3.4.0

changelog
package updates
2026-06-06 14:44:22 +08:00 · 2022-03-13 13:12:32 -07:00 · 2022-03-13 12:50:44 -07:00 · 2022-03-13 12:49:03 -07:00 · 2022-03-13 12:19:04 -07:00 · 2022-03-13 12:16:12 -07:00
161 changed files with 7159 additions and 5424 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,87 @@ Note that since we don't clearly distinguish between a public and private interf

 ## [Unreleased]

+## [v3.4.0] - 2022-03-13
+
+- Fix handling of mmcif with empty ``label_*`` fields
+- Improve saccharide detection (compare against list from CCD)
+- Fix legend label of hydrophobicity color theme
+- Add ``LoadTrajectory`` action
+- Add ``CustomImportControls`` to left panel
+- Add Zenodo import extension (load structures, trajectories, volumes, and zip files)
+- Fix loading of some compressed files within sessions
+- Fix wrong element assignment for atoms with Charmm ion names
+- Fix handling of empty symmetry cell data
+- Add support for ``trr`` and ``nctraj`` coordinates files
+- Add support for ``prmtop`` and ``top`` topology files
+
+## [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:
--- 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/README.md
+++ b/README.md
@@ -120,6 +120,9 @@ and navigate to `build/viewer`

    node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-ions.js src/mol-model/structure/model/types/ions.ts

+**Saccharide names**
+
+    node --max-old-space-size=4096 lib/commonjs/cli/chem-comp-dict/create-saccharides.js src/mol-model/structure/model/types/saccharides.ts

 **GraphQL schemas**

--- 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",
+  "version": "3.4.0",
  "description": "A comprehensive macromolecular library.",
  "homepage": "https://github.com/molstar/molstar#readme",
  "repository": {
@@ -13,7 +13,7 @@
  "scripts": {
    "lint": "eslint .",
    "lint-fix": "eslint . --fix",
-    "test": "npm run lint && jest",
+    "test": "npm install --no-save \"gl@^5.0.0\" && npm run lint && jest",
    "jest": "jest",
    "build": "npm run build-tsc && npm run build-extra && npm run build-webpack",
    "clean": "node ./scripts/clean.js",
@@ -92,72 +92,69 @@
  "license": "MIT",
  "devDependencies": {
    "@graphql-codegen/add": "^3.1.1",
-    "@graphql-codegen/cli": "^2.4.0",
+    "@graphql-codegen/cli": "^2.6.2",
    "@graphql-codegen/time": "^3.1.1",
-    "@graphql-codegen/typescript": "^2.4.2",
+    "@graphql-codegen/typescript": "^2.4.7",
    "@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": "^4.4.2",
+    "@graphql-codegen/typescript-operations": "^2.3.4",
    "@types/cors": "^2.8.12",
    "@types/gl": "^4.1.0",
-    "@types/jest": "^27.4.0",
-    "@typescript-eslint/eslint-plugin": "^5.10.0",
-    "@typescript-eslint/parser": "^5.10.0",
+    "@types/jest": "^27.4.1",
+    "@typescript-eslint/eslint-plugin": "^5.14.0",
+    "@typescript-eslint/parser": "^5.14.0",
    "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": "^6.7.1",
+    "eslint": "^8.11.0",
    "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": "^2.5.2",
+    "jest": "^27.5.1",
+    "mini-css-extract-plugin": "^2.6.0",
    "path-browserify": "^1.0.1",
    "raw-loader": "^4.0.2",
-    "sass": "^1.49.0",
-    "sass-loader": "^12.4.0",
-    "simple-git": "^2.48.0",
+    "sass": "^1.49.9",
+    "sass-loader": "^12.6.0",
+    "simple-git": "^3.3.0",
    "stream-browserify": "^3.0.0",
    "style-loader": "^3.3.1",
    "ts-jest": "^27.1.3",
-    "typescript": "^4.5.5",
-    "webpack": "^5.67.0",
-    "webpack-cli": "^4.9.1"
+    "typescript": "^4.6.2",
+    "webpack": "^5.70.0",
+    "webpack-cli": "^4.9.2"
  },
  "dependencies": {
    "@types/argparse": "^2.0.10",
    "@types/benchmark": "^2.1.1",
    "@types/compression": "1.7.2",
    "@types/express": "^4.17.13",
-    "@types/node": "^16.11.21",
-    "@types/node-fetch": "^2.5.12",
-    "@types/react": "^17.0.38",
-    "@types/react-dom": "^17.0.11",
+    "@types/node": "^16.11.26",
+    "@types/node-fetch": "^2.6.1",
+    "@types/react": "^17.0.40",
+    "@types/react-dom": "^17.0.13",
    "@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": "^2.6.7",
-    "rxjs": "^7.5.2",
-    "swagger-ui-dist": "^4.2.1",
+    "rxjs": "^7.5.5",
+    "swagger-ui-dist": "^4.6.2",
    "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
@@ -17,12 +17,15 @@ import { ModelExport } from '../../extensions/model-export';
 import { Mp4Export } from '../../extensions/mp4-export';
 import { PDBeStructureQualityReport } from '../../extensions/pdbe';
 import { RCSBAssemblySymmetry, RCSBValidationReport } from '../../extensions/rcsb';
+import { ZenodoImport } from '../../extensions/zenodo';
+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';
 import { PresetStructureRepresentations, StructureRepresentationPresetProvider } from '../../mol-plugin-state/builder/structure/representation-preset';
 import { DataFormatProvider } from '../../mol-plugin-state/formats/provider';
-import { BuildInStructureFormat } from '../../mol-plugin-state/formats/structure';
+import { BuiltInTopologyFormat } from '../../mol-plugin-state/formats/topology';
+import { BuiltInCoordinatesFormat } from '../../mol-plugin-state/formats/coordinates';
 import { BuiltInTrajectoryFormat } from '../../mol-plugin-state/formats/trajectory';
 import { BuildInVolumeFormat } from '../../mol-plugin-state/formats/volume';
 import { createVolumeRepresentationParams } from '../../mol-plugin-state/helpers/volume-representation-params';
@@ -62,6 +65,7 @@ const Extensions = {
    'mp4-export': PluginSpec.Behavior(Mp4Export),
    'geo-export': PluginSpec.Behavior(GeometryExport),
    'ma-quality-assessment': PluginSpec.Behavior(MAQualityAssessment),
+    'zenodo-import': PluginSpec.Behavior(ZenodoImport),
 };

 const DefaultViewerOptions = {
@@ -366,11 +370,13 @@ 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 }
                    }));
@@ -450,11 +456,11 @@ export interface VolumeIsovalueInfo {
 export interface LoadTrajectoryParams {
    model: { kind: 'model-url', url: string, format?: BuiltInTrajectoryFormat /* mmcif */, isBinary?: boolean }
    | { kind: 'model-data', data: string | number[] | ArrayBuffer | Uint8Array, format?: BuiltInTrajectoryFormat /* mmcif */ }
-    | { kind: 'topology-url', url: string, format: BuildInStructureFormat, isBinary?: boolean }
-    | { kind: 'topology-data', data: string | number[] | ArrayBuffer | Uint8Array, format: BuildInStructureFormat },
+    | { kind: 'topology-url', url: string, format: BuiltInTopologyFormat, isBinary?: boolean }
+    | { kind: 'topology-data', data: string | number[] | ArrayBuffer | Uint8Array, format: BuiltInTopologyFormat },
    modelLabel?: string,
-    coordinates: { kind: 'coordinates-url', url: string, format: BuildInStructureFormat, isBinary?: boolean }
-    | { kind: 'coordinates-data', data: string | number[] | ArrayBuffer | Uint8Array, format: BuildInStructureFormat },
+    coordinates: { kind: 'coordinates-url', url: string, format: BuiltInCoordinatesFormat, isBinary?: boolean }
+    | { kind: 'coordinates-data', data: string | number[] | ArrayBuffer | Uint8Array, format: BuiltInCoordinatesFormat },
    coordinatesLabel?: string,
    preset?: keyof PresetTrajectoryHierarchy
 }
--- a/src/cli/chem-comp-dict/create-saccharides.ts
+++ b/src/cli/chem-comp-dict/create-saccharides.ts
@@ -0,0 +1,77 @@
+#!/usr/bin/env node
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import * as argparse from 'argparse';
+import * as path from 'path';
+import util from 'util';
+import fs from 'fs';
+require('util.promisify').shim();
+const writeFile = util.promisify(fs.writeFile);
+
+import { DatabaseCollection } from '../../mol-data/db';
+import { CCD_Schema } from '../../mol-io/reader/cif/schema/ccd';
+import { ensureDataAvailable, readCCD } from './util';
+
+function extractSaccharideNames(ccd: DatabaseCollection<CCD_Schema>) {
+    const saccharideNames: string[] = [];
+    for (const k in ccd) {
+        const { chem_comp } = ccd[k];
+        const type = chem_comp.type.value(0).toUpperCase();
+        if (type.includes('SACCHARIDE')) {
+            saccharideNames.push(chem_comp.id.value(0));
+        }
+    }
+    // these are extra saccharides that don't have SACCHARIDE in their type
+    saccharideNames.push(
+        'UMQ', // UNDECYL-MALTOSIDE, via GlyFinder
+        'SQD', // SULFOQUINOVOSYLDIACYLGLYCEROL, via GlyFinder
+    );
+    return saccharideNames;
+}
+
+function writeSaccharideNamesFile(filePath: string, ionNames: string[]) {
+    const output = `/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Code-generated ion names params file. Names extracted from CCD components.
+ *
+ * @author molstar/cli/chem-comp-dict/create-saccharides
+ */
+
+export const SaccharideNames = new Set(${JSON.stringify(ionNames).replace(/"/g, "'").replace(/,/g, ', ')});
+`;
+    writeFile(filePath, output);
+}
+
+async function run(out: string, forceDownload = false) {
+    await ensureDataAvailable(forceDownload);
+    const ccd = await readCCD();
+    const saccharideNames = extractSaccharideNames(ccd);
+    if (!fs.existsSync(path.dirname(out))) {
+        fs.mkdirSync(path.dirname(out));
+    }
+    writeSaccharideNamesFile(out, saccharideNames);
+}
+
+const parser = new argparse.ArgumentParser({
+    add_help: true,
+    description: 'Extract and save SaccharideNames from CCD.'
+});
+parser.add_argument('out', {
+    help: 'Generated file output path.'
+});
+parser.add_argument('--forceDownload', '-f', {
+    action: 'store_true',
+    help: 'Force download of CCD and PVCD.'
+});
+interface Args {
+    out: string,
+    forceDownload?: boolean,
+}
+const args: Args = parser.parse_args();
+
+run(args.out, args.forceDownload);
--- 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/cellpack/model.ts
+++ b/src/extensions/cellpack/model.ts
@@ -32,6 +32,7 @@ import { Color } from '../../mol-util/color';
 import { objectForEach } from '../../mol-util/object';
 import { readFromFile } from '../../mol-util/data-source';
 import { ColorNames } from '../../mol-util/color/names';
+import { createBasic } from '../../mol-model-formats/structure/basic/schema';

 function getCellPackModelUrl(fileName: string, baseUrl: string) {
    return `${baseUrl}/results/${fileName}`;
@@ -310,7 +311,8 @@ async function getCurve(plugin: PluginContext, name: string, ingredient: Ingredi
    const cif = getCifCurve(name, transforms, model);
    const curveModelTask = Task.create('Curve Model', async ctx => {
        const format = MmcifFormat.fromFrame(cif);
-        const models = await createModels(format.data.db, format, ctx);
+        const basic = createBasic(format.data.db, true);
+        const models = await createModels(basic, format, ctx);
        return models.representative;
    });

--- 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/extensions/zenodo/index.ts
+++ b/src/extensions/zenodo/index.ts
@@ -0,0 +1,30 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { PluginBehavior } from '../../mol-plugin/behavior/behavior';
+import { ZenodoImportUI } from './ui';
+
+export const ZenodoImport = PluginBehavior.create<{ }>({
+    name: 'extension-zenodo-import',
+    category: 'misc',
+    display: {
+        name: 'Zenodo Export'
+    },
+    ctor: class extends PluginBehavior.Handler<{ }> {
+        register(): void {
+            this.ctx.customImportControls.set('zenodo-import', ZenodoImportUI as any);
+        }
+
+        update() {
+            return false;
+        }
+
+        unregister() {
+            this.ctx.customImportControls.delete('zenodo-import');
+        }
+    },
+    params: () => ({ })
+});
--- a/src/extensions/zenodo/ui.tsx
+++ b/src/extensions/zenodo/ui.tsx
@@ -0,0 +1,302 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { DownloadFile } from '../../mol-plugin-state/actions/file';
+import { DownloadStructure, LoadTrajectory } from '../../mol-plugin-state/actions/structure';
+import { DownloadDensity } from '../../mol-plugin-state/actions/volume';
+import { CoordinatesFormatCategory } from '../../mol-plugin-state/formats/coordinates';
+import { TopologyFormatCategory } from '../../mol-plugin-state/formats/topology';
+import { TrajectoryFormatCategory } from '../../mol-plugin-state/formats/trajectory';
+import { VolumeFormatCategory } from '../../mol-plugin-state/formats/volume';
+import { CollapsableControls, CollapsableState } from '../../mol-plugin-ui/base';
+import { Button } from '../../mol-plugin-ui/controls/common';
+import { OpenInBrowserSvg } from '../../mol-plugin-ui/controls/icons';
+import { ParameterControls } from '../../mol-plugin-ui/controls/parameters';
+import { PluginContext } from '../../mol-plugin/context';
+import { formatBytes } from '../../mol-util';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+
+type ZenodoFile = {
+    bucket: string
+    checksum: string
+    key: string
+    links: {
+        [key: string]: string
+        self: string
+    }
+    size: number
+    type: string
+}
+
+type ZenodoRecord = {
+    id: number
+    conceptdoi: string
+    conceptrecid: string
+    created: string
+    doi: string
+    files: ZenodoFile[]
+    revision: number
+    updated: string
+    metadata: {
+        title: string
+    }
+}
+
+interface State {
+    busy?: boolean
+    recordValues: PD.Values<typeof ZenodoImportParams>
+    importValues?: PD.Values<ImportParams>
+    importParams?: ImportParams
+    record?: ZenodoRecord
+    files?: ZenodoFile[]
+}
+
+const ZenodoImportParams = {
+    record: PD.Text('', { description: 'Zenodo ID.' })
+};
+
+function createImportParams(files: ZenodoFile[], plugin: PluginContext) {
+    const modelOpts: [string, string][] = [];
+    const topologyOpts: [string, string][] = [];
+    const coordinatesOpts: [string, string][] = [];
+    const volumeOpts: [string, string][] = [];
+    const compressedOpts: [string, string][] = [];
+
+    const structureExts = new Map<string, { format: string, isBinary: boolean }>();
+    const coordinatesExts = new Map<string, { format: string, isBinary: boolean }>();
+    const topologyExts = new Map<string, { format: string, isBinary: boolean }>();
+    const volumeExts = new Map<string, { format: string, isBinary: boolean }>();
+
+    for (const { provider: { category, binaryExtensions, stringExtensions }, name } of plugin.dataFormats.list) {
+        if (category === TrajectoryFormatCategory) {
+            if (binaryExtensions) for (const e of binaryExtensions) structureExts.set(e, { format: name, isBinary: true });
+            if (stringExtensions) for (const e of stringExtensions) structureExts.set(e, { format: name, isBinary: false });
+        } else if (category === VolumeFormatCategory) {
+            if (binaryExtensions) for (const e of binaryExtensions) volumeExts.set(e, { format: name, isBinary: true });
+            if (stringExtensions) for (const e of stringExtensions) volumeExts.set(e, { format: name, isBinary: false });
+        } else if (category === CoordinatesFormatCategory) {
+            if (binaryExtensions) for (const e of binaryExtensions) coordinatesExts.set(e, { format: name, isBinary: true });
+            if (stringExtensions) for (const e of stringExtensions) coordinatesExts.set(e, { format: name, isBinary: false });
+        } else if (category === TopologyFormatCategory) {
+            if (binaryExtensions) for (const e of binaryExtensions) topologyExts.set(e, { format: name, isBinary: true });
+            if (stringExtensions) for (const e of stringExtensions) topologyExts.set(e, { format: name, isBinary: false });
+        }
+    }
+
+    for (const file of files) {
+        const label = `${file.key} (${formatBytes(file.size)})`;
+        if (structureExts.has(file.type)) {
+            const { format, isBinary } = structureExts.get(file.type)!;
+            modelOpts.push([`${file.links.self}|${format}|${isBinary}`, label]);
+            topologyOpts.push([`${file.links.self}|${format}|${isBinary}`, label]);
+        } else if (volumeExts.has(file.type)) {
+            const { format, isBinary } = volumeExts.get(file.type)!;
+            volumeOpts.push([`${file.links.self}|${format}|${isBinary}`, label]);
+        } else if (topologyExts.has(file.type)) {
+            const { format, isBinary } = topologyExts.get(file.type)!;
+            topologyOpts.push([`${file.links.self}|${format}|${isBinary}`, label]);
+        } else if (coordinatesExts.has(file.type)) {
+            const { format, isBinary } = coordinatesExts.get(file.type)!;
+            coordinatesOpts.push([`${file.links.self}|${format}|${isBinary}`, label]);
+        } else if (file.type === 'zip') {
+            compressedOpts.push([`${file.links.self}|${file.type}|true`, label]);
+        }
+    }
+
+    const params: PD.Params = {};
+    let defaultType = '';
+
+    if (modelOpts.length) {
+        defaultType = 'structure';
+        params.structure = PD.Select(modelOpts[0][0], modelOpts);
+    }
+
+    if (topologyOpts.length && coordinatesOpts.length) {
+        if (!defaultType) defaultType = 'trajectory';
+        params.trajectory = PD.Group({
+            topology: PD.Select(topologyOpts[0][0], topologyOpts),
+            coordinates: PD.Select(coordinatesOpts[0][0], coordinatesOpts),
+        }, { isFlat: true });
+    }
+
+    if (volumeOpts.length) {
+        if (!defaultType) defaultType = 'volume';
+        params.volume = PD.Select(volumeOpts[0][0], volumeOpts);
+    }
+
+    if (compressedOpts.length) {
+        if (!defaultType) defaultType = 'compressed';
+        params.compressed = PD.Select(compressedOpts[0][0], compressedOpts);
+    }
+
+    return {
+        type: PD.MappedStatic(defaultType, Object.keys(params).length ? params : { '': PD.EmptyGroup() })
+    };
+}
+type ImportParams = ReturnType<typeof createImportParams>
+
+export class ZenodoImportUI extends CollapsableControls<{}, State> {
+    protected defaultState(): State & CollapsableState {
+        return {
+            header: 'Zenodo Import',
+            isCollapsed: true,
+            brand: { accent: 'cyan', svg: OpenInBrowserSvg },
+            recordValues: PD.getDefaultValues(ZenodoImportParams),
+            importValues: undefined,
+            importParams: undefined,
+            record: undefined,
+            files: undefined,
+        };
+    }
+
+    private recordParamsOnChange = (values: any) => {
+        this.setState({ recordValues: values });
+    };
+
+    private importParamsOnChange = (values: any) => {
+        this.setState({ importValues: values });
+    };
+
+    private loadRecord = async () => {
+        try {
+            this.setState({ busy: true });
+            const record: ZenodoRecord = await this.plugin.runTask(this.plugin.fetch({ url: `https://zenodo.org/api/records/${this.state.recordValues.record}`, type: 'json' }));
+            const importParams = createImportParams(record.files, this.plugin);
+            this.setState({
+                record,
+                files: record.files,
+                busy: false,
+                importValues: PD.getDefaultValues(importParams),
+                importParams
+            });
+        } catch (e) {
+            console.error(e);
+            this.plugin.log.error(`Failed to load Zenodo record '${this.state.recordValues.record}'`);
+            this.setState({ busy: false });
+        }
+    };
+
+    private loadFile = async (values: PD.Values<ImportParams>) => {
+        try {
+            this.setState({ busy: true });
+
+            const t = values.type;
+            if (t.name === 'structure') {
+                const defaultParams = DownloadStructure.createDefaultParams(this.plugin.state.data.root.obj!, this.plugin);
+
+                const [url, format, isBinary] = t.params.split('|');
+
+                await this.plugin.runTask(this.plugin.state.data.applyAction(DownloadStructure, {
+                    source: {
+                        name: 'url',
+                        params: {
+                            url,
+                            format: format as any,
+                            isBinary: isBinary === 'true',
+                            options: defaultParams.source.params.options,
+                        }
+                    }
+                }));
+            } else if (t.name === 'trajectory') {
+                const [topologyUrl, topologyFormat, topologyIsBinary] = t.params.topology.split('|');
+                const [coordinatesUrl, coordinatesFormat, coordinatesIsBinary] = t.params.coordinates.split('|');
+
+                await this.plugin.runTask(this.plugin.state.data.applyAction(LoadTrajectory, {
+                    source: {
+                        name: 'url',
+                        params: {
+                            model: {
+                                url: topologyUrl,
+                                format: topologyFormat as any,
+                                isBinary: topologyIsBinary === 'true',
+                            },
+                            coordinates: {
+                                url: coordinatesUrl,
+                                format: coordinatesFormat as any,
+                                isBinary: coordinatesIsBinary === 'true',
+                            },
+                        }
+                    }
+                }));
+            } else if (t.name === 'volume') {
+                const [url, format, isBinary] = t.params.split('|');
+
+                await this.plugin.runTask(this.plugin.state.data.applyAction(DownloadDensity, {
+                    source: {
+                        name: 'url',
+                        params: {
+                            url,
+                            format: format as any,
+                            isBinary: isBinary === 'true',
+                        }
+                    }
+                }));
+            } else if (t.name === 'compressed') {
+                const [url, format, isBinary] = t.params.split('|');
+
+                await this.plugin.runTask(this.plugin.state.data.applyAction(DownloadFile, {
+                    url,
+                    format: format as any,
+                    isBinary: isBinary === 'true',
+                    visuals: true
+                }));
+            }
+        } catch (e) {
+            console.error(e);
+            this.plugin.log.error(`Failed to load Zenodo file`);
+        } finally {
+            this.setState({ busy: false });
+        }
+    };
+
+    private clearRecord = () => {
+        this.setState({
+            importValues: undefined,
+            importParams: undefined,
+            record: undefined,
+            files: undefined
+        });
+    };
+
+    private renderLoadRecord() {
+        return <div style={{ marginBottom: 10 }}>
+            <ParameterControls params={ZenodoImportParams} values={this.state.recordValues} onChangeValues={this.recordParamsOnChange} isDisabled={this.state.busy} />
+            <Button onClick={this.loadRecord} style={{ marginTop: 1 }} disabled={this.state.busy || !this.state.recordValues.record}>
+                Load Record
+            </Button>
+        </div>;
+    }
+
+    private renderRecordInfo(record: ZenodoRecord) {
+        return <div style={{ marginBottom: 10 }}>
+            <div className='msp-help-text'>
+                <div>Record {`${record.id}`}: <i>{`${record.metadata.title}`}</i></div>
+            </div>
+            <Button onClick={this.clearRecord} style={{ marginTop: 1 }} disabled={this.state.busy}>
+                Clear
+            </Button>
+        </div>;
+    }
+
+    private renderImportFile(params: ImportParams, values: PD.Values<ImportParams>) {
+        return values.type.name ? <div style={{ marginBottom: 10 }}>
+            <ParameterControls params={params} values={this.state.importValues} onChangeValues={this.importParamsOnChange} isDisabled={this.state.busy} />
+            <Button onClick={() => this.loadFile(values)} style={{ marginTop: 1 }} disabled={this.state.busy}>
+                Import File
+            </Button>
+        </div> : <div className='msp-help-text' style={{ marginBottom: 10 }}>
+            <div>No supported files</div>
+        </div>;
+    }
+
+    protected renderControls(): JSX.Element | null {
+        return <>
+            {!this.state.record ? this.renderLoadRecord() : null}
+            {this.state.record ? this.renderRecordInfo(this.state.record) : null}
+            {this.state.importParams && this.state.importValues ? this.renderImportFile(this.state.importParams, this.state.importValues) : null}
+        </>;
+    }
+}
--- a/src/mol-canvas3d/camera.ts
+++ b/src/mol-canvas3d/camera.ts
@@ -10,6 +10,7 @@ import { Viewport, cameraProject, cameraUnproject } from './camera/util';
 import { CameraTransitionManager } from './camera/transition';
 import { BehaviorSubject } from 'rxjs';
 import { Scene } from '../mol-gl/scene';
+import { assertUnreachable } from '../mol-util/type-helpers';

 export { ICamera, Camera };

@@ -84,7 +85,7 @@ class Camera implements ICamera {
        switch (this.state.mode) {
            case 'orthographic': updateOrtho(this); break;
            case 'perspective': updatePers(this); break;
-            default: throw new Error('unknown camera mode');
+            default: assertUnreachable(this.state.mode);
        }

        const changed = !Mat4.areEqual(this.projection, this.prevProjection, EPSILON) || !Mat4.areEqual(this.view, this.prevView, EPSILON);
--- 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/text/text-builder.ts
+++ b/src/mol-geo/geometry/text/text-builder.ts
@@ -8,6 +8,7 @@ import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { ChunkedArray } from '../../../mol-data/util';
 import { Text } from './text';
 import { getFontAtlas } from './font-atlas';
+import { assertUnreachable } from '../../../mol-util/type-helpers';

 const quadIndices = new Uint16Array([
    0, 1, 2,
@@ -237,7 +238,7 @@ export namespace TextBuilder {
                            yBaseCenter = yTop;
                            break;
                        default:
-                            throw new Error('unsupported attachment');
+                            assertUnreachable(attachment);
                    }
                    caAdd2(mappings, xTip, yTip); // tip
                    caAdd2(mappings, xBaseA, yBaseA); // base A
--- 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-code.ts
+++ b/src/mol-gl/shader-code.ts
@@ -202,6 +202,7 @@ export const DirectVolumeShaderCode = ShaderCode('direct-volume', directVolume_v

 import { image_vert } from './shader/image.vert';
 import { image_frag } from './shader/image.frag';
+import { assertUnreachable } from '../mol-util/type-helpers';
 export const ImageShaderCode = ShaderCode('image', image_vert, image_frag, { drawBuffers: 'optional' }, {}, ignoreDefineUnlit);

 //
@@ -228,7 +229,7 @@ function getDefinesCode(defines: ShaderDefines, ignore?: IgnoreDefine) {
            } else if (typeof v === 'boolean') {
                if (v) lines.push(`#define ${name}`);
            } else {
-                throw new Error('unknown define type');
+                assertUnreachable(v);
            }
        }
    }
--- 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/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
@@ -8,7 +8,7 @@ import { WebGLContext } from './context';
 import { ValueCell } from '../../mol-util';
 import { RenderableSchema } from '../renderable/schema';
 import { idFactory } from '../../mol-util/id-factory';
-import { ValueOf } from '../../mol-util/type-helpers';
+import { assertUnreachable, ValueOf } from '../../mol-util/type-helpers';
 import { GLRenderingContext } from './compat';
 import { WebGLExtensions } from './extensions';
 import { WebGLState } from './state';
@@ -66,9 +66,8 @@ function dataTypeFromArray(gl: GLRenderingContext, array: ArrayType) {
        return gl.INT;
    } else if (array instanceof Float32Array) {
        return gl.FLOAT;
-    } else {
-        throw new Error('Should nevver happen');
    }
+    assertUnreachable(array);
 }

 export function getBufferType(gl: GLRenderingContext, bufferType: BufferType) {
--- 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/common/binary-cif/classifier.ts
+++ b/src/mol-io/common/binary-cif/classifier.ts
@@ -7,6 +7,7 @@

 import { ArrayEncoder, ArrayEncoding as E } from './array-encoder';
 import { getArrayDigitCount } from '../../../mol-util/number';
+import { assertUnreachable } from '../../../mol-util/type-helpers';

 export function classifyIntArray(xs: ArrayLike<number>) {
    return IntClassifier.classify(xs as number[]);
@@ -62,7 +63,7 @@ namespace IntClassifier {
        for (let i = 0, n = data.length; i < n; i++) {
            incSize(info, size, data[i]);
        }
-        return { ...byteSize(size), kind: 'pack' };
+        return { ...byteSize(size), kind: 'pack' as const };
    }

    function deltaSize(data: number[], info: IntColumnInfo) {
@@ -72,7 +73,7 @@ namespace IntClassifier {
            incSizeSigned(size, data[i] - prev);
            prev = data[i];
        }
-        return { ...byteSize(size), kind: 'delta' };
+        return { ...byteSize(size), kind: 'delta' as const };
    }

    function rleSize(data: number[], info: IntColumnInfo) {
@@ -90,7 +91,7 @@ namespace IntClassifier {
        incSize(info, size, data[data.length - 1]);
        incSize(info, size, run);

-        return { ...byteSize(size), kind: 'rle' };
+        return { ...byteSize(size), kind: 'rle' as const };
    }

    function deltaRleSize(data: number[], info: IntColumnInfo) {
@@ -111,7 +112,7 @@ namespace IntClassifier {
        incSizeSigned(size, prevValue);
        incSizeSigned(size, run);

-        return { ...byteSize(size), kind: 'delta-rle' };
+        return { ...byteSize(size), kind: 'delta-rle' as const };
    }

    export function getSize(data: number[]) {
@@ -132,9 +133,8 @@ namespace IntClassifier {
            case 'rle': return E.by(E.runLength).and(E.integerPacking);
            case 'delta': return E.by(E.delta).and(E.integerPacking);
            case 'delta-rle': return E.by(E.delta).and(E.runLength).and(E.integerPacking);
+            default: assertUnreachable(size);
        }
-
-        throw new Error('should not happen :)');
    }
 }

@@ -169,9 +169,8 @@ namespace FloatClassifier {
            case 'rle': return fp.and(E.runLength).and(E.integerPacking);
            case 'delta': return fp.and(E.delta).and(E.integerPacking);
            case 'delta-rle': return fp.and(E.delta).and(E.runLength).and(E.integerPacking);
+            default: assertUnreachable(size);
        }
-
-        throw new Error('should not happen :)');
    }

    function getMultiplier(mantissaDigits: number) {
--- a/src/mol-io/common/binary-cif/decoder.ts
+++ b/src/mol-io/common/binary-cif/decoder.ts
@@ -7,6 +7,7 @@

 import { Encoding, EncodedData } from './encoding';
 import { IsNativeEndianLittle, flipByteOrder } from '../binary';
+import { assertUnreachable } from '../../../mol-util/type-helpers';

 /**
 * Fixed point, delta, RLE, integer packing adopted from https://github.com/rcsb/mmtf-javascript/
@@ -33,7 +34,7 @@ function decodeStep(data: any, encoding: Encoding): any {
                case Encoding.IntDataType.Uint32: return uint32(data);
                case Encoding.FloatDataType.Float32: return float32(data);
                case Encoding.FloatDataType.Float64: return float64(data);
-                default: throw new Error('Unsupported ByteArray type.');
+                default: assertUnreachable(encoding.type);
            }
        }
        case 'FixedPoint': return fixedPoint(data, encoding);
@@ -53,7 +54,7 @@ function getIntArray(type: Encoding.IntDataType, size: number) {
        case Encoding.IntDataType.Uint8: return new Uint8Array(size);
        case Encoding.IntDataType.Uint16: return new Uint16Array(size);
        case Encoding.IntDataType.Uint32: return new Uint32Array(size);
-        default: throw new Error('Unsupported integer data type.');
+        default: assertUnreachable(type);
    }
 }

@@ -61,7 +62,7 @@ function getFloatArray(type: Encoding.FloatDataType, size: number) {
    switch (type) {
        case Encoding.FloatDataType.Float32: return new Float32Array(size);
        case Encoding.FloatDataType.Float64: return new Float64Array(size);
-        default: throw new Error('Unsupported floating data type.');
+        default: assertUnreachable(type);
    }
 }

--- a/src/mol-io/common/io-buffer.ts
+++ b/src/mol-io/common/io-buffer.ts
@@ -0,0 +1,453 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Adapted and converted to TypeScript from https://github.com/image-js/iobuffer
+ * MIT License, Copyright (c) 2015 Michaël Zasso
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { TypedArray } from '../../mol-util/type-helpers';
+
+const defaultByteLength = 1024 * 8;
+const charArray: string[] = [];
+
+export interface IOBufferParameters {
+    offset?: number // Ignore the first n bytes of the ArrayBuffer
+}
+
+/**
+ * Class for writing and reading binary data
+ */
+export class IOBuffer {
+    private _lastWrittenByte: number;
+    private _mark = 0;
+    private _marks: number[] = [];
+    private _data: DataView;
+
+    offset = 0; // The current offset of the buffer's pointer
+    littleEndian = true;
+    buffer: ArrayBuffer; // Reference to the internal ArrayBuffer object
+    length: number; // Byte length of the internal ArrayBuffer
+    byteLength: number; // Byte length of the internal ArrayBuffer
+    byteOffset: number; // Byte offset of the internal ArrayBuffer
+
+    /**
+     * If it's a number, it will initialize the buffer with the number as
+     * the buffer's length. If it's undefined, it will initialize the buffer
+     * with a default length of 8 Kb. If its an ArrayBuffer, a TypedArray,
+     * it will create a view over the underlying ArrayBuffer.
+     */
+    constructor(data: number | ArrayBuffer | TypedArray, params: IOBufferParameters = {}) {
+        let dataIsGiven = false;
+        if (data === undefined) {
+            data = defaultByteLength;
+        }
+        if (typeof data === 'number') {
+            data = new ArrayBuffer(data);
+        } else {
+            dataIsGiven = true;
+        }
+
+        const offset = params.offset ? params.offset >>> 0 : 0;
+        const byteLength = data.byteLength - offset;
+        let dvOffset = offset;
+        if (!(data instanceof ArrayBuffer)) {
+            if (data.byteLength !== data.buffer.byteLength) {
+                dvOffset = data.byteOffset + offset;
+            }
+            data = data.buffer;
+        }
+        if (dataIsGiven) {
+            this._lastWrittenByte = byteLength;
+        } else {
+            this._lastWrittenByte = 0;
+        }
+
+        this.buffer = data;
+        this.length = byteLength;
+        this.byteLength = byteLength;
+        this.byteOffset = dvOffset;
+
+        this._data = new DataView(this.buffer, dvOffset, byteLength);
+    }
+
+    /**
+     * Checks if the memory allocated to the buffer is sufficient to store more bytes after the offset
+     * @param byteLength The needed memory in bytes
+     */
+    available(byteLength: number = 1) {
+        return (this.offset + byteLength) <= this.length;
+    }
+
+    /**
+     * Check if little-endian mode is used for reading and writing multi-byte values
+     * Returns true if little-endian mode is used, false otherwise
+     */
+    isLittleEndian() {
+        return this.littleEndian;
+    }
+
+    /**
+     * Set little-endian mode for reading and writing multi-byte values
+     */
+    setLittleEndian() {
+        this.littleEndian = true;
+        return this;
+    }
+
+    /**
+     * Check if big-endian mode is used for reading and writing multi-byte values
+     * Returns true if big-endian mode is used, false otherwise
+     */
+    isBigEndian() {
+        return !this.littleEndian;
+    }
+
+    /**
+     * Switches to big-endian mode for reading and writing multi-byte values
+     */
+    setBigEndian() {
+        this.littleEndian = false;
+        return this;
+    }
+
+    /**
+     * Move the pointer n bytes forward
+     */
+    skip(n: number) {
+        if (n === undefined) n = 1;
+        this.offset += n;
+        return this;
+    }
+
+    /**
+     * Move the pointer to the given offset
+     */
+    seek(offset: number) {
+        this.offset = offset;
+        return this;
+    }
+
+    /**
+     * Store the current pointer offset.
+     */
+    mark() {
+        this._mark = this.offset;
+        return this;
+    }
+
+    /**
+     * Move the pointer back to the last pointer offset set by mark
+     */
+    reset() {
+        this.offset = this._mark;
+        return this;
+    }
+
+    /**
+     * Push the current pointer offset to the mark stack
+     */
+    pushMark() {
+        this._marks.push(this.offset);
+        return this;
+    }
+
+    /**
+     * Pop the last pointer offset from the mark stack, and set the current pointer offset to the popped value
+     */
+    popMark() {
+        const offset = this._marks.pop();
+        if (offset === undefined) throw new Error('Mark stack empty');
+        this.seek(offset);
+        return this;
+    }
+
+    /**
+     * Move the pointer offset back to 0
+     */
+    rewind() {
+        this.offset = 0;
+        return this;
+    }
+
+    /**
+     * Make sure the buffer has sufficient memory to write a given byteLength at the current pointer offset
+     * If the buffer's memory is insufficient, this method will create a new buffer (a copy) with a length
+     * that is twice (byteLength + current offset)
+     */
+    ensureAvailable(byteLength: number) {
+        if (byteLength === undefined) byteLength = 1;
+        if (!this.available(byteLength)) {
+            const lengthNeeded = this.offset + byteLength;
+            const newLength = lengthNeeded * 2;
+            const newArray = new Uint8Array(newLength);
+            newArray.set(new Uint8Array(this.buffer));
+            this.buffer = newArray.buffer;
+            this.length = this.byteLength = newLength;
+            this._data = new DataView(this.buffer);
+        }
+        return this;
+    }
+
+    /**
+     * Read a byte and return false if the byte's value is 0, or true otherwise
+     * Moves pointer forward
+     */
+    readBoolean() {
+        return this.readUint8() !== 0;
+    }
+
+    /**
+     * Read a signed 8-bit integer and move pointer forward
+     */
+    readInt8() {
+        return this._data.getInt8(this.offset++);
+    }
+
+    /**
+     * Read an unsigned 8-bit integer and move pointer forward
+     */
+    readUint8() {
+        return this._data.getUint8(this.offset++);
+    }
+
+    /**
+     * Alias for {@link IOBuffer#readUint8}
+     */
+    readByte() {
+        return this.readUint8();
+    }
+
+    /**
+     * Read n bytes and move pointer forward.
+     */
+    readBytes(n: number) {
+        if (n === undefined) n = 1;
+        const bytes = new Uint8Array(n);
+        for (let i = 0; i < n; i++) {
+            bytes[i] = this.readByte();
+        }
+        return bytes;
+    }
+
+    /**
+     * Read a 16-bit signed integer and move pointer forward
+     */
+    readInt16() {
+        const value = this._data.getInt16(this.offset, this.littleEndian);
+        this.offset += 2;
+        return value;
+    }
+
+    /**
+     * Read a 16-bit unsigned integer and move pointer forward
+     */
+    readUint16() {
+        const value = this._data.getUint16(this.offset, this.littleEndian);
+        this.offset += 2;
+        return value;
+    }
+
+    /**
+     * Read a 32-bit signed integer and move pointer forward
+     */
+    readInt32() {
+        const value = this._data.getInt32(this.offset, this.littleEndian);
+        this.offset += 4;
+        return value;
+    }
+
+    /**
+     * Read a 32-bit unsigned integer and move pointer forward
+     */
+    readUint32() {
+        const value = this._data.getUint32(this.offset, this.littleEndian);
+        this.offset += 4;
+        return value;
+    }
+
+    /**
+     * Read a 32-bit floating number and move pointer forward
+     */
+    readFloat32() {
+        const value = this._data.getFloat32(this.offset, this.littleEndian);
+        this.offset += 4;
+        return value;
+    }
+
+    /**
+     * Read a 64-bit floating number and move pointer forward
+     */
+    readFloat64() {
+        const value = this._data.getFloat64(this.offset, this.littleEndian);
+        this.offset += 8;
+        return value;
+    }
+
+    /**
+     * Read 1-byte ascii character and move pointer forward
+     */
+    readChar() {
+        return String.fromCharCode(this.readInt8());
+    }
+
+    /**
+     * Read n 1-byte ascii characters and move pointer forward
+     */
+    readChars(n = 1) {
+        charArray.length = n;
+        for (let i = 0; i < n; i++) {
+            charArray[i] = this.readChar();
+        }
+        return charArray.join('');
+    }
+
+    /**
+     * Write 0xff if the passed value is truthy, 0x00 otherwise
+     */
+    writeBoolean(value = false) {
+        this.writeUint8(value ? 0xff : 0x00);
+        return this;
+    }
+
+    /**
+     * Write value as an 8-bit signed integer
+     */
+    writeInt8(value: number) {
+        this.ensureAvailable(1);
+        this._data.setInt8(this.offset++, value);
+        this._updateLastWrittenByte();
+        return this;
+    }
+
+    /**
+     * Write value as a 8-bit unsigned integer
+     */
+    writeUint8(value: number) {
+        this.ensureAvailable(1);
+        this._data.setUint8(this.offset++, value);
+        this._updateLastWrittenByte();
+        return this;
+    }
+
+    /**
+     * An alias for IOBuffer#writeUint8
+     */
+    writeByte(value: number) {
+        return this.writeUint8(value);
+    }
+
+    /**
+     * Write bytes
+     */
+    writeBytes(bytes: number[] | Uint8Array) {
+        this.ensureAvailable(bytes.length);
+        for (let i = 0; i < bytes.length; i++) {
+            this._data.setUint8(this.offset++, bytes[i]);
+        }
+        this._updateLastWrittenByte();
+        return this;
+    }
+
+    /**
+     * Write value as an 16-bit signed integer
+     */
+    writeInt16(value: number) {
+        this.ensureAvailable(2);
+        this._data.setInt16(this.offset, value, this.littleEndian);
+        this.offset += 2;
+        this._updateLastWrittenByte();
+        return this;
+    }
+
+    /**
+     * Write value as a 16-bit unsigned integer
+     */
+    writeUint16(value: number) {
+        this.ensureAvailable(2);
+        this._data.setUint16(this.offset, value, this.littleEndian);
+        this.offset += 2;
+        this._updateLastWrittenByte();
+        return this;
+    }
+
+    /**
+     * Write a 32-bit signed integer at the current pointer offset
+     */
+    writeInt32(value: number) {
+        this.ensureAvailable(4);
+        this._data.setInt32(this.offset, value, this.littleEndian);
+        this.offset += 4;
+        this._updateLastWrittenByte();
+        return this;
+    }
+
+    /**
+     * Write a 32-bit unsigned integer at the current pointer offset
+     */
+    writeUint32(value: number) {
+        this.ensureAvailable(4);
+        this._data.setUint32(this.offset, value, this.littleEndian);
+        this.offset += 4;
+        this._updateLastWrittenByte();
+        return this;
+    }
+
+    /**
+     * Write a 32-bit floating number at the current pointer offset
+     */
+    writeFloat32(value: number) {
+        this.ensureAvailable(4);
+        this._data.setFloat32(this.offset, value, this.littleEndian);
+        this.offset += 4;
+        this._updateLastWrittenByte();
+        return this;
+    }
+
+    /**
+     * Write a 64-bit floating number at the current pointer offset
+     */
+    writeFloat64(value: number) {
+        this.ensureAvailable(8);
+        this._data.setFloat64(this.offset, value, this.littleEndian);
+        this.offset += 8;
+        this._updateLastWrittenByte();
+        return this;
+    }
+
+    /**
+     * Write the charCode of the passed string's first character to the current pointer offset
+     */
+    writeChar(str: string) {
+        return this.writeUint8(str.charCodeAt(0));
+    }
+
+    /**
+     * Write the charCodes of the passed string's characters to the current pointer offset
+     */
+    writeChars(str: string) {
+        for (let i = 0; i < str.length; i++) {
+            this.writeUint8(str.charCodeAt(i));
+        }
+        return this;
+    }
+
+    /**
+     * Export a Uint8Array view of the internal buffer.
+     * The view starts at the byte offset and its length
+     * is calculated to stop at the last written byte or the original length.
+     */
+    toArray() {
+        return new Uint8Array(this.buffer, this.byteOffset, this._lastWrittenByte);
+    }
+
+    /**
+     * Update the last written byte offset
+     */
+    private _updateLastWrittenByte() {
+        if (this.offset > this._lastWrittenByte) {
+            this._lastWrittenByte = this.offset;
+        }
+    }
+}
--- a/src/mol-io/common/netcdf/reader.ts
+++ b/src/mol-io/common/netcdf/reader.ts
@@ -0,0 +1,527 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Adapted from https://github.com/cheminfo-js/netcdfjs
+ * MIT License, Copyright (c) 2016 cheminfo
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+
+import { IOBuffer } from '../io-buffer';
+
+export interface NetCDFRecordDimension {
+    length: number,
+    id?: number,
+    name?: string,
+    recordStep?: number
+}
+
+export interface NetCDFVariable {
+    name: string
+    dimensions: any[]
+    attributes: any[]
+    type: string
+    size: number
+    offset: number
+    record: boolean
+}
+
+export interface NetCDFHeader {
+    recordDimension: NetCDFRecordDimension,
+    version: number,
+    dimensions: { name: string, size: number }[],
+    globalAttributes: { name: string, type: string, value: string | number }[],
+    variables: NetCDFVariable[]
+}
+
+export interface NetCDFDimension {
+    name: string,
+    size: number
+}
+
+/**
+ * Throws a non-valid NetCDF exception if the statement it's true
+ */
+function notNetcdf(statement: boolean, reason: string) {
+    if (statement) {
+        throw new TypeError('Not a valid NetCDF v3.x file: ' + reason);
+    }
+}
+
+/**
+ * Moves 1, 2, or 3 bytes to next 4-byte boundary
+ */
+function padding(buffer: IOBuffer) {
+    if ((buffer.offset % 4) !== 0) {
+        buffer.skip(4 - (buffer.offset % 4));
+    }
+}
+
+/**
+ * Reads the name
+ */
+function readName(buffer: IOBuffer) {
+    // Read name
+    const nameLength = buffer.readUint32();
+    const name = buffer.readChars(nameLength);
+
+    // validate name
+    // TODO
+
+    // Apply padding
+    padding(buffer);
+    return name;
+}
+
+const types = {
+    BYTE: 1,
+    CHAR: 2,
+    SHORT: 3,
+    INT: 4,
+    FLOAT: 5,
+    DOUBLE: 6
+};
+
+/**
+ * Parse a number into their respective type
+ */
+function num2str(type: number) {
+    switch (Number(type)) {
+        case types.BYTE:
+            return 'byte';
+        case types.CHAR:
+            return 'char';
+        case types.SHORT:
+            return 'short';
+        case types.INT:
+            return 'int';
+        case types.FLOAT:
+            return 'float';
+        case types.DOUBLE:
+            return 'double';
+        default:
+            return 'undefined';
+    }
+}
+
+/**
+ * Parse a number type identifier to his size in bytes
+ */
+function num2bytes(type: number) {
+    switch (Number(type)) {
+        case types.BYTE:
+            return 1;
+        case types.CHAR:
+            return 1;
+        case types.SHORT:
+            return 2;
+        case types.INT:
+            return 4;
+        case types.FLOAT:
+            return 4;
+        case types.DOUBLE:
+            return 8;
+        default:
+            return -1;
+    }
+}
+
+/**
+ * Reverse search of num2str
+ */
+function str2num(type: string) {
+    switch (String(type)) {
+        case 'byte':
+            return types.BYTE;
+        case 'char':
+            return types.CHAR;
+        case 'short':
+            return types.SHORT;
+        case 'int':
+            return types.INT;
+        case 'float':
+            return types.FLOAT;
+        case 'double':
+            return types.DOUBLE;
+        default:
+            return -1;
+    }
+}
+
+/**
+ * Auxiliary function to read numeric data
+ */
+function readNumber(size: number, bufferReader: Function) {
+    if (size !== 1) {
+        const numbers = new Array(size);
+        for (let i = 0; i < size; i++) {
+            numbers[i] = bufferReader();
+        }
+        return numbers;
+    } else {
+        return bufferReader();
+    }
+}
+
+/**
+ * Given a type and a size reads the next element
+ */
+function readType(buffer: IOBuffer, type: number, size: number) {
+    switch (type) {
+        case types.BYTE:
+            return buffer.readBytes(size);
+        case types.CHAR:
+            return trimNull(buffer.readChars(size));
+        case types.SHORT:
+            return readNumber(size, buffer.readInt16.bind(buffer));
+        case types.INT:
+            return readNumber(size, buffer.readInt32.bind(buffer));
+        case types.FLOAT:
+            return readNumber(size, buffer.readFloat32.bind(buffer));
+        case types.DOUBLE:
+            return readNumber(size, buffer.readFloat64.bind(buffer));
+        default:
+            notNetcdf(true, 'non valid type ' + type);
+            return undefined;
+    }
+}
+
+/**
+ * Removes null terminate value
+ */
+function trimNull(value: string) {
+    if (value.charCodeAt(value.length - 1) === 0) {
+        return value.substring(0, value.length - 1);
+    }
+    return value;
+}
+
+// const STREAMING = 4294967295;
+
+/**
+ * Read data for the given non-record variable
+ */
+function nonRecord(buffer: IOBuffer, variable: { type: string, size: number }) {
+    // variable type
+    const type = str2num(variable.type);
+
+    // size of the data
+    const size = variable.size / num2bytes(type);
+
+    // iterates over the data
+    const data = new Array(size);
+    for (let i = 0; i < size; i++) {
+        data[i] = readType(buffer, type, 1);
+    }
+
+    return data;
+}
+
+/**
+ * Read data for the given record variable
+ */
+function record(buffer: IOBuffer, variable: { type: string, size: number }, recordDimension: NetCDFRecordDimension) {
+    // variable type
+    const type = str2num(variable.type);
+    const width = variable.size ? variable.size / num2bytes(type) : 1;
+
+    // size of the data
+    // TODO streaming data
+    const size = recordDimension.length;
+
+    // iterates over the data
+    const data = new Array(size);
+    const step = recordDimension.recordStep;
+
+    for (let i = 0; i < size; i++) {
+        const currentOffset = buffer.offset;
+        data[i] = readType(buffer, type, width);
+        buffer.seek(currentOffset + step!);
+    }
+
+    return data;
+}
+
+// Grammar constants
+const ZERO = 0;
+const NC_DIMENSION = 10;
+const NC_VARIABLE = 11;
+const NC_ATTRIBUTE = 12;
+
+/**
+ * Read the header of the file
+ * Returns object with the fields:
+ *  - `recordDimension`: Number with the length of record dimension
+ *  - `dimensions`: List of dimensions
+ *  - `globalAttributes`: List of global attributes
+ *  - `variables`: List of variables
+ */
+function header(buffer: IOBuffer, version: number) {
+    // Length of record dimension
+    // sum of the varSize's of all the record variables.
+    const header: Partial<NetCDFHeader> = { recordDimension: { length: buffer.readUint32() } };
+
+    // Version
+    header.version = version;
+
+    // List of dimensions
+    const dimList = dimensionsList(buffer) as { dimensions: NetCDFDimension[], recordId: number, recordName: string };
+    header.recordDimension!.id = dimList.recordId;
+    header.recordDimension!.name = dimList.recordName;
+    header.dimensions = dimList.dimensions;
+
+    // List of global attributes
+    header.globalAttributes = attributesList(buffer);
+
+    // List of variables
+    const variables = variablesList(buffer, dimList.recordId, version) as { variables: any[], recordStep: number };
+    header.variables = variables.variables;
+    header.recordDimension!.recordStep = variables.recordStep;
+
+    return header;
+}
+
+/**
+ * List of dimensions
+ */
+function dimensionsList(buffer: IOBuffer) {
+    let dimensions: NetCDFDimension[], recordId, recordName;
+    const dimList = buffer.readUint32();
+    if (dimList === ZERO) {
+        notNetcdf((buffer.readUint32() !== ZERO), 'wrong empty tag for list of dimensions');
+        return [];
+    } else {
+        notNetcdf((dimList !== NC_DIMENSION), 'wrong tag for list of dimensions');
+
+        // Length of dimensions
+        const dimensionSize = buffer.readUint32();
+        dimensions = new Array(dimensionSize);
+        for (let dim = 0; dim < dimensionSize; dim++) {
+            // Read name
+            const name = readName(buffer);
+
+            // Read dimension size
+            const size = buffer.readUint32();
+            if (size === 0) {
+                recordId = dim;
+                recordName = name;
+            }
+
+            dimensions[dim] = {
+                name: name,
+                size: size
+            };
+        }
+        return {
+            dimensions: dimensions,
+            recordId: recordId,
+            recordName: recordName
+        };
+    }
+}
+
+/**
+ * List of attributes
+ */
+function attributesList(buffer: IOBuffer) {
+    let attributes: { name: string, type: ReturnType<typeof num2str>, value: any }[];
+    const gAttList = buffer.readUint32();
+    if (gAttList === ZERO) {
+        notNetcdf((buffer.readUint32() !== ZERO), 'wrong empty tag for list of attributes');
+        return [];
+    } else {
+        notNetcdf((gAttList !== NC_ATTRIBUTE), 'wrong tag for list of attributes');
+
+        // Length of attributes
+        const attributeSize = buffer.readUint32();
+        attributes = new Array(attributeSize);
+        for (let gAtt = 0; gAtt < attributeSize; gAtt++) {
+            // Read name
+            const name = readName(buffer);
+
+            // Read type
+            const type = buffer.readUint32();
+            notNetcdf(((type < 1) || (type > 6)), 'non valid type ' + type);
+
+            // Read attribute
+            const size = buffer.readUint32();
+            const value = readType(buffer, type, size);
+
+            // Apply padding
+            padding(buffer);
+
+            attributes[gAtt] = {
+                name: name,
+                type: num2str(type),
+                value: value
+            };
+        }
+    }
+    return attributes;
+}
+
+/**
+ * List of variables
+ */
+function variablesList(buffer: IOBuffer, recordId: number, version: number) {
+    const varList = buffer.readUint32();
+    let recordStep = 0;
+    let variables;
+    if (varList === ZERO) {
+        notNetcdf(
+            (buffer.readUint32() !== ZERO),
+            'wrong empty tag for list of variables'
+        );
+        return [];
+    } else {
+        notNetcdf((varList !== NC_VARIABLE), 'wrong tag for list of variables');
+
+        // Length of variables
+        const variableSize = buffer.readUint32();
+        variables = new Array(variableSize);
+        for (let v = 0; v < variableSize; v++) {
+            // Read name
+            const name = readName(buffer);
+
+            // Read dimensionality of the variable
+            const dimensionality = buffer.readUint32();
+
+            // Index into the list of dimensions
+            const dimensionsIds = new Array(dimensionality);
+            for (let dim = 0; dim < dimensionality; dim++) {
+                dimensionsIds[dim] = buffer.readUint32();
+            }
+
+            // Read variables size
+            const attributes = attributesList(buffer);
+
+            // Read type
+            const type = buffer.readUint32();
+            notNetcdf(((type < 1) && (type > 6)), 'non valid type ' + type);
+
+            // Read variable size
+            // The 32-bit varSize field is not large enough to contain the
+            // size of variables that require more than 2^32 - 4 bytes,
+            // so 2^32 - 1 is used in the varSize field for such variables.
+            const varSize = buffer.readUint32();
+
+            // Read offset
+            let offset = buffer.readUint32();
+            if (version === 2) {
+                notNetcdf((offset > 0), 'offsets larger than 4GB not supported');
+                offset = buffer.readUint32();
+            }
+
+            // Count amount of record variables
+            if (dimensionsIds[0] === recordId) {
+                recordStep += varSize;
+            }
+
+            variables[v] = {
+                name: name,
+                dimensions: dimensionsIds,
+                attributes: attributes,
+                type: num2str(type),
+                size: varSize,
+                offset: offset,
+                record: (dimensionsIds[0] === recordId)
+            };
+        }
+    }
+
+    return {
+        variables: variables,
+        recordStep: recordStep
+    };
+}
+
+/**
+ * Reads a NetCDF v3.x file
+ * https://www.unidata.ucar.edu/software/netcdf/docs/file_format_specifications.html
+ */
+export class NetcdfReader {
+    header: Partial<NetCDFHeader>;
+    buffer: IOBuffer;
+
+    constructor(data: ArrayBuffer) {
+        const buffer = new IOBuffer(data);
+        buffer.setBigEndian();
+
+        // Validate that it's a NetCDF file
+        notNetcdf((buffer.readChars(3) !== 'CDF'), 'should start with CDF');
+
+        // Check the NetCDF format
+        const version = buffer.readByte();
+        notNetcdf((version > 2), 'unknown version');
+
+        // Read the header
+        this.header = header(buffer, version);
+        this.buffer = buffer;
+    }
+
+    /**
+     * Version for the NetCDF format
+     */
+    get version() {
+        if (this.header.version === 1) {
+            return 'classic format';
+        } else {
+            return '64-bit offset format';
+        }
+    }
+
+    get recordDimension() {
+        return this.header.recordDimension;
+    }
+
+    get dimensions() {
+        return this.header.dimensions;
+    }
+
+    get globalAttributes() {
+        return this.header.globalAttributes;
+    }
+
+    get variables() {
+        return this.header.variables;
+    }
+
+    /**
+     * Checks if a variable is available
+     * @param {string|object} variableName - Name of the variable to check
+     * @return {Boolean} - Variable existence
+     */
+    hasDataVariable(variableName: string) {
+        return this.header.variables && this.header.variables.findIndex(val => val.name === variableName) !== -1;
+    }
+
+    /**
+     * Retrieves the data for a given variable
+     * @param {string|object} variableName - Name of the variable to search or variable object
+     * @return {Array} - List with the variable values
+     */
+    getDataVariable(variableName: string | NetCDFVariable) {
+        let variable: NetCDFVariable | undefined;
+        if (typeof variableName === 'string') {
+            // search the variable
+            variable = this.header.variables?.find((val) => val.name === variableName);
+        } else {
+            variable = variableName;
+        }
+
+        // throws if variable not found
+        if (variable === undefined) throw new Error('variable not found');
+
+        // go to the offset position
+        this.buffer.seek(variable.offset);
+
+        if (variable.record) {
+            // record variable case
+            return record(this.buffer, variable, this.header.recordDimension!);
+        } else {
+            // non-record variable case
+            return nonRecord(this.buffer, variable);
+        }
+    }
+}
--- 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/reader/nctraj/parser.ts
+++ b/src/mol-io/reader/nctraj/parser.ts
@@ -0,0 +1,89 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Task } from '../../../mol-task';
+import { Mutable } from '../../../mol-util/type-helpers';
+import { NetcdfReader } from '../../common/netcdf/reader';
+import { ReaderResult as Result } from '../result';
+
+export interface NctrajFile {
+    coordinates: number[][],
+    velocities?: number[][],
+    forces?: number[][],
+    cell_lengths?: number[][],
+    cell_angles?: number[][],
+    time?: number[],
+    timeOffset: number,
+    deltaTime: number
+}
+
+async function parseInternal(data: Uint8Array) {
+    // http://ambermd.org/netcdf/nctraj.xhtml
+
+    const nc = new NetcdfReader(data);
+
+    const f: Mutable<NctrajFile> = {
+        coordinates: [],
+        time: [],
+        timeOffset: 0,
+        deltaTime: 1
+    };
+
+    for (const c of nc.getDataVariable('coordinates')) f.coordinates.push(c);
+
+    if (nc.hasDataVariable('velocities')) {
+        const velocities: number[][] = [];
+        for (const v of nc.getDataVariable('velocities')) velocities.push(v);
+        f.velocities = velocities;
+    }
+
+    if (nc.hasDataVariable('forces')) {
+        const forces: number[][] = [];
+        for (const f of nc.getDataVariable('forces')) forces.push(f);
+        f.forces = forces;
+    }
+
+    if (nc.hasDataVariable('cell_lengths')) {
+        const cell_lengths: number[][] = [];
+        for (const l of nc.getDataVariable('cell_lengths')) cell_lengths.push(l);
+        f.cell_lengths = cell_lengths;
+    }
+
+    if (nc.hasDataVariable('cell_angles')) {
+        const cell_angles: number[][] = [];
+        for (const a of nc.getDataVariable('cell_angles')) cell_angles.push(a);
+        f.cell_angles = cell_angles;
+    }
+
+    if (nc.hasDataVariable('time')) {
+        const time: number[] = [];
+        for (const t of nc.getDataVariable('time')) time.push(t);
+        f.time = time;
+    }
+
+    if (f.time) {
+        if (f.time.length >= 1) {
+            f.timeOffset = f.time[0];
+        }
+        if (f.time.length >= 2) {
+            f.deltaTime = f.time[1] - f.time[0];
+        }
+    }
+
+    return f;
+}
+
+export function parseNctraj(data: Uint8Array) {
+    return Task.create<Result<NctrajFile>>('Parse NCTRAJ', async ctx => {
+        try {
+            ctx.update({ canAbort: true, message: 'Parsing trajectory...' });
+            const file = await parseInternal(data);
+            return Result.success(file);
+        } catch (e) {
+            return Result.error('' + e);
+        }
+    });
+}
--- a/src/mol-io/reader/prmtop/parser.ts
+++ b/src/mol-io/reader/prmtop/parser.ts
@@ -0,0 +1,176 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Task, RuntimeContext } from '../../../mol-task';
+import { Tokenizer, TokenBuilder, Tokens } from '../common/text/tokenizer';
+import { ReaderResult as Result } from '../result';
+import { TokenColumnProvider as TokenColumn } from '../common/text/column/token';
+import { Column } from '../../../mol-data/db';
+import { Mutable } from '../../../mol-util/type-helpers';
+
+// http://ambermd.org/prmtop.pdf
+// https://ambermd.org/FileFormats.php#topology
+
+const Pointers = {
+    'NATOM': '', 'NTYPES': '', 'NBONH': '', 'MBONA': '', 'NTHETH': '', 'MTHETA': '',
+    'NPHIH': '', 'MPHIA': '', 'NHPARM': '', 'NPARM': '', 'NNB': '', 'NRES': '',
+    'NBONA': '', 'NTHETA': '', 'NPHIA': '', 'NUMBND': '', 'NUMANG': '', 'NPTRA': '',
+    'NATYP': '', 'NPHB': '', 'IFPERT': '', 'NBPER': '', 'NGPER': '', 'NDPER': '',
+    'MBPER': '', 'MGPER': '', 'MDPER': '', 'IFBOX': '', 'NMXRS': '', 'IFCAP': '',
+    'NUMEXTRA': '', 'NCOPY': '',
+};
+type PointerName = keyof typeof Pointers;
+const PointersNames = Object.keys(Pointers) as PointerName[];
+
+export interface PrmtopFile {
+    readonly version: string
+    readonly title: ReadonlyArray<string>
+    readonly pointers: Readonly<Record<PointerName, number>>
+    readonly atomName: Column<string>
+    readonly charge: Column<number>
+    readonly mass: Column<number>
+    readonly residueLabel: Column<string>
+    readonly residuePointer: Column<number>
+    readonly bondsIncHydrogen: Column<number>
+    readonly bondsWithoutHydrogen: Column<number>
+    readonly radii: Column<number>
+}
+
+const { readLine, markLine, trim } = Tokenizer;
+
+function State(tokenizer: Tokenizer, runtimeCtx: RuntimeContext) {
+    return {
+        tokenizer,
+        runtimeCtx,
+    };
+}
+type State = ReturnType<typeof State>
+
+function handleTitle(state: State): string[] {
+    const { tokenizer } = state;
+    const title: string[] = [];
+
+    while (tokenizer.tokenEnd < tokenizer.length) {
+        if (tokenizer.data[tokenizer.position] === '%') break;
+        const line = readLine(tokenizer).trim();
+        if (line) title.push(line);
+    }
+
+    return title;
+}
+
+function handlePointers(state: State): Record<PointerName, number> {
+    const { tokenizer } = state;
+
+    const pointers: Record<PointerName, number> = Object.create(null);
+    PointersNames.forEach(name => { pointers[name] = 0; });
+
+    let curIdx = 0;
+    while (tokenizer.tokenEnd < tokenizer.length) {
+        if (tokenizer.data[tokenizer.position] === '%') break;
+        const line = readLine(tokenizer);
+
+        const n = Math.min(curIdx + 10, 32);
+        for (let i = 0; curIdx < n; ++i, ++curIdx) {
+            pointers[PointersNames[curIdx]] = parseInt(
+                line.substring(i * 8, i * 8 + 8).trim()
+            );
+        }
+    }
+
+    return pointers;
+}
+
+function handleTokens(state: State, count: number, countPerLine: number, itemSize: number): Tokens {
+    const { tokenizer } = state;
+
+    const tokens = TokenBuilder.create(tokenizer.data, count * 2);
+
+    let curIdx = 0;
+    while (tokenizer.tokenEnd < tokenizer.length) {
+        if (tokenizer.data[tokenizer.position] === '%') break;
+
+        tokenizer.tokenStart = tokenizer.position;
+        const n = Math.min(curIdx + countPerLine, count);
+        for (let i = 0; curIdx < n; ++i, ++curIdx) {
+            const p = tokenizer.position;
+            trim(tokenizer, tokenizer.position, tokenizer.position + itemSize);
+            TokenBuilder.addUnchecked(tokens, tokenizer.tokenStart, tokenizer.tokenEnd);
+            tokenizer.position = p + itemSize;
+        }
+
+        markLine(tokenizer);
+    }
+
+    return tokens;
+}
+
+async function parseInternal(data: string, ctx: RuntimeContext): Promise<Result<PrmtopFile>> {
+    const t = Tokenizer(data);
+    const state = State(t, ctx);
+
+    const result: Mutable<PrmtopFile> = Object.create(null);
+    let prevPosition = 0;
+
+    while (t.tokenEnd < t.length) {
+        if (t.position - prevPosition > 100000 && ctx.shouldUpdate) {
+            prevPosition = t.position;
+            await ctx.update({ current: t.position, max: t.length });
+        }
+
+        const line = readLine(state.tokenizer).trim();
+        if (line.startsWith('%VERSION')) {
+            result.version = line.substring(8).trim();
+        } else if (line.startsWith('%FLAG')) {
+            const flag = line.substring(5).trim();
+            const formatLine = readLine(state.tokenizer).trim();
+            if (!formatLine.startsWith('%FORMAT')) throw new Error('expected %FORMAT');
+
+            if (flag === 'TITLE') {
+                result.title = handleTitle(state);
+            } else if (flag === 'POINTERS') {
+                result.pointers = handlePointers(state);
+            } else if (flag === 'ATOM_NAME') {
+                const tokens = handleTokens(state, result.pointers['NATOM'], 20, 4);
+                result.atomName = TokenColumn(tokens)(Column.Schema.str);
+            } else if (flag === 'CHARGE') {
+                const tokens = handleTokens(state, result.pointers['NATOM'], 5, 16);
+                result.charge = TokenColumn(tokens)(Column.Schema.float);
+            } else if (flag === 'MASS') {
+                const tokens = handleTokens(state, result.pointers['NATOM'], 5, 16);
+                result.mass = TokenColumn(tokens)(Column.Schema.float);
+            } else if (flag === 'RESIDUE_LABEL') {
+                const tokens = handleTokens(state, result.pointers['NRES'], 20, 4);
+                result.residueLabel = TokenColumn(tokens)(Column.Schema.str);
+            } else if (flag === 'RESIDUE_POINTER') {
+                const tokens = handleTokens(state, result.pointers['NRES'], 10, 8);
+                result.residuePointer = TokenColumn(tokens)(Column.Schema.int);
+            } else if (flag === 'BONDS_INC_HYDROGEN') {
+                const tokens = handleTokens(state, result.pointers['NBONH'] * 3, 10, 8);
+                result.bondsIncHydrogen = TokenColumn(tokens)(Column.Schema.int);
+            } else if (flag === 'BONDS_WITHOUT_HYDROGEN') {
+                const tokens = handleTokens(state, result.pointers['NBONA'] * 3, 10, 8);
+                result.bondsWithoutHydrogen = TokenColumn(tokens)(Column.Schema.int);
+            } else if (flag === 'RADII') {
+                const tokens = handleTokens(state, result.pointers['NATOM'], 5, 16);
+                result.radii = TokenColumn(tokens)(Column.Schema.float);
+            } else {
+                while (t.tokenEnd < t.length) {
+                    if (t.data[t.position] === '%') break;
+                    markLine(t);
+                }
+            }
+        }
+    }
+
+    return Result.success(result);
+}
+
+export function parsePrmtop(data: string) {
+    return Task.create<Result<PrmtopFile>>('Parse PRMTOP', async ctx => {
+        return await parseInternal(data, ctx);
+    });
+}
--- a/src/mol-io/reader/top/parser.ts
+++ b/src/mol-io/reader/top/parser.ts
@@ -0,0 +1,303 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Task, RuntimeContext } from '../../../mol-task';
+import { Tokenizer, TokenBuilder } from '../common/text/tokenizer';
+import { ReaderResult as Result } from '../result';
+import { TokenColumnProvider as TokenColumn } from '../common/text/column/token';
+import { Column, Table } from '../../../mol-data/db';
+import { Mutable } from '../../../mol-util/type-helpers';
+
+// https://manual.gromacs.org/2021-current/reference-manual/file-formats.html#top
+
+const AtomsSchema = {
+    nr: Column.Schema.Int(),
+    type: Column.Schema.Str(),
+    resnr: Column.Schema.Int(),
+    residu: Column.Schema.Str(),
+    atom: Column.Schema.Str(),
+    cgnr: Column.Schema.Int(),
+    charge: Column.Schema.Float(),
+    mass: Column.Schema.Float(),
+};
+
+const BondsSchema = {
+    ai: Column.Schema.Int(),
+    aj: Column.Schema.Int(),
+};
+
+const MoleculesSchema = {
+    compound: Column.Schema.Str(),
+    molCount: Column.Schema.Int(),
+};
+
+type Compound = {
+    atoms: Table<typeof AtomsSchema>
+    bonds?: Table<typeof BondsSchema>
+}
+
+export interface TopFile {
+    readonly system: string
+    readonly molecules: Table<typeof MoleculesSchema>
+    readonly compounds: Record<string, Compound>
+}
+
+const { readLine, markLine, skipWhitespace, markStart, eatValue, eatLine } = Tokenizer;
+
+function State(tokenizer: Tokenizer, runtimeCtx: RuntimeContext) {
+    return {
+        tokenizer,
+        runtimeCtx,
+    };
+}
+type State = ReturnType<typeof State>
+
+const reField = /\[ (.+) \]/;
+const reWhitespace = /\s+/;
+
+function handleMoleculetype(state: State) {
+    const { tokenizer } = state;
+
+    let molName: string | undefined = undefined;
+
+    while (tokenizer.tokenEnd < tokenizer.length) {
+        skipWhitespace(tokenizer);
+        const c = tokenizer.data[tokenizer.position];
+        if (c === '[') break;
+        if (c === ';' || c === '*') {
+            markLine(tokenizer);
+            continue;
+        }
+
+        if (molName !== undefined) throw new Error('more than one molName');
+
+        const line = readLine(tokenizer);
+        molName = line.split(reWhitespace)[0];
+    }
+
+    if (molName === undefined) throw new Error('missing molName');
+
+    return molName;
+}
+
+function handleAtoms(state: State) {
+    const { tokenizer } = state;
+
+    const nr = TokenBuilder.create(tokenizer.data, 64);
+    const type = TokenBuilder.create(tokenizer.data, 64);
+    const resnr = TokenBuilder.create(tokenizer.data, 64);
+    const residu = TokenBuilder.create(tokenizer.data, 64);
+    const atom = TokenBuilder.create(tokenizer.data, 64);
+    const cgnr = TokenBuilder.create(tokenizer.data, 64);
+    const charge = TokenBuilder.create(tokenizer.data, 64);
+    const mass = TokenBuilder.create(tokenizer.data, 64);
+
+    while (tokenizer.tokenEnd < tokenizer.length) {
+        skipWhitespace(tokenizer);
+        const c = tokenizer.data[tokenizer.position];
+        if (c === '[') break;
+        if (c === ';' || c === '*') {
+            markLine(tokenizer);
+            continue;
+        }
+
+        for (let j = 0; j < 8; ++j) {
+            skipWhitespace(tokenizer);
+            markStart(tokenizer);
+            eatValue(tokenizer);
+
+            switch (j) {
+                case 0: TokenBuilder.add(nr, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+                case 1: TokenBuilder.add(type, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+                case 2: TokenBuilder.add(resnr, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+                case 3: TokenBuilder.add(residu, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+                case 4: TokenBuilder.add(atom, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+                case 5: TokenBuilder.add(cgnr, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+                case 6: TokenBuilder.add(charge, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+                case 7: TokenBuilder.add(mass, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+            }
+        }
+        // ignore any extra columns
+        markLine(tokenizer);
+    }
+
+    return Table.ofColumns(AtomsSchema, {
+        nr: TokenColumn(nr)(Column.Schema.int),
+        type: TokenColumn(type)(Column.Schema.str),
+        resnr: TokenColumn(resnr)(Column.Schema.int),
+        residu: TokenColumn(residu)(Column.Schema.str),
+        atom: TokenColumn(atom)(Column.Schema.str),
+        cgnr: TokenColumn(cgnr)(Column.Schema.int),
+        charge: TokenColumn(charge)(Column.Schema.float),
+        mass: TokenColumn(mass)(Column.Schema.float),
+    });
+}
+
+function handleBonds(state: State) {
+    const { tokenizer } = state;
+
+    const ai = TokenBuilder.create(tokenizer.data, 64);
+    const aj = TokenBuilder.create(tokenizer.data, 64);
+
+    while (tokenizer.tokenEnd < tokenizer.length) {
+        skipWhitespace(tokenizer);
+        const c = tokenizer.data[tokenizer.position];
+        if (c === '[') break;
+        if (c === ';' || c === '*') {
+            markLine(tokenizer);
+            continue;
+        }
+
+        for (let j = 0; j < 2; ++j) {
+            skipWhitespace(tokenizer);
+            markStart(tokenizer);
+            eatValue(tokenizer);
+
+            switch (j) {
+                case 0: TokenBuilder.add(ai, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+                case 1: TokenBuilder.add(aj, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+            }
+        }
+        // ignore any extra columns
+        markLine(tokenizer);
+    }
+
+    return Table.ofColumns(BondsSchema, {
+        ai: TokenColumn(ai)(Column.Schema.int),
+        aj: TokenColumn(aj)(Column.Schema.int),
+    });
+}
+
+function handleSystem(state: State) {
+    const { tokenizer } = state;
+
+    let system: string | undefined = undefined;
+
+    while (tokenizer.tokenEnd < tokenizer.length) {
+        skipWhitespace(tokenizer);
+        const c = tokenizer.data[tokenizer.position];
+        if (c === '[') break;
+        if (c === ';' || c === '*') {
+            markLine(tokenizer);
+            continue;
+        }
+
+        if (system !== undefined) throw new Error('more than one system');
+        system = readLine(tokenizer).trim();
+    }
+
+    if (system === undefined) throw new Error('missing system');
+
+    return system;
+}
+
+function handleMolecules(state: State) {
+    const { tokenizer } = state;
+
+    const compound = TokenBuilder.create(tokenizer.data, 64);
+    const molCount = TokenBuilder.create(tokenizer.data, 64);
+
+    while (tokenizer.tokenEnd < tokenizer.length) {
+        skipWhitespace(tokenizer);
+        if (tokenizer.position >= tokenizer.length) break;
+
+        const c = tokenizer.data[tokenizer.position];
+        if (c === '[') break;
+        if (c === ';' || c === '*') {
+            markLine(tokenizer);
+            continue;
+        }
+
+        for (let j = 0; j < 2; ++j) {
+            skipWhitespace(tokenizer);
+            markStart(tokenizer);
+            eatValue(tokenizer);
+
+            switch (j) {
+                case 0: TokenBuilder.add(compound, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+                case 1: TokenBuilder.add(molCount, tokenizer.tokenStart, tokenizer.tokenEnd); break;
+            }
+        }
+        // ignore any extra columns
+        eatLine(tokenizer);
+        markStart(tokenizer);
+    }
+
+    return Table.ofColumns(MoleculesSchema, {
+        compound: TokenColumn(compound)(Column.Schema.str),
+        molCount: TokenColumn(molCount)(Column.Schema.int),
+    });
+}
+
+async function parseInternal(data: string, ctx: RuntimeContext): Promise<Result<TopFile>> {
+    const t = Tokenizer(data);
+    const state = State(t, ctx);
+
+    const result: Mutable<TopFile> = Object.create(null);
+    let prevPosition = 0;
+
+    result.compounds = {};
+    let currentCompound: Partial<Compound> = {};
+    let currentMolName = '';
+
+    function addMol() {
+        if (currentMolName && currentCompound.atoms) {
+            result.compounds[currentMolName] = currentCompound as Compound;
+            currentCompound = {};
+            currentMolName = '';
+        }
+    }
+
+    while (t.tokenEnd < t.length) {
+        if (t.position - prevPosition > 100000 && ctx.shouldUpdate) {
+            prevPosition = t.position;
+            await ctx.update({ current: t.position, max: t.length });
+        }
+
+        const line = readLine(state.tokenizer).trim();
+
+        if (!line || line[0] === '*' || line[0] === ';') {
+            continue;
+        }
+
+        if (line.startsWith('#include')) {
+            throw new Error('#include statements not allowed');
+        }
+
+        if (line.startsWith('[')) {
+            const fieldMatch = line.match(reField);
+            if (fieldMatch === null) throw new Error('expected field name');
+
+            const fieldName = fieldMatch[1];
+            if (fieldName === 'moleculetype') {
+                addMol();
+                currentMolName = handleMoleculetype(state);
+            } else if (fieldName === 'atoms') {
+                currentCompound.atoms = handleAtoms(state);
+            } else if (fieldName === 'bonds') {
+                currentCompound.bonds = handleBonds(state);
+            } else if (fieldName === 'system') {
+                result.system = handleSystem(state);
+            } else if (fieldName === 'molecules') {
+                addMol(); // add the last compound
+                result.molecules = handleMolecules(state);
+            } else {
+                while (t.tokenEnd < t.length) {
+                    if (t.data[t.position] === '[') break;
+                    markLine(t);
+                }
+            }
+        }
+    }
+
+    return Result.success(result);
+}
+
+export function parseTop(data: string) {
+    return Task.create<Result<TopFile>>('Parse TOP', async ctx => {
+        return await parseInternal(data, ctx);
+    });
+}
--- a/src/mol-io/reader/trr/parser.ts
+++ b/src/mol-io/reader/trr/parser.ts
@@ -0,0 +1,157 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * Adapted from NGL.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Task } from '../../../mol-task';
+import { ReaderResult as Result } from '../result';
+
+export interface TrrFile {
+    frames: { count: number, x: Float32Array, y: Float32Array, z: Float32Array }[],
+    boxes: number[][],
+    times: number[],
+    timeOffset: number,
+    deltaTime: number
+}
+
+async function parseInternal(data: Uint8Array) {
+    // https://github.com/gromacs/gromacs/blob/master/src/gromacs/fileio/trrio.cpp
+
+    const dv = new DataView(data.buffer);
+
+    const f: TrrFile = {
+        frames: [],
+        boxes: [],
+        times: [],
+        timeOffset: 0,
+        deltaTime: 0
+    };
+    const coordinates = f.frames;
+    const boxes = f.boxes;
+    const times = f.times;
+
+    let offset = 0;
+
+    while (true) {
+        // const magicnum = dv.getInt32(offset)
+        // const i1 = dv.getFloat32(offset + 4)
+        offset += 8;
+
+        const versionSize = dv.getInt32(offset);
+        offset += 4;
+        offset += versionSize;
+
+        // const irSize = dv.getInt32(offset)
+        // const eSize = dv.getInt32(offset + 4)
+        const boxSize = dv.getInt32(offset + 8);
+        const virSize = dv.getInt32(offset + 12);
+        const presSize = dv.getInt32(offset + 16);
+        // const topSize = dv.getInt32(offset + 20)
+        // const symSize = dv.getInt32(offset + 24)
+        const coordSize = dv.getInt32(offset + 28);
+        const velocitySize = dv.getInt32(offset + 32);
+        const forceSize = dv.getInt32(offset + 36);
+        const natoms = dv.getInt32(offset + 40);
+        // const step = dv.getInt32(offset + 44)
+        // const nre = dv.getInt32(offset + 48)
+        offset += 52;
+
+        const floatSize = boxSize / 9;
+        const natoms3 = natoms * 3;
+
+        // let lambda
+        if (floatSize === 8) {
+            times.push(dv.getFloat64(offset));
+            // lambda = dv.getFloat64(offset + 8)
+        } else {
+            times.push(dv.getFloat32(offset));
+            // lambda = dv.getFloat32(offset + 4)
+        }
+        offset += 2 * floatSize;
+
+        if (boxSize) {
+            const box = new Float32Array(9);
+            if (floatSize === 8) {
+                for (let i = 0; i < 9; ++i) {
+                    box[i] = dv.getFloat64(offset) * 10;
+                    offset += 8;
+                }
+            } else {
+                for (let i = 0; i < 9; ++i) {
+                    box[i] = dv.getFloat32(offset) * 10;
+                    offset += 4;
+                }
+            }
+            boxes.push(box as unknown as number[]);
+        }
+
+        // ignore, unused
+        offset += virSize;
+
+        // ignore, unused
+        offset += presSize;
+
+        if (coordSize) {
+            const x = new Float32Array(natoms);
+            const y = new Float32Array(natoms);
+            const z = new Float32Array(natoms);
+            if (floatSize === 8) {
+                for (let i = 0; i < natoms; ++i) {
+                    x[i] = dv.getFloat64(offset) * 10;
+                    y[i] = dv.getFloat64(offset + 8) * 10;
+                    z[i] = dv.getFloat64(offset + 16) * 10;
+                    offset += 24;
+                }
+            } else {
+                const tmp = new Uint32Array(data.buffer, offset, natoms3);
+                for (let i = 0; i < natoms3; ++i) {
+                    const value = tmp[i];
+                    tmp[i] = (
+                        ((value & 0xFF) << 24) | ((value & 0xFF00) << 8) |
+                        ((value >> 8) & 0xFF00) | ((value >> 24) & 0xFF)
+                    );
+                }
+                const frameCoords = new Float32Array(data.buffer, offset, natoms3);
+                for (let i = 0; i < natoms; ++i) {
+                    x[i] = frameCoords[i * 3] * 10;
+                    y[i] = frameCoords[i * 3 + 1] * 10;
+                    z[i] = frameCoords[i * 3 + 2] * 10;
+                    offset += 12;
+                }
+            }
+            coordinates.push({ count: natoms, x, y, z });
+        }
+
+        // ignore, unused
+        offset += velocitySize;
+
+        // ignore, unused
+        offset += forceSize;
+
+        if (offset >= data.byteLength) break;
+    }
+
+    if (times.length >= 1) {
+        f.timeOffset = times[0];
+    }
+    if (times.length >= 2) {
+        f.deltaTime = times[1] - times[0];
+    }
+
+    return f;
+}
+
+export function parseTrr(data: Uint8Array) {
+    return Task.create<Result<TrrFile>>('Parse TRR', async ctx => {
+        try {
+            ctx.update({ canAbort: true, message: 'Parsing trajectory...' });
+            const file = await parseInternal(data);
+            return Result.success(file);
+        } catch (e) {
+            return Result.error('' + e);
+        }
+    });
+}
--- a/src/mol-io/writer/cif/encoder.ts
+++ b/src/mol-io/writer/cif/encoder.ts
@@ -11,6 +11,7 @@ import { Tensor } from '../../../mol-math/linear-algebra';
 import { Encoder as EncoderBase } from '../encoder';
 import { ArrayEncoder, ArrayEncoding } from '../../common/binary-cif';
 import { BinaryEncodingProvider } from './encoder/binary';
+import { assertUnreachable } from '../../../mol-util/type-helpers';

 // TODO: support for "coordinate fields", make "coordinate precision" a parameter of the encoder
 // TODO: automatically detect "precision" of floating point arrays.
@@ -324,7 +325,7 @@ function cifFieldsFromTableSchema(schema: Table.Schema) {
        } else if (t.valueType === 'tensor') {
            fields.push(...getTensorDefinitions(k, t.space));
        } else {
-            throw new Error(`Unknown valueType ${t.valueType}`);
+            assertUnreachable(t.valueType);
        }
    }
    return fields;
--- 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-model-formats/structure/basic/atomic.ts
+++ b/src/mol-model-formats/structure/basic/atomic.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>
@@ -45,15 +45,6 @@ function findHierarchyOffsets(atom_site: AtomSite) {
    return { residues, chains };
 }

-function substUndefinedColumn<T extends Table<any>>(table: T, a: keyof T, b: keyof T) {
-    if (!(table as any)[a].isDefined) {
-        (table as any)[a] = (table as any)[b];
-    }
-    if (!(table as any)[b].isDefined) {
-        (table as any)[b] = (table as any)[a];
-    }
-}
-
 function createHierarchyData(atom_site: AtomSite, sourceIndex: Column<number>, offsets: { residues: ArrayLike<number>, chains: ArrayLike<number> }): AtomicData {
    const atoms = Table.ofColumns(AtomsSchema, {
        type_symbol: Column.ofArray({ array: Column.mapToArray(atom_site.type_symbol, ElementSymbol), schema: Column.Schema.Aliased<ElementSymbol>(Column.Schema.str) }),
@@ -87,12 +78,6 @@ function createHierarchyData(atom_site: AtomSite, sourceIndex: Column<number>, o
    Table.columnToArray(residues, 'label_seq_id', Int32Array);
    Table.columnToArray(residues, 'auth_seq_id', Int32Array);

-    // Fix possibly missing auth_/label_ columns
-    substUndefinedColumn(atoms, 'label_atom_id', 'auth_atom_id');
-    substUndefinedColumn(atoms, 'label_comp_id', 'auth_comp_id');
-    substUndefinedColumn(residues, 'label_seq_id', 'auth_seq_id');
-    substUndefinedColumn(chains, 'label_asym_id', 'auth_asym_id');
-
    return { atoms, residues, chains, atomSourceIndex: sourceIndex };
 }

--- a/src/mol-model-formats/structure/basic/parser.ts
+++ b/src/mol-model-formats/structure/basic/parser.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>
@@ -186,8 +186,6 @@ function splitTable<T extends Table<any>>(table: T, col: Column<number>) {
    return ret;
 }

-
-
 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`
--- a/src/mol-model-formats/structure/basic/schema.ts
+++ b/src/mol-model-formats/structure/basic/schema.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>
 */
@@ -7,6 +7,7 @@
 import { mmCIF_Schema } from '../../../mol-io/reader/cif/schema/mmcif';
 import { Table } from '../../../mol-data/db';
 import { mmCIF_chemComp_schema } from '../../../mol-io/reader/cif/schema/mmcif-extras';
+import { getNormalizedAtomSite } from './util';

 // TODO split into conformation and hierarchy parts

@@ -68,7 +69,7 @@ export interface BasicData {
    pdbx_molecule: Molecule
 }

-export function createBasic(data: Partial<BasicData>): BasicData {
+export function createBasic(data: Partial<BasicData>, normalize = false): BasicData {
    const basic = Object.create(null);
    for (const name of Object.keys(BasicSchema)) {
        if (name in data) {
@@ -77,5 +78,8 @@ export function createBasic(data: Partial<BasicData>): BasicData {
            basic[name] = Table.ofUndefinedColumns(BasicSchema[name as keyof typeof BasicSchema], 0);
        }
    }
+    if (normalize) {
+        basic.atom_site = getNormalizedAtomSite(basic.atom_site);
+    }
    return basic;
 }
--- a/src/mol-model-formats/structure/basic/util.ts
+++ b/src/mol-model-formats/structure/basic/util.ts
@@ -1,12 +1,12 @@
 /**
- * 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>
 */

-import { BasicData } from './schema';
-import { Table } from '../../../mol-data/db';
+import { AtomSite, BasicData } from './schema';
+import { Column, Table } from '../../../mol-data/db';

 export function getModelGroupName(model_id: number, data: BasicData) {
    const { ihm_model_group, ihm_model_group_link } = data;
@@ -17,4 +17,28 @@ export function getModelGroupName(model_id: number, data: BasicData) {
        if (group) return group.name;
    }
    return '';
+}
+
+//
+
+function hasPresentValues(column: Column<any>) {
+    for (let i = 0, il = column.rowCount; i < il; i++) {
+        if (column.valueKind(i) === Column.ValueKind.Present) return true;
+    }
+    return false;
+}
+
+function substUndefinedColumn<T extends Table<any>>(table: T, a: keyof T, b: keyof T) {
+    if (!table[a].isDefined || !hasPresentValues(table[a])) table[a] = table[b];
+    if (!table[b].isDefined || !hasPresentValues(table[b])) table[b] = table[a];
+}
+
+/** Fix possibly missing auth_/label_ columns */
+export function getNormalizedAtomSite(atom_site: AtomSite) {
+    const normalized = Table.ofColumns(atom_site._schema, atom_site);
+    substUndefinedColumn(normalized, 'label_atom_id', 'auth_atom_id');
+    substUndefinedColumn(normalized, 'label_comp_id', 'auth_comp_id');
+    substUndefinedColumn(normalized, 'label_seq_id', 'auth_seq_id');
+    substUndefinedColumn(normalized, 'label_asym_id', 'auth_asym_id');
+    return normalized;
 }
--- a/src/mol-model-formats/structure/cif-core.ts
+++ b/src/mol-model-formats/structure/cif-core.ts
@@ -100,7 +100,7 @@ async function getModels(db: CifCore_Database, format: CifCoreFormat, ctx: Runti
        const element_symbol = new Array<string>(atomCount);
        for (let i = 0; i < atomCount; ++i) {
            // TODO can take as is if type_symbol not given?
-            element_symbol[i] = guessElementSymbolString(label.value(i));
+            element_symbol[i] = guessElementSymbolString(label.value(i), '');
        }
        typeSymbol = Column.ofStringArray(element_symbol);
        formalCharge = Column.Undefined(atomCount, Column.Schema.int);
@@ -146,13 +146,13 @@ async function getModels(db: CifCore_Database, format: CifCoreFormat, ctx: Runti
    componentBuilder.setNames([['MOL', name || 'Unknown Molecule']]);
    componentBuilder.add('MOL', 0);

-    const basics = createBasic({
+    const basic = createBasic({
        entity: entityBuilder.getEntityTable(),
        chem_comp: componentBuilder.getChemCompTable(),
        atom_site
    });

-    const models = await createModels(basics, format, ctx);
+    const models = await createModels(basic, format, ctx);

    if (models.frameCount > 0) {
        const first = models.representative;
--- 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>
 */
@@ -9,6 +9,7 @@ import { WaterNames, PolymerNames } from '../../../mol-model/structure/model/typ
 import { SetUtils } from '../../../mol-util/set';
 import { BasicSchema } from '../basic/schema';
 import { mmCIF_chemComp_schema } from '../../../mol-io/reader/cif/schema/mmcif-extras';
+import { SaccharideCompIdMap } from '../../../mol-model/structure/structure/carbohydrates/constants';

 type Component = Table.Row<Pick<mmCIF_chemComp_schema, 'id' | 'name' | 'type'>>

@@ -30,7 +31,7 @@ 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 () {
@@ -156,8 +157,10 @@ 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 if (SaccharideCompIdMap.has(compId.toUpperCase())) {
+                this.set({ id: compId, name: this.namesMap.get(compId) || compId, type: 'saccharide' });
            } else {
                const atomIds = this.getAtomIds(index);
                if (atomIds.size === 1 && CharmmIonComponents.has(compId)) {
--- 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/cube.ts
+++ b/src/mol-model-formats/structure/cube.ts
@@ -53,13 +53,13 @@ async function getModels(cube: CubeFile, ctx: RuntimeContext) {
    componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
    componentBuilder.add('MOL', 0);

-    const basics = createBasic({
+    const basic = createBasic({
        entity: entityBuilder.getEntityTable(),
        chem_comp: componentBuilder.getChemCompTable(),
        atom_site
    });

-    return await createModels(basics, MolFormat.create(cube), ctx);
+    return await createModels(basic, MolFormat.create(cube), ctx);
 }

 //
--- a/src/mol-model-formats/structure/gro.ts
+++ b/src/mol-model-formats/structure/gro.ts
@@ -27,6 +27,7 @@ function getBasic(atoms: GroAtoms, modelNum: number): BasicData {
    const asymIds = new Array<string>(atoms.count);
    const seqIds = new Uint32Array(atoms.count);
    const ids = new Uint32Array(atoms.count);
+    const typeSymbol = new Array<string>(atoms.count);

    const entityBuilder = new EntityBuilder();
    const componentBuilder = new ComponentBuilder(atoms.residueNumber, atoms.atomName);
@@ -66,6 +67,8 @@ function getBasic(atoms: GroAtoms, modelNum: number): BasicData {
        asymIds[i] = currentAsymId;
        seqIds[i] = currentSeqId;
        ids[i] = i;
+
+        typeSymbol[i] = guessElementSymbolString(atoms.atomName.value(i), atoms.residueName.value(i));
    }

    const auth_asym_id = Column.ofStringArray(asymIds);
@@ -87,7 +90,7 @@ function getBasic(atoms: GroAtoms, modelNum: number): BasicData {
        label_entity_id: Column.ofStringArray(entityIds),

        occupancy: Column.ofConst(1, atoms.count, Column.Schema.float),
-        type_symbol: Column.ofStringArray(Column.mapToArray(atoms.atomName, s => guessElementSymbolString(s))),
+        type_symbol: Column.ofStringArray(typeSymbol),

        pdbx_PDB_model_num: Column.ofConst(modelNum, atoms.count, Column.Schema.int),
    }, atoms.count);
--- a/src/mol-model-formats/structure/mmcif.ts
+++ b/src/mol-model-formats/structure/mmcif.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>
@@ -19,6 +19,7 @@ import { ComponentBond } from './property/bonds/chem_comp';
 import { StructConn } from './property/bonds/struct_conn';
 import { Trajectory } from '../../mol-model/structure';
 import { GlobalModelTransformInfo } from '../../mol-model/structure/model/properties/global-transform';
+import { createBasic } from './basic/schema';

 function modelSymmetryFromMmcif(model: Model) {
    if (!MmcifFormat.is(model.sourceData)) return;
@@ -100,5 +101,6 @@ namespace MmcifFormat {

 export function trajectoryFromMmCIF(frame: CifFrame): Task<Trajectory> {
    const format = MmcifFormat.fromFrame(frame);
-    return Task.create('Create mmCIF Model', ctx => createModels(format.data.db, format, ctx));
+    const basic = createBasic(format.data.db, true);
+    return Task.create('Create mmCIF Model', ctx => createModels(basic, format, ctx));
 }
--- a/src/mol-model-formats/structure/mol.ts
+++ b/src/mol-model-formats/structure/mol.ts
@@ -68,13 +68,13 @@ export async function getMolModels(mol: MolFile, format: ModelFormat<any> | unde
    componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
    componentBuilder.add('MOL', 0);

-    const basics = createBasic({
+    const basic = createBasic({
        entity: entityBuilder.getEntityTable(),
        chem_comp: componentBuilder.getChemCompTable(),
        atom_site
    });

-    const models = await createModels(basics, format ?? MolFormat.create(mol), ctx);
+    const models = await createModels(basic, format ?? MolFormat.create(mol), ctx);

    if (models.frameCount > 0) {
        const indexA = Column.ofIntArray(Column.mapToArray(bonds.atomIdxA, x => x - 1, Int32Array));
--- a/src/mol-model-formats/structure/mol2.ts
+++ b/src/mol-model-formats/structure/mol2.ts
@@ -41,7 +41,7 @@ async function getModels(mol2: Mol2File, ctx: RuntimeContext) {
        for (let i = 0; i < atoms.count; ++i) {
            type_symbol[i] = hasAtomType
                ? atoms.atom_type.value(i).split('.')[0].toUpperCase()
-                : guessElementSymbolString(atoms.atom_name.value(i));
+                : guessElementSymbolString(atoms.atom_name.value(i), atoms.subst_name.value(i));
        }

        const atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
@@ -75,13 +75,13 @@ async function getModels(mol2: Mol2File, ctx: RuntimeContext) {
            componentBuilder.add(atoms.subst_name.value(i), i);
        }

-        const basics = createBasic({
+        const basic = createBasic({
            entity: entityBuilder.getEntityTable(),
            chem_comp: componentBuilder.getChemCompTable(),
            atom_site
        });

-        const _models = await createModels(basics, Mol2Format.create(mol2), ctx);
+        const _models = await createModels(basic, Mol2Format.create(mol2), ctx);

        if (_models.frameCount > 0) {
            const indexA = Column.ofIntArray(Column.mapToArray(bonds.origin_atom_id, x => x - 1, Int32Array));
@@ -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/nctraj.ts
+++ b/src/mol-model-formats/structure/nctraj.ts
@@ -0,0 +1,52 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Task } from '../../mol-task';
+import { NctrajFile } from '../../mol-io/reader/nctraj/parser';
+import { Coordinates, Frame, Time } from '../../mol-model/structure/coordinates';
+import { Cell } from '../../mol-math/geometry/spacegroup/cell';
+import { Vec3 } from '../../mol-math/linear-algebra';
+import { Mutable } from '../../mol-util/type-helpers';
+
+export function coordinatesFromNctraj(file: NctrajFile): Task<Coordinates> {
+    return Task.create('Parse NCTRAJ', async ctx => {
+        await ctx.update('Converting to coordinates');
+
+        const deltaTime = Time(file.deltaTime, 'step');
+        const offsetTime = Time(file.timeOffset, deltaTime.unit);
+
+        const frames: Frame[] = [];
+        for (let i = 0, il = file.coordinates.length; i < il; ++i) {
+            const c = file.coordinates[i];
+            const elementCount = c.length / 3;
+            const x = new Float32Array(elementCount);
+            const y = new Float32Array(elementCount);
+            const z = new Float32Array(elementCount);
+            for (let j = 0, jl = c.length; j < jl; j += 3) {
+                x[j / 3] = c[j];
+                y[j / 3] = c[j + 1];
+                z[j / 3] = c[j + 2];
+            }
+            const frame: Mutable<Frame> = {
+                elementCount,
+                x, y, z,
+                xyzOrdering: { isIdentity: true },
+                time: Time(offsetTime.value + deltaTime.value * i, deltaTime.unit)
+            };
+            // TODO: handle case where cell_lengths and cell_angles are set, i.e., angles not 90deg
+            if (file.cell_lengths) {
+                const lengths = file.cell_lengths[i];
+                const x = Vec3.scale(Vec3(), Vec3.unitX, lengths[0]);
+                const y = Vec3.scale(Vec3(), Vec3.unitY, lengths[1]);
+                const z = Vec3.scale(Vec3(), Vec3.unitZ, lengths[2]);
+                frame.cell = Cell.fromBasis(x, y, z);
+            }
+            frames.push(frame);
+        }
+
+        return Coordinates.create(frames, deltaTime, offsetTime);
+    });
+}
--- a/src/mol-model-formats/structure/pdb.ts
+++ b/src/mol-model-formats/structure/pdb.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 David Sehnal <david.sehnal@gmail.com>
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -14,6 +14,7 @@ import { Column } from '../../mol-data/db';
 import { AtomPartialCharge } from './property/partial-charge';
 import { Trajectory } from '../../mol-model/structure';
 import { ModelFormat } from '../format';
+import { createBasic } from './basic/schema';

 export { PdbFormat };

@@ -34,7 +35,8 @@ export function trajectoryFromPDB(pdb: PdbFile): Task<Trajectory> {
        await ctx.update('Converting to mmCIF');
        const cif = await pdbToMmCif(pdb);
        const format = MmcifFormat.fromFrame(cif, undefined, PdbFormat.create(pdb));
-        const models = await createModels(format.data.db, format, ctx);
+        const basic = createBasic(format.data.db, true);
+        const models = await createModels(basic, format, ctx);
        const partial_charge = cif.categories['atom_site']?.getField('partial_charge');
        if (partial_charge) {
            // TODO works only for single, unsorted model, to work generally
--- a/src/mol-model-formats/structure/prmtop.ts
+++ b/src/mol-model-formats/structure/prmtop.ts
@@ -0,0 +1,174 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Column, Table } from '../../mol-data/db';
+import { PrmtopFile } from '../../mol-io/reader/prmtop/parser';
+import { getMoleculeType, MoleculeType } from '../../mol-model/structure/model/types';
+import { Topology } from '../../mol-model/structure/topology/topology';
+import { Task } from '../../mol-task';
+import { ModelFormat } from '../format';
+import { BasicSchema, createBasic } from './basic/schema';
+import { ComponentBuilder } from './common/component';
+import { EntityBuilder } from './common/entity';
+import { getChainId } from './common/util';
+import { guessElementSymbolString } from './util';
+
+function getBasic(prmtop: PrmtopFile) {
+    const { pointers, residuePointer, residueLabel, atomName } = prmtop;
+    const atomCount = pointers.NATOM;
+    const residueCount = pointers.NRES;
+
+    //
+
+    const residueIds = new Uint32Array(atomCount);
+    const residueNames: string[] = [];
+
+    const addResidue = (i: number, from: number, to: number) => {
+        const rn = residueLabel.value(i);
+        for (let j = from, jl = to; j < jl; ++j) {
+            residueIds[j] = i + 1;
+            residueNames[j] = rn;
+        }
+    };
+
+    for (let i = 0, il = residueCount - 1; i < il; ++i) {
+        addResidue(i, residuePointer.value(i) - 1, residuePointer.value(i + 1) - 1);
+
+    }
+    addResidue(residueCount - 1, residuePointer.value(residueCount - 1) - 1, atomCount);
+
+    const residueId = Column.ofIntArray(residueIds);
+    const residueName = Column.ofStringArray(residueNames);
+
+    //
+
+    const entityIds = new Array<string>(atomCount);
+    const asymIds = new Array<string>(atomCount);
+    const seqIds = new Uint32Array(atomCount);
+    const ids = new Uint32Array(atomCount);
+
+    const entityBuilder = new EntityBuilder();
+    const componentBuilder = new ComponentBuilder(residueId, atomName);
+
+    let currentEntityId = '';
+    let currentAsymIndex = 0;
+    let currentAsymId = '';
+    let currentSeqId = 0;
+    let prevMoleculeType = MoleculeType.Unknown;
+    let prevResidueNumber = -1;
+
+    for (let i = 0, il = atomCount; i < il; ++i) {
+        const residueNumber = residueId.value(i);
+        if (residueNumber !== prevResidueNumber) {
+            const compId = residueName.value(i);
+            const moleculeType = getMoleculeType(componentBuilder.add(compId, i).type, compId);
+
+            if (moleculeType !== prevMoleculeType) {
+                currentAsymId = getChainId(currentAsymIndex);
+                currentAsymIndex += 1;
+                currentSeqId = 0;
+            }
+
+            currentEntityId = entityBuilder.getEntityId(compId, moleculeType, currentAsymId);
+            currentSeqId += 1;
+
+            prevResidueNumber = residueNumber;
+            prevMoleculeType = moleculeType;
+        }
+
+        entityIds[i] = currentEntityId;
+        asymIds[i] = currentAsymId;
+        seqIds[i] = currentSeqId;
+        ids[i] = i;
+    }
+
+    const id = Column.ofIntArray(ids);
+    const asym_id = Column.ofStringArray(asymIds);
+
+    //
+
+    const type_symbol = new Array<string>(atomCount);
+    for (let i = 0; i < atomCount; ++i) {
+        type_symbol[i] = guessElementSymbolString(atomName.value(i), residueName.value(i));
+    }
+
+    const atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
+        auth_asym_id: asym_id,
+        auth_atom_id: Column.asArrayColumn(atomName),
+        auth_comp_id: residueName,
+        auth_seq_id: residueId,
+        id: Column.asArrayColumn(id),
+
+        label_asym_id: asym_id,
+        label_atom_id: Column.asArrayColumn(atomName),
+        label_comp_id: residueName,
+        label_seq_id: Column.ofIntArray(seqIds),
+        label_entity_id: Column.ofStringArray(entityIds),
+
+        occupancy: Column.ofConst(1, atomCount, Column.Schema.float),
+        type_symbol: Column.ofStringArray(type_symbol),
+
+        pdbx_PDB_model_num: Column.ofConst(1, atomCount, Column.Schema.int),
+    }, atomCount);
+
+    const basic = createBasic({
+        entity: entityBuilder.getEntityTable(),
+        chem_comp: componentBuilder.getChemCompTable(),
+        atom_site
+    });
+
+    return basic;
+}
+
+//
+
+export { PrmtopFormat };
+
+type PrmtopFormat = ModelFormat<PrmtopFile>
+
+namespace PrmtopFormat {
+    export function is(x?: ModelFormat): x is PrmtopFormat {
+        return x?.kind === 'prmtop';
+    }
+
+    export function fromPrmtop(prmtop: PrmtopFile): PrmtopFormat {
+        return { kind: 'prmtop', name: prmtop.title.join(' ') || 'PRMTOP', data: prmtop };
+    }
+}
+
+export function topologyFromPrmtop(prmtop: PrmtopFile): Task<Topology> {
+    return Task.create('Parse PRMTOP', async ctx => {
+        const format = PrmtopFormat.fromPrmtop(prmtop);
+        const basic = getBasic(prmtop);
+
+        const { pointers: { NBONH, NBONA }, bondsIncHydrogen, bondsWithoutHydrogen } = prmtop;
+        const bondCount = NBONH + NBONA;
+
+        const bonds = {
+            indexA: Column.ofLambda({
+                value: (row: number) => {
+                    return row < NBONH
+                        ? bondsIncHydrogen.value(row * 3) / 3
+                        : bondsWithoutHydrogen.value((row - NBONH) * 3) / 3;
+                },
+                rowCount: bondCount,
+                schema: Column.Schema.int,
+            }),
+            indexB: Column.ofLambda({
+                value: (row: number) => {
+                    return row < NBONH
+                        ? bondsIncHydrogen.value(row * 3 + 1) / 3
+                        : bondsWithoutHydrogen.value((row - NBONH) * 3 + 1) / 3;
+                },
+                rowCount: bondCount,
+                schema: Column.Schema.int,
+            }),
+            order: Column.ofConst(1, bondCount, Column.Schema.int)
+        };
+
+        return Topology.create(prmtop.title.join(' ') || 'PRMTOP', basic, bonds, format);
+    });
+}
--- 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-formats/structure/property/symmetry.ts
+++ b/src/mol-model-formats/structure/property/symmetry.ts
@@ -63,10 +63,21 @@ function getSpacegroupNameOrNumber(symmetry: Table<mmCIF_Schema['symmetry']>) {

 function getSpacegroup(symmetry: Table<mmCIF_Schema['symmetry']>, cell: Table<mmCIF_Schema['cell']>): Spacegroup {
    if (symmetry._rowCount === 0 || cell._rowCount === 0) return Spacegroup.ZeroP1;
+
+    const a = cell.length_a.value(0);
+    const b = cell.length_b.value(0);
+    const c = cell.length_c.value(0);
+    if (a === 0 || b === 0 || c === 0) return Spacegroup.ZeroP1;
+
+    const alpha = cell.angle_alpha.value(0);
+    const beta = cell.angle_beta.value(0);
+    const gamma = cell.angle_gamma.value(0);
+    if (alpha === 0 || beta === 0 || gamma === 0) return Spacegroup.ZeroP1;
+
    const nameOrNumber = getSpacegroupNameOrNumber(symmetry);
    const spaceCell = SpacegroupCell.create(nameOrNumber,
-        Vec3.create(cell.length_a.value(0), cell.length_b.value(0), cell.length_c.value(0)),
-        Vec3.scale(Vec3.zero(), Vec3.create(cell.angle_alpha.value(0), cell.angle_beta.value(0), cell.angle_gamma.value(0)), Math.PI / 180));
+        Vec3.create(a, b, c),
+        Vec3.scale(Vec3(), Vec3.create(alpha, beta, gamma), Math.PI / 180));

    return Spacegroup.create(spaceCell);
 }
--- a/src/mol-model-formats/structure/psf.ts
+++ b/src/mol-model-formats/structure/psf.ts
@@ -21,6 +21,7 @@ function getBasic(atoms: PsfFile['atoms']) {
    const asymIds = new Array<string>(atoms.count);
    const seqIds = new Uint32Array(atoms.count);
    const ids = new Uint32Array(atoms.count);
+    const typeSymbol = new Array<string>(atoms.count);

    const entityBuilder = new EntityBuilder();
    const componentBuilder = new ComponentBuilder(atoms.residueId, atoms.atomName);
@@ -68,6 +69,8 @@ function getBasic(atoms: PsfFile['atoms']) {
        asymIds[i] = currentAsymId;
        seqIds[i] = currentSeqId;
        ids[i] = i;
+
+        typeSymbol[i] = guessElementSymbolString(atoms.atomName.value(i), atoms.residueName.value(i));
    }

    const atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
@@ -84,7 +87,7 @@ function getBasic(atoms: PsfFile['atoms']) {
        label_entity_id: Column.ofStringArray(entityIds),

        occupancy: Column.ofConst(1, atoms.count, Column.Schema.float),
-        type_symbol: Column.ofStringArray(Column.mapToArray(atoms.atomName, s => guessElementSymbolString(s))),
+        type_symbol: Column.ofStringArray(typeSymbol),

        pdbx_PDB_model_num: Column.ofConst(1, atoms.count, Column.Schema.int),
    }, atoms.count);
--- a/src/mol-model-formats/structure/top.ts
+++ b/src/mol-model-formats/structure/top.ts
@@ -0,0 +1,226 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Column, Table } from '../../mol-data/db';
+import { TopFile } from '../../mol-io/reader/top/parser';
+import { getMoleculeType, MoleculeType } from '../../mol-model/structure/model/types';
+import { Topology } from '../../mol-model/structure/topology/topology';
+import { Task } from '../../mol-task';
+import { ModelFormat } from '../format';
+import { BasicSchema, createBasic } from './basic/schema';
+import { ComponentBuilder } from './common/component';
+import { EntityBuilder } from './common/entity';
+import { getChainId } from './common/util';
+import { guessElementSymbolString } from './util';
+
+function getBasic(top: TopFile) {
+    const { molecules, compounds } = top;
+
+    const singleResidue: Record<string, boolean> = {};
+    let atomCount = 0;
+
+    for (let i = 0, il = molecules._rowCount; i < il; ++i) {
+        const mol = molecules.compound.value(i);
+        const count = molecules.molCount.value(i);
+        const { atoms } = compounds[mol];
+
+        Column.asArrayColumn(atoms.atom);
+        Column.asArrayColumn(atoms.resnr);
+        Column.asArrayColumn(atoms.residu);
+
+        atomCount += count * atoms._rowCount;
+
+        let prevResnr = atoms.resnr.value(0);
+        singleResidue[mol] = true;
+        for (let j = 1, jl = atoms._rowCount; j < jl; ++j) {
+            const resnr = atoms.resnr.value(j);
+            if (resnr !== prevResnr) {
+                singleResidue[mol] = false;
+                break;
+            }
+            prevResnr = resnr;
+        }
+    }
+
+    //
+
+    const atomNames = new Array<string>(atomCount);
+    const residueIds = new Uint32Array(atomCount);
+    const residueNames = new Array<string>(atomCount);
+
+    let k = 0;
+    for (let i = 0, il = molecules._rowCount; i < il; ++i) {
+        const mol = molecules.compound.value(i);
+        const count = molecules.molCount.value(i);
+        const { atoms } = compounds[mol];
+        const isSingleResidue = singleResidue[mol];
+        for (let j = 0; j < count; ++j) {
+            for (let l = 0, ll = atoms._rowCount; l < ll; ++l) {
+                atomNames[k] = atoms.atom.value(l);
+                residueIds[k] = atoms.resnr.value(l);
+                residueNames[k] = atoms.residu.value(l);
+
+                if (isSingleResidue) residueIds[k] += j;
+
+                k += 1;
+            }
+        }
+    }
+
+    const atomName = Column.ofStringArray(atomNames);
+    const residueId = Column.ofIntArray(residueIds);
+    const residueName = Column.ofStringArray(residueNames);
+
+    //
+
+    const entityIds = new Array<string>(atomCount);
+    const asymIds = new Array<string>(atomCount);
+    const seqIds = new Uint32Array(atomCount);
+    const ids = new Uint32Array(atomCount);
+
+    const entityBuilder = new EntityBuilder();
+    const componentBuilder = new ComponentBuilder(residueId, atomName);
+
+    let currentEntityId = '';
+    let currentAsymIndex = 0;
+    let currentAsymId = '';
+    let currentSeqId = 0;
+    let prevMoleculeType = MoleculeType.Unknown;
+    let prevResidueNumber = -1;
+
+    for (let i = 0, il = atomCount; i < il; ++i) {
+        const residueNumber = residueId.value(i);
+        if (residueNumber !== prevResidueNumber) {
+            const compId = residueName.value(i);
+            const moleculeType = getMoleculeType(componentBuilder.add(compId, i).type, compId);
+
+            if (moleculeType !== prevMoleculeType) {
+                currentAsymId = getChainId(currentAsymIndex);
+                currentAsymIndex += 1;
+                currentSeqId = 0;
+            }
+
+            currentEntityId = entityBuilder.getEntityId(compId, moleculeType, currentAsymId);
+            currentSeqId += 1;
+
+            prevResidueNumber = residueNumber;
+            prevMoleculeType = moleculeType;
+        }
+
+        entityIds[i] = currentEntityId;
+        asymIds[i] = currentAsymId;
+        seqIds[i] = currentSeqId;
+        ids[i] = i;
+    }
+
+    const id = Column.ofIntArray(ids);
+    const asym_id = Column.ofStringArray(asymIds);
+
+    //
+
+    const type_symbol = new Array<string>(atomCount);
+    for (let i = 0; i < atomCount; ++i) {
+        type_symbol[i] = guessElementSymbolString(atomName.value(i), residueName.value(i));
+    }
+
+    const atom_site = Table.ofPartialColumns(BasicSchema.atom_site, {
+        auth_asym_id: asym_id,
+        auth_atom_id: Column.asArrayColumn(atomName),
+        auth_comp_id: residueName,
+        auth_seq_id: residueId,
+        id: Column.asArrayColumn(id),
+
+        label_asym_id: asym_id,
+        label_atom_id: Column.asArrayColumn(atomName),
+        label_comp_id: residueName,
+        label_seq_id: Column.ofIntArray(seqIds),
+        label_entity_id: Column.ofStringArray(entityIds),
+
+        occupancy: Column.ofConst(1, atomCount, Column.Schema.float),
+        type_symbol: Column.ofStringArray(type_symbol),
+
+        pdbx_PDB_model_num: Column.ofConst(1, atomCount, Column.Schema.int),
+    }, atomCount);
+
+    const basic = createBasic({
+        entity: entityBuilder.getEntityTable(),
+        chem_comp: componentBuilder.getChemCompTable(),
+        atom_site
+    });
+
+    return basic;
+}
+
+function getBonds(top: TopFile) {
+    const { molecules, compounds } = top;
+
+    const indexA: number[] = [];
+    const indexB: number[] = [];
+
+    let atomOffset = 0;
+
+    for (let i = 0, il = molecules._rowCount; i < il; ++i) {
+        const mol = molecules.compound.value(i);
+        const count = molecules.molCount.value(i);
+        const { atoms, bonds } = compounds[mol];
+
+
+
+        if (bonds) {
+            for (let j = 0; j < count; ++j) {
+
+                for (let l = 0, ll = bonds._rowCount; l < ll; ++l) {
+                    indexA.push(bonds.ai.value(l) - 1 + atomOffset);
+                    indexB.push(bonds.aj.value(l) - 1 + atomOffset);
+                }
+
+                atomOffset += atoms._rowCount;
+            }
+        } else if (mol === 'TIP3') {
+            for (let j = 0; j < count; ++j) {
+                indexA.push(0 + atomOffset);
+                indexB.push(1 + atomOffset);
+                indexA.push(0 + atomOffset);
+                indexB.push(2 + atomOffset);
+                atomOffset += atoms._rowCount;
+            }
+        } else {
+            atomOffset += count * atoms._rowCount;
+        }
+    }
+
+    return {
+        indexA: Column.ofIntArray(indexA),
+        indexB: Column.ofIntArray(indexB),
+        order: Column.ofConst(1, indexA.length, Column.Schema.int)
+    };
+}
+
+//
+
+export { TopFormat };
+
+type TopFormat = ModelFormat<TopFile>
+
+namespace TopFormat {
+    export function is(x?: ModelFormat): x is TopFormat {
+        return x?.kind === 'top';
+    }
+
+    export function fromTop(top: TopFile): TopFormat {
+        return { kind: 'top', name: top.system || 'TOP', data: top };
+    }
+}
+
+export function topologyFromTop(top: TopFile): Task<Topology> {
+    return Task.create('Parse TOP', async ctx => {
+        const format = TopFormat.fromTop(top);
+        const basic = getBasic(top);
+        const bonds = getBonds(top);
+
+        return Topology.create(top.system || 'TOP', basic, bonds, format);
+    });
+}
--- a/src/mol-model-formats/structure/trr.ts
+++ b/src/mol-model-formats/structure/trr.ts
@@ -0,0 +1,39 @@
+/**
+ * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { Task } from '../../mol-task';
+import { TrrFile } from '../../mol-io/reader/trr/parser';
+import { Coordinates, Frame, Time } from '../../mol-model/structure/coordinates';
+import { Cell } from '../../mol-math/geometry/spacegroup/cell';
+import { Vec3 } from '../../mol-math/linear-algebra';
+
+export function coordinatesFromTrr(file: TrrFile): Task<Coordinates> {
+    return Task.create('Parse TRR', async ctx => {
+        await ctx.update('Converting to coordinates');
+
+        const deltaTime = Time(file.deltaTime, 'step');
+        const offsetTime = Time(file.timeOffset, deltaTime.unit);
+
+        const frames: Frame[] = [];
+        for (let i = 0, il = file.frames.length; i < il; ++i) {
+            const box = file.boxes[i];
+            const x = Vec3.fromArray(Vec3(), box, 0);
+            const y = Vec3.fromArray(Vec3(), box, 3);
+            const z = Vec3.fromArray(Vec3(), box, 6);
+            frames.push({
+                elementCount: file.frames[i].count,
+                cell: Cell.fromBasis(x, y, z),
+                x: file.frames[i].x,
+                y: file.frames[i].y,
+                z: file.frames[i].z,
+                xyzOrdering: { isIdentity: true },
+                time: Time(offsetTime.value + deltaTime.value * i, deltaTime.unit)
+            });
+        }
+
+        return Coordinates.create(frames, deltaTime, offsetTime);
+    });
+}
--- a/src/mol-model-formats/structure/util.ts
+++ b/src/mol-model-formats/structure/util.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>
 */
@@ -46,31 +46,30 @@ export function guessElementSymbolTokens(tokens: Tokens, str: string, start: num
    TokenBuilder.add(tokens, s, s); // no reasonable guess, add empty token
 }

+const TwoCharElementNames = new Set(['NA', 'CL', 'FE', 'SI', 'BR', 'AS']);
+const OneCharElementNames = new Set(['C', 'H', 'N', 'O', 'P', 'S']);
+
 const reTrimSpacesAndNumbers = /^[\s\d]+|[\s\d]+$/g;
-export function guessElementSymbolString(str: string) {
+export function guessElementSymbolString(atomId: string, compId: string) {
    // trim spaces and numbers, convert to upper case
-    str = str.replace(reTrimSpacesAndNumbers, '').toUpperCase();
-    const l = str.length;
+    atomId = atomId.replace(reTrimSpacesAndNumbers, '').toUpperCase();
+    const l = atomId.length;

-    if (l === 0) return str; // empty
-    if (l === 1) return str; // one char
+    if (l === 0) return atomId; // empty
+    if (l === 1) return atomId; // one char
+    if (TwoCharElementNames.has(atomId)) return atomId; // two chars

-    if (l === 2) { // two chars
-        if (str === 'NA' || str === 'CL' || str === 'FE' || str === 'SI' ||
-            str === 'BR' || str === 'AS'
-        ) return str;
+    // check for Charmm ion names where component and atom id are the same
+    if (l === 3 && compId === atomId) {
+        if (atomId === 'SOD') return 'NA';
+        if (atomId === 'POT') return 'K';
+        if (atomId === 'CES') return 'CS';
+        if (atomId === 'CAL') return 'CA';
+        if (atomId === 'CLA') return 'CL';
    }

-    if (l === 3) { // three chars
-        if (str === 'SOD') return 'NA';
-        if (str === 'POT') return 'K';
-        if (str === 'CES') return 'CS';
-        if (str === 'CAL') return 'CA';
-        if (str === 'CLA') return 'CL';
-    }
-
-    const c = str[0];
-    if (c === 'C' || c === 'H' || c === 'N' || c === 'O' || c === 'P' || c === 'S') return c;
+    if (OneCharElementNames.has(atomId[0])) return atomId[0];

    return ''; // no reasonable guess, return empty string
-}
+}
+
--- a/src/mol-model-formats/structure/xyz.ts
+++ b/src/mol-model-formats/structure/xyz.ts
@@ -78,13 +78,13 @@ function getModels(mol: XyzFile, ctx: RuntimeContext) {
    componentBuilder.setNames([['MOL', 'Unknown Molecule']]);
    componentBuilder.add('MOL', 0);

-    const basics = createBasic({
+    const basic = createBasic({
        entity: entityBuilder.getEntityTable(),
        chem_comp: componentBuilder.getChemCompTable(),
        atom_site
    });

-    return createModels(basics, XyzFormat.create(mol), ctx);
+    return createModels(basic, XyzFormat.create(mol), ctx);
 }

 //
--- 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
@@ -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;
 }
@@ -164,7 +176,6 @@ function eachInteraction(loci: Loci, structureGroup: StructureGroup, apply: (int
            const unitIdx = group.unitIndexMap.get(e.unit.id);
            if (unitIdx === undefined) continue;

-            __contactIndicesSet.clear();
            OrderedSet.forEach(e.indices, v => {
                for (let i = fOffsets[v], il = fOffsets[v + 1]; i < il; ++i) {
                    const fI = fIndices[i];
@@ -188,6 +199,8 @@ function eachInteraction(loci: Loci, structureGroup: StructureGroup, apply: (int

                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
@@ -11,30 +11,43 @@ import { Model } from '../../mol-model/structure';
 import { StructureElement } from '../../mol-model/structure/structure';
 import { CustomModelProperty } from '../common/custom-model-property';

-export { BestDatabaseSequenceMapping };
+export { SIFTSMapping as SIFTSMapping };

-interface BestDatabaseSequenceMapping {
+interface SIFTSMappingMapping {
    readonly dbName: string[],
    readonly accession: string[],
-    readonly num: number[],
+    readonly num: string[],
    readonly residue: string[]
 }

-namespace BestDatabaseSequenceMapping {
-    export const Provider: CustomModelProperty.Provider<{}, BestDatabaseSequenceMapping> = CustomModelProperty.createProvider({
-        label: 'Best Database Sequence Mapping',
+namespace SIFTSMapping {
+    export const Provider: CustomModelProperty.Provider<{}, SIFTSMappingMapping> = CustomModelProperty.createProvider({
+        label: 'SIFTS Mapping',
        descriptor: CustomPropertyDescriptor({
-            name: 'molstar_best_database_sequence_mapping'
+            name: 'sifts_sequence_mapping'
        }),
        type: 'static',
        defaultParams: {},
        getParams: () => ({}),
-        isApplicable: (data: Model) => MmcifFormat.is(data.sourceData) && data.sourceData.data.frame.categories?.atom_site?.fieldNames.indexOf('pdbx_sifts_xref_db_name') >= 0,
+        isApplicable: (data: Model) => isAvailable(data),
        obtain: async (ctx, data) => {
            return { value: fromCif(data) };
        }
    });

+    export function isAvailable(model: Model) {
+        if (!MmcifFormat.is(model.sourceData)) return false;
+
+        const {
+            pdbx_sifts_xref_db_name: db_name,
+            pdbx_sifts_xref_db_acc: db_acc,
+            pdbx_sifts_xref_db_num: db_num,
+            pdbx_sifts_xref_db_res: db_res
+        } = model.sourceData.data.db.atom_site;
+
+        return db_name.isDefined && db_acc.isDefined && db_num.isDefined && db_res.isDefined;
+    }
+
    export function getKey(loc: StructureElement.Location) {
        const model = loc.unit.model;
        const data = Provider.get(model).value;
@@ -55,22 +68,23 @@ namespace BestDatabaseSequenceMapping {
        return `${dbName} ${data.accession[rI]} ${data.num[rI]} ${data.residue[rI]}`;
    }

-    function fromCif(model: Model): BestDatabaseSequenceMapping | undefined {
+    function fromCif(model: Model): SIFTSMappingMapping | undefined {
        if (!MmcifFormat.is(model.sourceData)) return;

-        const { atom_site } = model.sourceData.data.frame.categories;
-        const db_name = atom_site.getField('pdbx_sifts_xref_db_name');
-        const db_acc = atom_site.getField('pdbx_sifts_xref_db_acc');
-        const db_num = atom_site.getField('pdbx_sifts_xref_db_num');
-        const db_res = atom_site.getField('pdbx_sifts_xref_db_res');
+        const {
+            pdbx_sifts_xref_db_name: db_name,
+            pdbx_sifts_xref_db_acc: db_acc,
+            pdbx_sifts_xref_db_num: db_num,
+            pdbx_sifts_xref_db_res: db_res
+        } = model.sourceData.data.db.atom_site;

-        if (!db_name || !db_acc || !db_num || !db_res) return;
+        if (!db_name.isDefined || !db_acc.isDefined || !db_num.isDefined || !db_res.isDefined) return;

        const { atomSourceIndex } = model.atomicHierarchy;
        const { count, offsets: residueOffsets } = model.atomicHierarchy.residueAtomSegments;
        const dbName = new Array<string>(count);
        const accession = new Array<string>(count);
-        const num = new Array<number>(count);
+        const num = new Array<string>(count);
        const residue = new Array<string>(count);

        for (let i = 0; i < count; i++) {
@@ -79,15 +93,15 @@ namespace BestDatabaseSequenceMapping {
            if (db_name.valueKind(row) !== Column.ValueKind.Present) {
                dbName[i] = '';
                accession[i] = '';
-                num[i] = 0;
+                num[i] = '';
                residue[i] = '';
                continue;
            }

-            dbName[i] = db_name.str(row);
-            accession[i] = db_acc.str(row);
-            num[i] = db_num.int(row);
-            residue[i] = db_res.str(row);
+            dbName[i] = db_name.value(row);
+            accession[i] = db_acc.value(row);
+            num[i] = db_num.value(row);
+            residue[i] = db_res.value(row);
        }

        return { dbName, accession, num, residue };
--- 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/sequence/sequence.ts
+++ b/src/mol-model/sequence/sequence.ts
@@ -7,6 +7,7 @@

 import { AminoAlphabet, NuclecicAlphabet, getProteinOneLetterCode, getRnaOneLetterCode, getDnaOneLetterCode } from './constants';
 import { Column } from '../../mol-data/db';
+import { assertUnreachable } from '../../mol-util/type-helpers';

 // TODO add mapping support to other sequence spaces, e.g. uniprot

@@ -66,7 +67,7 @@ namespace Sequence {
            case Kind.DNA: code = getDnaOneLetterCode; break;
            case Kind.RNA: code = getRnaOneLetterCode; break;
            case Kind.Generic: code = () => 'X'; break;
-            default: throw new Error(`unknown kind '${kind}'`);
+            default: assertUnreachable(kind);
        }
        if (map && map.size > 0) {
            return (name: string) => {
--- 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/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/types/saccharides.ts
+++ b/src/mol-model/structure/model/types/saccharides.ts
--- a/src/mol-model/structure/structure/carbohydrates/constants.ts
+++ b/src/mol-model/structure/structure/carbohydrates/constants.ts
@@ -1,11 +1,12 @@
 /**
- * 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>
 */

 import { Color, ColorMap } from '../../../../mol-util/color';
+import { SaccharideNames } from '../../model/types/saccharides';

 // follows community standard from https://www.ncbi.nlm.nih.gov/glycans/snfg.html

@@ -302,13 +303,6 @@ const CommonSaccharideNames: { [k: string]: string[] } = {
    Psi: ['PSV', 'SF6', 'SF9', 'TTV'],
 };

-const UnknownSaccharideNames = [
-    'NGZ', // via CCD
-    'LAT', // BETA-LACTOSE, Gal-Glc di-saccharide via GlyFinder
-
-    'PUF', 'GDA', '9WJ', // via updated CCD
-];
-
 /**
 * From http://glycam.org/docs/othertoolsservice/2016/06/09/3d-snfg-list-of-residue-names/#CHARMM
 */
@@ -354,9 +348,9 @@ export const SaccharideCompIdMap = (function () {
            }
        }
    }
-    for (let i = 0, il = UnknownSaccharideNames.length; i < il; ++i) {
-        map.set(UnknownSaccharideNames[i], UnknownSaccharideComponent);
-    }
+    SaccharideNames.forEach(name => {
+        if (!map.has(name)) map.set(name, UnknownSaccharideComponent);
+    });
    return map;
 })();

--- 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/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
@@ -1,28 +1,34 @@
 /**
- * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
 */

 import { Segmentation } from '../../../../mol-data/int';
-import { Mat4 } from '../../../../mol-math/linear-algebra';
 import { MinimizeRmsd } from '../../../../mol-math/linear-algebra/3d/minimize-rmsd';
-import { BestDatabaseSequenceMapping } from '../../../../mol-model-props/sequence/best-database-mapping';
+import { SIFTSMapping } from '../../../../mol-model-props/sequence/sifts-mapping';
 import { ElementIndex } from '../../model/indexing';
 import { Structure } from '../structure';
 import { Unit } from '../unit';

-export interface AlignmentResult {
+export interface AlignmentResultEntry {
    transform: MinimizeRmsd.Result,
    pivot: number,
    other: number
 }

-export function alignAndSuperposeWithBestDatabaseMapping(structures: Structure[]): AlignmentResult[] {
+export interface AlignmentResult {
+    entries: AlignmentResultEntry[],
+    zeroOverlapPairs: [number, number][],
+    failedPairs: [number, number][]
+}
+
+export function alignAndSuperposeWithSIFTSMapping(structures: Structure[], options?: { traceOnly?: boolean }): AlignmentResult {
    const indexMap = new Map<string, IndexEntry>();

    for (let i = 0; i < structures.length; i++) {
-        buildIndex(structures[i], indexMap, i);
+        buildIndex(structures[i], indexMap, i, options?.traceOnly ?? true);
    }

    const index = Array.from(indexMap.values());
@@ -30,15 +36,26 @@ export function alignAndSuperposeWithBestDatabaseMapping(structures: Structure[]
    // TODO: support non-first structure pivots
    const pairs = findPairs(structures.length, index);

-    const ret: AlignmentResult[] = [];
+    const zeroOverlapPairs: AlignmentResult['zeroOverlapPairs'] = [];
+    const failedPairs: AlignmentResult['failedPairs'] = [];
+
+
+    const entries: AlignmentResultEntry[] = [];
    for (const p of pairs) {
-        const [a, b] = getPositionTables(index, p.i, p.j, p.count);
-        const transform = MinimizeRmsd.compute({ a, b });
-        console.log(Mat4.makeTable(transform.bTransform), transform.rmsd);
-        ret.push({ transform, pivot: p.i, other: p.j });
+        if (p.count === 0) {
+            zeroOverlapPairs.push([p.i, p.j]);
+        } else {
+            const [a, b] = getPositionTables(index, p.i, p.j, p.count);
+            const transform = MinimizeRmsd.compute({ a, b });
+            if (Number.isNaN(transform.rmsd)) {
+                failedPairs.push([p.i, p.j]);
+            } else {
+                entries.push({ transform, pivot: p.i, other: p.j });
+            }
+        }
    }

-    return ret;
+    return { entries, zeroOverlapPairs, failedPairs };
 }

 function getPositionTables(index: IndexEntry[], pivot: number, other: number, N: number) {
@@ -53,7 +70,6 @@ function getPositionTables(index: IndexEntry[], pivot: number, other: number, N:

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

-        // TODO: allow to use just backbone atoms?
        // TODO: check if residue types match?
        for (let i = 0; i < l; i++) {
            let eI = (a[1] + i) as ElementIndex;
@@ -121,19 +137,20 @@ interface IndexEntry {
    pivots: { [i: number]: [unit: Unit.Atomic, start: ElementIndex, end: ElementIndex] | undefined }
 }

-function buildIndex(structure: Structure, index: Map<string, IndexEntry>, sI: number) {
+function buildIndex(structure: Structure, index: Map<string, IndexEntry>, sI: number, traceOnly: boolean) {
    for (const unit of structure.units) {
        if (unit.kind !== Unit.Kind.Atomic) continue;

        const { elements, model } = unit;

-        const map = BestDatabaseSequenceMapping.Provider.get(model).value;
+        const map = SIFTSMapping.Provider.get(model).value;
        if (!map) return;

        const { dbName, accession, num } = map;

        const chainsIt = Segmentation.transientSegments(unit.model.atomicHierarchy.chainAtomSegments, elements);
        const residuesIt = Segmentation.transientSegments(unit.model.atomicHierarchy.residueAtomSegments, elements);
+        const traceElementIndex = unit.model.atomicHierarchy.derived.residue.traceElementIndex;

        while (chainsIt.hasNext) {
            const chainSegment = chainsIt.move();
@@ -144,8 +161,15 @@ function buildIndex(structure: Structure, index: Map<string, IndexEntry>, sI: nu

                if (!dbName[rI]) continue;

-                const start = elements[residueSegment.start];
-                const end = elements[residueSegment.end - 1] + 1 as ElementIndex;
+                let start, end;
+                if (traceOnly) {
+                    start = traceElementIndex[rI];
+                    if (start === -1) continue;
+                    end = start + 1 as ElementIndex;
+                } else {
+                    start = elements[residueSegment.start];
+                    end = elements[residueSegment.end - 1] + 1 as ElementIndex;
+                }

                const key = `${dbName[rI]}-${accession[rI]}-${num[rI]}`;

@@ -161,6 +185,4 @@ function buildIndex(structure: Structure, index: Map<string, IndexEntry>, sI: nu
            }
        }
    }
-
-    console.log(index);
 }
--- 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
@@ -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>
 */
@@ -13,6 +13,27 @@ import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { unzip } from '../../mol-util/zip/zip';
 import { PluginStateObject } from '../objects';

+async function processFile(file: Asset.File, plugin: PluginContext, format: string, visuals: boolean) {
+    const info = getFileInfo(file.file!);
+    const isBinary = plugin.dataFormats.binaryExtensions.has(info.ext);
+    const { data } = await plugin.builders.data.readFile({ file, isBinary });
+    const provider = format === 'auto'
+        ? plugin.dataFormats.auto(info, data.cell?.obj!)
+        : plugin.dataFormats.get(format);
+
+    if (!provider) {
+        plugin.log.warn(`OpenFiles: could not find data provider for '${info.ext}'`);
+        await plugin.state.data.build().delete(data).commit();
+        return;
+    }
+
+    // need to await so that the enclosing Task finishes after the update is done.
+    const parsed = await provider.parse(plugin, data);
+    if (visuals) {
+        await provider.visuals?.(plugin, parsed);
+    }
+};
+
 export const OpenFiles = StateAction.build({
    display: { name: 'Open Files', description: 'Load one or more files and optionally create default visuals' },
    from: PluginStateObject.Root,
@@ -36,36 +57,19 @@ export const OpenFiles = StateAction.build({
            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 {
                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);
+                        if (!(filedata instanceof Uint8Array) || filedata.length === 0) continue;
+
+                        const asset = Asset.File(new File([filedata], fn));
+                        await processFile(asset, plugin, 'auto', params.visuals);
                    }
                } else {
-                    await processFile(file);
+                    const format = params.format.name === 'auto' ? 'auto' : params.format.params;
+                    await processFile(file, plugin, format, params.visuals);
                }
            } catch (e) {
                console.error(e);
@@ -79,7 +83,7 @@ export const DownloadFile = StateAction.build({
    display: { name: 'Download File', description: 'Load one or more file from an URL' },
    from: PluginStateObject.Root,
    params: (a, ctx: PluginContext) => {
-        const { options } = ctx.dataFormats;
+        const options = [...ctx.dataFormats.options, ['zip', 'Zip'] as const];
        return {
            url: PD.Url(''),
            format: PD.Select(options[0][0], options),
@@ -92,16 +96,30 @@ export const DownloadFile = StateAction.build({

    await state.transaction(async () => {
        try {
-            const provider = plugin.dataFormats.get(params.format);
-            if (!provider) {
-                plugin.log.warn(`DownloadFile: could not find data provider for '${params.format}'`);
-                return;
-            }
+            if (params.format === 'zip') {
+                // TODO: add ReadZipFile transformer so this can be saved as a simple state snaphot,
+                //       would need support for extracting individual files from zip
+                const data = await plugin.builders.data.download({ url: params.url, isBinary: true });
+                const zippedFiles = await unzip(taskCtx, (data.obj?.data as Uint8Array).buffer);
+                for (const [fn, filedata] of Object.entries(zippedFiles)) {
+                    if (!(filedata instanceof Uint8Array) || filedata.length === 0) continue;

-            const data = await plugin.builders.data.download({ url: params.url, isBinary: params.isBinary });
-            const parsed = await provider.parse(plugin, data);
-            if (params.visuals) {
-                await provider.visuals?.(plugin, parsed);
+                    const asset = Asset.File(new File([filedata], fn));
+
+                    await processFile(asset, plugin, 'auto', params.visuals);
+                }
+            } else {
+                const provider = plugin.dataFormats.get(params.format);
+                if (!provider) {
+                    plugin.log.warn(`DownloadFile: could not find data provider for '${params.format}'`);
+                    return;
+                }
+
+                const data = await plugin.builders.data.download({ url: params.url, isBinary: params.isBinary });
+                const parsed = await provider.parse(plugin, data);
+                if (params.visuals) {
+                    await provider.visuals?.(plugin, parsed);
+                }
            }
        } catch (e) {
            console.error(e);
--- a/src/mol-plugin-state/actions/structure.ts
+++ b/src/mol-plugin-state/actions/structure.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>
@@ -10,16 +10,18 @@ import { StateAction, StateSelection, StateTransformer } from '../../mol-state';
 import { Task } from '../../mol-task';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { PresetStructureRepresentations, StructureRepresentationPresetProvider } from '../builder/structure/representation-preset';
-import { BuiltInTrajectoryFormat, BuiltInTrajectoryFormats } from '../formats/trajectory';
+import { BuiltInTrajectoryFormat, BuiltInTrajectoryFormats, TrajectoryFormatCategory } from '../formats/trajectory';
 import { RootStructureDefinition } from '../helpers/root-structure';
 import { PluginStateObject } from '../objects';
 import { StateTransforms } from '../transforms';
 import { Download } from '../transforms/data';
-import { CustomModelProperties, CustomStructureProperties, TrajectoryFromModelAndCoordinates } from '../transforms/model';
+import { CustomModelProperties, CustomStructureProperties, ModelFromTrajectory, TrajectoryFromModelAndCoordinates } from '../transforms/model';
 import { Asset } from '../../mol-util/assets';
 import { PluginConfig } from '../../mol-plugin/config';
 import { getFileInfo } from '../../mol-util/file-info';
 import { assertUnreachable } from '../../mol-util/type-helpers';
+import { TopologyFormatCategory } from '../formats/topology';
+import { CoordinatesFormatCategory } from '../formats/coordinates';

 const DownloadModelRepresentationOptions = (plugin: PluginContext) => {
    const representationDefault = plugin.config.get(PluginConfig.Structure.DefaultRepresentationPreset) || PresetStructureRepresentations.auto.id;
@@ -155,7 +157,7 @@ const DownloadStructure = StateAction.build({
            asTrajectory = !!src.params.options.asTrajectory;
            format = 'mol';
            break;
-        default: throw new Error(`${(src as any).name} not supported.`);
+        default: assertUnreachable(src);
    }

    const representationPreset: any = params.source.params.options.representation || plugin.config.get(PluginConfig.Structure.DefaultRepresentationPreset) || PresetStructureRepresentations.auto.id;
@@ -311,4 +313,127 @@ export const AddTrajectory = StateAction.build({
        const structure = await ctx.builders.structure.createStructure(model.selector);
        await ctx.builders.structure.representation.applyPreset(structure, 'auto');
    }).runInContext(taskCtx);
+}));
+
+export const LoadTrajectory = StateAction.build({
+    display: { name: 'Load Trajectory', description: 'Load trajectory of model/topology and coordinates from URL or file.' },
+    from: PluginStateObject.Root,
+    params(a, ctx: PluginContext) {
+        const { options } = ctx.dataFormats;
+        const modelOptions = options.filter(o => o[2] === TrajectoryFormatCategory || o[2] === TopologyFormatCategory);
+        const coordinatesOptions = options.filter(o => o[2] === CoordinatesFormatCategory);
+
+        const modelExts: string[] = [];
+        const coordinatesExts: string[] = [];
+        for (const { provider } of ctx.dataFormats.list) {
+            if (provider.category === TrajectoryFormatCategory || provider.category === TopologyFormatCategory) {
+                if (provider.binaryExtensions) modelExts.push(...provider.binaryExtensions);
+                if (provider.stringExtensions) modelExts.push(...provider.stringExtensions);
+            } else if (provider.category === CoordinatesFormatCategory) {
+                if (provider.binaryExtensions) coordinatesExts.push(...provider.binaryExtensions);
+                if (provider.stringExtensions) coordinatesExts.push(...provider.stringExtensions);
+            }
+        }
+
+        return {
+            source: PD.MappedStatic('file', {
+                url: PD.Group({
+                    model: PD.Group({
+                        url: PD.Url(''),
+                        format: PD.Select(modelOptions[0][0], modelOptions),
+                        isBinary: PD.Boolean(false),
+                    }, { isExpanded: true }),
+                    coordinates: PD.Group({
+                        url: PD.Url(''),
+                        format: PD.Select(coordinatesOptions[0][0], coordinatesOptions),
+                    }, { isExpanded: true })
+                }, { isFlat: true }),
+                file: PD.Group({
+                    model: PD.File({ accept: modelExts.map(e => `.${e}`).join(','), label: 'Model' }),
+                    coordinates: PD.File({ accept: coordinatesExts.map(e => `.${e}`).join(','), label: 'Coordinates' }),
+                }, { isFlat: true }),
+            }, { options: [['url', 'URL'], ['file', 'File']] })
+        };
+    }
+})(({ params, state }, ctx: PluginContext) => Task.create('Load Trajectory', taskCtx => {
+    return state.transaction(async () => {
+        const s = params.source;
+
+        if (s.name === 'file' && (s.params.model === null || s.params.coordinates === null)) {
+            ctx.log.error('No file(s) selected');
+            return;
+        }
+
+        if (s.name === 'url' && (!s.params.model || !s.params.coordinates)) {
+            ctx.log.error('No URL(s) given');
+            return;
+        }
+
+        const processUrl = async (url: string | Asset.Url, format: string, isBinary: boolean) => {
+            const data = await ctx.builders.data.download({ url, isBinary });
+            const provider = ctx.dataFormats.get(format);
+
+            if (!provider) {
+                ctx.log.warn(`LoadTrajectory: could not find data provider for '${format}'`);
+                return;
+            }
+
+            return provider.parse(ctx, data);
+        };
+
+        const processFile = async (file: Asset.File | null) => {
+            if (!file) throw new Error('No file selected');
+
+            const info = getFileInfo(file.file!);
+            const isBinary = ctx.dataFormats.binaryExtensions.has(info.ext);
+            const { data } = await ctx.builders.data.readFile({ file, isBinary });
+            const provider = ctx.dataFormats.auto(info, data.cell?.obj!);
+
+            if (!provider) {
+                ctx.log.warn(`LoadTrajectory: could not find data provider for '${info.ext}'`);
+                await ctx.state.data.build().delete(data).commit();
+                return;
+            }
+
+            return provider.parse(ctx, data);
+        };
+
+        try {
+            const modelParsed = s.name === 'url'
+                ? await processUrl(s.params.model.url, s.params.model.format, s.params.model.isBinary)
+                : await processFile(s.params.model);
+
+            let model;
+            if ('trajectory' in modelParsed) {
+                model = await state.build().to(modelParsed.trajectory)
+                    .apply(ModelFromTrajectory, { modelIndex: 0 })
+                    .commit();
+            } else {
+                model = modelParsed.topology;
+            }
+
+            //
+
+            const coordinates = s.name === 'url'
+                ? await processUrl(s.params.coordinates.url, s.params.coordinates.format, true)
+                : await processFile(s.params.coordinates);
+
+            //
+
+            const dependsOn = [model.ref, coordinates.ref];
+            const traj = state.build().toRoot()
+                .apply(TrajectoryFromModelAndCoordinates, {
+                    modelRef: model.ref,
+                    coordinatesRef: coordinates.ref
+                }, { dependsOn })
+                .apply(StateTransforms.Model.ModelFromTrajectory, { modelIndex: 0 });
+
+            await state.updateTree(traj).runInContext(taskCtx);
+            const structure = await ctx.builders.structure.createStructure(traj.selector);
+            await ctx.builders.structure.representation.applyPreset(structure, 'auto');
+        } catch (e) {
+            console.error(e);
+            ctx.log.error(`Error loading trajectory`);
+        }
+    }).runInContext(taskCtx);
 }));
--- 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>
@@ -15,6 +15,7 @@ import { Download } from '../transforms/data';
 import { DataFormatProvider } from '../formats/provider';
 import { Asset } from '../../mol-util/assets';
 import { StateTransforms } from '../transforms';
+import { assertUnreachable } from '../../mol-util/type-helpers';

 export type EmdbDownloadProvider = 'pdbe' | 'rcsb'

@@ -75,8 +76,8 @@ 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}`
            } : {
@@ -109,7 +110,7 @@ const DownloadDensity = StateAction.build({
                label: `RCSB PDB X-ray Density Server: ${src.params.provider.id}`
            };
            break;
-        default: throw new Error(`${(src as any).name} not supported.`);
+        default: assertUnreachable(src);
    }

    const data = await plugin.builders.data.download(downloadParams);
@@ -131,7 +132,7 @@ const DownloadDensity = StateAction.build({
            entryId = src.params.provider.id;
            provider = plugin.dataFormats.get('dscif');
            break;
-        default: throw new Error(`${(src as any).name} not supported.`);
+        default: assertUnreachable(src);
    }

    if (!provider) {
--- 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/Show More
+++ b/Show More
Author	SHA1	Message	Date
Alexander Rose	23ec35d1f9	3.4.0	2022-03-13 13:12:32 -07:00
Alexander Rose	ff089c2b9f	changelog	2022-03-13 12:50:44 -07:00
Alexander Rose	1ab088718a	package updates	2022-03-13 12:49:03 -07:00
Alexander Rose	0cb2e5857a	Merge pull request #393 from molstar/zenodo-import Zenodo import	2022-03-13 12:19:04 -07:00
Alexander Rose	7c5ae5d7ee	tweak guessElementSymbolString	2022-03-13 12:16:12 -07:00
Alexander Rose	6e2665d98d	Merge branch 'master' of https://github.com/molstar/molstar into zenodo-import	2022-03-12 18:03:45 -08:00
Alexander Rose	b3b4692237	add top format support	2022-03-12 17:46:29 -08:00
Alexander Rose	55ff1d4999	add nctraj format support	2022-03-12 14:17:58 -08:00
Alexander Rose	511c839237	add prmtop format support	2022-03-12 13:48:10 -08:00
Alexander Rose	384cd6e5d9	add trr format support	2022-03-12 13:02:50 -08:00
Alexander Rose	6fd9dcc72e	split structure formats into topology & coordinates	2022-03-12 11:51:03 -08:00
Alexander Rose	12ca06fe91	fix handling of empty symmetry cell data	2022-03-12 11:44:27 -08:00
Alexander Rose	652f6c651b	fix wrong element assignment	2022-03-12 10:58:33 -08:00
Alexander Rose	7dd808a772	add custom import controls	2022-03-12 10:52:43 -08:00
Alexander Rose	945e55f8a7	add formated file size	2022-03-07 22:06:22 -08:00
Alexander Rose	866a30abe5	cleanup getFileInfo	2022-03-07 22:05:11 -08:00
Alexander Rose	f0e33e1e4e	fix legend of hydrophobicity color theme	2022-03-07 21:44:57 -08:00
Alexander Rose	8723ca38b4	improve saccharide detection	2022-03-07 21:31:33 -08:00
Alexander Rose	efffca0026	zenode import fixes	2022-03-06 21:57:42 -08:00
Alexander Rose	6c5eb3035f	remove default record id	2022-03-06 17:55:52 -08:00
Alexander Rose	0bf385f2ca	add zip file support to zenodo extension	2022-03-06 17:37:39 -08:00
Alexander Rose	9d5f51f513	improve handling of compressed files - fix loading of some compressed files within sessions - ignore some hidden MACOSX files	2022-03-06 17:32:56 -08:00
Alexander Rose	a1448131d8	add Zenodo import extension	2022-03-06 11:12:21 -08:00
Alexander Rose	664cacc7ac	add LoadTrajectory action	2022-03-06 11:11:16 -08:00
Alexander Rose	1aec37dd05	fix	2022-03-06 11:09:51 -08:00
Alexander Rose	3ff2c0840e	Merge pull request #392 from molstar/assert-unreachable make use of assertUnreachable	2022-03-06 11:06:04 -08:00
Alexander Rose	5ca3c3ac52	Update src/mol-script/language/parser.ts	2022-03-06 11:04:58 -08:00
Alexander Rose	714ee50965	Update src/mol-script/language/parser.ts Co-authored-by: David Sehnal <dsehnal@users.noreply.github.com>	2022-03-06 11:03:33 -08:00
Alexander Rose	ae1df3c5aa	Update src/mol-script/language/parser.ts Co-authored-by: David Sehnal <dsehnal@users.noreply.github.com>	2022-03-06 11:03:28 -08:00
Alexander Rose	28afb39550	make use of assertUnreachable	2022-03-05 10:18:40 -08:00
Alexander Rose	3466a8a024	Merge pull request #389 from molstar/cif-check-present fix handling of mmcif with empty label_asym_id	2022-03-05 09:20:19 -08:00
Alexander Rose	90db3321f5	changelog Co-authored-by: David Sehnal <dsehnal@users.noreply.github.com>	2022-03-05 09:20:04 -08:00
Alexander Rose	bf4e5ed7c2	normalize mmcif data	2022-03-04 22:47:14 -08:00
Alexander Rose	d3b2c20c26	normalize atom_site early	2022-03-03 18:31:54 -08:00
Alexander Rose	c3afabb4b1	spelling	2022-03-02 19:50:30 -08:00
Alexander Rose	18cc9790d1	fix handling of mmcif with empty label_asym_id	2022-03-02 19:17:31 -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