bf5fb	citation tweak	2022-01-29 16:05:17 -08:00
Alexander Rose	26dceabf83	add citation file	2022-01-29 15:56:39 -08:00
Alexander Rose	abe506182e	fix multi-instance entity label display - fix empty elements created in extendToAllInstances	2022-01-29 11:21:48 -08:00
Alexander Rose	582a0e2a38	fix Sphere.expand for highly directional extrema	2022-01-29 11:13:19 -08:00
dsehnal	2784ccf379	3.0.1	2022-01-27 12:15:53 +01:00
dsehnal	0ad1d578fe	changelog	2022-01-27 12:13:22 +01:00
David Sehnal	31fd1c9c68	Merge pull request #353 from molstar/drag-tweak emit drag event whenever started within viewport	2022-01-27 12:12:07 +01:00
David Sehnal	9c961297a2	Merge branch 'master' into drag-tweak	2022-01-27 12:11:59 +01:00
David Sehnal	b920053349	Merge pull request #352 from molstar/var-fixes Various fixes	2022-01-27 12:09:39 +01:00
David Sehnal	0a5c764e4a	Merge pull request #351 from molstar/volume-server-data-fix Volume server data fix	2022-01-27 11:37:31 +01:00
Alexander Rose	b9a71c83ff	emit drag event whenever started within viewport	2022-01-26 21:32:14 -08:00
Alexander Rose	3255f207d0	Merge branch 'master' of https://github.com/molstar/molstar into var-fixes	2022-01-26 20:46:11 -08:00
Alexander Rose	e3b4ca8862	add entity-id and entity-source as carbonColor	2022-01-26 20:42:38 -08:00
Alexander Rose	6810793015	fix marking of InteractionsInterUnitVisual	2022-01-26 20:40:12 -08:00
Alexander Rose	1feb3c2095	fix entity-id coloring broken for non-ihm models	2022-01-26 20:38:46 -08:00
Alexander Rose	f2da6033d0	fix pdbe xray maps url	2022-01-26 20:36:52 -08:00
Alexander Rose	28bc212132	fix marking pass for transparentBackground	2022-01-26 20:35:38 -08:00
dsehnal	1a7c62eec6	remove gl from dependencies & install it on demand instead - installing gl on M1 Mac was taking several minutes to compile on each update	2022-01-26 23:12:12 +01:00
dsehnal	de67dbacba	iso-value adjustment for VolumeServer data in default Viewer	2022-01-26 17:47:23 +01:00
dsehnal	57223a0f9a	Fix VolumeServer/query CLI	2022-01-26 16:49:18 +01:00
Alexander Rose	2ad0754b90	3.0.0	2022-01-23 18:12:48 -08:00
Alexander Rose	3ecb3af57b	changelog	2022-01-23 18:08:01 -08:00
Alexander Rose	ec4f15f549	improve/fix InteractionsIntraUnitVisual marking	2022-01-23 17:55:51 -08:00
Alexander Rose	2458ea7b92	Merge pull request #349 from molstar/custom-theme-colors add custom theme colors	2022-01-23 15:13:24 -08:00
Alexander Rose	c5e6bedf11	Merge branch 'master' into custom-theme-colors	2022-01-23 13:54:57 -08:00
dsehnal	8528e5a666	Support/bugfixes for atom_site.pdbx_sifts_xref categories	2022-01-23 20:46:49 +01:00
dsehnal	6ed232b3d9	fix using default values for webgl1/wboit features in the default viewer app	2022-01-23 19:25:09 +01:00
dsehnal	f8aae8cbd1	skip Coarse models in export extension	2022-01-23 16:13:02 +01:00
Alexander Rose	00c2517045	package updates	2022-01-22 14:06:26 -08:00
Alexander Rose	99b043a929	avoid circular dependency	2022-01-22 11:10:41 -08:00
Alexander Rose	5900e27e39	add custom theme colors - element-symbol - molecule-type - residue-name - secondary-structure	2022-01-22 10:51:41 -08:00
Alexander Rose	1b79d34907	fix marking of carbohydrate visuals	2022-01-22 08:53:47 -08:00
Alexander Rose	fc52e29c92	re-add using _struct_asym cat in getStructAsymMap - needed for ihm model support	2022-01-22 08:50:29 -08:00
Alexander Rose	df23b3c0fe	fix coarse model support in entity-id color theme - add StructureProperties.coarse.entity_id	2022-01-22 08:48:07 -08:00
David Sehnal	5e25716c98	Merge pull request #334 from molstar/export-extension Model export extension & related improvements	2022-01-18 13:23:11 +01:00
dsehnal	f70a10bc56	add info about CIF export failure	2022-01-18 13:20:53 +01:00
dsehnal	0ccb045f4e	Merge branch 'master' of https://github.com/molstar/molstar into export-extension	2022-01-18 12:30:45 +01:00
dsehnal	fbb60c9493	Treat empty string as non-present value in BinaryCIF	2022-01-17 16:21:14 +01:00
dsehnal	9f953ef51c	add Model Export overlay	2022-01-17 15:47:56 +01:00
dsehnal	4871f1547c	Generate structAsymMap from normalized atomic hierarchy - Fixes issue with remapped chains - Requires to parse PRD separately	2022-01-17 14:52:53 +01:00
dsehnal	d6413529f4	PR feedback	2022-01-17 13:58:20 +01:00
dsehnal	b6847907ca	Add ModelExport to viewer/app.ts	2022-01-17 11:37:49 +01:00
dsehnal	fb54a1aed7	Merge branch 'master' of https://github.com/molstar/molstar into export-extension	2022-01-17 11:37:16 +01:00
dsehnal	c0880b647f	changelog	2022-01-03 13:51:09 +01:00
dsehnal	039dc6a76b	changelog	2022-01-03 13:49:59 +01:00
dsehnal	042a7625ad	isWithoutOperator tweak	2022-01-03 13:46:13 +01:00
dsehnal	41827c478d	open zip files with multiple entries	2022-01-03 13:42:37 +01:00
dsehnal	9a73180c3c	support transformed export & structAsymMap parsing fix	2022-01-03 13:15:51 +01:00
dsehnal	333ee85fdb	omit suffix for identity assembly operators	2022-01-03 12:52:05 +01:00
dsehnal	fa8ca45b6a	do not include assembly categories in export if an operator has been applied	2022-01-03 12:34:37 +01:00
dsehnal	c2bae1aeb7	model export extension	2022-01-03 12:26:36 +01:00