2.3.6

changelog
prefer webgl1 in safari 15.1
2026-06-04 21:34:23 +08:00 · 2021-11-08 18:57:06 +01:00 · 2021-11-08 18:54:52 +01:00 · 2021-11-08 18:50:16 +01:00 · 2021-11-08 18:40:51 +01:00 · 2021-11-08 18:30:52 +01:00
478 changed files with 24169 additions and 21843 deletions
--- a/.eslintrc.json
+++ b/.eslintrc.json
@@ -38,7 +38,24 @@
                "selector": "ExportDefaultDeclaration",
                "message": "Default exports are not allowed"
            }
-        ]
+        ],
+        "no-throw-literal": "error",
+        "key-spacing": "error",
+        "object-curly-spacing": ["error", "always"],
+        "array-bracket-spacing": "error",
+        "space-in-parens": "error",
+        "computed-property-spacing": "error",
+        "prefer-const": ["error", {
+            "destructuring": "all",
+            "ignoreReadBeforeAssign": false
+        }],
+        "space-before-function-paren": "off",
+        "func-call-spacing": "off",
+        "no-multi-spaces": "error",
+        "block-spacing": "error",
+        "keyword-spacing": "off",
+        "space-before-blocks": "error",
+        "semi-spacing": "error"
    },
    "overrides": [
        {
@@ -89,7 +106,14 @@
                    "error",
                    "1tbs", { "allowSingleLine": true }
                ],
-                "@typescript-eslint/comma-spacing": "error"
+                "@typescript-eslint/comma-spacing": "error",
+                "@typescript-eslint/space-before-function-paren": ["error", {
+                    "anonymous": "always",
+                    "named": "never",
+                    "asyncArrow": "always"
+                }],
+                "@typescript-eslint/func-call-spacing": ["error"],
+                "@typescript-eslint/keyword-spacing": ["error"]
            }
        }
    ]
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -1,18 +0,0 @@
-on:
-  push:
-  pull_request:
-
-jobs:
-  eslint:
-    name: eslint
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v1
-    - name: install node v12
-      uses: actions/setup-node@v1
-      with:
-        node-version: 12
-    - name: yarn install
-      run: yarn install
-    - name: eslint
-      uses: icrawl/action-eslint@v1
--- a/.github/workflows/node.yml
+++ b/.github/workflows/node.yml
@@ -0,0 +1,20 @@
+on:
+  push:
+  pull_request:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-node@v2
+      with:
+        node-version: 14
+    - run: npm ci
+    - run: sudo apt-get install xvfb
+    - name: Lint
+      run: npm run lint
+    - name: Test
+      run: xvfb-run --auto-servernum npm run jest
+    - name: Build
+      run: npm run build
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,81 @@ Note that since we don't clearly distinguish between a public and private interf

 ## [Unreleased]

+## [v2.3.6] - 2021-11-8
+
+- Add additional measurement controls: orientation (box, axes, ellipsoid) & plane (best fit)
+- Improve aromatic bond visuals (add ``aromaticScale``, ``aromaticSpacing``, ``aromaticDashCount`` params)
+- [Breaking] Change ``adjustCylinderLength`` default to ``false`` (set to true for focus representation)
+- Fix marker highlight color overriding select color
+- CellPack extension update
+    - add binary model support
+    - add compartment (including membrane) geometry support
+    - add latest mycoplasma model example
+- Prefer WebGL1 in Safari 15.1.
+
+## [v2.3.5] - 2021-10-19
+
+- Fix sequence viewer for PDB files with COMPND record and multichain entities.
+- Fix index pair bonds order assignment
+
+## [v2.3.4] - 2021-10-12
+
+- Fix pickScale not taken into account in line/point shader
+- Add pixel-scale, pick-scale & pick-padding GET params to Viewer app
+- Fix selecting bonds not adding their atoms in selection manager
+- Add ``preferAtoms`` option to SelectLoci/HighlightLoci behaviors
+- Make the implicit atoms of bond visuals pickable
+    - Add ``preferAtomPixelPadding`` to Canvas3dInteractionHelper
+- Add points & crosses visuals to Line representation
+- Add ``pickPadding`` config option (look around in case target pixel is empty)
+- Add ``multipleBonds`` param to bond visuals with options: off, symmetric, offset
+- Fix ``argparse`` config in servers.
+
+## [v2.3.3] - 2021-10-01
+
+- Fix direct volume shader
+
+## [v2.3.2] - 2021-10-01
+
+- Prefer WebGL1 on iOS devices until WebGL2 support has stabilized.
+
+## [v2.3.1] - 2021-09-28
+
+- Add Charmm saccharide names
+- Treat missing occupancy column as occupancy of 1
+- Fix line shader not accounting for aspect ratio
+- [Breaking] Fix point repr & shader
+    - Was unusable with ``wboit``
+    - Replaced ``pointFilledCircle`` & ``pointEdgeBleach`` params by ``pointStyle`` (square, circle, fuzzy)
+    - Set ``pointSizeAttenuation`` to false by default
+    - Set ``sizeTheme`` to ``uniform`` by default
+- Add ``markerPriority`` option to Renderer (useful in combination with edges of marking pass)
+- Add support support for ``chem_comp_bond`` and ``struct_conn`` categories (fixes ModelServer behavior where these categories should have been present)
+- Model and VolumeServer: fix argparse config
+
+## [v2.3.0] - 2021-09-06
+
+- Take include/exclude flags into account when displaying aromatic bonds
+- Improve marking performance
+    - Avoid unnecessary draw calls/ui updates when marking
+    - Check if loci is superset of visual
+    - Check if loci overlaps with unit visual
+    - Ensure ``Interval`` is used for ranges instead of ``SortedArray``
+    - Add uniform marker type
+    - Special case for reversing previous mark
+- Add optional marking pass
+    - Outlines visible and hidden parts of highlighted/selected groups
+    - Add highlightStrength/selectStrength renderer params
+
+## [v2.2.3] - 2021-08-25
+
+- Add ``invertCantorPairing`` helper function
+- Add ``Mesh`` processing helper ``.smoothEdges``
+- Smooth border of molecular-surface with ``includeParent`` enabled
+- Hide ``includeParent`` option from gaussian-surface visuals (not particularly useful)
+- Improved ``StructureElement.Loci.size`` performance (for marking large cellpack models)
+- Fix new ``TransformData`` issues (camera/bounding helper not showing up)
+- Improve marking performance (avoid superfluous calls to ``StructureElement.Loci.isWholeStructure``)

 ## [v2.2.2] - 2021-08-11

@@ -90,29 +165,22 @@ Note that since we don't clearly distinguish between a public and private interf
 - Fixed Measurements UI labels (#166)

 ## [v2.0.3] - 2021-04-09
-### Added
- Support for ``ColorTheme.palette`` designed for providing gradient-like coloring.

-### Changed
+- Add support for ``ColorTheme.palette`` designed for providing gradient-like coloring.
 - [Breaking] The ``zip`` function is now asynchronous and expects a ``RuntimeContext``. Also added ``Zip()`` returning a ``Task``.
 - [Breaking] Add ``CubeGridFormat`` in ``alpha-orbitals`` extension.

 ## [v2.0.2] - 2021-03-29
-### Added
- ``Canvas3D.getRenderObjects``.
+
+- Add ``Canvas3D.getRenderObjects``.
 - [WIP] Animate state interpolating, including model trajectories
-
-### Changed
 - Recognise MSE, SEP, TPO, PTR and PCA as non-standard amino-acids.
-
-### Fixed
- VolumeFromDensityServerCif transform label
-
+- Fix VolumeFromDensityServerCif transform label

 ## [v2.0.1] - 2021-03-23
-### Fixed
+
 - Exclude tsconfig.commonjs.tsbuildinfo from npm bundle

-
 ## [v2.0.0] - 2021-03-23
+
 Too many changes to list as this is the start of the changelog... Notably, default exports are now forbidden.
--- a/README.md
+++ b/README.md
@@ -122,9 +122,9 @@ and navigate to `build/viewer`

 **Convert any CIF to BinaryCIF**

-    node lib/servers/model/preprocess -i file.cif -ob file.bcif
+    node lib/commonjs/servers/model/preprocess -i file.cif -ob file.bcif

-To see all available commands, use ``node lib/servers/model/preprocess -h``.
+To see all available commands, use ``node lib/commonjs/servers/model/preprocess -h``.

 Or

--- a/data/cif-field-names/cif-core-field-names.csv
+++ b/data/cif-field-names/cif-core-field-names.csv
@@ -2,11 +2,11 @@ audit.block_doi

 database_code.depnum_ccdc_archive
 database_code.depnum_ccdc_fiz
-database_code.ICSD
-database_code.MDF
-database_code.NBS
-database_code.CSD
-database_code.COD
+database_code.icsd
+database_code.mdf
+database_code.nbs
+database_code.csd
+database_code.cod

 chemical.name_systematic
 chemical.name_common
@@ -24,8 +24,8 @@ atom_type_scat.dispersion_imag
 atom_type_scat.source

 space_group.crystal_system
-space_group.name_H-M_full
-space_group.IT_number
+space_group.name_h-m_full
+space_group.it_number
 space_group_symop.operation_xyz

 cell.length_a
@@ -35,14 +35,14 @@ cell.angle_alpha
 cell.angle_beta
 cell.angle_gamma
 cell.volume
-cell.formula_units_Z
+cell.formula_units_z

 atom_site.label
 atom_site.type_symbol
 atom_site.fract_x
 atom_site.fract_y
 atom_site.fract_z
-atom_site.U_iso_or_equiv
+atom_site.u_iso_or_equiv
 atom_site.adp_type
 atom_site.occupancy
 atom_site.calc_flag
@@ -52,20 +52,13 @@ atom_site.disorder_group
 atom_site.site_symmetry_multiplicity

 atom_site_aniso.label
-atom_site_aniso.U
-atom_site_aniso.U_11
-atom_site_aniso.U_22
-atom_site_aniso.U_33
-atom_site_aniso.U_23
-atom_site_aniso.U_13
-atom_site_aniso.U_12
-atom_site_aniso.U_su
-atom_site_aniso.U_11_su
-atom_site_aniso.U_22_su
-atom_site_aniso.U_33_su
-atom_site_aniso.U_23_su
-atom_site_aniso.U_13_su
-atom_site_aniso.U_12_su
+atom_site_aniso.u
+atom_site_aniso.u_11
+atom_site_aniso.u_22
+atom_site_aniso.u_33
+atom_site_aniso.u_23
+atom_site_aniso.u_13
+atom_site_aniso.u_12

 geom_bond.atom_site_label_1
 geom_bond.atom_site_label_2
--- a/package-lock.json
+++ b/package-lock.json
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
  "name": "molstar",
-  "version": "2.2.2",
+  "version": "2.3.6",
  "description": "A comprehensive macromolecular library.",
  "homepage": "https://github.com/molstar/molstar#readme",
  "repository": {
@@ -88,68 +88,72 @@
  ],
  "license": "MIT",
  "devDependencies": {
-    "@graphql-codegen/add": "^2.0.2",
-    "@graphql-codegen/cli": "^1.19.4",
-    "@graphql-codegen/time": "^2.0.2",
-    "@graphql-codegen/typescript": "^1.19.0",
-    "@graphql-codegen/typescript-graphql-files-modules": "^1.18.1",
-    "@graphql-codegen/typescript-graphql-request": "^2.0.3",
-    "@graphql-codegen/typescript-operations": "^1.17.12",
-    "@types/cors": "^2.8.8",
-    "@typescript-eslint/eslint-plugin": "^4.9.1",
-    "@typescript-eslint/parser": "^4.9.1",
+    "@graphql-codegen/add": "^3.1.0",
+    "@graphql-codegen/cli": "^2.2.0",
+    "@graphql-codegen/time": "^3.1.0",
+    "@graphql-codegen/typescript": "^2.2.2",
+    "@graphql-codegen/typescript-graphql-files-modules": "^2.1.0",
+    "@graphql-codegen/typescript-graphql-request": "^4.1.4",
+    "@graphql-codegen/typescript-operations": "^2.1.6",
+    "@types/cors": "^2.8.12",
+    "@types/gl": "^4.1.0",
+    "@typescript-eslint/eslint-plugin": "^4.32.0",
+    "@typescript-eslint/parser": "^4.32.0",
    "benchmark": "^2.1.4",
-    "concurrently": "^5.3.0",
-    "cpx2": "^3.0.0",
+    "concurrently": "^6.3.0",
+    "cpx2": "^4.0.0",
    "crypto-browserify": "^3.12.0",
-    "css-loader": "^5.0.1",
-    "eslint": "^7.15.0",
+    "css-loader": "^6.3.0",
+    "eslint": "^7.32.0",
    "extra-watch-webpack-plugin": "^1.0.3",
    "file-loader": "^6.2.0",
-    "fs-extra": "^9.0.1",
-    "graphql": "^15.4.0",
-    "http-server": "^0.12.3",
-    "jest": "^26.6.3",
-    "mini-css-extract-plugin": "^1.3.2",
-    "node-sass": "^6.0.0",
+    "fs-extra": "^10.0.0",
+    "graphql": "^15.6.0",
+    "http-server": "^13.0.2",
+    "jest": "^27.2.4",
+    "mini-css-extract-plugin": "^2.3.0",
+    "node-sass": "^6.0.1",
    "path-browserify": "^1.0.1",
    "raw-loader": "^4.0.2",
-    "sass-loader": "^11.1.1",
-    "simple-git": "^2.25.0",
+    "sass-loader": "^12.1.0",
+    "simple-git": "^2.46.0",
    "stream-browserify": "^3.0.0",
-    "style-loader": "^2.0.0",
-    "ts-jest": "^26.4.4",
-    "typescript": "^4.2.4",
-    "webpack": "^5.37.1",
-    "webpack-cli": "^4.7.0",
+    "style-loader": "^3.3.0",
+    "ts-jest": "^27.0.5",
+    "typescript": "^4.4.3",
+    "webpack": "^5.56.0",
+    "webpack-cli": "^4.8.0",
    "webpack-version-file-plugin": "^0.4.0"
  },
  "dependencies": {
-    "@types/argparse": "^1.0.38",
-    "@types/benchmark": "^2.1.0",
-    "@types/compression": "1.7.0",
-    "@types/express": "^4.17.9",
-    "@types/jest": "^26.0.18",
-    "@types/node": "^14.14.11",
-    "@types/node-fetch": "^2.5.7",
-    "@types/react": "^17.0.0",
-    "@types/react-dom": "^17.0.0",
-    "@types/swagger-ui-dist": "3.30.0",
-    "argparse": "^1.0.10",
+    "@types/argparse": "^2.0.10",
+    "@types/benchmark": "^2.1.1",
+    "@types/compression": "1.7.2",
+    "@types/express": "^4.17.13",
+    "@types/jest": "^27.0.2",
+    "@types/node": "^16.10.2",
+    "@types/node-fetch": "^2.5.12",
+    "@types/react": "^17.0.27",
+    "@types/react-dom": "^17.0.9",
+    "@types/swagger-ui-dist": "3.30.1",
+    "argparse": "^2.0.1",
    "body-parser": "^1.19.0",
    "compression": "^1.7.4",
    "cors": "^2.8.5",
    "express": "^4.17.1",
    "h264-mp4-encoder": "^1.0.12",
-    "immer": "^8.0.1",
+    "immer": "^9.0.6",
    "immutable": "^3.8.2",
-    "node-fetch": "^2.6.1",
-    "react": "^17.0.1",
-    "react-dom": "^17.0.1",
-    "rxjs": "^6.6.6",
-    "swagger-ui-dist": "^3.37.2",
-    "tslib": "^2.1.0",
-    "util.promisify": "^1.0.1",
-    "xhr2": "^0.2.0"
+    "node-fetch": "^2.6.2",
+    "react": "^17.0.2",
+    "react-dom": "^17.0.2",
+    "rxjs": "^7.3.1",
+    "swagger-ui-dist": "^3.52.3",
+    "tslib": "^2.3.1",
+    "util.promisify": "^1.1.1",
+    "xhr2": "^0.2.1"
+  },
+  "optionalDependencies": {
+    "gl": "^4.9.2"
  }
 }
--- a/src/apps/docking-viewer/viewport.tsx
+++ b/src/apps/docking-viewer/viewport.tsx
@@ -238,7 +238,7 @@ export class ViewportComponent extends PluginUIComponent {
    pocketPreset = () => this.set(PocketPreset);
    interactionsPreset = () => this.set(InteractionsPreset);

-    get showButtons () {
+    get showButtons() {
        return this.plugin.config.get(ShowButtons);
    }

--- a/src/apps/viewer/index.html
+++ b/src/apps/viewer/index.html
@@ -52,12 +52,22 @@
            var collapseLeftPanel = getParam('collapse-left-panel', '[^&]+').trim() === '1';
            var pdbProvider = getParam('pdb-provider', '[^&]+').trim().toLowerCase();
            var emdbProvider = getParam('emdb-provider', '[^&]+').trim().toLowerCase();
+            var mapProvider = getParam('map-provider', '[^&]+').trim().toLowerCase();
+            var pixelScale = getParam('pixel-scale', '[^&]+').trim();
+            var pickScale = getParam('pick-scale', '[^&]+').trim();
+            var pickPadding = getParam('pick-padding', '[^&]+').trim();
            var viewer = new molstar.Viewer('app', {
                layoutShowControls: !hideControls,
                viewportShowExpand: false,
                collapseLeftPanel: collapseLeftPanel,
                pdbProvider: pdbProvider || 'pdbe',
                emdbProvider: emdbProvider || 'pdbe',
+                volumeStreamingServer: (mapProvider || 'pdbe') === 'rcsb'
+                    ? 'https://maps.rcsb.org'
+                    : 'https://www.ebi.ac.uk/pdbe/densities',
+                pixelScale: parseFloat(pixelScale) || 1,
+                pickScale: parseFloat(pickScale) || 0.25,
+                pickPadding: isNaN(parseFloat(pickPadding)) ? 1 : parseFloat(pickPadding),
            });

            var snapshotId = getParam('snapshot-id', '[^&]+').trim();
--- a/src/apps/viewer/index.ts
+++ b/src/apps/viewer/index.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -71,9 +71,11 @@ const DefaultViewerOptions = {
    layoutShowLog: true,
    layoutShowLeftPanel: true,
    collapseLeftPanel: false,
-    disableAntialiasing: false,
-    pixelScale: 1,
-    enableWboit: true,
+    disableAntialiasing: PluginConfig.General.DisableAntialiasing.defaultValue,
+    pixelScale: PluginConfig.General.PixelScale.defaultValue,
+    pickScale: PluginConfig.General.PickScale.defaultValue,
+    pickPadding: PluginConfig.General.PickPadding.defaultValue,
+    enableWboit: PluginConfig.General.EnableWboit.defaultValue,

    viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
    viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
@@ -130,6 +132,8 @@ export class Viewer {
            config: [
                [PluginConfig.General.DisableAntialiasing, o.disableAntialiasing],
                [PluginConfig.General.PixelScale, o.pixelScale],
+                [PluginConfig.General.PickScale, o.pickScale],
+                [PluginConfig.General.PickPadding, o.pickPadding],
                [PluginConfig.General.EnableWboit, o.enableWboit],
                [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
                [PluginConfig.Viewport.ShowControls, o.viewportShowControls],
@@ -325,7 +329,7 @@ export class Viewer {
    }

    handleResize() {
-        this.plugin.layout.events.updated.next();
+        this.plugin.layout.events.updated.next(void 0);
    }
 }

--- a/src/cli/chem-comp-dict/create-ions.ts
+++ b/src/cli/chem-comp-dict/create-ions.ts
@@ -19,7 +19,7 @@ import { ensureDataAvailable, readCCD } from './util';
 function extractIonNames(ccd: DatabaseCollection<CCD_Schema>) {
    const ionNames: string[] = [];
    for (const k in ccd) {
-        const {chem_comp} = ccd[k];
+        const { chem_comp } = ccd[k];
        if (chem_comp.name.value(0).toUpperCase().includes(' ION')) {
            ionNames.push(chem_comp.id.value(0));
        }
@@ -54,20 +54,20 @@ async function run(out: string, forceDownload = false) {
 }

 const parser = new argparse.ArgumentParser({
-    addHelp: true,
+    add_help: true,
    description: 'Extract and save IonNames from CCD.'
 });
-parser.addArgument('out', {
+parser.add_argument('out', {
    help: 'Generated file output path.'
 });
-parser.addArgument([ '--forceDownload', '-f' ], {
-    action: 'storeTrue',
+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.parseArgs();
+const args: Args = parser.parse_args();

 run(args.out, args.forceDownload);
--- a/src/cli/chem-comp-dict/create-table.ts
+++ b/src/cli/chem-comp-dict/create-table.ts
@@ -171,7 +171,7 @@ async function createBonds(
        pdbx_aromatic_flag, pdbx_stereo_config, molstar_protonation_variant
    });

-    const bondDatabase =  Database.ofTables(
+    const bondDatabase = Database.ofTables(
        CCB_TABLE_NAME,
        { chem_comp_bond: mmCIF_chemCompBond_schema },
        { chem_comp_bond: bondTable }
@@ -265,21 +265,21 @@ const CCB_TABLE_NAME = 'CHEM_COMP_BONDS';
 const CCA_TABLE_NAME = 'CHEM_COMP_ATOMS';

 const parser = new argparse.ArgumentParser({
-    addHelp: true,
+    add_help: true,
    description: 'Create a cif file with one big table of all chem_comp_bond entries from the CCD and PVCD.'
 });
-parser.addArgument('out', {
+parser.add_argument('out', {
    help: 'Generated file output path.'
 });
-parser.addArgument([ '--forceDownload', '-f' ], {
-    action: 'storeTrue',
+parser.add_argument('--forceDownload', '-f', {
+    action: 'store_true',
    help: 'Force download of CCD and PVCD.'
 });
-parser.addArgument([ '--binary', '-b' ], {
-    action: 'storeTrue',
+parser.add_argument('--binary', '-b', {
+    action: 'store_true',
    help: 'Output as BinaryCIF.'
 });
-parser.addArgument(['--ccaOut', '-a'], {
+parser.add_argument('--ccaOut', '-a', {
    help: 'Optional generated file output path for chem_comp_atom data.',
    required: false
 });
@@ -289,6 +289,6 @@ interface Args {
    binary?: boolean,
    ccaOut?: string
 }
-const args: Args = parser.parseArgs();
+const args: Args = parser.parse_args();

 run(args.out, args.binary, args.forceDownload, args.ccaOut);
--- a/src/cli/cif2bcif/index.ts
+++ b/src/cli/cif2bcif/index.ts
@@ -37,20 +37,20 @@ function run(args: Args) {
 }

 const parser = new argparse.ArgumentParser({
-    addHelp: true,
+    add_help: true,
    description: 'Convert any CIF file to a BCIF file'
 });
-parser.addArgument([ 'src' ], {
+parser.add_argument('src', {
    help: 'Source CIF path'
 });
-parser.addArgument([ 'out' ], {
+parser.add_argument('out', {
    help: 'Output BCIF path'
 });
-parser.addArgument([ '-c', '--config' ], {
+parser.add_argument('-c', '--config', {
    help: 'Optional encoding strategy/precision config path',
    required: false
 });
-parser.addArgument([ '-f', '--filter' ], {
+parser.add_argument('-f', '--filter', {
    help: 'Optional filter whitelist/blacklist path',
    required: false
 });
@@ -61,7 +61,7 @@ interface Args {
    config?: string
    filter?: string
 }
-const args: Args = parser.parseArgs();
+const args: Args = parser.parse_args();

 if (args) {
    run(args);
--- a/src/cli/cifschema/index.ts
+++ b/src/cli/cifschema/index.ts
@@ -124,15 +124,15 @@ async function getFieldNamesFilter(fieldNamesPath: string): Promise<Filter> {
    const csvFile = parsed.result;

    const fieldNamesCol = csvFile.table.getColumn('0');
-    if (!fieldNamesCol) throw 'error getting fields columns';
+    if (!fieldNamesCol) throw new Error('error getting fields columns');
    const fieldNames = fieldNamesCol.toStringArray();

    const filter: Filter = {};
    fieldNames.forEach((name, i) => {
-        const [ category, field ] = name.split('.');
+        const [category, field] = name.split('.');
        // console.log(category, field)
-        if (!filter[ category ]) filter[ category ] = {};
-        filter[ category ][ field ] = true;
+        if (!filter[category]) filter[category] = {};
+        filter[category][field] = true;
    });
    return filter;
 }
@@ -178,44 +178,44 @@ const CIF_CORE_ATTR_PATH = `${DIC_DIR}/templ_attr.cif`;
 const CIF_CORE_ATTR_URL = 'https://raw.githubusercontent.com/COMCIFS/cif_core/master/templ_attr.cif';

 const parser = new argparse.ArgumentParser({
-    addHelp: true,
+    add_help: true,
    description: 'Create schema from mmcif dictionary (v50 plus IHM and entity_branch extensions, downloaded from wwPDB)'
 });
-parser.addArgument([ '--preset', '-p' ], {
-    defaultValue: '',
+parser.add_argument('--preset', '-p', {
+    default: '',
    choices: ['', 'mmCIF', 'CCD', 'BIRD', 'CifCore'],
    help: 'Preset name'
 });
-parser.addArgument([ '--name', '-n' ], {
-    defaultValue: '',
+parser.add_argument('--name', '-n', {
+    default: '',
    help: 'Schema name'
 });
-parser.addArgument([ '--out', '-o' ], {
+parser.add_argument('--out', '-o', {
    help: 'Generated schema output path, if not given printed to stdout'
 });
-parser.addArgument([ '--targetFormat', '-tf' ], {
-    defaultValue: 'typescript-molstar',
+parser.add_argument('--targetFormat', '-tf', {
+    default: 'typescript-molstar',
    choices: ['typescript-molstar', 'json-internal'],
    help: 'Target format'
 });
-parser.addArgument([ '--dicPath', '-d' ], {
-    defaultValue: '',
+parser.add_argument('--dicPath', '-d', {
+    default: '',
    help: 'Path to dictionary'
 });
-parser.addArgument([ '--fieldNamesPath', '-fn' ], {
-    defaultValue: '',
+parser.add_argument('--fieldNamesPath', '-fn', {
+    default: '',
    help: 'Field names to include'
 });
-parser.addArgument([ '--forceDicDownload', '-f' ], {
-    action: 'storeTrue',
+parser.add_argument('--forceDicDownload', '-f', {
+    action: 'store_true',
    help: 'Force download of dictionaries'
 });
-parser.addArgument([ '--moldataImportPath', '-mip' ], {
-    defaultValue: 'molstar/lib/mol-data',
+parser.add_argument('--moldataImportPath', '-mip', {
+    default: 'molstar/lib/mol-data',
    help: 'mol-data import path (for typescript target only)'
 });
-parser.addArgument([ '--addAliases', '-aa' ], {
-    action: 'storeTrue',
+parser.add_argument('--addAliases', '-aa', {
+    action: 'store_true',
    help: 'Add field name/path aliases'
 });
 interface Args {
@@ -230,7 +230,7 @@ interface Args {
    moldataImportPath: string
    addAliases: boolean
 }
-const args: Args = parser.parseArgs();
+const args: Args = parser.parse_args();

 const FORCE_DIC_DOWNLOAD = args.forceDicDownload;

--- a/src/cli/cifschema/util/cif-dic.ts
+++ b/src/cli/cifschema/util/cif-dic.ts
@@ -34,6 +34,8 @@ export function getFieldType(type: string, description: string, values?: string[
        case 'seq-one-letter-code':
        case 'author':
        case 'orcid_id':
+        case 'pdbx_PDB_obsoleted_db_id':
+        case 'pdbx_related_db_id':
        case 'sequence_dep':
        case 'pdb_id':
        case 'emd_id':
@@ -79,7 +81,7 @@ export function getFieldType(type: string, description: string, values?: string[
        case 'List(Real,Real)':
        case 'List(Real,Real,Real,Real)':
        case 'Date':
-        case 'Datetime':
+        case 'DateTime':
        case 'Tag':
        case 'Implied':
            return wrapContainer('str', ',', description, container);
@@ -187,7 +189,7 @@ function getContainer(d: Data.CifFrame, imports: Imports, ctx: FrameData) {
 function getCode(d: Data.CifFrame, imports: Imports, ctx: FrameData): [string, string[] | undefined, string | undefined ] | undefined {
    const code = getField('item_type', 'code', d, imports, ctx) || getField('type', 'contents', d, imports, ctx);
    if (code) {
-        return [ code.str(0), getEnums(d, imports, ctx), getContainer(d, imports, ctx) ];
+        return [code.str(0), getEnums(d, imports, ctx), getContainer(d, imports, ctx)];
    } else {
        console.log(`item_type.code or type.contents not found for '${d.header}'`);
    }
@@ -232,29 +234,26 @@ const FORCE_INT_FIELDS = [
    '_struct_sheet_range.end_auth_seq_id',
 ];

+/**
+ * Note that name and mapped name must share a prefix. This is not always the case in
+ * the cifCore dictionary, but for downstream code to work a container field with the
+ * same prefix as the member fields must be given here and in the field names filter
+ * list.
+ */
 const FORCE_MATRIX_FIELDS_MAP: { [k: string]: string } = {
-    'atom_site_aniso.U_11': 'U',
-    'atom_site_aniso.U_22': 'U',
-    'atom_site_aniso.U_33': 'U',
-    'atom_site_aniso.U_23': 'U',
-    'atom_site_aniso.U_13': 'U',
-    'atom_site_aniso.U_12': 'U',
-    'atom_site_aniso.U_11_su': 'U_su',
-    'atom_site_aniso.U_22_su': 'U_su',
-    'atom_site_aniso.U_33_su': 'U_su',
-    'atom_site_aniso.U_23_su': 'U_su',
-    'atom_site_aniso.U_13_su': 'U_su',
-    'atom_site_aniso.U_12_su': 'U_su',
+    'atom_site_aniso.u_11': 'u', // is matrix_u in the the dic
+    'atom_site_aniso.u_22': 'u',
+    'atom_site_aniso.u_33': 'u',
+    'atom_site_aniso.u_23': 'u',
+    'atom_site_aniso.u_13': 'u',
+    'atom_site_aniso.u_12': 'u',
 };
 const FORCE_MATRIX_FIELDS = Object.keys(FORCE_MATRIX_FIELDS_MAP);

 const EXTRA_ALIASES: Database['aliases'] = {
-    'atom_site_aniso.U': [
-        'atom_site_anisotrop_U'
-    ],
-    'atom_site_aniso.U_su': [
-        'atom_site_aniso_U_esd',
-        'atom_site_anisotrop_U_esd',
+    'atom_site_aniso.matrix_u': [
+        'atom_site_anisotrop_U',
+        'atom_site_aniso.U'
    ],
 };

@@ -317,7 +316,7 @@ export function generateSchema(frames: CifFrame[], imports: Imports = new Map())
    frames.forEach(d => {
        // category definitions in mmCIF start with '_' and don't include a '.'
        // category definitions in cifCore don't include a '.'
-        if (d.header[0] === '_'  || d.header.includes('.')) return;
+        if (d.header[0] === '_' || d.header.includes('.')) return;
        const categoryName = d.header.toLowerCase();
        // console.log(d.header, d.categoryNames, d.categories)
        let descriptionField: Data.CifField | undefined;
@@ -372,7 +371,7 @@ export function generateSchema(frames: CifFrame[], imports: Imports = new Map())
            const parent_name = item_linked.getField('parent_name');
            if (child_name && parent_name) {
                for (let i = 0; i < item_linked.rowCount; ++i) {
-                    const childName = child_name.str(i);
+                    const childName: string = child_name.str(i);
                    const parentName = parent_name.str(i);
                    if (childName in links && links[childName] !== parentName) {
                        console.log(`${childName} linked to ${links[childName]}, ignoring link to ${parentName}`);
--- a/src/cli/cifschema/util/generate.ts
+++ b/src/cli/cifschema/util/generate.ts
@@ -8,7 +8,7 @@ import { Database, Filter, Column } from './schema';
 import { indentString } from '../../../mol-util/string';
 import { FieldPath } from '../../../mol-io/reader/cif/schema';

-function header (name: string, info: string, moldataImportPath: string) {
+function header(name: string, info: string, moldataImportPath: string) {
    return `/**
 * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
@@ -22,7 +22,7 @@ import { Database, Column } from '${moldataImportPath}/db';
 import Schema = Column.Schema;`;
 }

-function footer (name: string) {
+function footer(name: string) {
    return `
 export type ${name}_Schema = typeof ${name}_Schema;
 export interface ${name}_Database extends Database<${name}_Schema> {};`;
@@ -89,7 +89,7 @@ function doc(description: string, spacesCount: number) {
    ].join('\n');
 }

-export function generate (name: string, info: string, schema: Database, fields: Filter | undefined, moldataImportPath: string, addAliases: boolean) {
+export function generate(name: string, info: string, schema: Database, fields: Filter | undefined, moldataImportPath: string, addAliases: boolean) {
    const codeLines: string[] = [];

    if (fields) {
@@ -128,7 +128,7 @@ export function generate (name: string, info: string, schema: Database, fields:
        codeLines.push('');
        codeLines.push(`export const ${name}_Aliases = {`);
        Object.keys(schema.aliases).forEach(path => {
-            const [ table, columnName ] = path.split('.');
+            const [table, columnName] = path.split('.');
            if (fields && !fields[table]) return;
            if (fields && !fields[table][columnName]) return;

--- a/src/cli/cifschema/util/helper.ts
+++ b/src/cli/cifschema/util/helper.ts
@@ -10,8 +10,8 @@ export function parseImportGet(s: string): Import[] {
    // [{'save':hi_ang_Fox_coeffs  'file':templ_attr.cif}   {'save':hi_ang_Fox_c0  'file':templ_enum.cif}]
    // [{"file":'templ_enum.cif' "save":'H_M_ref'}]
    return s.trim().substring(2, s.length - 2).split(/}[ \n\t]*{/g).map(s => {
-        const save = s.match(/('save'|"save"):([^ \t\n]+)/);
-        const file = s.match(/('file'|"file"):([^ \t\n]+)/);
+        const save = s.match(/('save'|"save"):([^ \t\n{}]+)/);
+        const file = s.match(/('file'|"file"):([^ \t\n{}]+)/);
        return {
            save: save ? save[0].substr(7).replace(/['"]/g, '') : undefined,
            file: file ? file[0].substr(7).replace(/['"]/g, '') : undefined
--- a/src/cli/cifschema/util/schema.ts
+++ b/src/cli/cifschema/util/schema.ts
@@ -51,13 +51,13 @@ export function ListCol(subType: 'int' | 'str' | 'float' | 'coord', separator: s

 export type Filter = { [ table: string ]: { [ column: string ]: true } }

-export function mergeFilters (...filters: Filter[]) {
+export function mergeFilters(...filters: Filter[]) {
    const n = filters.length;
    const mergedFilter: Filter = {};
    const fields: Map<string, number> = new Map();
    filters.forEach(filter => {
        Object.keys(filter).forEach(category => {
-            Object.keys(filter[ category ]).forEach(field => {
+            Object.keys(filter[category]).forEach(field => {
                const key = `${category}.${field}`;
                const value = fields.get(key) || 0;
                fields.set(key, value + 1);
--- a/src/cli/lipid-params/index.ts
+++ b/src/cli/lipid-params/index.ts
@@ -70,21 +70,21 @@ export const LipidNames = new Set(${lipidNames.replace(/"/g, "'").replace(/,/g,
 }

 const parser = new argparse.ArgumentParser({
-    addHelp: true,
+    add_help: true,
    description: 'Create lipid params (from martini lipids itp)'
 });
-parser.addArgument([ '--out', '-o' ], {
+parser.add_argument('--out', '-o', {
    help: 'Generated lipid params output path, if not given printed to stdout'
 });
-parser.addArgument([ '--forceDownload', '-f' ], {
-    action: 'storeTrue',
+parser.add_argument('--forceDownload', '-f', {
+    action: 'store_true',
    help: 'Force download of martini lipids itp'
 });
 interface Args {
    out: string
    forceDownload: boolean
 }
-const args: Args = parser.parseArgs();
+const args: Args = parser.parse_args();

 const FORCE_DOWNLOAD = args.forceDownload;

--- a/src/cli/structure-info/model.ts
+++ b/src/cli/structure-info/model.ts
@@ -63,7 +63,7 @@ export function printSecStructure(model: Model) {
    const count = residues._rowCount;
    let rI = 0;
    while (rI < count) {
-        let start = rI;
+        const start = rI;
        while (rI < count && key[start] === key[rI]) rI++;
        rI--;

@@ -230,21 +230,21 @@ async function runFile(filename: string, args: Args) {
 }

 const parser = new argparse.ArgumentParser({
-    addHelp: true,
+    add_help: true,
    description: 'Print info about a structure, mainly to test and showcase the mol-model module'
 });
-parser.addArgument(['--download', '-d'], { help: 'Pdb entry id' });
-parser.addArgument(['--file', '-f'], { help: 'filename' });
+parser.add_argument('--download', '-d', { help: 'Pdb entry id' });
+parser.add_argument('--file', '-f', { help: 'filename' });

-parser.addArgument(['--models'], { help: 'print models info', action: 'storeTrue' });
-parser.addArgument(['--seq'], { help: 'print sequence', action: 'storeTrue' });
-parser.addArgument(['--units'], { help: 'print units', action: 'storeTrue' });
-parser.addArgument(['--sym'], { help: 'print symmetry', action: 'storeTrue' });
-parser.addArgument(['--rings'], { help: 'print rings', action: 'storeTrue' });
-parser.addArgument(['--intraBonds'], { help: 'print intra unit bonds', action: 'storeTrue' });
-parser.addArgument(['--interBonds'], { help: 'print inter unit bonds', action: 'storeTrue' });
-parser.addArgument(['--mod'], { help: 'print modified residues', action: 'storeTrue' });
-parser.addArgument(['--sec'], { help: 'print secoundary structure', action: 'storeTrue' });
+parser.add_argument('--models', { help: 'print models info', action: 'store_true' });
+parser.add_argument('--seq', { help: 'print sequence', action: 'store_true' });
+parser.add_argument('--units', { help: 'print units', action: 'store_true' });
+parser.add_argument('--sym', { help: 'print symmetry', action: 'store_true' });
+parser.add_argument('--rings', { help: 'print rings', action: 'store_true' });
+parser.add_argument('--intraBonds', { help: 'print intra unit bonds', action: 'store_true' });
+parser.add_argument('--interBonds', { help: 'print inter unit bonds', action: 'store_true' });
+parser.add_argument('--mod', { help: 'print modified residues', action: 'store_true' });
+parser.add_argument('--sec', { help: 'print secoundary structure', action: 'store_true' });
 interface Args {
    download?: string,
    file?: string,
@@ -260,7 +260,7 @@ interface Args {
    mod?: boolean,
    sec?: boolean,
 }
-const args: Args = parser.parseArgs();
+const args: Args = parser.parse_args();

 if (args.download) runDL(args.download, args);
 else if (args.file) runFile(args.file, args);
--- a/src/cli/structure-info/volume.ts
+++ b/src/cli/structure-info/volume.ts
@@ -38,7 +38,7 @@ function print(volume: Volume) {
 }

 async function doMesh(volume: Volume, filename: string) {
-    const mesh = await Task.create('', runtime => createVolumeIsosurfaceMesh({ runtime }, volume, Theme.createEmpty(), { isoValue: Volume.IsoValue.absolute(1.5) } )).run();
+    const mesh = await Task.create('', runtime => createVolumeIsosurfaceMesh({ runtime }, volume, Theme.createEmpty(), { isoValue: Volume.IsoValue.absolute(1.5) })).run();
    console.log({ vc: mesh.vertexCount, tc: mesh.triangleCount });

    // Export the mesh in OBJ format.
@@ -75,13 +75,13 @@ async function run(url: string, meshFilename: string) {
 }

 const parser = new argparse.ArgumentParser({
-    addHelp: true,
+    add_help: true,
    description: 'Info about VolumeData from mol-model module'
 });
-parser.addArgument([ '--emdb', '-e' ], {
+parser.add_argument('--emdb', '-e', {
    help: 'EMDB id, for example 8116',
 });
-parser.addArgument([ '--mesh' ], {
+parser.add_argument('--mesh', {
    help: 'Mesh filename',
    required: true
 });
@@ -89,6 +89,6 @@ interface Args {
    emdb?: string,
    mesh: string
 }
-const args: Args = parser.parseArgs();
+const args: Args = parser.parse_args();

 run(`https://ds.litemol.org/em/emd-${args.emdb}/cell?detail=4`, args.mesh);
--- a/src/examples/domain-annotation-server/mapping.ts
+++ b/src/examples/domain-annotation-server/mapping.ts
@@ -38,7 +38,7 @@ type MappingRow = Table.Row<S.mapping>;

 function writeDomain(enc: CifWriter.Encoder, domain: DomainAnnotation | undefined) {
    if (!domain) return;
-    enc.writeCategory({ name: `pdbx_${domain.name}_domain_annotation`, instance: () =>  CifWriter.Category.ofTable(domain.domains) });
+    enc.writeCategory({ name: `pdbx_${domain.name}_domain_annotation`, instance: () => CifWriter.Category.ofTable(domain.domains) });
    enc.writeCategory({ name: `pdbx_${domain.name}_domain_mapping`, instance: () => CifWriter.Category.ofTable(domain.mappings) });
 }

--- a/src/examples/domain-annotation-server/server.ts
+++ b/src/examples/domain-annotation-server/server.ts
@@ -15,7 +15,7 @@ async function getMappings(id: string) {
 };


-let PORT = process.env.port || 1338;
+const PORT = process.env.port || 1338;

 const app = express();

--- a/src/examples/lighting/index.ts
+++ b/src/examples/lighting/index.ts
@@ -105,7 +105,7 @@ class LightingDemo {
                ...this.plugin.canvas3d!.props.postprocessing,
                ...props.postprocessing
            },
-        }});
+        } });
    }

    async load({ url, format = 'mmcif', isBinary = true, assemblyId = '' }: LoadParams, radius: number, bias: number) {
--- a/src/examples/proteopedia-wrapper/index.ts
+++ b/src/examples/proteopedia-wrapper/index.ts
@@ -250,7 +250,7 @@ class MolStarProteopediaWrapper {
    setBackground(color: number) {
        if (!this.plugin.canvas3d) return;
        const renderer = this.plugin.canvas3d.props.renderer;
-        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { renderer: { ...renderer,  backgroundColor: Color(color) } } });
+        PluginCommands.Canvas3D.SetSettings(this.plugin, { settings: { renderer: { ...renderer, backgroundColor: Color(color) } } });
    }

    toggleSpin() {
--- a/src/extensions/anvil/algorithm.ts
+++ b/src/extensions/anvil/algorithm.ts
@@ -39,22 +39,34 @@ interface ANVILContext {
 };

 export const ANVILParams = {
-    numberOfSpherePoints: PD.Numeric(140, { min: 35, max: 700, step: 1 }, { description: 'Number of spheres/directions to test for membrane placement. Original value is 350.' }),
+    numberOfSpherePoints: PD.Numeric(175, { min: 35, max: 700, step: 1 }, { description: 'Number of spheres/directions to test for membrane placement. Original value is 350.' }),
    stepSize: PD.Numeric(1, { min: 0.25, max: 4, step: 0.25 }, { description: 'Thickness of membrane slices that will be tested' }),
-    minThickness: PD.Numeric(20, { min: 10, max: 30, step: 1}, { description: 'Minimum membrane thickness used during refinement' }),
-    maxThickness: PD.Numeric(40, { min: 30, max: 50, step: 1}, { description: 'Maximum membrane thickness used during refinement' }),
+    minThickness: PD.Numeric(20, { min: 10, max: 30, step: 1 }, { description: 'Minimum membrane thickness used during refinement' }),
+    maxThickness: PD.Numeric(40, { min: 30, max: 50, step: 1 }, { description: 'Maximum membrane thickness used during refinement' }),
    asaCutoff: PD.Numeric(40, { min: 10, max: 100, step: 1 }, { description: 'Relative ASA cutoff above which residues will be considered' }),
-    adjust: PD.Numeric(14, { min: 0, max: 30, step: 1 }, { description: 'Minimum length of membrane-spanning regions (original values: 14 for alpha-helices and 5 for beta sheets). Set to 0 to not optimize membrane thickness.' })
+    adjust: PD.Numeric(14, { min: 0, max: 30, step: 1 }, { description: 'Minimum length of membrane-spanning regions (original values: 14 for alpha-helices and 5 for beta sheets). Set to 0 to not optimize membrane thickness.' }),
+    tmdetDefinition: PD.Boolean(false, { description: `Use TMDET's classification of membrane-favoring amino acids. TMDET's classification shows better performance on porins and other beta-barrel structures.` })
 };
 export type ANVILParams = typeof ANVILParams
 export type ANVILProps = PD.Values<ANVILParams>

+/** ANVIL-specific (not general) definition of membrane-favoring amino acids */
+const ANVIL_DEFINITION = new Set(['ALA', 'CYS', 'GLY', 'HIS', 'ILE', 'LEU', 'MET', 'PHE', 'SER', 'TRP', 'VAL']);
+/** TMDET-specific (not general) definition of membrane-favoring amino acids */
+const TMDET_DEFINITION = new Set(['LEU', 'ILE', 'VAL', 'PHE', 'MET', 'GLY', 'TRP', 'TYR']);
+
 /**
 * Implements:
 * Membrane positioning for high- and low-resolution protein structures through a binary classification approach
 * Guillaume Postic, Yassine Ghouzam, Vincent Guiraud, and Jean-Christophe Gelly
 * Protein Engineering, Design & Selection, 2015, 1–5
 * doi: 10.1093/protein/gzv063
+ *
+ * ANVIL is derived from TMDET, the corresponding classification of hydrophobic amino acids is provided as optional parameter:
+ * Gabor E. Tusnady, Zsuzsanna Dosztanyi and Istvan Simon
+ * Transmembrane proteins in the Protein Data Bank: identification and classification
+ * Bioinformatics, 2004, 2964-2972
+ * doi: 10.1093/bioinformatics/bth340
 */
 export function computeANVIL(structure: Structure, props: ANVILProps) {
    return Task.create('Compute Membrane Orientation', async runtime => {
@@ -87,6 +99,11 @@ async function initialize(structure: Structure, props: ANVILProps, accessibleSur
    const offsets = new Array<number>();
    const exposed = new Array<number>();
    const hydrophobic = new Array<boolean>();
+    const definition = props.tmdetDefinition ? TMDET_DEFINITION : ANVIL_DEFINITION;
+
+    function isPartOfEntity(l: StructureElement.Location): boolean {
+        return !Unit.isAtomic(l.unit) ? notAtomic() : l.unit.model.atomicHierarchy.residues.label_seq_id.valueKind(l.unit.residueIndex[l.element]) === 0;
+    }

    const vec = v3zero();
    for (let i = 0, il = structure.units.length; i < il; ++i) {
@@ -98,8 +115,8 @@ async function initialize(structure: Structure, props: ANVILProps, accessibleSur
            const eI = elements[j];
            l.element = eI;

-            // consider only amino acids
-            if (getElementMoleculeType(unit, eI) !== MoleculeType.Protein) {
+            // consider only amino acids in chains
+            if (getElementMoleculeType(unit, eI) !== MoleculeType.Protein || !isPartOfEntity(l)) {
                continue;
            }

@@ -121,7 +138,7 @@ async function initialize(structure: Structure, props: ANVILProps, accessibleSur
            offsets.push(structure.serialMapping.getSerialIndex(l.unit, l.element));
            if (AccessibleSurfaceArea.getValue(l, accessibleSurfaceArea) / MaxAsa[label_comp_id(l)] > asaCutoff) {
                exposed.push(structure.serialMapping.getSerialIndex(l.unit, l.element));
-                hydrophobic.push(isHydrophobic(label_comp_id(l)));
+                hydrophobic.push(isHydrophobic(definition, label_comp_id(l)));
            }
        }
    }
@@ -166,7 +183,7 @@ export async function calculate(runtime: RuntimeContext, structure: Structure, p
    }

    const normalVector = v3zero();
-    const center =  v3zero();
+    const center = v3zero();
    v3sub(normalVector, membrane.planePoint1, membrane.planePoint2);
    v3normalize(normalVector, normalVector);

@@ -344,7 +361,7 @@ function membraneSegments(ctx: ANVILContext, membrane: MembraneCandidate): Array
    // collect all residues in membrane layer
    for (let k = 0, kl = offsets.length; k < kl; k++) {
        const unit = units[unitIndices[offsets[k]]];
-        if (!Unit.isAtomic(unit)) throw 'Property only available for atomic models.';
+        if (!Unit.isAtomic(unit)) notAtomic();
        const elementIndex = elementIndices[offsets[k]];

        authAsymId = unit.model.atomicHierarchy.chains.auth_asym_id.value(unit.chainIndex[elementIndex]);
@@ -365,7 +382,7 @@ function membraneSegments(ctx: ANVILContext, membrane: MembraneCandidate): Array

    for (let k = 0, kl = offsets.length; k < kl; k++) {
        const unit = units[unitIndices[offsets[k]]];
-        if (!Unit.isAtomic(unit)) throw 'Property only available for atomic models.';
+        if (!Unit.isAtomic(unit)) notAtomic();
        const elementIndex = elementIndices[offsets[k]];

        authAsymId = unit.model.atomicHierarchy.chains.auth_asym_id.value(unit.chainIndex[elementIndex]);
@@ -387,7 +404,7 @@ function membraneSegments(ctx: ANVILContext, membrane: MembraneCandidate): Array
                }
                lastAuthSeqId = authSeqId;
                endOffset = k;
-            } else  {
+            } else {
                lastAuthSeqId++;
                endOffset++;
            }
@@ -428,6 +445,10 @@ function membraneSegments(ctx: ANVILContext, membrane: MembraneCandidate): Array
    return refinedSegments;
 }

+function notAtomic(): never {
+    throw new Error('Property only available for atomic models.');
+}
+
 /** Filter for membrane residues and calculate the final extent of the membrane layer */
 function adjustExtent(ctx: ANVILContext, membrane: MembraneCandidate, centroid: Vec3): number {
    const { offsets, structure } = ctx;
@@ -455,11 +476,11 @@ function adjustExtent(ctx: ANVILContext, membrane: MembraneCandidate, centroid:
 }

 function qValue(currentStats: HphobHphil, initialStats: HphobHphil): number {
-    if(initialStats.hphob < 1) {
+    if (initialStats.hphob < 1) {
        initialStats.hphob = 0.1;
    }

-    if(initialStats.hphil < 1) {
+    if (initialStats.hphil < 1) {
        initialStats.hphil += 1;
    }

@@ -484,7 +505,7 @@ function generateSpherePoints(ctx: ANVILContext, numberOfSpherePoints: number):
    const { centroid, extent } = ctx;
    const points = [];
    let oldPhi = 0, h, theta, phi;
-    for(let k = 1, kl = numberOfSpherePoints + 1; k < kl; k++) {
+    for (let k = 1, kl = numberOfSpherePoints + 1; k < kl; k++) {
        h = -1 + 2 * (k - 1) / (2 * numberOfSpherePoints - 1);
        theta = Math.acos(h);
        phi = (k === 1 || k === numberOfSpherePoints) ? 0 : (oldPhi + 3.6 / Math.sqrt(2 * numberOfSpherePoints * (1 - h * h))) % (2 * Math.PI);
@@ -566,11 +587,9 @@ namespace HphobHphil {
    }
 }

-/** ANVIL-specific (not general) definition of membrane-favoring amino acids */
-const HYDROPHOBIC_AMINO_ACIDS = new Set(['ALA', 'CYS', 'GLY', 'HIS', 'ILE', 'LEU', 'MET', 'PHE', 'SER', 'TRP', 'VAL']);
-/** Returns true if ANVIL considers this as amino acid that favors being embedded in a membrane */
-export function isHydrophobic(label_comp_id: string): boolean {
-    return HYDROPHOBIC_AMINO_ACIDS.has(label_comp_id);
+/** Returns true if the definition considers this as membrane-favoring amino acid */
+export function isHydrophobic(definition: Set<string>, label_comp_id: string): boolean {
+    return definition.has(label_comp_id);
 }

 /** Accessible surface area used for normalization. ANVIL uses 'Total-Side REL' values from NACCESS, from: Hubbard, S. J., & Thornton, J. M. (1993). naccess. Computer Program, Department of Biochemistry and Molecular Biology, University College London, 2(1). */
--- a/src/extensions/anvil/behavior.ts
+++ b/src/extensions/anvil/behavior.ts
@@ -52,7 +52,7 @@ export const ANVILMembraneOrientation = PluginBehavior.create<{ autoAttach: bool
        }

        update(p: { autoAttach: boolean }) {
-            let updated = this.params.autoAttach !== p.autoAttach;
+            const updated = this.params.autoAttach !== p.autoAttach;
            this.params.autoAttach = p.autoAttach;
            this.ctx.customStructureProperties.setDefaultAutoAttach(this.provider.descriptor.name, this.params.autoAttach);
            return updated;
@@ -150,7 +150,7 @@ export const MembraneOrientationPreset = StructureRepresentationPresetProvider({
    params: () => StructureRepresentationPresetProvider.CommonParams,
    async apply(ref, params, plugin) {
        const structureCell = StateObjectRef.resolveAndCheck(plugin.state.data, ref);
-        const structure  = structureCell?.obj?.data;
+        const structure = structureCell?.obj?.data;
        if (!structureCell || !structure) return {};

        if (!MembraneOrientationProvider.get(structure).value) {
--- a/src/extensions/cellpack/color/generate.ts
+++ b/src/extensions/cellpack/color/generate.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */
@@ -33,7 +33,7 @@ export function CellPackGenerateColorTheme(ctx: ThemeDataContext, props: PD.Valu

    if (ctx.structure && info) {
        const colors = distinctColors(info.packingsCount);
-        let hcl = Hcl.fromColor(Hcl(), colors[info.packingIndex]);
+        const hcl = Hcl.fromColor(Hcl(), colors[info.packingIndex]);

        const hue = [Math.max(0, hcl[0] - 35), Math.min(360, hcl[0] + 35)] as [number, number];

@@ -48,7 +48,7 @@ export function CellPackGenerateColorTheme(ctx: ThemeDataContext, props: PD.Valu
                hue, chroma: [30, 80], luminance: [15, 85],
                clusteringStepCount: 50, minSampleCount: 800, maxCount: 75
            }
-        }}, { minLabel: 'Min', maxLabel: 'Max' });
+        } }, { minLabel: 'Min', maxLabel: 'Max' });
        legend = palette.legend;
        const modelColor = new Map<number, Color>();
        for (let i = 0, il = models.length; i < il; ++i) {
--- a/src/extensions/cellpack/color/provided.ts
+++ b/src/extensions/cellpack/color/provided.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */
--- a/src/extensions/cellpack/curve.ts
+++ b/src/extensions/cellpack/curve.ts
@@ -1,7 +1,7 @@
 /**
- * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
- * @author Ludovic Autin <autin@scripps.edu>
+ * @author Ludovic Autin <ludovic.autin@gmail.com>
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */

@@ -49,7 +49,7 @@ function ResampleControlPoints(points: NumberArray, segmentLength: number) {
    // controlPoints.Insert(0, controlPoints[0] + (controlPoints[0] - controlPoints[1]) / 2.0f);
    // controlPoints.Add(controlPoints[nP - 1] + (controlPoints[nP - 1] - controlPoints[nP - 2]) / 2.0f);

-    let resampledControlPoints: Vec3[] = [];
+    const resampledControlPoints: Vec3[] = [];
    // resampledControlPoints.Add(controlPoints[0]);
    // resampledControlPoints.Add(controlPoints[1]);

@@ -111,7 +111,7 @@ function GetSmoothNormals(points: Vec3[]) {
    let p1 = points[1];
    let p2 = points[2];
    const p21 = Vec3.sub(tmpV1, p2, p1);
-    const p01 =  Vec3.sub(tmpV2, p0, p1);
+    const p01 = Vec3.sub(tmpV2, p0, p1);
    const p0121 = Vec3.cross(tmpV3, p01, p21);
    Vec3.normalize(prevV, p0121);
    smoothNormals.push(Vec3.clone(prevV));
@@ -179,7 +179,7 @@ function GetMiniFrame(points: Vec3[], normals: Vec3[]) {
        const v1t = Vec3.scale(mfTmpV5, v1, (2.0 / c1) * Vec3.dot(v1, frames[i].t));
        const tan_L_i = Vec3.sub(mfTmpV6, frames[i].t, v1t);
        // # compute reflection vector of R_2
-        const v2 =  Vec3.sub(mfTmpV7, t2, tan_L_i);
+        const v2 = Vec3.sub(mfTmpV7, t2, tan_L_i);
        const c2 = Vec3.dot(v2, v2);
        // compute r_(i+1) = R_2 * r_i^L
        const v2l = Vec3.scale(mfTmpV8, v1, (2.0 / c2) * Vec3.dot(v2, ref_L_i));
@@ -195,7 +195,7 @@ export function getMatFromResamplePoints(points: NumberArray, segmentLength: num
    let new_points: Vec3[] = [];
    if (resample) new_points = ResampleControlPoints(points, segmentLength);
    else {
-        for (let idx = 0; idx < points.length / 3; ++idx){
+        for (let idx = 0; idx < points.length / 3; ++idx) {
            new_points.push(Vec3.fromArray(Vec3.zero(), points, idx * 3));
        }
    }
@@ -211,7 +211,7 @@ export function getMatFromResamplePoints(points: NumberArray, segmentLength: num
        if (d >= segmentLength) {
            // use twist or random?
            const quat = Quat.rotationTo(Quat.zero(), Vec3.create(0, 0, 1), frames[i].t); // Quat.rotationTo(Quat.zero(), Vec3.create(0,0,1),new_normal[i]);//Quat.rotationTo(Quat.zero(), Vec3.create(0,0,1),direction);new_normal
-            const rq = Quat.setAxisAngle(Quat.zero(), frames[i].t, Math.random() * 3.60 ); // Quat.setAxisAngle(Quat.zero(),direction, Math.random()*3.60 );//Quat.identity();//
+            const rq = Quat.setAxisAngle(Quat.zero(), frames[i].t, Math.random() * 3.60); // Quat.setAxisAngle(Quat.zero(),direction, Math.random()*3.60 );//Quat.identity();//
            const m = Mat4.fromQuat(Mat4.zero(), Quat.multiply(Quat.zero(), rq, quat)); // Mat4.fromQuat(Mat4.zero(),Quat.multiply(Quat.zero(),quat1,quat2));//Mat4.fromQuat(Mat4.zero(),quat);//Mat4.identity();//Mat4.fromQuat(Mat4.zero(),Quat.multiply(Quat.zero(),rq,quat));
            // let pos:Vec3 = Vec3.add(Vec3.zero(),pti1,pti)
            // pos = Vec3.scale(pos,pos,1.0/2.0);
--- a/src/extensions/cellpack/data.ts
+++ b/src/extensions/cellpack/data.ts
@@ -13,16 +13,27 @@ export interface CellPack {

 export interface CellPacking {
    name: string,
-    location: 'surface' | 'interior' | 'cytoplasme',
+    location: 'surface' | 'interior' | 'cytoplasme'
    ingredients: Packing['ingredients']
+    compartment?: CellCompartment
 }

-//
+export interface CellCompartment {
+    filename?: string
+    geom_type?: 'raw' | 'file' | 'sphere' | 'mb' | 'None'
+    compartment_primitives?: CompartmentPrimitives
+}

 export interface Cell {
    recipe: Recipe
+    options?: RecipeOptions
    cytoplasme?: Packing
    compartments?: { [key: string]: Compartment }
+    mapping_ids?: { [key: number]: [number, string] }
+}
+
+export interface RecipeOptions {
+    resultfile?: string
 }

 export interface Recipe {
@@ -35,8 +46,29 @@ export interface Recipe {
 export interface Compartment {
    surface?: Packing
    interior?: Packing
+    geom?: unknown
+    geom_type?: 'raw' | 'file' | 'sphere' | 'mb' | 'None'
+    mb?: CompartmentPrimitives
 }

+// Primitives discribing a compartment
+export const enum CompartmentPrimitiveType {
+    MetaBall = 0,
+    Sphere = 1,
+    Cube = 2,
+    Cylinder = 3,
+    Cone = 4,
+    Plane = 5,
+    None = 6
+}
+
+export interface CompartmentPrimitives{
+    positions?: number[];
+    radii?: number[];
+    types?: CompartmentPrimitiveType[];
+}
+
+
 export interface Packing {
    ingredients: { [key: string]: Ingredient }
 }
@@ -64,18 +96,20 @@ export interface Ingredient {
    [curveX: string]: unknown;
    /** the orientation in the membrane */
    principalAxis?: Vec3;
+    principalVector?: Vec3;
    /** offset along membrane */
    offset?: Vec3;
    ingtype?: string;
    color?: Vec3;
    confidence?: number;
+    Type?: string;
 }

 export interface IngredientSource {
    pdb: string;
-    bu?: string;  /** biological unit e.g AU,BU1,etc.. */
+    bu?: string; /** biological unit e.g AU,BU1,etc.. */
    selection?: string; /** NGL selection or :A or :B etc.. */
-    model?: string;     /** model number e.g 0,1,2... */
+    model?: string; /** model number e.g 0,1,2... */
    transform: {
        center: boolean;
        translate?: Vec3;
--- a/src/extensions/cellpack/index.ts
+++ b/src/extensions/cellpack/index.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */
--- a/src/extensions/cellpack/model.ts
+++ b/src/extensions/cellpack/model.ts
@@ -2,13 +2,14 @@
 * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Ludovic Autin <ludovic.autin@gmail.com>
 */

 import { StateAction, StateBuilder, StateTransformer, State } from '../../mol-state';
 import { PluginContext } from '../../mol-plugin/context';
 import { PluginStateObject as PSO } from '../../mol-plugin-state/objects';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
-import { Ingredient, IngredientSource, CellPacking } from './data';
+import { Ingredient, CellPacking, CompartmentPrimitives } from './data';
 import { getFromPdb, getFromCellPackDB, IngredientFiles, parseCif, parsePDBfile, getStructureMean, getFromOPM } from './util';
 import { Model, Structure, StructureSymmetry, StructureSelection, QueryContext, Unit, Trajectory } from '../../mol-model/structure';
 import { trajectoryFromMmCIF, MmcifFormat } from '../../mol-model-formats/structure/mmcif';
@@ -17,7 +18,7 @@ import { Mat4, Vec3, Quat } from '../../mol-math/linear-algebra';
 import { SymmetryOperator } from '../../mol-math/geometry';
 import { Task, RuntimeContext } from '../../mol-task';
 import { StateTransforms } from '../../mol-plugin-state/transforms';
-import { ParseCellPack, StructureFromCellpack, DefaultCellPackBaseUrl, StructureFromAssemblies } from './state';
+import { ParseCellPack, StructureFromCellpack, DefaultCellPackBaseUrl, StructureFromAssemblies, CreateCompartmentSphere } from './state';
 import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
 import { getMatFromResamplePoints } from './curve';
 import { compile } from '../../mol-script/runtime/query/compiler';
@@ -28,8 +29,9 @@ import { createModels } from '../../mol-model-formats/structure/basic/parser';
 import { CellpackPackingPreset, CellpackMembranePreset } from './preset';
 import { Asset } from '../../mol-util/assets';
 import { Color } from '../../mol-util/color';
-import { readFromFile } from '../../mol-util/data-source';
 import { objectForEach } from '../../mol-util/object';
+import { readFromFile } from '../../mol-util/data-source';
+import { ColorNames } from '../../mol-util/color/names';

 function getCellPackModelUrl(fileName: string, baseUrl: string) {
    return `${baseUrl}/results/${fileName}`;
@@ -41,12 +43,16 @@ class TrajectoryCache {
    get(id: string) { return this.map.get(id); }
 }

-async function getModel(plugin: PluginContext, id: string, ingredient: Ingredient, baseUrl: string, trajCache: TrajectoryCache, file?: Asset.File) {
+async function getModel(plugin: PluginContext, id: string, ingredient: Ingredient,
+    baseUrl: string, trajCache: TrajectoryCache, location: string,
+    file?: Asset.File
+) {
    const assetManager = plugin.managers.asset;
    const modelIndex = (ingredient.source.model) ? parseInt(ingredient.source.model) : 0;
-    const surface = (ingredient.ingtype) ? (ingredient.ingtype === 'transmembrane') : false;
+    let surface = (ingredient.ingtype) ? (ingredient.ingtype === 'transmembrane') : false;
+    if (location === 'surface') surface = true;
    let trajectory = trajCache.get(id);
-    let assets: Asset.Wrapper[] = [];
+    const assets: Asset.Wrapper[] = [];
    if (!trajectory) {
        if (file) {
            if (file.name.endsWith('.cif')) {
@@ -68,10 +74,11 @@ async function getModel(plugin: PluginContext, id: string, ingredient: Ingredien
                throw new Error(`unsupported file type '${file.name}'`);
            }
        } else if (id.match(/^[1-9][a-zA-Z0-9]{3,3}$/i)) {
-            if (surface){
+            if (surface) {
                try {
                    const data = await getFromOPM(plugin, id, assetManager);
                    assets.push(data.asset);
+                    data.pdb.id! = id.toUpperCase();
                    trajectory = await plugin.runTask(trajectoryFromPDB(data.pdb));
                } catch (e) {
                    // fallback to getFromPdb
@@ -100,7 +107,7 @@ async function getModel(plugin: PluginContext, id: string, ingredient: Ingredien
    return { model, assets };
 }

-async function getStructure(plugin: PluginContext, model: Model, source: IngredientSource, props: { assembly?: string } = {}) {
+async function getStructure(plugin: PluginContext, model: Model, source: Ingredient, props: { assembly?: string } = {}) {
    let structure = Structure.ofModel(model);
    const { assembly } = props;

@@ -108,11 +115,12 @@ async function getStructure(plugin: PluginContext, model: Model, source: Ingredi
        structure = await plugin.runTask(StructureSymmetry.buildAssembly(structure, assembly));
    }
    let query;
-    if (source.selection){
-        const asymIds: string[] = source.selection.replace(' ', '').replace(':', '').split('or');
+    if (source.source.selection) {
+        const sel = source.source.selection;
+        // selection can have the model ID as well. remove it
+        const asymIds: string[] = sel.replace(/ /g, '').replace(/:/g, '').split('or').slice(1);
        query = MS.struct.modifier.union([
            MS.struct.generator.atomGroups({
-                'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
                'chain-test': MS.core.set.has([MS.set(...asymIds), MS.ammp('auth_asym_id')])
            })
        ]);
@@ -123,11 +131,11 @@ async function getStructure(plugin: PluginContext, model: Model, source: Ingredi
            })
        ]);
    }
-
    const compiled = compile<StructureSelection>(query);
    const result = compiled(new QueryContext(structure));
    structure = StructureSelection.unionStructure(result);
-
+    // change here if possible the label ?
+    // structure.label =  source.name;
    return structure;
 }

@@ -141,9 +149,9 @@ function getTransformLegacy(trans: Vec3, rot: Quat) {
 }

 function getTransform(trans: Vec3, rot: Quat) {
-    const q: Quat = Quat.create(rot[0], rot[1], rot[2], rot[3]);
+    const q: Quat = Quat.create(-rot[0], rot[1], rot[2], -rot[3]);
    const m: Mat4 = Mat4.fromQuat(Mat4.zero(), q);
-    const p: Vec3 = Vec3.create(trans[0], trans[1], trans[2]);
+    const p: Vec3 = Vec3.create(-trans[0], trans[1], trans[2]);
    Mat4.setTranslation(m, p);
    return m;
 }
@@ -157,9 +165,9 @@ function getCurveTransforms(ingredient: Ingredient) {
    const n = ingredient.nbCurve || 0;
    const instances: Mat4[] = [];
    let segmentLength = 3.4;
-    if (ingredient.uLength){
+    if (ingredient.uLength) {
        segmentLength = ingredient.uLength;
-    } else if (ingredient.radii){
+    } else if (ingredient.radii) {
        segmentLength = ingredient.radii[0].radii
            ? ingredient.radii[0].radii[0] * 2.0
            : 3.4;
@@ -168,7 +176,7 @@ function getCurveTransforms(ingredient: Ingredient) {
    for (let i = 0; i < n; ++i) {
        const cname = `curve${i}`;
        if (!(cname in ingredient)) {
-            // console.warn(`Expected '${cname}' in ingredient`)
+            console.warn(`Expected '${cname}' in ingredient`);
            continue;
        }
        const _points = ingredient[cname] as Vec3[];
@@ -177,9 +185,9 @@ function getCurveTransforms(ingredient: Ingredient) {
            continue;
        }
        // test for resampling
-        let distance: number = Vec3.distance(_points[0], _points[1]);
+        const distance: number = Vec3.distance(_points[0], _points[1]);
        if (distance >= segmentLength + 2.0) {
-            console.info(distance);
+            // console.info(distance);
            resampling = true;
        }
        const points = new Float32Array(_points.length * 3);
@@ -190,13 +198,13 @@ function getCurveTransforms(ingredient: Ingredient) {
    return instances;
 }

-function getAssembly(transforms: Mat4[], structure: Structure) {
-    const builder = Structure.Builder();
+function getAssembly(name: string, transforms: Mat4[], structure: Structure) {
+    const builder = Structure.Builder({ label: name });
    const { units } = structure;

    for (let i = 0, il = transforms.length; i < il; ++i) {
        const id = `${i + 1}`;
-        const op = SymmetryOperator.create(id, transforms[i], { assembly: { id, operId: i, operList: [ id ] } });
+        const op = SymmetryOperator.create(id, transforms[i], { assembly: { id, operId: i, operList: [id] } });
        for (const unit of units) {
            builder.addWithOperator(unit, op);
        }
@@ -307,13 +315,13 @@ async function getCurve(plugin: PluginContext, name: string, ingredient: Ingredi
    });

    const curveModel = await plugin.runTask(curveModelTask);
-    return getStructure(plugin, curveModel, ingredient.source);
+    // ingredient.source.selection = undefined;
+    return getStructure(plugin, curveModel, ingredient);
 }

-async function getIngredientStructure(plugin: PluginContext, ingredient: Ingredient, baseUrl: string, ingredientFiles: IngredientFiles, trajCache: TrajectoryCache) {
+async function getIngredientStructure(plugin: PluginContext, ingredient: Ingredient, baseUrl: string, ingredientFiles: IngredientFiles, trajCache: TrajectoryCache, location: 'surface' | 'interior' | 'cytoplasme') {
    const { name, source, results, nbCurve } = ingredient;
    if (source.pdb === 'None') return;
-
    const file = ingredientFiles[source.pdb];
    if (!file) {
        // TODO can these be added to the library?
@@ -325,72 +333,79 @@ async function getIngredientStructure(plugin: PluginContext, ingredient: Ingredi
    }

    // model id in case structure is NMR
-    const { model, assets } = await getModel(plugin, source.pdb || name, ingredient, baseUrl, trajCache, file);
+    const { model, assets } = await getModel(plugin, source.pdb || name, ingredient, baseUrl, trajCache, location, file);
    if (!model) return;
-
    let structure: Structure;
    if (nbCurve) {
        structure = await getCurve(plugin, name, ingredient, getCurveTransforms(ingredient), model);
    } else {
+        if ((!results || results.length === 0)) return;
        let bu: string|undefined = source.bu ? source.bu : undefined;
-        if (bu){
+        if (bu) {
            if (bu === 'AU') {
                bu = undefined;
            } else {
                bu = bu.slice(2);
            }
        }
-        structure = await getStructure(plugin, model, source, { assembly: bu });
+        structure = await getStructure(plugin, model, ingredient, { assembly: bu });
        // transform with offset and pcp
        let legacy: boolean = true;
-        if (ingredient.offset || ingredient.principalAxis){
+        const pcp = ingredient.principalVector ? ingredient.principalVector : ingredient.principalAxis;
+        if (pcp) {
            legacy = false;
            const structureMean = getStructureMean(structure);
            Vec3.negate(structureMean, structureMean);
            const m1: Mat4 = Mat4.identity();
            Mat4.setTranslation(m1, structureMean);
            structure = Structure.transform(structure, m1);
-            if (ingredient.offset){
-                if (!Vec3.exactEquals(ingredient.offset, Vec3.zero())){
+            if (ingredient.offset) {
+                const o: Vec3 = Vec3.create(ingredient.offset[0], ingredient.offset[1], ingredient.offset[2]);
+                if (!Vec3.exactEquals(o, Vec3.zero())) { // -1, 1, 4e-16 ??
+                    if (location !== 'surface') {
+                        Vec3.negate(o, o);
+                    }
                    const m: Mat4 = Mat4.identity();
-                    Mat4.setTranslation(m, ingredient.offset);
+                    Mat4.setTranslation(m, o);
                    structure = Structure.transform(structure, m);
                }
            }
-            if (ingredient.principalAxis){
-                if (!Vec3.exactEquals(ingredient.principalAxis, Vec3.unitZ)){
+            if (pcp) {
+                const p: Vec3 = Vec3.create(pcp[0], pcp[1], pcp[2]);
+                if (!Vec3.exactEquals(p, Vec3.unitZ)) {
                    const q: Quat = Quat.identity();
-                    Quat.rotationTo(q, ingredient.principalAxis, Vec3.unitZ);
+                    Quat.rotationTo(q, p, Vec3.unitZ);
                    const m: Mat4 = Mat4.fromQuat(Mat4.zero(), q);
                    structure = Structure.transform(structure, m);
                }
            }
        }
-        structure = getAssembly(getResultTransforms(results, legacy), structure);
+
+        structure = getAssembly(name, getResultTransforms(results, legacy), structure);
    }

    return { structure, assets };
 }

+
 export function createStructureFromCellPack(plugin: PluginContext, packing: CellPacking, baseUrl: string, ingredientFiles: IngredientFiles) {
    return Task.create('Create Packing Structure', async ctx => {
-        const { ingredients, name } = packing;
+        const { ingredients, location, name } = packing;
        const assets: Asset.Wrapper[] = [];
        const trajCache = new TrajectoryCache();
        const structures: Structure[] = [];
        const colors: Color[] = [];
-        let skipColors: boolean = false;
        for (const iName in ingredients) {
            if (ctx.shouldUpdate) await ctx.update(iName);
-            const ingredientStructure = await getIngredientStructure(plugin, ingredients[iName], baseUrl, ingredientFiles, trajCache);
+            const ingredientStructure = await getIngredientStructure(plugin, ingredients[iName], baseUrl, ingredientFiles, trajCache, location);
            if (ingredientStructure) {
                structures.push(ingredientStructure.structure);
                assets.push(...ingredientStructure.assets);
                const c = ingredients[iName].color;
-                if (c){
+                if (c) {
                    colors.push(Color.fromNormalizedRgb(c[0], c[1], c[2]));
                } else {
-                    skipColors = true;
+                    colors.push(Color.fromNormalizedRgb(1, 0, 0));
                }
            }
        }
@@ -402,7 +417,7 @@ export function createStructureFromCellPack(plugin: PluginContext, packing: Cell
        for (const s of structures) {
            if (ctx.shouldUpdate) await ctx.update(`${s.label}`);
            let maxInvariantId = 0;
-            let maxChainGroupId = 0;
+            const maxChainGroupId = 0;
            for (const u of s.units) {
                const invariantId = u.invariantId + offsetInvariantId;
                const chainGroupId = u.chainGroupId + offsetChainGroupId;
@@ -414,21 +429,20 @@ export function createStructureFromCellPack(plugin: PluginContext, packing: Cell
        }

        if (ctx.shouldUpdate) await ctx.update(`${name} - structure`);
-        const structure = Structure.create(units);
-        for( let i = 0, il = structure.models.length; i < il; ++i) {
+        const structure = Structure.create(units, { label: name + '.' + location });
+        for (let i = 0, il = structure.models.length; i < il; ++i) {
            Model.TrajectoryInfo.set(structure.models[i], { size: il, index: i });
        }
-        return { structure, assets, colors: skipColors ? undefined : colors };
+        return { structure, assets, colors: colors };
    });
 }

 async function handleHivRna(plugin: PluginContext, packings: CellPacking[], baseUrl: string) {
    for (let i = 0, il = packings.length; i < il; ++i) {
-        if (packings[i].name === 'HIV1_capsid_3j3q_PackInner_0_1_0') {
+        if (packings[i].name === 'HIV1_capsid_3j3q_PackInner_0_1_0' || packings[i].name === 'HIV_capsid') {
            const url = Asset.getUrlAsset(plugin.managers.asset, `${baseUrl}/extras/rna_allpoints.json`);
            const json = await plugin.runTask(plugin.managers.asset.resolve(url, 'json', false));
            const points = json.data.points as number[];
-
            const curve0: Vec3[] = [];
            for (let j = 0, jl = points.length; j < jl; j += 3) {
                curve0.push(Vec3.fromArray(Vec3(), points, j));
@@ -454,7 +468,7 @@ async function loadMembrane(plugin: PluginContext, name: string, state: State, p
                break;
            }
        }
-        if (!file){
+        if (!file) {
            // check for cif directly
            const cifileName = `${name}.cif`;
            for (const f of params.ingredients) {
@@ -465,7 +479,8 @@ async function loadMembrane(plugin: PluginContext, name: string, state: State, p
            }
        }
    }
-
+    let legacy_membrane: boolean = false; // temporary variable until all membrane are converted to the new correct cif format
+    let geometry_membrane: boolean = false; // membrane can be a mesh geometry
    let b = state.build().toRoot();
    if (file) {
        if (file.name.endsWith('.cif')) {
@@ -474,27 +489,82 @@ async function loadMembrane(plugin: PluginContext, name: string, state: State, p
            b = b.apply(StateTransforms.Data.ReadFile, { file, isBinary: true, label: file.name }, { state: { isGhost: true } });
        }
    } else {
-        const url = Asset.getUrlAsset(plugin.managers.asset, `${params.baseUrl}/membranes/${name}.bcif`);
-        b = b.apply(StateTransforms.Data.Download, { url, isBinary: true, label: name }, { state: { isGhost: true } });
+        if (name.toLowerCase().endsWith('.bcif')) {
+            const url = Asset.getUrlAsset(plugin.managers.asset, `${params.baseUrl}/membranes/${name}`);
+            b = b.apply(StateTransforms.Data.Download, { url, isBinary: true, label: name }, { state: { isGhost: true } });
+        } else if (name.toLowerCase().endsWith('.cif')) {
+            const url = Asset.getUrlAsset(plugin.managers.asset, `${params.baseUrl}/membranes/${name}`);
+            b = b.apply(StateTransforms.Data.Download, { url, isBinary: false, label: name }, { state: { isGhost: true } });
+        } else if (name.toLowerCase().endsWith('.ply')) {
+            const url = Asset.getUrlAsset(plugin.managers.asset, `${params.baseUrl}/geometries/${name}`);
+            b = b.apply(StateTransforms.Data.Download, { url, isBinary: false, label: name }, { state: { isGhost: true } });
+            geometry_membrane = true;
+        } else {
+            const url = Asset.getUrlAsset(plugin.managers.asset, `${params.baseUrl}/membranes/${name}.bcif`);
+            b = b.apply(StateTransforms.Data.Download, { url, isBinary: true, label: name }, { state: { isGhost: true } });
+            legacy_membrane = true;
+        }
    }
-
-    const membrane = await b.apply(StateTransforms.Data.ParseCif, undefined, { state: { isGhost: true } })
-        .apply(StateTransforms.Model.TrajectoryFromMmCif, undefined, { state: { isGhost: true } })
-        .apply(StateTransforms.Model.ModelFromTrajectory, undefined, { state: { isGhost: true } })
-        .apply(StructureFromAssemblies, undefined, { state: { isGhost: true } })
-        .commit({ revertOnError: true });
-
-    const membraneParams = {
-        representation: params.preset.representation,
+    const props = {
+        type: {
+            name: 'assembly' as const,
+            params: { id: '1' }
+        }
    };
+    if (legacy_membrane) {
+        // old membrane
+        const membrane = await b.apply(StateTransforms.Data.ParseCif, undefined, { state: { isGhost: true } })
+            .apply(StateTransforms.Model.TrajectoryFromMmCif, undefined, { state: { isGhost: true } })
+            .apply(StateTransforms.Model.ModelFromTrajectory, undefined, { state: { isGhost: true } })
+            .apply(StructureFromAssemblies, undefined, { state: { isGhost: true } })
+            .commit({ revertOnError: true });
+        const membraneParams = {
+            representation: params.preset.representation,
+        };
+        await CellpackMembranePreset.apply(membrane, membraneParams, plugin);
+    } else if (geometry_membrane) {
+        await b.apply(StateTransforms.Data.ParsePly, undefined, { state: { isGhost: true } })
+            .apply(StateTransforms.Model.ShapeFromPly)
+            .apply(StateTransforms.Representation.ShapeRepresentation3D, { xrayShaded: true,
+                doubleSided: true, coloring: { name: 'uniform', params: { color: ColorNames.orange } } })
+            .commit({ revertOnError: true });
+    } else {
+        const membrane = await b.apply(StateTransforms.Data.ParseCif, undefined, { state: { isGhost: true } })
+            .apply(StateTransforms.Model.TrajectoryFromMmCif, undefined, { state: { isGhost: true } })
+            .apply(StateTransforms.Model.ModelFromTrajectory, undefined, { state: { isGhost: true } })
+            .apply(StateTransforms.Model.StructureFromModel, props, { state: { isGhost: true } })
+            .commit({ revertOnError: true });
+        const membraneParams = {
+            representation: params.preset.representation,
+        };
+        await CellpackMembranePreset.apply(membrane, membraneParams, plugin);
+    }
+}

-    await CellpackMembranePreset.apply(membrane, membraneParams, plugin);
+async function handleMembraneSpheres(state: State, primitives: CompartmentPrimitives) {
+    const nSpheres = primitives.positions!.length / 3;
+    // console.log('ok mb ', nSpheres);
+    // TODO : take in account the type of the primitives.
+    for (let j = 0; j < nSpheres; j++) {
+        await state.build()
+            .toRoot()
+            .apply(CreateCompartmentSphere, {
+                center: Vec3.create(
+                    primitives.positions![j * 3 + 0],
+                    primitives.positions![j * 3 + 1],
+                    primitives.positions![j * 3 + 2]
+                ),
+                radius: primitives!.radii![j]
+            })
+            .commit();
+    }
 }

 async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, state: State, params: LoadCellPackModelParams) {
    const ingredientFiles = params.ingredients || [];

    let cellPackJson: StateBuilder.To<PSO.Format.Json, StateTransformer<PSO.Data.String, PSO.Format.Json>>;
+    let resultsFile: Asset.File | null = params.results;
    if (params.source.name === 'id') {
        const url = Asset.getUrlAsset(plugin.managers.asset, getCellPackModelUrl(params.source.params, params.baseUrl));
        cellPackJson = state.build().toRoot()
@@ -506,29 +576,36 @@ async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, stat
            return;
        }

-        let jsonFile: Asset.File;
+        let modelFile: Asset.File;
        if (file.name.toLowerCase().endsWith('.zip')) {
            const data = await readFromFile(file.file, 'zip').runInContext(runtime);
-            jsonFile = Asset.File(new File([data['model.json']], 'model.json'));
+            if (data['model.json']) {
+                modelFile = Asset.File(new File([data['model.json']], 'model.json'));
+            } else {
+                throw new Error('model.json missing from zip file');
+            }
+            if (data['results.bin']) {
+                resultsFile = Asset.File(new File([data['results.bin']], 'results.bin'));
+            }
            objectForEach(data, (v, k) => {
                if (k === 'model.json') return;
+                if (k === 'results.bin') return;
                ingredientFiles.push(Asset.File(new File([v], k)));
            });
        } else {
-            jsonFile = file;
+            modelFile = file;
        }
-
        cellPackJson = state.build().toRoot()
-            .apply(StateTransforms.Data.ReadFile, { file: jsonFile, isBinary: false, label: jsonFile.name }, { state: { isGhost: true } });
+            .apply(StateTransforms.Data.ReadFile, { file: modelFile, isBinary: false, label: modelFile.name }, { state: { isGhost: true } });
    }

    const cellPackBuilder = cellPackJson
        .apply(StateTransforms.Data.ParseJson, undefined, { state: { isGhost: true } })
-        .apply(ParseCellPack);
+        .apply(ParseCellPack, { resultsFile, baseUrl: params.baseUrl });

    const cellPackObject = await state.updateTree(cellPackBuilder).runInContext(runtime);
-    const { packings } = cellPackObject.obj!.data;

+    const { packings } = cellPackObject.obj!.data;
    await handleHivRna(plugin, packings, params.baseUrl);

    for (let i = 0, il = packings.length; i < il; ++i) {
@@ -544,8 +621,30 @@ async function loadPackings(plugin: PluginContext, runtime: RuntimeContext, stat
            representation: params.preset.representation,
        };
        await CellpackPackingPreset.apply(packing, packingParams, plugin);
-        if ( packings[i].location === 'surface' && params.membrane){
-            await loadMembrane(plugin, packings[i].name, state, params);
+        if (packings[i].compartment) {
+            if (params.membrane === 'lipids') {
+                if (packings[i].compartment!.geom_type) {
+                    if (packings[i].compartment!.geom_type === 'file') {
+                        // TODO: load mesh files or vertex,faces data
+                        await loadMembrane(plugin, packings[i].compartment!.filename!, state, params);
+                    } else if (packings[i].compartment!.compartment_primitives) {
+                        await handleMembraneSpheres(state, packings[i].compartment!.compartment_primitives!);
+                    }
+                } else {
+                    // try loading membrane from repo as a bcif file or from the given list of files.
+                    if (params.membrane === 'lipids') {
+                        await loadMembrane(plugin, packings[i].name, state, params);
+                    }
+                }
+            } else if (params.membrane === 'geometry') {
+                if (packings[i].compartment!.compartment_primitives) {
+                    await handleMembraneSpheres(state, packings[i].compartment!.compartment_primitives!);
+                } else if (packings[i].compartment!.geom_type === 'file') {
+                    if (packings[i].compartment!.filename!.toLowerCase().endsWith('.ply')) {
+                        await loadMembrane(plugin, packings[i].compartment!.filename!, state, params);
+                    }
+                }
+            }
        }
    }
 }
@@ -555,19 +654,19 @@ const LoadCellPackModelParams = {
        'id': PD.Select('InfluenzaModel2.json', [
            ['blood_hiv_immature_inside.json', 'Blood HIV immature'],
            ['HIV_immature_model.json', 'HIV immature'],
-            ['BloodHIV1.0_mixed_fixed_nc1.cpr', 'Blood HIV'],
-            ['HIV-1_0.1.6-8_mixed_radii_pdb.cpr', 'HIV'],
+            ['Blood_HIV.json', 'Blood HIV'],
+            ['HIV-1_0.1.6-8_mixed_radii_pdb.json', 'HIV'],
            ['influenza_model1.json', 'Influenza envelope'],
-            ['InfluenzaModel2.json', 'Influenza Complete'],
+            ['InfluenzaModel2.json', 'Influenza complete'],
            ['ExosomeModel.json', 'Exosome Model'],
-            ['Mycoplasma1.5_mixed_pdb_fixed.cpr', 'Mycoplasma simple'],
-            ['MycoplasmaModel.json', 'Mycoplasma WholeCell model'],
+            ['MycoplasmaGenitalium.json', 'Mycoplasma Genitalium curated model'],
        ] as const, { description: 'Download the model definition with `id` from the server at `baseUrl.`' }),
-        'file': PD.File({ accept: '.json,.cpr,.zip', description: 'Open model definition from .json/.cpr file or open .zip file containing model definition plus ingredients.' }),
+        'file': PD.File({ accept: '.json,.cpr,.zip', description: 'Open model definition from .json/.cpr file or open .zip file containing model definition plus ingredients.', label: 'Recipe file' }),
    }, { options: [['id', 'Id'], ['file', 'File']] }),
    baseUrl: PD.Text(DefaultCellPackBaseUrl),
-    membrane: PD.Boolean(true),
-    ingredients: PD.FileList({ accept: '.cif,.bcif,.pdb', label: 'Ingredients' }),
+    results: PD.File({ accept: '.bin', description: 'open results file in binary format from cellpackgpu for the specified recipe', label: 'Results file' }),
+    membrane: PD.Select('lipids', PD.arrayToOptions(['lipids', 'geometry', 'none'])),
+    ingredients: PD.FileList({ accept: '.cif,.bcif,.pdb', label: 'Ingredient files' }),
    preset: PD.Group({
        traceOnly: PD.Boolean(false),
        representation: PD.Select('gaussian-surface', PD.arrayToOptions(['spacefill', 'gaussian-surface', 'point', 'orientation']))
@@ -581,4 +680,4 @@ export const LoadCellPackModel = StateAction.build({
    from: PSO.Root
 })(({ state, params }, ctx: PluginContext) => Task.create('CellPack Loader', async taskCtx => {
    await loadPackings(ctx, taskCtx, state, params);
-}));
+}));
--- a/src/extensions/cellpack/preset.ts
+++ b/src/extensions/cellpack/preset.ts
@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Ludovic Autin <ludovic.autin@gmail.com>
 */

 import { StateObjectRef } from '../../mol-state';
@@ -9,8 +10,6 @@ import { StructureRepresentationPresetProvider, presetStaticComponent } from '..
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ColorNames } from '../../mol-util/color/names';
 import { CellPackGenerateColorThemeProvider } from './color/generate';
-import { CellPackInfoProvider } from './property';
-import { CellPackProvidedColorThemeProvider } from './color/provided';

 export const CellpackPackingPresetParams = {
    traceOnly: PD.Boolean(true),
@@ -42,8 +41,8 @@ export const CellpackPackingPreset = StructureRepresentationPresetProvider({
            Object.assign(reprProps, { sizeFactor: 2 });
        }

-        const info = structureCell.obj?.data && CellPackInfoProvider.get(structureCell.obj?.data).value;
-        const color = info?.colors ? CellPackProvidedColorThemeProvider.name : CellPackGenerateColorThemeProvider.name;
+        // default is generated
+        const color = CellPackGenerateColorThemeProvider.name;

        const { update, builder, typeParams } = StructureRepresentationPresetProvider.reprBuilder(plugin, {});
        const representations = {
@@ -92,4 +91,4 @@ export const CellpackMembranePreset = StructureRepresentationPresetProvider({

        return { components, representations };
    }
-});
+});
--- a/src/extensions/cellpack/property.ts
+++ b/src/extensions/cellpack/property.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */
@@ -34,4 +34,4 @@ export const CellPackInfoProvider: CustomStructureProperty.Provider<typeof CellP
            value: { ...CellPackInfoParams.info.defaultValue, ...props.info }
        };
    }
-});
+});
--- a/src/extensions/cellpack/representation.ts
+++ b/src/extensions/cellpack/representation.ts
@@ -0,0 +1,70 @@
+/**
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Ludovic Autin <ludovic.autin@gmail.com>
+ */
+
+import { ShapeRepresentation } from '../../mol-repr/shape/representation';
+import { Shape } from '../../mol-model/shape';
+import { ColorNames } from '../../mol-util/color/names';
+import { RuntimeContext } from '../../mol-task';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Mesh } from '../../mol-geo/geometry/mesh/mesh';
+import { MeshBuilder } from '../../mol-geo/geometry/mesh/mesh-builder';
+// import { Polyhedron, DefaultPolyhedronProps } from '../../mol-geo/primitive/polyhedron';
+// import { Icosahedron } from '../../mol-geo/primitive/icosahedron';
+import { Sphere } from '../../mol-geo/primitive/sphere';
+import { Mat4, Vec3 } from '../../mol-math/linear-algebra';
+import { RepresentationParamsGetter, Representation, RepresentationContext } from '../../mol-repr/representation';
+
+
+interface MembraneSphereData {
+    radius: number
+    center: Vec3
+}
+
+
+const MembraneSphereParams = {
+    ...Mesh.Params,
+    cellColor: PD.Color(ColorNames.orange),
+    cellScale: PD.Numeric(2, { min: 0.1, max: 5, step: 0.1 }),
+    radius: PD.Numeric(2, { min: 0.1, max: 5, step: 0.1 }),
+    center: PD.Vec3(Vec3.create(0, 0, 0)),
+    quality: { ...Mesh.Params.quality, isEssential: false },
+};
+
+type MeshParams = typeof MembraneSphereParams
+
+const MembraneSphereVisuals = {
+    'mesh': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<MembraneSphereData, MeshParams>) => ShapeRepresentation(getMBShape, Mesh.Utils),
+};
+
+export const MBParams = {
+    ...MembraneSphereParams
+};
+export type MBParams = typeof MBParams
+export type UnitcellProps = PD.Values<MBParams>
+
+function getMBMesh(data: MembraneSphereData, props: UnitcellProps, mesh?: Mesh) {
+    const state = MeshBuilder.createState(256, 128, mesh);
+    const radius = props.radius;
+    const asphere = Sphere(3);
+    const trans: Mat4 = Mat4.identity();
+    Mat4.fromScaling(trans, Vec3.create(radius, radius, radius));
+    state.currentGroup = 1;
+    MeshBuilder.addPrimitive(state, trans, asphere);
+    const m = MeshBuilder.getMesh(state);
+    return m;
+}
+
+function getMBShape(ctx: RuntimeContext, data: MembraneSphereData, props: UnitcellProps, shape?: Shape<Mesh>) {
+    const geo = getMBMesh(data, props, shape && shape.geometry);
+    const label = 'mb';
+    return Shape.create(label, data, geo, () => props.cellColor, () => 1, () => label);
+}
+
+export type MBRepresentation = Representation<MembraneSphereData, MBParams>
+export function MBRepresentation(ctx: RepresentationContext, getParams: RepresentationParamsGetter<MembraneSphereData, MBParams>): MBRepresentation {
+    return Representation.createMulti('MB', ctx, getParams, Representation.StateBuilder, MembraneSphereVisuals as unknown as Representation.Def<MembraneSphereData, MBParams>);
+}
--- a/src/extensions/cellpack/state.ts
+++ b/src/extensions/cellpack/state.ts
@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Ludovic Autin <ludovic.autin@gmail.com>
 */

 import { PluginStateObject as PSO, PluginStateTransform } from '../../mol-plugin-state/objects';
@@ -15,9 +16,13 @@ import { PluginContext } from '../../mol-plugin/context';
 import { CellPackInfoProvider } from './property';
 import { Structure, StructureSymmetry, Unit, Model } from '../../mol-model/structure';
 import { ModelSymmetry } from '../../mol-model-formats/structure/property/symmetry';
+import { Vec3, Quat } from '../../mol-math/linear-algebra';
+import { StateTransformer } from '../../mol-state';
+import { MBRepresentation, MBParams } from './representation';
+import { IsNativeEndianLittle, flipByteOrder } from '../../mol-io/common/binary';
+import { getFloatValue } from './util';

-export const DefaultCellPackBaseUrl = 'https://mesoscope.scripps.edu/data/cellPACK_data/cellPACK_database_1.1.0/';
-
+export const DefaultCellPackBaseUrl = 'https://raw.githubusercontent.com/mesoscope/cellPACK_data/master/cellPACK_database_1.1.0';
 export class CellPack extends PSO.Create<_CellPack>({ name: 'CellPack', typeClass: 'Object' }) { }

 export { ParseCellPack };
@@ -26,26 +31,173 @@ const ParseCellPack = PluginStateTransform.BuiltIn({
    name: 'parse-cellpack',
    display: { name: 'Parse CellPack', description: 'Parse CellPack from JSON data' },
    from: PSO.Format.Json,
-    to: CellPack
+    to: CellPack,
+    params: a => {
+        return {
+            resultsFile: PD.File({ accept: '.bin' }),
+            baseUrl: PD.Text(DefaultCellPackBaseUrl)
+        };
+    }
 })({
-    apply({ a }) {
+    apply({ a, params, cache }, plugin: PluginContext) {
        return Task.create('Parse CellPack', async ctx => {
            const cell = a.data as Cell;
-
+            let counter_id = 0;
+            let fiber_counter_id = 0;
+            let comp_counter = 0;
            const packings: CellPacking[] = [];
            const { compartments, cytoplasme } = cell;
+            if (!cell.mapping_ids) cell.mapping_ids = {};
+            if (cytoplasme) {
+                packings.push({ name: 'Cytoplasme', location: 'cytoplasme', ingredients: cytoplasme.ingredients });
+                for (const iName in cytoplasme.ingredients) {
+                    if (cytoplasme.ingredients[iName].ingtype === 'fiber') {
+                        cell.mapping_ids[-(fiber_counter_id + 1)] = [comp_counter, iName];
+                        if (!cytoplasme.ingredients[iName].nbCurve) cytoplasme.ingredients[iName].nbCurve = 0;
+                        fiber_counter_id++;
+                    } else {
+                        cell.mapping_ids[counter_id] = [comp_counter, iName];
+                        if (!cytoplasme.ingredients[iName].results) { cytoplasme.ingredients[iName].results = []; }
+                        counter_id++;
+                    }
+                }
+                comp_counter++;
+            }
            if (compartments) {
                for (const name in compartments) {
                    const { surface, interior } = compartments[name];
-                    if (surface) packings.push({ name, location: 'surface', ingredients: surface.ingredients });
-                    if (interior) packings.push({ name, location: 'interior', ingredients: interior.ingredients });
+                    let filename = '';
+                    if (compartments[name].geom_type === 'file') {
+                        filename = (compartments[name].geom) ? compartments[name].geom as string : '';
+                    }
+                    const compartment = { filename: filename, geom_type: compartments[name].geom_type, compartment_primitives: compartments[name].mb };
+                    if (surface) {
+                        packings.push({ name, location: 'surface', ingredients: surface.ingredients, compartment: compartment });
+                        for (const iName in surface.ingredients) {
+                            if (surface.ingredients[iName].ingtype === 'fiber') {
+                                cell.mapping_ids[-(fiber_counter_id + 1)] = [comp_counter, iName];
+                                if (!surface.ingredients[iName].nbCurve) surface.ingredients[iName].nbCurve = 0;
+                                fiber_counter_id++;
+                            } else {
+                                cell.mapping_ids[counter_id] = [comp_counter, iName];
+                                if (!surface.ingredients[iName].results) { surface.ingredients[iName].results = []; }
+                                counter_id++;
+                            }
+                        }
+                        comp_counter++;
+                    }
+                    if (interior) {
+                        if (!surface) packings.push({ name, location: 'interior', ingredients: interior.ingredients, compartment: compartment });
+                        else packings.push({ name, location: 'interior', ingredients: interior.ingredients });
+                        for (const iName in interior.ingredients) {
+                            if (interior.ingredients[iName].ingtype === 'fiber') {
+                                cell.mapping_ids[-(fiber_counter_id + 1)] = [comp_counter, iName];
+                                if (!interior.ingredients[iName].nbCurve) interior.ingredients[iName].nbCurve = 0;
+                                fiber_counter_id++;
+                            } else {
+                                cell.mapping_ids[counter_id] = [comp_counter, iName];
+                                if (!interior.ingredients[iName].results) { interior.ingredients[iName].results = []; }
+                                counter_id++;
+                            }
+                        }
+                        comp_counter++;
+                    }
                }
            }
-            if (cytoplasme) packings.push({ name: 'Cytoplasme', location: 'cytoplasme', ingredients: cytoplasme.ingredients });
+            const { options } = cell;
+            let resultsAsset: Asset.Wrapper<'binary'> | undefined;
+            if (params.resultsFile) {
+                resultsAsset = await plugin.runTask(plugin.managers.asset.resolve(params.resultsFile, 'binary', true));
+            } else if (options?.resultfile) {
+                const url = `${params.baseUrl}/results/${options.resultfile}`;
+                resultsAsset = await plugin.runTask(plugin.managers.asset.resolve(Asset.getUrlAsset(plugin.managers.asset, url), 'binary', true));
+            }
+            if (resultsAsset) {
+                (cache as any).asset = resultsAsset;
+                const results = resultsAsset.data;
+                // flip the byte order if needed
+                const buffer = IsNativeEndianLittle ? results.buffer : flipByteOrder(results, 4);
+                const numbers = new DataView(buffer);
+                const ninst = getFloatValue(numbers, 0);
+                const npoints = getFloatValue(numbers, 4);
+                const ncurve = getFloatValue(numbers, 8);

+                let offset = 12;
+
+                if (ninst !== 0) {
+                    const pos = new Float32Array(buffer, offset, ninst * 4);
+                    offset += ninst * 4 * 4;
+                    const quat = new Float32Array(buffer, offset, ninst * 4);
+                    offset += ninst * 4 * 4;
+
+                    for (let i = 0; i < ninst; i++) {
+                        const x: number = pos[i * 4 + 0];
+                        const y: number = pos[i * 4 + 1];
+                        const z: number = pos[i * 4 + 2];
+                        const ingr_id = pos[i * 4 + 3] as number;
+                        const pid = cell.mapping_ids![ingr_id];
+                        if (!packings[pid[0]].ingredients[pid[1]].results) {
+                            packings[pid[0]].ingredients[pid[1]].results = [];
+                        }
+                        packings[pid[0]].ingredients[pid[1]].results.push([Vec3.create(x, y, z),
+                            Quat.create(quat[i * 4 + 0], quat[i * 4 + 1], quat[i * 4 + 2], quat[i * 4 + 3])]);
+                    }
+                }
+
+                if (npoints !== 0) {
+                    const ctr_pos = new Float32Array(buffer, offset, npoints * 4);
+                    offset += npoints * 4 * 4;
+                    offset += npoints * 4 * 4;
+                    const ctr_info = new Float32Array(buffer, offset, npoints * 4);
+                    offset += npoints * 4 * 4;
+                    const curve_ids = new Float32Array(buffer, offset, ncurve * 4);
+                    offset += ncurve * 4 * 4;
+
+                    let counter = 0;
+                    let ctr_points: Vec3[] = [];
+                    let prev_ctype = 0;
+                    let prev_cid = 0;
+
+                    for (let i = 0; i < npoints; i++) {
+                        const x: number = -ctr_pos[i * 4 + 0];
+                        const y: number = ctr_pos[i * 4 + 1];
+                        const z: number = ctr_pos[i * 4 + 2];
+                        const cid: number = ctr_info[i * 4 + 0]; // curve id
+                        const ctype: number = curve_ids[cid * 4 + 0]; // curve type
+                        // cid  148 165 -1 0
+                        // console.log("cid ",cid,ctype,prev_cid,prev_ctype);//165,148
+                        if (prev_ctype !== ctype) {
+                            const pid = cell.mapping_ids![-prev_ctype - 1];
+                            const cname = `curve${counter}`;
+                            packings[pid[0]].ingredients[pid[1]].nbCurve = counter + 1;
+                            packings[pid[0]].ingredients[pid[1]][cname] = ctr_points;
+                            ctr_points = [];
+                            counter = 0;
+                        } else if (prev_cid !== cid) {
+                            ctr_points = [];
+                            const pid = cell.mapping_ids![-prev_ctype - 1];
+                            const cname = `curve${counter}`;
+                            packings[pid[0]].ingredients[pid[1]][cname] = ctr_points;
+                            counter += 1;
+                        }
+                        ctr_points.push(Vec3.create(x, y, z));
+                        prev_ctype = ctype;
+                        prev_cid = cid;
+                    }
+
+                    // do the last one
+                    const pid = cell.mapping_ids![-prev_ctype - 1];
+                    const cname = `curve${counter}`;
+                    packings[pid[0]].ingredients[pid[1]].nbCurve = counter + 1;
+                    packings[pid[0]].ingredients[pid[1]][cname] = ctr_points;
+                }
+            }
            return new CellPack({ cell, packings });
        });
-    }
+    },
+    dispose({ cache }) {
+        ((cache as any)?.asset as Asset.Wrapper | undefined)?.dispose();
+    },
 });

 export { StructureFromCellpack };
@@ -77,14 +229,13 @@ const StructureFromCellpack = PluginStateTransform.BuiltIn({
            await CellPackInfoProvider.attach({ runtime: ctx, assetManager: plugin.managers.asset }, structure, {
                info: { packingsCount: a.data.packings.length, packingIndex: params.packing, colors }
            });
-
            (cache as any).assets = assets;
-            return new PSO.Molecule.Structure(structure, { label: packing.name });
+            return new PSO.Molecule.Structure(structure, { label: packing.name + '.' + packing.location });
        });
    },
    dispose({ b, cache }) {
        const assets = (cache as any).assets as Asset.Wrapper[];
-        if(assets) {
+        if (assets) {
            for (const a of assets) a.dispose();
        }

@@ -115,17 +266,17 @@ const StructureFromAssemblies = PluginStateTransform.BuiltIn({
            // TODO: optimze
            // TODO: think of ways how to fast-track changes to this for animations
            const model = a.data;
-            let initial_structure = Structure.ofModel(model);
+            const initial_structure = Structure.ofModel(model);
            const structures: Structure[] = [];
            let structure: Structure = initial_structure;
            // the list of asambly *?
            const symmetry = ModelSymmetry.Provider.get(model);
-            if (symmetry && symmetry.assemblies.length !== 0){
+            if (symmetry && symmetry.assemblies.length !== 0) {
                for (const a of symmetry.assemblies) {
                    const s = await StructureSymmetry.buildAssembly(initial_structure, a.id).runInContext(ctx);
                    structures.push(s);
                }
-                const builder = Structure.Builder();
+                const builder = Structure.Builder({ label: 'Membrane' });
                let offsetInvariantId = 0;
                for (const s of structures) {
                    let maxInvariantId = 0;
@@ -137,7 +288,7 @@ const StructureFromAssemblies = PluginStateTransform.BuiltIn({
                    offsetInvariantId += maxInvariantId + 1;
                }
                structure = builder.getStructure();
-                for( let i = 0, il = structure.models.length; i < il; ++i) {
+                for (let i = 0, il = structure.models.length; i < il; ++i) {
                    Model.TrajectoryInfo.set(structure.models[i], { size: il, index: i });
                }
            }
@@ -148,3 +299,28 @@ const StructureFromAssemblies = PluginStateTransform.BuiltIn({
        b?.data.customPropertyDescriptors.dispose();
    }
 });
+
+const CreateTransformer = StateTransformer.builderFactory('cellPACK');
+export const CreateCompartmentSphere = CreateTransformer({
+    name: 'create-compartment-sphere',
+    display: 'CompartmentSphere',
+    from: PSO.Root, // or whatever data source
+    to: PSO.Shape.Representation3D,
+    params: {
+        center: PD.Vec3(Vec3()),
+        radius: PD.Numeric(1),
+        label: PD.Text(`Compartment Sphere`)
+    }
+})({
+    canAutoUpdate({ oldParams, newParams }) {
+        return true;
+    },
+    apply({ a, params }, plugin: PluginContext) {
+        return Task.create('Compartment Sphere', async ctx => {
+            const data = params;
+            const repr = MBRepresentation({ webgl: plugin.canvas3d?.webgl, ...plugin.representation.structure.themes }, () => (MBParams));
+            await repr.createOrUpdate({ ...params, quality: 'custom', xrayShaded: true, doubleSided: true }, data).runInContext(ctx);
+            return new PSO.Shape.Representation3D({ repr, sourceData: a }, { label: data.label });
+        });
+    }
+});
--- a/src/extensions/cellpack/util.ts
+++ b/src/extensions/cellpack/util.ts
@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Ludovic Autin <ludovic.autin@gmail.com>
 */

 import { CIF } from '../../mol-io/reader/cif';
@@ -37,11 +38,11 @@ async function downloadPDB(plugin: PluginContext, url: string, id: string, asset
 }

 export async function getFromPdb(plugin: PluginContext, pdbId: string, assetManager: AssetManager) {
-    const { cif, asset } = await downloadCif(plugin, `https://models.rcsb.org/${pdbId.toUpperCase()}.bcif`, true, assetManager);
+    const { cif, asset } = await downloadCif(plugin, `https://models.rcsb.org/${pdbId}.bcif`, true, assetManager);
    return { mmcif: cif.blocks[0], asset };
 }

-export async function getFromOPM(plugin: PluginContext, pdbId: string, assetManager: AssetManager){
+export async function getFromOPM(plugin: PluginContext, pdbId: string, assetManager: AssetManager) {
    const asset = await plugin.runTask(assetManager.resolve(Asset.getUrlAsset(assetManager, `https://opm-assets.storage.googleapis.com/pdb/${pdbId.toLowerCase()}.pdb`), 'string'));
    return { pdb: await parsePDBfile(plugin, asset.data, pdbId), asset };
 }
@@ -74,4 +75,35 @@ export function getStructureMean(structure: Structure) {
    }
    const { elementCount } = structure;
    return Vec3.create(xSum / elementCount, ySum / elementCount, zSum / elementCount);
+}
+
+export function getFloatValue(value: DataView, offset: number) {
+    // if the last byte is a negative value (MSB is 1), the final
+    // float should be too
+    const negative = value.getInt8(offset + 2) >>> 31;
+
+    // this is how the bytes are arranged in the byte array/DataView
+    // buffer
+    const [b0, b1, b2, exponent] = [
+        // get first three bytes as unsigned since we only care
+        // about the last 8 bits of 32-bit js number returned by
+        // getUint8().
+        // Should be the same as: getInt8(offset) & -1 >>> 24
+        value.getUint8(offset),
+        value.getUint8(offset + 1),
+        value.getUint8(offset + 2),
+
+        // get the last byte, which is the exponent, as a signed int
+        // since it's already correct
+        value.getInt8(offset + 3)
+    ];
+
+    let mantissa = b0 | (b1 << 8) | (b2 << 16);
+    if (negative) {
+        // need to set the most significant 8 bits to 1's since a js
+        // number is 32 bits but our mantissa is only 24.
+        mantissa |= 255 << 24;
+    }
+
+    return mantissa * Math.pow(10, exponent);
 }
--- a/src/extensions/dnatco/confal-pyramids/behavior.ts
+++ b/src/extensions/dnatco/confal-pyramids/behavior.ts
@@ -41,10 +41,10 @@ export const DnatcoConfalPyramidsPreset = StructureRepresentationPresetProvider(

        let pyramidsRepr;
        if (representations)
-            pyramidsRepr = builder.buildRepresentation(update, pyramids,  { type: ConfalPyramidsRepresentationProvider, typeParams, color: ConfalPyramidsColorThemeProvider }, { tag: 'confal-pyramdis' } );
+            pyramidsRepr = builder.buildRepresentation(update, pyramids, { type: ConfalPyramidsRepresentationProvider, typeParams, color: ConfalPyramidsColorThemeProvider }, { tag: 'confal-pyramdis' });

        await update.commit({ revertOnError: true });
-        return  { components: { ...components, pyramids }, representations: { ...representations, pyramidsRepr } };
+        return { components: { ...components, pyramids }, representations: { ...representations, pyramidsRepr } };
    }
 });

--- a/src/extensions/dnatco/confal-pyramids/color.ts
+++ b/src/extensions/dnatco/confal-pyramids/color.ts
@@ -27,7 +27,7 @@ const ColorMapping: ReadonlyMap<ConformerClasses, Color> = new Map([
    ['B', Color(0xC8CFFF)],
    ['BII', Color(0x0059DA)],
    ['miB', Color(0x3BE8FB)],
-    ['Z',  Color(0x01F60E)],
+    ['Z', Color(0x01F60E)],
    ['IC', Color(0xFA5CFB)],
    ['OPN', Color(0xE90000)],
    ['SYN', Color(0xFFFF01)],
@@ -165,8 +165,8 @@ export function ConfalPyramidsColorTheme(ctx: ThemeDataContext, props: PD.Values
        legend: TableLegend(iterableToArray(ColorMapping.entries()).map(([conformer, color]) => {
            return [conformer, color] as [string, Color];
        }).concat([
-            [ 'Error', ErrorColor ],
-            [ 'Unknown', DefaultColor ]
+            ['Error', ErrorColor],
+            ['Unknown', DefaultColor]
        ]))
    };
 }
--- a/src/extensions/dnatco/confal-pyramids/util.ts
+++ b/src/extensions/dnatco/confal-pyramids/util.ts
@@ -95,7 +95,7 @@ export namespace ConfalPyramidsUtil {
            const first = residueInfoFromLocation(locFirst);
            const second = residueInfoFromLocation(locSecond);
            const model_id = this.hasMultipleModels ? `-m${modelNum}` : '';
-            const alt_id_1 =  fakeAltId_1 !== '' ? `.${fakeAltId_1}` : (first.alt_id.length ? `.${first.alt_id}` : '');
+            const alt_id_1 = fakeAltId_1 !== '' ? `.${fakeAltId_1}` : (first.alt_id.length ? `.${first.alt_id}` : '');
            const alt_id_2 = fakeAltId_2 !== '' ? `.${fakeAltId_2}` : (second.alt_id.length ? `.${second.alt_id}` : '');
            const ins_code_1 = first.ins_code.length ? `.${first.ins_code}` : '';
            const ins_code_2 = second.ins_code.length ? `.${second.ins_code}` : '';
--- a/src/extensions/g3d/model.ts
+++ b/src/extensions/g3d/model.ts
@@ -61,7 +61,7 @@ function getColumns(block: G3dDataBlock) {
    objectForEach(data, (hs, h) => {
        objectForEach(hs, (chs, ch) => {
            const entity_id = `${ch}-${h}`;
-            const l =  chs.start.length;
+            const l = chs.start.length;
            if (l === 0) return;

            let x = chs.x[0];
--- a/src/extensions/geo-export/glb-exporter.ts
+++ b/src/extensions/geo-export/glb-exporter.ts
@@ -53,7 +53,7 @@ export class GlbExporter extends MeshExporter<GlbData> {
                max[j] = Math.max(a[i + j], max[j]);
            }
        }
-        return [ min, max ];
+        return [min, max];
    }

    private addBuffer(buffer: ArrayBuffer, componentType: number, type: string, count: number, target: number, min?: any, max?: any, normalized?: boolean) {
@@ -108,7 +108,7 @@ export class GlbExporter extends MeshExporter<GlbData> {
            indexArray = indices!.slice(0, drawCount);
        }

-        const [ vertexMin, vertexMax ] = GlbExporter.vec3MinMax(vertexArray);
+        const [vertexMin, vertexMax] = GlbExporter.vec3MinMax(vertexArray);

        let vertexBuffer = vertexArray.buffer;
        let normalBuffer = normalArray.buffer;
@@ -273,14 +273,14 @@ export class GlbExporter extends MeshExporter<GlbData> {
            if (padding) {
                chunk.push(padding.buffer);
            }
-            return [ chunk, 8 + byteLength ];
+            return [chunk, 8 + byteLength];
        };
        const jsonString = JSON.stringify(gltf);
        const jsonBuffer = new Uint8Array(jsonString.length);
        asciiWrite(jsonBuffer, jsonString);

-        const [ jsonChunk, jsonChunkLength ] = createChunk(0x4E4F534A, [jsonBuffer.buffer], jsonBuffer.length, 0x20);
-        const [ binaryChunk, binaryChunkLength ] = createChunk(0x004E4942, this.binaryBuffer, binaryBufferLength, 0x00);
+        const [jsonChunk, jsonChunkLength] = createChunk(0x4E4F534A, [jsonBuffer.buffer], jsonBuffer.length, 0x20);
+        const [binaryChunk, binaryChunkLength] = createChunk(0x004E4942, this.binaryBuffer, binaryBufferLength, 0x00);

        const glbBufferLength = 12 + jsonChunkLength + binaryChunkLength;
        const header = new ArrayBuffer(12);
--- a/src/extensions/geo-export/mesh-exporter.ts
+++ b/src/extensions/geo-export/mesh-exporter.ts
@@ -102,7 +102,7 @@ export abstract class MeshExporter<D extends RenderObjectExportData> implements
        }
        const framebuffer = webgl.namedFramebuffers[GeoExportName];

-        const [ width, height ] = colorTexDim;
+        const [width, height] = colorTexDim;
        const colorGrid = new Uint8Array(width * height * 4);

        framebuffer.bind();
@@ -357,7 +357,7 @@ export abstract class MeshExporter<D extends RenderObjectExportData> implements
        }
        const framebuffer = webgl.namedFramebuffers[GeoExportName];

-        const [ width, height ] = values.uGeoTexDim.ref.value;
+        const [width, height] = values.uGeoTexDim.ref.value;
        const vertices = new Float32Array(width * height * 4);
        const normals = new Float32Array(width * height * 4);
        const groups = webgl.isWebGL2 ? new Uint8Array(width * height * 4) : new Float32Array(width * height * 4);
--- a/src/extensions/pdbe/preferred-assembly.ts
+++ b/src/extensions/pdbe/preferred-assembly.ts
@@ -62,7 +62,7 @@ export namespace PDBePreferredAssembly {
        if (model.customProperties.has(Descriptor)) return true;

        let asmName: string | undefined = fromCifData(model);
-        if (asmName === void 0 &&  params.PDBe_apiSourceJson) {
+        if (asmName === void 0 && params.PDBe_apiSourceJson) {
            const data = await params.PDBe_apiSourceJson(model);
            if (!data) return false;
            asmName = asmNameFromJson(model, data);
--- a/src/extensions/pdbe/structure-quality-report/behavior.ts
+++ b/src/extensions/pdbe/structure-quality-report/behavior.ts
@@ -52,7 +52,7 @@ export const PDBeStructureQualityReport = PluginBehavior.create<{ autoAttach: bo
        }

        update(p: { autoAttach: boolean, showTooltip: boolean }) {
-            let updated = this.params.autoAttach !== p.autoAttach;
+            const updated = this.params.autoAttach !== p.autoAttach;
            this.params.autoAttach = p.autoAttach;
            this.params.showTooltip = p.showTooltip;
            this.ctx.customModelProperties.setDefaultAutoAttach(this.provider.descriptor.name, this.params.autoAttach);
--- a/src/extensions/pdbe/structure-quality-report/color.ts
+++ b/src/extensions/pdbe/structure-quality-report/color.ts
@@ -87,7 +87,7 @@ export function StructureQualityReportColorTheme(ctx: ThemeDataContext, props: P
    };
 }

-export const StructureQualityReportColorThemeProvider: ColorTheme.Provider<Params, 'pdbe-structure-quality-report'> =  {
+export const StructureQualityReportColorThemeProvider: ColorTheme.Provider<Params, 'pdbe-structure-quality-report'> = {
    name: 'pdbe-structure-quality-report',
    label: 'Structure Quality Report',
    category: ColorTheme.Category.Validation,
--- a/src/extensions/pdbe/structure-quality-report/prop.ts
+++ b/src/extensions/pdbe/structure-quality-report/prop.ts
@@ -73,7 +73,7 @@ namespace StructureQualityReport {
    }

    export function fromCif(ctx: CustomProperty.Context, model: Model, props: StructureQualityReportProps): StructureQualityReport | undefined {
-        let info = PropertyWrapper.tryGetInfoFromCif('pdbe_structure_quality_report', model);
+        const info = PropertyWrapper.tryGetInfoFromCif('pdbe_structure_quality_report', model);
        if (!info) return;
        const data = getCifData(model);
        const issueMap = createIssueMapFromCif(model, data.residues, data.groups);
--- a/src/extensions/rcsb/assembly-symmetry/behavior.ts
+++ b/src/extensions/rcsb/assembly-symmetry/behavior.ts
@@ -47,7 +47,7 @@ export const RCSBAssemblySymmetry = PluginBehavior.create<{ autoAttach: boolean
        }

        update(p: { autoAttach: boolean }) {
-            let updated = this.params.autoAttach !== p.autoAttach;
+            const updated = this.params.autoAttach !== p.autoAttach;
            this.params.autoAttach = p.autoAttach;
            this.ctx.customStructureProperties.setDefaultAutoAttach(this.provider.descriptor.name, this.params.autoAttach);
            return updated;
@@ -85,7 +85,7 @@ export const InitAssemblySymmetry3D = StateAction.build({
        const assemblySymmetryData = AssemblySymmetryDataProvider.get(a.data).value;
        const symmetryIndex = assemblySymmetryData ? AssemblySymmetry.firstNonC1(assemblySymmetryData) : -1;
        await AssemblySymmetryProvider.attach(propCtx, a.data, { symmetryIndex });
-    } catch(e) {
+    } catch (e) {
        plugin.log.error(`Assembly Symmetry: ${e}`);
        return;
    }
--- a/src/extensions/rcsb/assembly-symmetry/prop.ts
+++ b/src/extensions/rcsb/assembly-symmetry/prop.ts
@@ -130,7 +130,7 @@ export function getSymmetrySelectParam(structure?: Structure) {
            for (let i = 0, il = assemblySymmetryData.length; i < il; ++i) {
                const { symbol, kind } = assemblySymmetryData[i];
                if (symbol !== 'C1') {
-                    options.push([ i, `${i + 1}: ${symbol} ${kind}` ]);
+                    options.push([i, `${i + 1}: ${symbol} ${kind}`]);
                }
            }
            if (options.length > 1) {
--- a/src/extensions/rcsb/assembly-symmetry/representation.ts
+++ b/src/extensions/rcsb/assembly-symmetry/representation.ts
@@ -310,7 +310,7 @@ function setSymbolTransform(t: Mat4, symbol: string, axes: AssemblySymmetry.Rota
    }
 }

-const unitCircleDirections = (function() {
+const unitCircleDirections = (function () {
    const dirs: Vec3[] = [];
    const circle = polygon(12, false, 1);
    for (let i = 0, il = circle.length; i < il; i += 3) {
--- a/src/extensions/rcsb/assembly-symmetry/ui.tsx
+++ b/src/extensions/rcsb/assembly-symmetry/ui.tsx
@@ -7,7 +7,7 @@
 import { CollapsableState, CollapsableControls } from '../../../mol-plugin-ui/base';
 import { ApplyActionControl } from '../../../mol-plugin-ui/state/apply-action';
 import { InitAssemblySymmetry3D, AssemblySymmetry3D, AssemblySymmetryPreset, tryCreateAssemblySymmetry } from './behavior';
-import { AssemblySymmetryProvider,  AssemblySymmetryProps, AssemblySymmetryDataProvider, AssemblySymmetry } from './prop';
+import { AssemblySymmetryProvider, AssemblySymmetryProps, AssemblySymmetryDataProvider, AssemblySymmetry } from './prop';
 import { ParameterControls } from '../../../mol-plugin-ui/controls/parameters';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { StructureHierarchyManager } from '../../../mol-plugin-state/manager/structure/hierarchy';
--- a/src/extensions/rcsb/graphql/codegen.yml
+++ b/src/extensions/rcsb/graphql/codegen.yml
@@ -1,12 +1,13 @@
 schema: https://data.rcsb.org/graphql
 documents: './src/extensions/rcsb/graphql/symmetry.gql.ts'
 generates:
-  './src/extensions/rcsb/graphql/types.ts':
-    plugins:
-      - add: '/* eslint-disable */'
-      - time
-      - typescript
-      - typescript-operations
-    config:
-      immutableTypes: true
-      skipTypename: true
+    './src/extensions/rcsb/graphql/types.ts':
+        plugins:
+            - add:
+                content: '/* eslint-disable */'
+            - time
+            - typescript
+            - typescript-operations
+        config:
+            immutableTypes: true
+            skipTypename: true
--- a/src/extensions/rcsb/graphql/types.ts
+++ b/src/extensions/rcsb/graphql/types.ts
--- a/src/extensions/rcsb/validation-report/behavior.ts
+++ b/src/extensions/rcsb/validation-report/behavior.ts
@@ -63,7 +63,7 @@ export const RCSBValidationReport = PluginBehavior.create<{ autoAttach: boolean,
        }

        update(p: { autoAttach: boolean, showTooltip: boolean }) {
-            let updated = this.params.autoAttach !== p.autoAttach;
+            const updated = this.params.autoAttach !== p.autoAttach;
            this.params.autoAttach = p.autoAttach;
            this.params.showTooltip = p.showTooltip;
            this.ctx.customStructureProperties.setDefaultAutoAttach(this.provider.descriptor.name, this.params.autoAttach);
--- a/src/extensions/rcsb/validation-report/prop.ts
+++ b/src/extensions/rcsb/validation-report/prop.ts
@@ -112,7 +112,7 @@ namespace ValidationReport {
    }

    export async function obtain(ctx: CustomProperty.Context, model: Model, props: ValidationReportProps): Promise<CustomProperty.Data<ValidationReport>> {
-        switch(props.source.name) {
+        switch (props.source.name) {
            case 'file': return open(ctx, model, props.source.params);
            case 'server': return fetch(ctx, model, props.source.params);
        }
@@ -208,8 +208,8 @@ function createInterUnitClashes(structure: Structure, clashes: ValidationReport[

        for (let i = 0, il = clashes.edgeCount * 2; i < il; ++i) {
            // TODO create lookup
-            let indexA = SortedArray.indexOf(elementsA, a[i]);
-            let indexB = SortedArray.indexOf(elementsB, b[i]);
+            const indexA = SortedArray.indexOf(elementsA, a[i]);
+            const indexB = SortedArray.indexOf(elementsB, b[i]);

            if (indexA !== -1 && indexB !== -1) {
                unitA.conformation.position(a[i], pA);
@@ -250,8 +250,8 @@ function createIntraUnitClashes(unit: Unit.Atomic, clashes: ValidationReport['cl

    for (let i = 0, il = edgeCount * 2; i < il; ++i) {
        // TODO create lookup
-        let indexA = SortedArray.indexOf(elements, a[i]);
-        let indexB = SortedArray.indexOf(elements, b[i]);
+        const indexA = SortedArray.indexOf(elements, a[i]);
+        const indexB = SortedArray.indexOf(elements, b[i]);

        if (indexA !== -1 && indexB !== -1) {
            unit.conformation.position(a[i], pA);
@@ -431,7 +431,7 @@ function parseValidationReportXml(xml: XMLDocument, model: Model): ValidationRep

    const groups = xml.getElementsByTagName('ModelledSubgroup');
    for (let i = 0, il = groups.length; i < il; ++i) {
-        const g = groups[ i ];
+        const g = groups[i];
        const ga = g.attributes;

        const pdbx_PDB_model_num = parseInt(getItem(ga, 'model'));
--- a/src/extensions/rcsb/validation-report/representation.ts
+++ b/src/extensions/rcsb/validation-report/representation.ts
@@ -107,7 +107,7 @@ function getIntraClashLabel(structure: Structure, unit: Unit.Atomic, clashes: In

 function IntraClashLoci(structure: Structure, unit: Unit.Atomic, clashes: IntraUnitClashes, elements: number[]) {
    return DataLoci('intra-clashes', { unit, clashes }, elements,
-        (boundingSphere: Sphere3D) =>  getIntraClashBoundingSphere(unit, clashes, elements, boundingSphere),
+        (boundingSphere: Sphere3D) => getIntraClashBoundingSphere(unit, clashes, elements, boundingSphere),
        () => getIntraClashLabel(structure, unit, clashes, elements));
 }

@@ -125,7 +125,7 @@ function getIntraClashLoci(pickingId: PickingId, structureGroup: StructureGroup,
 }

 function eachIntraClash(loci: Loci, structureGroup: StructureGroup, apply: (interval: Interval) => boolean) {
-    let changed = false;
+    const changed = false;
    // TODO
    return changed;
 }
@@ -226,7 +226,7 @@ function getInterClashLabel(structure: Structure, clashes: InterUnitClashes, ele

 function InterClashLoci(structure: Structure, clashes: InterUnitClashes, elements: number[]) {
    return DataLoci('inter-clashes', clashes, elements,
-        (boundingSphere: Sphere3D) =>  getInterClashBoundingSphere(structure, clashes, elements, boundingSphere),
+        (boundingSphere: Sphere3D) => getInterClashBoundingSphere(structure, clashes, elements, boundingSphere),
        () => getInterClashLabel(structure, clashes, elements));
 }

@@ -240,7 +240,7 @@ function getInterClashLoci(pickingId: PickingId, structure: Structure, id: numbe
 }

 function eachInterClash(loci: Loci, structure: Structure, apply: (interval: Interval) => boolean) {
-    let changed = false;
+    const changed = false;
    // TODO
    return changed;
 }
--- a/src/mol-canvas3d/camera.ts
+++ b/src/mol-canvas3d/camera.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -27,6 +27,10 @@ interface ICamera {
    readonly fogNear: number,
 }

+const tmpPos1 = Vec3();
+const tmpPos2 = Vec3();
+const tmpClip = Vec4();
+
 class Camera implements ICamera {
    readonly view: Mat4 = Mat4.identity();
    readonly projection: Mat4 = Mat4.identity();
@@ -34,7 +38,7 @@ class Camera implements ICamera {
    readonly inverseProjectionView: Mat4 = Mat4.identity();

    private pixelScale: number
-    get pixelRatio () {
+    get pixelRatio() {
        const dpr = (typeof window !== 'undefined') ? window.devicePixelRatio : 1;
        return dpr * this.pixelScale;
    }
@@ -155,14 +159,32 @@ class Camera implements ICamera {
        }
    }

+    /** Transform point into 2D window coordinates. */
    project(out: Vec4, point: Vec3) {
        return cameraProject(out, point, this.viewport, this.projectionView);
    }

-    unproject(out: Vec3, point: Vec3) {
+    /**
+     * Transform point from screen space to 3D coordinates.
+     * The point must have `x` and `y` set to 2D window coordinates
+     * and `z` between 0 (near) and 1 (far); the optional `w` is not used.
+     */
+    unproject(out: Vec3, point: Vec3 | Vec4) {
        return cameraUnproject(out, point, this.viewport, this.inverseProjectionView);
    }

+    /** World space pixel size at given `point` */
+    getPixelSize(point: Vec3) {
+        // project -> unproject of `point` does not exactly return the same
+        // to get a sufficiently accurate measure we unproject the original
+        // clip position in addition to the one shifted bey one pixel
+        this.project(tmpClip, point);
+        this.unproject(tmpPos1, tmpClip);
+        tmpClip[0] += 1;
+        this.unproject(tmpPos2, tmpClip);
+        return Vec3.distance(tmpPos1, tmpPos2);
+    }
+
    constructor(state?: Partial<Camera.Snapshot>, viewport = Viewport.create(0, 0, 128, 128), props: Partial<{ pixelScale: number }> = {}) {
        this.viewport = viewport;
        this.pixelScale = props.pixelScale || 1;
@@ -178,7 +200,7 @@ namespace Camera {
    /**
     * Sets an offseted view in a larger frustum. This is useful for
     * - multi-window or multi-monitor/multi-machine setups
-     * - jittering the camera position for
+     * - jittering the camera position for sampling
     */
    export interface ViewOffset {
        enabled: boolean,
--- a/src/mol-canvas3d/camera/util.ts
+++ b/src/mol-canvas3d/camera/util.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */
@@ -55,14 +55,11 @@ namespace Viewport {

 //

-const NEAR_RANGE = 0;
-const FAR_RANGE = 1;
-
 const tmpVec4 = Vec4();

 /** Transform point into 2D window coordinates. */
-export function cameraProject (out: Vec4, point: Vec3, viewport: Viewport, projectionView: Mat4) {
-    const { x: vX, y: vY, width: vWidth, height: vHeight } = viewport;
+export function cameraProject(out: Vec4, point: Vec3, viewport: Viewport, projectionView: Mat4) {
+    const { x, y, width, height } = viewport;

    // clip space -> NDC -> window coordinates, implicit 1.0 for w component
    Vec4.set(tmpVec4, point[0], point[1], point[2], 1.0);
@@ -78,27 +75,28 @@ export function cameraProject (out: Vec4, point: Vec3, viewport: Viewport, proje
        tmpVec4[2] /= w;
    }

-    // transform into window coordinates, set fourth component is (1/clip.w) as in gl_FragCoord.w
-    out[0] = vX + vWidth / 2 * tmpVec4[0] + (0 + vWidth / 2);
-    out[1] = vY + vHeight / 2 * tmpVec4[1] + (0 + vHeight / 2);
-    out[2] = (FAR_RANGE - NEAR_RANGE) / 2 * tmpVec4[2] + (FAR_RANGE + NEAR_RANGE) / 2;
+    // transform into window coordinates, set fourth component to 1 / clip.w as in gl_FragCoord.w
+    out[0] = (tmpVec4[0] + 1) * width * 0.5 + x;
+    out[1] = (1 - tmpVec4[1]) * height * 0.5 + y; // flip Y
+    out[2] = (tmpVec4[2] + 1) * 0.5;
    out[3] = w === 0 ? 0 : 1 / w;
    return out;
 }

 /**
 * Transform point from screen space to 3D coordinates.
- * The point must have x and y set to 2D window coordinates and z between 0 (near) and 1 (far).
+ * The point must have `x` and `y` set to 2D window coordinates
+ * and `z` between 0 (near) and 1 (far); the optional `w` is not used.
 */
-export function cameraUnproject (out: Vec3, point: Vec3, viewport: Viewport, inverseProjectionView: Mat4) {
-    const { x: vX, y: vY, width: vWidth, height: vHeight } = viewport;
+export function cameraUnproject(out: Vec3, point: Vec3 | Vec4, viewport: Viewport, inverseProjectionView: Mat4) {
+    const { x, y, width, height } = viewport;

-    const x = point[0] - vX;
-    const y = (vHeight - point[1] - 1) - vY;
-    const z = point[2];
+    const px = point[0] - x;
+    const py = (height - point[1] - 1) - y;
+    const pz = point[2];

-    out[0] = (2 * x) / vWidth - 1;
-    out[1] = (2 * y) / vHeight - 1;
-    out[2] = 2 * z - 1;
+    out[0] = (2 * px) / width - 1;
+    out[1] = (2 * py) / height - 1;
+    out[2] = 2 * pz - 1;
    return Vec3.transformMat4(out, out, inverseProjectionView);
 }
--- a/src/mol-canvas3d/canvas3d.ts
+++ b/src/mol-canvas3d/canvas3d.ts
@@ -23,7 +23,7 @@ import { Camera } from './camera';
 import { ParamDefinition as PD } from '../mol-util/param-definition';
 import { DebugHelperParams } from './helper/bounding-sphere-helper';
 import { SetUtils } from '../mol-util/set';
-import { Canvas3dInteractionHelper } from './helper/interaction-events';
+import { Canvas3dInteractionHelper, Canvas3dInteractionHelperParams } from './helper/interaction-events';
 import { PostprocessingParams } from './passes/postprocessing';
 import { MultiSampleHelper, MultiSampleParams, MultiSamplePass } from './passes/multi-sample';
 import { PickData } from './passes/pick';
@@ -38,6 +38,7 @@ import { StereoCamera, StereoCameraParams } from './camera/stereo';
 import { Helper } from './helper/helper';
 import { Passes } from './passes/passes';
 import { shallowEqual } from '../mol-util';
+import { MarkingParams } from './passes/marking';

 export const Canvas3DParams = {
    camera: PD.Group({
@@ -80,8 +81,10 @@ export const Canvas3DParams = {

    multiSample: PD.Group(MultiSampleParams),
    postprocessing: PD.Group(PostprocessingParams),
+    marking: PD.Group(MarkingParams),
    renderer: PD.Group(RendererParams),
    trackball: PD.Group(TrackballControlsParams),
+    interaction: PD.Group(Canvas3dInteractionHelperParams),
    debug: PD.Group(DebugHelperParams),
    handle: PD.Group(HandleHelperParams),
 };
@@ -113,19 +116,23 @@ namespace Canvas3DContext {
        preserveDrawingBuffer: true,
        pixelScale: 1,
        pickScale: 0.25,
-        enableWboit: true
+        /** extra pixels to around target to check in case target is empty */
+        pickPadding: 1,
+        enableWboit: true,
+        preferWebGl1: false
    };
    export type Attribs = typeof DefaultAttribs

    export function fromCanvas(canvas: HTMLCanvasElement, attribs: Partial<Attribs> = {}): Canvas3DContext {
        const a = { ...DefaultAttribs, ...attribs };
-        const { antialias, preserveDrawingBuffer, pixelScale } = a;
+        const { antialias, preserveDrawingBuffer, pixelScale, preferWebGl1 } = a;
        const gl = getGLContext(canvas, {
            antialias,
            preserveDrawingBuffer,
            alpha: true, // the renderer requires an alpha channel
            depth: true, // the renderer requires a depth buffer
            premultipliedAlpha: true, // the renderer outputs PMA
+            preferWebGl1
        });
        if (gl === null) throw new Error('Could not create a WebGL rendering context');

@@ -228,7 +235,7 @@ 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): void
+    mark(loci: Representation.Loci, action: MarkerAction, noDraw?: boolean): void
    getLoci(pickingId: PickingId | undefined): Representation.Loci

    notifyDidDraw: boolean,
@@ -303,8 +310,8 @@ namespace Canvas3D {
        const renderer = Renderer.create(webgl, p.renderer);
        const helper = new Helper(webgl, scene, p);

-        const pickHelper = new PickHelper(webgl, renderer, scene, helper, passes.pick, { x, y, width, height });
-        const interactionHelper = new Canvas3dInteractionHelper(identify, getLoci, input, camera);
+        const pickHelper = new PickHelper(webgl, renderer, scene, helper, passes.pick, { x, y, width, height }, attribs.pickPadding);
+        const interactionHelper = new Canvas3dInteractionHelper(identify, getLoci, input, camera, p.interaction);
        const multiSampleHelper = new MultiSampleHelper(passes.multiSample);

        let cameraResetRequested = false;
@@ -337,7 +344,7 @@ namespace Canvas3D {
            return { loci, repr };
        }

-        function mark(reprLoci: Representation.Loci, action: MarkerAction) {
+        function mark(reprLoci: Representation.Loci, action: MarkerAction, noDraw = false) {
            const { repr, loci } = reprLoci;
            let changed = false;
            if (repr) {
@@ -347,7 +354,7 @@ namespace Canvas3D {
                changed = helper.camera.mark(loci, action) || changed;
                reprRenderObjects.forEach((_, _repr) => { changed = _repr.mark(loci, action) || changed; });
            }
-            if (changed) {
+            if (changed && !noDraw) {
                scene.update(void 0, true);
                helper.handle.scene.update(void 0, true);
                helper.camera.scene.update(void 0, true);
@@ -390,7 +397,7 @@ namespace Canvas3D {
                if (MultiSamplePass.isEnabled(p.multiSample)) {
                    multiSampleHelper.render(renderer, cam, scene, helper, true, p.transparentBackground, p);
                } else {
-                    passes.draw.render(renderer, cam, scene, helper, true, p.transparentBackground, p.postprocessing);
+                    passes.draw.render(renderer, cam, scene, helper, true, p.transparentBackground, p.postprocessing, p.marking);
                }
                pickHelper.dirty = true;
                didRender = true;
@@ -636,9 +643,11 @@ namespace Canvas3D {
                viewport: p.viewport,

                postprocessing: { ...p.postprocessing },
+                marking: { ...p.marking },
                multiSample: { ...p.multiSample },
                renderer: { ...renderer.props },
                trackball: { ...controls.props },
+                interaction: { ...interactionHelper.props },
                debug: { ...helper.debug.props },
                handle: { ...helper.handle.props },
            };
@@ -729,7 +738,7 @@ namespace Canvas3D {
            resized,
            setProps: (properties, doNotRequestDraw = false) => {
                const props: PartialCanvas3DProps = typeof properties === 'function'
-                    ? produce(getProps(), properties)
+                    ? produce(getProps(), properties as any)
                    : properties;

                const cameraState: Partial<Camera.Snapshot> = Object.create(null);
@@ -771,9 +780,11 @@ namespace Canvas3D {
                }

                if (props.postprocessing) Object.assign(p.postprocessing, props.postprocessing);
+                if (props.marking) Object.assign(p.marking, props.marking);
                if (props.multiSample) Object.assign(p.multiSample, props.multiSample);
                if (props.renderer) renderer.setProps(props.renderer);
                if (props.trackball) controls.setProps(props.trackball);
+                if (props.interaction) interactionHelper.setProps(props.interaction);
                if (props.debug) helper.debug.setProps(props.debug);
                if (props.handle) helper.handle.setProps(props.handle);

@@ -835,9 +846,6 @@ namespace Canvas3D {
                height = Math.round(p.viewport.params.height * gl.drawingBufferHeight);
                y = Math.round(gl.drawingBufferHeight - height - p.viewport.params.y * gl.drawingBufferHeight);
                width = Math.round(p.viewport.params.width * gl.drawingBufferWidth);
-                // if (x + width >= gl.drawingBufferWidth) width = gl.drawingBufferWidth - x;
-                // if (y + height >= gl.drawingBufferHeight) height = gl.drawingBufferHeight - y - 1;
-                // console.log({ x, y, width, height });
            }

            if (oldX !== x || oldY !== y || oldWidth !== width || oldHeight !== height) {
--- a/src/mol-canvas3d/helper/bounding-sphere-helper.ts
+++ b/src/mol-canvas3d/helper/bounding-sphere-helper.ts
@@ -121,7 +121,7 @@ export class BoundingSphereHelper {
    }
    get props() { return this._props as Readonly<DebugHelperProps>; }

-    setProps (props: Partial<DebugHelperProps>) {
+    setProps(props: Partial<DebugHelperProps>) {
        Object.assign(this._props, props);
        if (this.isEnabled) this.update();
    }
--- a/src/mol-canvas3d/helper/interaction-events.ts
+++ b/src/mol-canvas3d/helper/interaction-events.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 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 +11,8 @@ import { InputObserver, ModifiersKeys, ButtonsType } from '../../mol-util/input/
 import { RxEventHelper } from '../../mol-util/rx-event-helper';
 import { Vec2, Vec3 } from '../../mol-math/linear-algebra';
 import { Camera } from '../camera';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { Bond } from '../../mol-model/structure';

 type Canvas3D = import('../canvas3d').Canvas3D
 type HoverEvent = import('../canvas3d').Canvas3D.HoverEvent
@@ -19,6 +21,17 @@ type ClickEvent = import('../canvas3d').Canvas3D.ClickEvent

 const enum InputEvent { Move, Click, Drag }

+const tmpPosA = Vec3();
+const tmpPos = Vec3();
+const tmpNorm = Vec3();
+
+export const Canvas3dInteractionHelperParams = {
+    maxFps: PD.Numeric(30, { min: 10, max: 60, step: 10 }),
+    preferAtomPixelPadding: PD.Numeric(3, { min: 0, max: 20, step: 1 }, { description: 'Number of extra pixels at which to prefer atoms over bonds.' }),
+};
+export type Canvas3dInteractionHelperParams = typeof Canvas3dInteractionHelperParams
+export type Canvas3dInteractionHelperProps = PD.Values<Canvas3dInteractionHelperParams>
+
 export class Canvas3dInteractionHelper {
    private ev = RxEventHelper.create();

@@ -48,6 +61,12 @@ export class Canvas3dInteractionHelper {
    private button: ButtonsType.Flag = ButtonsType.create(0);
    private modifiers: ModifiersKeys = ModifiersKeys.None;

+    readonly props: Canvas3dInteractionHelperProps;
+
+    setProps(props: Partial<Canvas3dInteractionHelperProps>) {
+        Object.assign(this.props, props);
+    }
+
    private identify(e: InputEvent, t: number) {
        const xyChanged = this.startX !== this.endX || this.startY !== this.endY;

@@ -70,7 +89,7 @@ export class Canvas3dInteractionHelper {
        }

        if (e === InputEvent.Click) {
-            const loci = this.getLoci(this.id);
+            const loci = this.getLoci(this.id, this.position);
            this.events.click.next({ current: loci, buttons: this.buttons, button: this.button, modifiers: this.modifiers, page: Vec2.create(this.endX, this.endY), position: this.position });
            this.prevLoci = loci;
            return;
@@ -78,13 +97,13 @@ export class Canvas3dInteractionHelper {

        if (!this.inside || this.currentIdentifyT !== t || !xyChanged || this.outsideViewport(this.endX, this.endY)) return;

-        const loci = this.getLoci(this.id);
+        const loci = this.getLoci(this.id, this.position);
        this.events.hover.next({ current: loci, buttons: this.buttons, button: this.button, modifiers: this.modifiers, page: Vec2.create(this.endX, this.endY), position: this.position });
        this.prevLoci = loci;
    }

    tick(t: number) {
-        if (this.inside && t - this.prevT > 1000 / this.maxFps) {
+        if (this.inside && t - this.prevT > 1000 / this.props.maxFps) {
            this.prevT = t;
            this.currentIdentifyT = t;
            this.identify(this.isInteracting ? InputEvent.Drag : InputEvent.Move, t);
@@ -144,18 +163,41 @@ export class Canvas3dInteractionHelper {
        );
    }

+    private getLoci(pickingId: PickingId | undefined, position: Vec3 | undefined) {
+        const { repr, loci } = this.lociGetter(pickingId);
+        if (position && repr && Bond.isLoci(loci) && loci.bonds.length === 2) {
+            const { aUnit, aIndex } = loci.bonds[0];
+            aUnit.conformation.position(aUnit.elements[aIndex], tmpPosA);
+            Vec3.sub(tmpNorm, this.camera.state.position, this.camera.state.target);
+            Vec3.projectPointOnPlane(tmpPos, position, tmpNorm, tmpPosA);
+            const pixelSize = this.camera.getPixelSize(tmpPos);
+            let radius = repr.theme.size.size(loci.bonds[0]) * (repr.props.sizeFactor ?? 1);
+            if (repr.props.lineSizeAttenuation === false) {
+                // divide by two to get radius
+                radius *= pixelSize / 2;
+            }
+            radius += this.props.preferAtomPixelPadding * pixelSize;
+            if (Vec3.distance(tmpPos, tmpPosA) < radius) {
+                return { repr, loci: Bond.toFirstStructureElementLoci(loci) };
+            }
+        }
+        return { repr, loci };
+    }
+
    dispose() {
        this.ev.dispose();
    }

-    constructor(private canvasIdentify: Canvas3D['identify'], private getLoci: Canvas3D['getLoci'], private input: InputObserver, private camera: Camera, private maxFps: number = 30) {
-        input.drag.subscribe(({x, y, buttons, button, modifiers }) => {
+    constructor(private canvasIdentify: Canvas3D['identify'], private lociGetter: Canvas3D['getLoci'], private input: InputObserver, private camera: Camera, props: Partial<Canvas3dInteractionHelperProps> = {}) {
+        this.props = { ...PD.getDefaultValues(Canvas3dInteractionHelperParams), ...props };
+
+        input.drag.subscribe(({ x, y, buttons, button, modifiers }) => {
            this.isInteracting = true;
            // console.log('drag');
            this.drag(x, y, buttons, button, modifiers);
        });

-        input.move.subscribe(({x, y, inside, buttons, button, modifiers }) => {
+        input.move.subscribe(({ x, y, inside, buttons, button, modifiers }) => {
            if (!inside || this.isInteracting) return;
            // console.log('move');
            this.move(x, y, buttons, button, modifiers);
@@ -166,7 +208,7 @@ export class Canvas3dInteractionHelper {
            this.leave();
        });

-        input.click.subscribe(({x, y, buttons, button, modifiers }) => {
+        input.click.subscribe(({ x, y, buttons, button, modifiers }) => {
            if (this.outsideViewport(x, y)) return;
            // console.log('click');
            this.click(x, y, buttons, button, modifiers);
--- a/src/mol-canvas3d/passes/draw.ts
+++ b/src/mol-canvas3d/passes/draw.ts
@@ -26,6 +26,7 @@ import { copy_frag } from '../../mol-gl/shader/copy.frag';
 import { StereoCamera } from '../camera/stereo';
 import { WboitPass } from './wboit';
 import { AntialiasingPass, PostprocessingPass, PostprocessingProps } from './postprocessing';
+import { MarkingPass, MarkingProps } from './marking';

 const DepthMergeSchema = {
    ...QuadSchema,
@@ -57,8 +58,8 @@ const CopySchema = {
    tColor: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
    uTexSize: UniformSpec('v2'),
 };
-const  CopyShaderCode = ShaderCode('copy', quad_vert, copy_frag);
-type  CopyRenderable = ComputeRenderable<Values<typeof CopySchema>>
+const CopyShaderCode = ShaderCode('copy', quad_vert, copy_frag);
+type CopyRenderable = ComputeRenderable<Values<typeof CopySchema>>

 function getCopyRenderable(ctx: WebGLContext, colorTexture: Texture): CopyRenderable {
    const values: Values<typeof CopySchema> = {
@@ -92,6 +93,7 @@ export class DrawPass {
    private copyFboPostprocessing: CopyRenderable

    private wboit: WboitPass | undefined
+    private readonly marking: MarkingPass
    readonly postprocessing: PostprocessingPass
    private readonly antialiasing: AntialiasingPass

@@ -122,6 +124,7 @@ export class DrawPass {
        this.depthMerge = getDepthMergeRenderable(webgl, this.depthTexturePrimitives, this.depthTextureVolumes, this.packedDepth);

        this.wboit = enableWboit ? new WboitPass(webgl, width, height) : undefined;
+        this.marking = new MarkingPass(webgl, width, height);
        this.postprocessing = new PostprocessingPass(webgl, this);
        this.antialiasing = new AntialiasingPass(webgl, this);

@@ -162,6 +165,7 @@ export class DrawPass {
                this.wboit.setSize(width, height);
            }

+            this.marking.setSize(width, height);
            this.postprocessing.setSize(width, height);
            this.antialiasing.setSize(width, height);
        }
@@ -281,10 +285,11 @@ export class DrawPass {
        renderer.renderBlendedTransparent(scene.primitives, camera, null);
    }

-    private _render(renderer: Renderer, camera: ICamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, transparentBackground: boolean, postprocessingProps: PostprocessingProps) {
+    private _render(renderer: Renderer, camera: ICamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, transparentBackground: boolean, postprocessingProps: PostprocessingProps, markingProps: MarkingProps) {
        const volumeRendering = scene.volumes.renderables.length > 0;
        const postprocessingEnabled = PostprocessingPass.isEnabled(postprocessingProps);
        const antialiasingEnabled = AntialiasingPass.isEnabled(postprocessingProps);
+        const markingEnabled = MarkingPass.isEnabled(markingProps);

        const { x, y, width, height } = camera.viewport;
        renderer.setViewport(x, y, width, height);
@@ -309,6 +314,22 @@ export class DrawPass {
            this.drawTarget.bind();
        }

+        if (markingEnabled) {
+            const markingDepthTest = markingProps.ghostEdgeStrength < 1;
+            if (markingDepthTest) {
+                this.marking.depthTarget.bind();
+                renderer.clear(false);
+                renderer.renderMarkingDepth(scene.primitives, camera, null);
+            }
+
+            this.marking.maskTarget.bind();
+            renderer.clear(false);
+            renderer.renderMarkingMask(scene.primitives, camera, markingDepthTest ? this.marking.depthTarget.texture : null);
+
+            this.marking.update(markingProps);
+            this.marking.render(camera.viewport, postprocessingEnabled ? this.postprocessing.target : this.colorTarget);
+        }
+
        if (helper.debug.isEnabled) {
            helper.debug.syncVisibility();
            renderer.renderBlended(helper.debug.scene, camera, null);
@@ -338,15 +359,16 @@ export class DrawPass {
        this.webgl.gl.flush();
    }

-    render(renderer: Renderer, camera: Camera | StereoCamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, transparentBackground: boolean, postprocessingProps: PostprocessingProps) {
+    render(renderer: Renderer, camera: Camera | StereoCamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, transparentBackground: boolean, postprocessingProps: PostprocessingProps, markingProps: MarkingProps) {
        renderer.setTransparentBackground(transparentBackground);
        renderer.setDrawingBufferSize(this.colorTarget.getWidth(), this.colorTarget.getHeight());
+        renderer.setPixelRatio(this.webgl.pixelRatio);

        if (StereoCamera.is(camera)) {
-            this._render(renderer, camera.left, scene, helper, toDrawingBuffer, transparentBackground, postprocessingProps);
-            this._render(renderer, camera.right, scene, helper, toDrawingBuffer, transparentBackground, postprocessingProps);
+            this._render(renderer, camera.left, scene, helper, toDrawingBuffer, transparentBackground, postprocessingProps, markingProps);
+            this._render(renderer, camera.right, scene, helper, toDrawingBuffer, transparentBackground, postprocessingProps, markingProps);
        } else {
-            this._render(renderer, camera, scene, helper, toDrawingBuffer, transparentBackground, postprocessingProps);
+            this._render(renderer, camera, scene, helper, toDrawingBuffer, transparentBackground, postprocessingProps, markingProps);
        }
    }

--- a/src/mol-canvas3d/passes/image.ts
+++ b/src/mol-canvas3d/passes/image.ts
@@ -17,11 +17,13 @@ import { Viewport } from '../camera/util';
 import { PixelData } from '../../mol-util/image';
 import { Helper } from '../helper/helper';
 import { CameraHelper, CameraHelperParams } from '../helper/camera-helper';
+import { MarkingParams } from './marking';

 export const ImageParams = {
    transparentBackground: PD.Boolean(false),
    multiSample: PD.Group(MultiSampleParams),
    postprocessing: PD.Group(PostprocessingParams),
+    marking: PD.Group(MarkingParams),

    cameraHelper: PD.Group(CameraHelperParams),
 };
@@ -85,7 +87,7 @@ export class ImagePass {
            this.multiSampleHelper.render(this.renderer, this._camera, this.scene, this.helper, false, this.props.transparentBackground, this.props);
            this._colorTarget = this.multiSamplePass.colorTarget;
        } else {
-            this.drawPass.render(this.renderer, this._camera, this.scene, this.helper, false, this.props.transparentBackground, this.props.postprocessing);
+            this.drawPass.render(this.renderer, this._camera, this.scene, this.helper, false, this.props.transparentBackground, this.props.postprocessing, this.props.marking);
            this._colorTarget = this.drawPass.getColorTarget(this.props.postprocessing);
        }
    }
--- a/src/mol-canvas3d/passes/marking.ts
+++ b/src/mol-canvas3d/passes/marking.ts
@@ -0,0 +1,194 @@
+/**
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+
+import { QuadSchema, QuadValues } from '../../mol-gl/compute/util';
+import { ComputeRenderable, createComputeRenderable } from '../../mol-gl/renderable';
+import { DefineSpec, TextureSpec, UniformSpec, Values } from '../../mol-gl/renderable/schema';
+import { ShaderCode } from '../../mol-gl/shader-code';
+import { WebGLContext } from '../../mol-gl/webgl/context';
+import { createComputeRenderItem } from '../../mol-gl/webgl/render-item';
+import { Texture } from '../../mol-gl/webgl/texture';
+import { Vec2, Vec3 } from '../../mol-math/linear-algebra';
+import { ValueCell } from '../../mol-util';
+import { ParamDefinition as PD } from '../../mol-util/param-definition';
+import { quad_vert } from '../../mol-gl/shader/quad.vert';
+import { overlay_frag } from '../../mol-gl/shader/marking/overlay.frag';
+import { Viewport } from '../camera/util';
+import { RenderTarget } from '../../mol-gl/webgl/render-target';
+import { Color } from '../../mol-util/color';
+import { edge_frag } from '../../mol-gl/shader/marking/edge.frag';
+
+export const MarkingParams = {
+    enabled: PD.Boolean(false),
+    highlightEdgeColor: PD.Color(Color.darken(Color.fromNormalizedRgb(1.0, 0.4, 0.6), 1.0)),
+    selectEdgeColor: PD.Color(Color.darken(Color.fromNormalizedRgb(0.2, 1.0, 0.1), 1.0)),
+    edgeScale: PD.Numeric(1, { min: 1, max: 3, step: 1 }, { description: 'Thickness of the edge.' }),
+    ghostEdgeStrength: PD.Numeric(0.3, { min: 0, max: 1, step: 0.1 }, { description: 'Opacity of the hidden edges that are covered by other geometry. When set to 1, one less geometry render pass is done.' }),
+    innerEdgeFactor: PD.Numeric(1.5, { min: 0, max: 3, step: 0.1 }, { description: 'Factor to multiply the inner edge color with - for added contrast.' }),
+};
+export type MarkingProps = PD.Values<typeof MarkingParams>
+
+export class MarkingPass {
+    static isEnabled(props: MarkingProps) {
+        return props.enabled;
+    }
+
+    readonly depthTarget: RenderTarget
+    readonly maskTarget: RenderTarget
+    private readonly edgesTarget: RenderTarget
+
+    private readonly edge: EdgeRenderable
+    private readonly overlay: OverlayRenderable
+
+    constructor(private webgl: WebGLContext, width: number, height: number) {
+        this.depthTarget = webgl.createRenderTarget(width, height);
+        this.maskTarget = webgl.createRenderTarget(width, height);
+        this.edgesTarget = webgl.createRenderTarget(width, height);
+
+        this.edge = getEdgeRenderable(webgl, this.maskTarget.texture);
+        this.overlay = getOverlayRenderable(webgl, this.edgesTarget.texture);
+    }
+
+    private setEdgeState(viewport: Viewport) {
+        const { gl, state } = this.webgl;
+
+        state.enable(gl.SCISSOR_TEST);
+        state.enable(gl.BLEND);
+        state.blendFunc(gl.ONE, gl.ONE);
+        state.blendEquation(gl.FUNC_ADD);
+        state.disable(gl.DEPTH_TEST);
+        state.depthMask(false);
+
+        const { x, y, width, height } = viewport;
+        gl.viewport(x, y, width, height);
+        gl.scissor(x, y, width, height);
+
+        state.clearColor(0, 0, 0, 0);
+        gl.clear(gl.COLOR_BUFFER_BIT);
+    }
+
+    private setOverlayState(viewport: Viewport) {
+        const { gl, state } = this.webgl;
+
+        state.enable(gl.SCISSOR_TEST);
+        state.enable(gl.BLEND);
+        state.blendFunc(gl.SRC_ALPHA, gl.ONE_MINUS_SRC_ALPHA);
+        state.blendEquation(gl.FUNC_ADD);
+        state.disable(gl.DEPTH_TEST);
+        state.depthMask(false);
+
+        const { x, y, width, height } = viewport;
+        gl.viewport(x, y, width, height);
+        gl.scissor(x, y, width, height);
+    }
+
+    setSize(width: number, height: number) {
+        const w = this.depthTarget.getWidth();
+        const h = this.depthTarget.getHeight();
+
+        if (width !== w || height !== h) {
+            this.depthTarget.setSize(width, height);
+            this.maskTarget.setSize(width, height);
+            this.edgesTarget.setSize(width, height);
+
+            ValueCell.update(this.edge.values.uTexSizeInv, Vec2.set(this.edge.values.uTexSizeInv.ref.value, 1 / width, 1 / height));
+            ValueCell.update(this.overlay.values.uTexSizeInv, Vec2.set(this.overlay.values.uTexSizeInv.ref.value, 1 / width, 1 / height));
+        }
+    }
+
+    update(props: MarkingProps) {
+        const { highlightEdgeColor, selectEdgeColor, edgeScale, innerEdgeFactor, ghostEdgeStrength } = props;
+
+        const { values: edgeValues } = this.edge;
+        const _edgeScale = Math.round(edgeScale * this.webgl.pixelRatio);
+        if (edgeValues.dEdgeScale.ref.value !== _edgeScale) {
+            ValueCell.update(edgeValues.dEdgeScale, _edgeScale);
+            this.edge.update();
+        }
+
+        const { values: overlayValues } = this.overlay;
+        ValueCell.update(overlayValues.uHighlightEdgeColor, Color.toVec3Normalized(overlayValues.uHighlightEdgeColor.ref.value, highlightEdgeColor));
+        ValueCell.update(overlayValues.uSelectEdgeColor, Color.toVec3Normalized(overlayValues.uSelectEdgeColor.ref.value, selectEdgeColor));
+        ValueCell.update(overlayValues.uInnerEdgeFactor, innerEdgeFactor);
+        ValueCell.update(overlayValues.uGhostEdgeStrength, ghostEdgeStrength);
+    }
+
+    render(viewport: Viewport, target: RenderTarget | undefined) {
+        this.edgesTarget.bind();
+        this.setEdgeState(viewport);
+        this.edge.render();
+
+        if (target) {
+            target.bind();
+        } else {
+            this.webgl.unbindFramebuffer();
+        }
+        this.setOverlayState(viewport);
+        this.overlay.render();
+    }
+}
+
+//
+
+const EdgeSchema = {
+    ...QuadSchema,
+    tMaskTexture: TextureSpec('texture', 'rgba', 'ubyte', 'linear'),
+    uTexSizeInv: UniformSpec('v2'),
+    dEdgeScale: DefineSpec('number'),
+};
+const EdgeShaderCode = ShaderCode('edge', quad_vert, edge_frag);
+type EdgeRenderable = ComputeRenderable<Values<typeof EdgeSchema>>
+
+function getEdgeRenderable(ctx: WebGLContext, maskTexture: Texture): EdgeRenderable {
+    const width = maskTexture.getWidth();
+    const height = maskTexture.getHeight();
+
+    const values: Values<typeof EdgeSchema> = {
+        ...QuadValues,
+        tMaskTexture: ValueCell.create(maskTexture),
+        uTexSizeInv: ValueCell.create(Vec2.create(1 / width, 1 / height)),
+        dEdgeScale: ValueCell.create(1),
+    };
+
+    const schema = { ...EdgeSchema };
+    const renderItem = createComputeRenderItem(ctx, 'triangles', EdgeShaderCode, schema, values);
+
+    return createComputeRenderable(renderItem, values);
+}
+
+//
+
+const OverlaySchema = {
+    ...QuadSchema,
+    tEdgeTexture: TextureSpec('texture', 'rgba', 'ubyte', 'linear'),
+    uTexSizeInv: UniformSpec('v2'),
+    uHighlightEdgeColor: UniformSpec('v3'),
+    uSelectEdgeColor: UniformSpec('v3'),
+    uGhostEdgeStrength: UniformSpec('f'),
+    uInnerEdgeFactor: UniformSpec('f'),
+};
+const OverlayShaderCode = ShaderCode('overlay', quad_vert, overlay_frag);
+type OverlayRenderable = ComputeRenderable<Values<typeof OverlaySchema>>
+
+function getOverlayRenderable(ctx: WebGLContext, edgeTexture: Texture): OverlayRenderable {
+    const width = edgeTexture.getWidth();
+    const height = edgeTexture.getHeight();
+
+    const values: Values<typeof OverlaySchema> = {
+        ...QuadValues,
+        tEdgeTexture: ValueCell.create(edgeTexture),
+        uTexSizeInv: ValueCell.create(Vec2.create(1 / width, 1 / height)),
+        uHighlightEdgeColor: ValueCell.create(Vec3()),
+        uSelectEdgeColor: ValueCell.create(Vec3()),
+        uGhostEdgeStrength: ValueCell.create(0),
+        uInnerEdgeFactor: ValueCell.create(0),
+    };
+
+    const schema = { ...OverlaySchema };
+    const renderItem = createComputeRenderItem(ctx, 'triangles', OverlayShaderCode, schema, values);
+
+    return createComputeRenderable(renderItem, values);
+}
--- a/src/mol-canvas3d/passes/multi-sample.ts
+++ b/src/mol-canvas3d/passes/multi-sample.ts
@@ -22,9 +22,9 @@ import { Renderer } from '../../mol-gl/renderer';
 import { Scene } from '../../mol-gl/scene';
 import { Helper } from '../helper/helper';
 import { StereoCamera } from '../camera/stereo';
-
 import { quad_vert } from '../../mol-gl/shader/quad.vert';
 import { compose_frag } from '../../mol-gl/shader/compose.frag';
+import { MarkingProps } from './marking';

 const ComposeSchema = {
    ...QuadSchema,
@@ -55,7 +55,11 @@ export const MultiSampleParams = {
 };
 export type MultiSampleProps = PD.Values<typeof MultiSampleParams>

-type Props = { multiSample: MultiSampleProps, postprocessing: PostprocessingProps }
+type Props = {
+    multiSample: MultiSampleProps
+    postprocessing: PostprocessingProps
+    marking: MarkingProps
+}

 export class MultiSamplePass {
    static isEnabled(props: MultiSampleProps) {
@@ -119,7 +123,7 @@ export class MultiSamplePass {
        //
        // This manual approach to MSAA re-renders the scene once for
        // each sample with camera jitter and accumulates the results.
-        const offsetList = JitterVectors[ Math.max(0, Math.min(props.multiSample.sampleLevel, 5)) ];
+        const offsetList = JitterVectors[Math.max(0, Math.min(props.multiSample.sampleLevel, 5))];

        const { x, y, width, height } = camera.viewport;
        const baseSampleWeight = 1.0 / offsetList.length;
@@ -144,7 +148,7 @@ export class MultiSamplePass {
            ValueCell.update(compose.values.uWeight, sampleWeight);

            // render scene
-            drawPass.render(renderer, camera, scene, helper, false, transparentBackground, props.postprocessing);
+            drawPass.render(renderer, camera, scene, helper, false, transparentBackground, props.postprocessing, props.marking);

            // compose rendered scene with compose target
            composeTarget.bind();
@@ -186,7 +190,7 @@ export class MultiSamplePass {
        //
        // This manual approach to MSAA re-renders the scene once for
        // each sample with camera jitter and accumulates the results.
-        const offsetList = JitterVectors[ Math.max(0, Math.min(props.multiSample.sampleLevel, 5)) ];
+        const offsetList = JitterVectors[Math.max(0, Math.min(props.multiSample.sampleLevel, 5))];

        if (sampleIndex === -2 || sampleIndex >= offsetList.length) return -2;

@@ -194,7 +198,7 @@ export class MultiSamplePass {
        const sampleWeight = 1.0 / offsetList.length;

        if (sampleIndex === -1) {
-            drawPass.render(renderer, camera, scene, helper, false, transparentBackground, props.postprocessing);
+            drawPass.render(renderer, camera, scene, helper, false, transparentBackground, props.postprocessing, props.marking);
            ValueCell.update(compose.values.uWeight, 1.0);
            ValueCell.update(compose.values.tColor, drawPass.getColorTarget(props.postprocessing).texture);
            compose.update();
@@ -222,7 +226,7 @@ export class MultiSamplePass {
                camera.update();

                // render scene
-                drawPass.render(renderer, camera, scene, helper, false, transparentBackground, props.postprocessing);
+                drawPass.render(renderer, camera, scene, helper, false, transparentBackground, props.postprocessing, props.marking);

                // compose rendered scene with compose target
                composeTarget.bind();
@@ -240,7 +244,7 @@ export class MultiSamplePass {
                compose.render();

                sampleIndex += 1;
-                if (sampleIndex >= offsetList.length ) break;
+                if (sampleIndex >= offsetList.length) break;
            }
        }

@@ -274,33 +278,33 @@ export class MultiSamplePass {

 const JitterVectors = [
    [
-        [ 0, 0 ]
+        [0, 0]
    ],
    [
-        [ 4, 4 ], [ -4, -4 ]
+        [4, 4], [-4, -4]
    ],
    [
-        [ -2, -6 ], [ 6, -2 ], [ -6, 2 ], [ 2, 6 ]
+        [-2, -6], [6, -2], [-6, 2], [2, 6]
    ],
    [
-        [ 1, -3 ], [ -1, 3 ], [ 5, 1 ], [ -3, -5 ],
-        [ -5, 5 ], [ -7, -1 ], [ 3, 7 ], [ 7, -7 ]
+        [1, -3], [-1, 3], [5, 1], [-3, -5],
+        [-5, 5], [-7, -1], [3, 7], [7, -7]
    ],
    [
-        [ 1, 1 ], [ -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 ]
+        [1, 1], [-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 ],
-        [ -1, -4 ], [ -2, -2 ], [ -6, -1 ], [ -4, 0 ],
-        [ -7, 1 ], [ -1, 2 ], [ -6, 3 ], [ -3, 3 ],
-        [ -7, 6 ], [ -3, 6 ], [ -5, 7 ], [ -1, 7 ],
-        [ 5, -7 ], [ 1, -6 ], [ 6, -5 ], [ 4, -4 ],
-        [ 2, -3 ], [ 7, -2 ], [ 1, -1 ], [ 4, -1 ],
-        [ 2, 1 ], [ 6, 2 ], [ 0, 4 ], [ 4, 4 ],
-        [ 2, 5 ], [ 7, 5 ], [ 5, 6 ], [ 3, 7 ]
+        [-4, -7], [-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],
+        [5, -7], [1, -6], [6, -5], [4, -4],
+        [2, -3], [7, -2], [1, -1], [4, -1],
+        [2, 1], [6, 2], [0, 4], [4, 4],
+        [2, 5], [7, 5], [5, 6], [3, 7]
    ]
 ];

--- a/src/mol-canvas3d/passes/pick.ts
+++ b/src/mol-canvas3d/passes/pick.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */
@@ -11,6 +11,7 @@ import { WebGLContext } from '../../mol-gl/webgl/context';
 import { GraphicsRenderVariant } from '../../mol-gl/webgl/render-item';
 import { RenderTarget } from '../../mol-gl/webgl/render-target';
 import { Vec3 } from '../../mol-math/linear-algebra';
+import { spiral2d } from '../../mol-math/misc';
 import { decodeFloatRGB, unpackRGBAToDepth } from '../../mol-util/float-packing';
 import { Camera, ICamera } from '../camera';
 import { StereoCamera } from '../camera/stereo';
@@ -88,6 +89,7 @@ export class PickPass {

        this.groupPickTarget.bind();
        this.renderVariant(renderer, camera, scene, helper, 'pickGroup');
+        // printTexture(this.webgl, this.groupPickTarget.texture, { id: 'group' })

        this.depthPickTarget.bind();
        this.renderVariant(renderer, camera, scene, helper, 'depth');
@@ -111,6 +113,8 @@ export class PickHelper {
    private pickHeight: number
    private halfPickWidth: number

+    private spiral: [number, number][]
+
    private setupBuffers() {
        const bufferSize = this.pickWidth * this.pickHeight * 4;
        if (!this.objectBuffer || this.objectBuffer.length !== bufferSize) {
@@ -138,6 +142,8 @@ export class PickHelper {

            this.setupBuffers();
        }
+
+        this.spiral = spiral2d(Math.round(this.pickScale * this.pickPadding));
    }

    private syncBuffers() {
@@ -177,6 +183,7 @@ export class PickHelper {

        renderer.setTransparentBackground(false);
        renderer.setDrawingBufferSize(this.pickPass.objectPickTarget.getWidth(), this.pickPass.objectPickTarget.getHeight());
+        renderer.setPixelRatio(this.pickScale);

        if (StereoCamera.is(camera)) {
            renderer.setViewport(pickX, pickY, halfPickWidth, pickHeight);
@@ -192,7 +199,7 @@ export class PickHelper {
        this.dirty = false;
    }

-    identify(x: number, y: number, camera: Camera | StereoCamera): PickData | undefined {
+    private identifyInternal(x: number, y: number, camera: Camera | StereoCamera): PickData | undefined {
        const { webgl, pickScale } = this;
        if (webgl.isContextLost) return;

@@ -251,7 +258,14 @@ export class PickHelper {
        return { id: { objectId, instanceId, groupId }, position };
    }

-    constructor(private webgl: WebGLContext, private renderer: Renderer, private scene: Scene, private helper: Helper, private pickPass: PickPass, viewport: Viewport) {
+    identify(x: number, y: number, camera: Camera | StereoCamera): PickData | undefined {
+        for (const d of this.spiral) {
+            const pickData = this.identifyInternal(x + d[0], y + d[1], camera);
+            if (pickData) return pickData;
+        }
+    }
+
+    constructor(private webgl: WebGLContext, private renderer: Renderer, private scene: Scene, private helper: Helper, private pickPass: PickPass, viewport: Viewport, readonly pickPadding = 1) {
        this.setViewport(viewport.x, viewport.y, viewport.width, viewport.height);
    }
 }
--- a/src/mol-canvas3d/passes/postprocessing.ts
+++ b/src/mol-canvas3d/passes/postprocessing.ts
@@ -154,10 +154,10 @@ function getSsaoBlurRenderable(ctx: WebGLContext, ssaoDepthTexture: Texture, dir
 }

 function getBlurKernel(kernelSize: number): number[] {
-    let sigma = kernelSize / 3.0;
-    let halfKernelSize = Math.floor((kernelSize + 1) / 2);
+    const sigma = kernelSize / 3.0;
+    const halfKernelSize = Math.floor((kernelSize + 1) / 2);

-    let kernel = [];
+    const kernel = [];
    for (let x = 0; x < halfKernelSize; x++) {
        kernel.push((1.0 / ((Math.sqrt(2 * Math.PI)) * sigma)) * Math.exp(-x * x / (2 * sigma * sigma)));
    }
@@ -166,7 +166,7 @@ function getBlurKernel(kernelSize: number): number[] {
 }

 function getSamples(vectorSamples: Vec3[], nSamples: number): number[] {
-    let samples = [];
+    const samples = [];
    for (let i = 0; i < nSamples; i++) {
        let scale = (i * i + 2.0 * i + 1) / (nSamples * nSamples);
        scale = 0.1 + scale * (1.0 - 0.1);
@@ -241,7 +241,7 @@ function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, d
 export const PostprocessingParams = {
    occlusion: PD.MappedStatic('on', {
        on: PD.Group({
-            samples: PD.Numeric(32, {min: 1, max: 256, step: 1}),
+            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.' }),
            bias: PD.Numeric(0.8, { min: 0, max: 3, step: 0.1 }),
            blurKernelSize: PD.Numeric(15, { min: 1, max: 25, step: 2 }),
@@ -314,7 +314,7 @@ export class PostprocessingPass {

        this.randomHemisphereVector = [];
        for (let i = 0; i < 256; i++) {
-            let v = Vec3();
+            const v = Vec3();
            v[0] = Math.random() * 2.0 - 1.0;
            v[1] = Math.random() * 2.0 - 1.0;
            v[2] = Math.random();
@@ -376,7 +376,7 @@ export class PostprocessingPass {
        const outlinesEnabled = props.outline.name === 'on';
        const occlusionEnabled = props.occlusion.name === 'on';

-        let invProjection = Mat4.identity();
+        const invProjection = Mat4.identity();
        Mat4.invert(invProjection, camera.projection);

        if (props.occlusion.name === 'on') {
--- a/src/mol-canvas3d/passes/smaa.ts
+++ b/src/mol-canvas3d/passes/smaa.ts
@@ -25,8 +25,8 @@ import { Viewport } from '../camera/util';
 import { isDebugMode } from '../../mol-util/debug';

 export const SmaaParams = {
-    edgeThreshold:PD.Numeric(0.1, { min: 0.05, max: 0.15, step: 0.01 }),
-    maxSearchSteps:PD.Numeric(16, { min: 0, max: 32, step: 1 }),
+    edgeThreshold: PD.Numeric(0.1, { min: 0.05, max: 0.15, step: 0.01 }),
+    maxSearchSteps: PD.Numeric(16, { min: 0, max: 32, step: 1 }),
 };
 export type SmaaProps = PD.Values<typeof SmaaParams>

--- a/src/mol-canvas3d/util.ts
+++ b/src/mol-canvas3d/util.ts
@@ -12,7 +12,7 @@ export function setCanvasSize(canvas: HTMLCanvasElement, width: number, height:
 }

 /** Resize canvas to container element taking `devicePixelRatio` into account */
-export function resizeCanvas (canvas: HTMLCanvasElement, container: HTMLElement, scale = 1) {
+export function resizeCanvas(canvas: HTMLCanvasElement, container: HTMLElement, scale = 1) {
    let width = window.innerWidth;
    let height = window.innerHeight;
    if (container !== document.body) {
--- a/src/mol-data/db/_spec/table.spec.ts
+++ b/src/mol-data/db/_spec/table.spec.ts
@@ -100,7 +100,7 @@ describe('table', () => {
            n: Column.ofArray({ array: ['row1', 'row2'], schema: Column.Schema.str }),
        });
        const s = { x: Column.Schema.int, y: Column.Schema.int };
-        const picked = Table.pickColumns(s, t, { y: Column.ofArray({ array: [3, 4], schema: Column.Schema.int })});
+        const picked = Table.pickColumns(s, t, { y: Column.ofArray({ array: [3, 4], schema: Column.Schema.int }) });
        expect(picked._columns).toEqual(['x', 'y']);
        expect(picked._rowCount).toEqual(2);
        expect(picked.x.toArray()).toEqual([10, -1]);
--- a/src/mol-data/generic/_spec/linked-list.spec.ts
+++ b/src/mol-data/generic/_spec/linked-list.spec.ts
@@ -33,21 +33,21 @@ describe('linked list', () => {
        expect(list.count).toBe(5);
    });

-    it ('remove', () => {
+    it('remove', () => {
        const list = create([1, 2, 3, 4]);
-        let fst = list.removeFirst();
+        const fst = list.removeFirst();
        expect(fst).toBe(1);
        expect(list.last!.value).toBe(4);
        expect(list.count).toBe(3);
        expect(toArray(list)).toEqual([2, 3, 4]);

-        let last = list.removeLast();
+        const last = list.removeLast();
        expect(last).toBe(4);
        expect(list.last!.value).toBe(3);
        expect(list.count).toBe(2);
        expect(toArray(list)).toEqual([2, 3]);

-        let n3 = list.find(3)!;
+        const n3 = list.find(3)!;
        list.remove(n3);
        expect(list.first!.value).toBe(2);
        expect(list.last!.value).toBe(2);
--- a/src/mol-data/int/impl/interval.ts
+++ b/src/mol-data/int/impl/interval.ts
@@ -16,7 +16,7 @@ export const start = Tuple.fst;
 export const end = Tuple.snd;
 export const min = Tuple.fst;
 export function max(i: Tuple) { return Tuple.snd(i) - 1; }
-export function size(i: Tuple) { return Tuple.snd(i) - Tuple.fst(i); }
+export const size = Tuple.diff;
 export const hashCode = Tuple.hashCode;
 export const toString = Tuple.toString;

--- a/src/mol-data/int/impl/ordered-set.ts
+++ b/src/mol-data/int/impl/ordered-set.ts
@@ -19,7 +19,7 @@ export const ofBounds = I.ofBounds;
 export function ofSortedArray(xs: Nums): OrderedSetImpl {
    if (!xs.length) return Empty;
    // check if the array is just a range
-    if (xs[xs.length - 1] - xs[0] + 1 === xs.length) return I.ofRange(xs[0], xs[xs.length - 1]);
+    if (S.isRange(xs)) return I.ofRange(xs[0], xs[xs.length - 1]);
    return xs as any;
 }

--- a/src/mol-data/int/impl/sorted-array.ts
+++ b/src/mol-data/int/impl/sorted-array.ts
@@ -22,9 +22,10 @@ export function ofRange(min: number, max: number) {
    return ret;
 }
 export function is(xs: any): xs is Nums { return xs && (Array.isArray(xs) || !!xs.buffer); }
+export function isRange(xs: Nums) { return xs[xs.length - 1] - xs[0] + 1 === xs.length; }

 export function start(xs: Nums) { return xs[0]; }
-export function end(xs: Nums) { return xs[xs.length - 1] + 1;  }
+export function end(xs: Nums) { return xs[xs.length - 1] + 1; }
 export function min(xs: Nums) { return xs[0]; }
 export function max(xs: Nums) { return xs[xs.length - 1]; }
 export function size(xs: Nums) { return xs.length; }
@@ -59,9 +60,11 @@ export function getAt(xs: Nums, i: number) { return xs[i]; }

 export function areEqual(a: Nums, b: Nums) {
    if (a === b) return true;
-    const aSize = a.length;
+    let aSize = a.length;
    if (aSize !== b.length || a[0] !== b[0] || a[aSize - 1] !== b[aSize - 1]) return false;
-    for (let i = 0; i < aSize; i++) {
+    if (isRange(a)) return true;
+    aSize--;
+    for (let i = 1; i < aSize; i++) {
        if (a[i] !== b[i]) return false;
    }
    return true;
@@ -340,7 +343,7 @@ export function deduplicate(xs: Nums) {
 }

 export function indicesOf(a: Nums, b: Nums): Nums {
-    if (a === b) return ofSortedArray(createRangeArray(0, a.length - 1));
+    if (areEqual(a, b)) return ofSortedArray(createRangeArray(0, a.length - 1));

    const { startI: sI, startJ: sJ, endI, endJ } = getSuitableIntersectionRange(a, b);
    let i = sI, j = sJ;
--- a/src/mol-data/int/sorted-array.ts
+++ b/src/mol-data/int/sorted-array.ts
@@ -17,6 +17,7 @@ namespace SortedArray {
    /** create sorted array [min, max) (it does NOT contain the max value) */
    export const ofBounds: <T extends number = number>(min: T, max: T) => SortedArray<T> = (min, max) => Impl.ofRange(min, max - 1) as any;
    export const is: <T extends number = number>(v: any) => v is SortedArray<T> = Impl.is as any;
+    export const isRange: <T extends number = number>(array: ArrayLike<number>) => boolean = Impl.isRange as any;

    export const has: <T extends number = number>(array: SortedArray<T>, x: T) => boolean = Impl.has as any;
    /** Returns the index of `x` in `set` or -1 if not found. */
--- a/src/mol-data/int/tuple.ts
+++ b/src/mol-data/int/tuple.ts
@@ -15,7 +15,7 @@ interface IntTuple { '@type': 'int-tuple' }
 namespace IntTuple {
    export const Zero: IntTuple = 0 as any;

-    const { _int32, _float64, _int32_1, _float64_1 } = (function() {
+    const { _int32, _float64, _int32_1, _float64_1 } = (function () {
        const data = new ArrayBuffer(8);
        const data_1 = new ArrayBuffer(8);
        return {
@@ -36,6 +36,12 @@ namespace IntTuple {
        return _float64[0] as any;
    }

+    /** snd - fst */
+    export function diff(t: IntTuple) {
+        _float64[0] = t as any;
+        return _int32[1] - _int32[0];
+    }
+
    export function fst(t: IntTuple): number {
        _float64[0] = t as any;
        return _int32[0];
--- a/src/mol-data/util/_spec/chunked-array.spec.ts
+++ b/src/mol-data/util/_spec/chunked-array.spec.ts
@@ -8,14 +8,14 @@ import { ChunkedArray } from '../chunked-array';

 describe('Chunked Array', () => {
    it('creation', () => {
-        const arr  = ChunkedArray.create<number, 2>(Array, 2, 2);
+        const arr = ChunkedArray.create<number, 2>(Array, 2, 2);
        ChunkedArray.add2(arr, 1, 2);
        ChunkedArray.add2(arr, 3, 4);
        expect(ChunkedArray.compact(arr)).toEqual([1, 2, 3, 4]);
    });

    it('initial', () => {
-        const arr  = ChunkedArray.create(Int32Array, 2, 6, new Int32Array([1, 2, 3, 4]));
+        const arr = ChunkedArray.create(Int32Array, 2, 6, new Int32Array([1, 2, 3, 4]));
        ChunkedArray.add2(arr, 4, 3);
        ChunkedArray.add2(arr, 2, 1);
        ChunkedArray.add2(arr, 5, 6);
@@ -23,13 +23,13 @@ describe('Chunked Array', () => {
    });

    it('add many', () => {
-        const arr  = ChunkedArray.create<number, 2>(Array, 2, 2);
+        const arr = ChunkedArray.create<number, 2>(Array, 2, 2);
        ChunkedArray.addMany(arr, [1, 2, 3, 4]);
        expect(ChunkedArray.compact(arr)).toEqual([1, 2, 3, 4]);
    });

    it('resize', () => {
-        const arr  = ChunkedArray.create<number, 2>(Int32Array, 2, 2);
+        const arr = ChunkedArray.create<number, 2>(Int32Array, 2, 2);
        ChunkedArray.add2(arr, 1, 2);
        ChunkedArray.add2(arr, 3, 4);
        ChunkedArray.add2(arr, 5, 6);
@@ -39,7 +39,7 @@ describe('Chunked Array', () => {
    });

    it('resize-fraction', () => {
-        const arr  = ChunkedArray.create<number, 2>(Int32Array, 2, 2.5);
+        const arr = ChunkedArray.create<number, 2>(Int32Array, 2, 2.5);
        ChunkedArray.add2(arr, 1, 2);
        ChunkedArray.add2(arr, 3, 4);
        ChunkedArray.add2(arr, 5, 6);
--- a/src/mol-data/util/chunked-array.ts
+++ b/src/mol-data/util/chunked-array.ts
@@ -36,7 +36,7 @@ namespace ChunkedArray {
    }

    function allocateNext(array: ChunkedArray<any, any>) {
-        let nextSize = array.growBy * array.elementSize;
+        const nextSize = array.growBy * array.elementSize;
        array.currentSize = nextSize;
        array.currentIndex = 0;
        array.currentChunk = new array.ctor(nextSize);
--- a/src/mol-data/util/hash-functions.ts
+++ b/src/mol-data/util/hash-functions.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2021 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>
@@ -70,6 +70,15 @@ export function sortedCantorPairing(a: number, b: number) {
    return a < b ? cantorPairing(a, b) : cantorPairing(b, a);
 }

+export function invertCantorPairing(out: [number, number], z: number) {
+    const w = Math.floor((Math.sqrt(8 * z + 1) - 1) / 2);
+    const t = (w * w + w) / 2;
+    const y = z - t;
+    out[0] = w - y;
+    out[1] = y;
+    return out;
+}
+
 /**
 * 32 bit FNV-1a hash, see http://isthe.com/chongo/tech/comp/fnv/
 */
--- a/src/mol-geo/geometry/base.ts
+++ b/src/mol-geo/geometry/base.ts
@@ -52,8 +52,8 @@ export namespace BaseGeometry {
        if (!transform) transform = createIdentityTransform();
        const locationIterator = LocationIterator(1, transform.instanceCount.ref.value, 1, () => NullLocation, false, () => false);
        const theme: Theme = {
-            color: UniformColorTheme({}, { value: colorValue}),
-            size: UniformSizeTheme({}, { value: sizeValue})
+            color: UniformColorTheme({}, { value: colorValue }),
+            size: UniformSizeTheme({}, { value: sizeValue })
        };
        return { transform, locationIterator, theme };
    }
--- a/src/mol-geo/geometry/cylinders/cylinders.ts
+++ b/src/mol-geo/geometry/cylinders/cylinders.ts
@@ -6,7 +6,7 @@

 import { ValueCell } from '../../../mol-util';
 import { Mat4, Vec3, Vec4 } from '../../../mol-math/linear-algebra';
-import { transformPositionArray, GroupMapping, createGroupMapping} from '../../util';
+import { transformPositionArray, GroupMapping, createGroupMapping } from '../../util';
 import { GeometryUtils } from '../geometry';
 import { createColors } from '../color-data';
 import { createMarkers } from '../marker-data';
--- a/src/mol-geo/geometry/direct-volume/direct-volume.ts
+++ b/src/mol-geo/geometry/direct-volume/direct-volume.ts
@@ -9,7 +9,7 @@ import { LocationIterator, PositionLocation } from '../../../mol-geo/util/locati
 import { RenderableState } from '../../../mol-gl/renderable';
 import { DirectVolumeValues } from '../../../mol-gl/renderable/direct-volume';
 import { calculateTransformBoundingSphere } from '../../../mol-gl/renderable/util';
-import { Texture } from '../../../mol-gl/webgl/texture';
+import { createNullTexture, Texture } from '../../../mol-gl/webgl/texture';
 import { Box3D, Sphere3D } from '../../../mol-math/geometry';
 import { Mat4, Vec2, Vec3, Vec4 } from '../../../mol-math/linear-algebra';
 import { Theme } from '../../../mol-theme/theme';
@@ -129,7 +129,15 @@ export namespace DirectVolume {
    }

    export function createEmpty(directVolume?: DirectVolume): DirectVolume {
-        return {} as DirectVolume; // TODO
+        const bbox = Box3D();
+        const gridDimension = Vec3();
+        const transform = Mat4.identity();
+        const unitToCartn = Mat4.identity();
+        const cellDim = Vec3();
+        const texture = createNullTexture();
+        const stats = Grid.One.stats;
+        const packedGroup = false;
+        return create(bbox, gridDimension, transform, unitToCartn, cellDim, texture, stats, packedGroup, directVolume);
    }

    export function createRenderModeParam(stats?: Grid['stats']) {
--- a/src/mol-geo/geometry/image/image.ts
+++ b/src/mol-geo/geometry/image/image.ts
@@ -7,7 +7,7 @@
 import { hashFnv32a } from '../../../mol-data/util';
 import { LocationIterator } from '../../../mol-geo/util/location-iterator';
 import { RenderableState } from '../../../mol-gl/renderable';
-import { calculateTransformBoundingSphere, TextureImage } from '../../../mol-gl/renderable/util';
+import { calculateTransformBoundingSphere, createTextureImage, TextureImage } from '../../../mol-gl/renderable/util';
 import { Sphere3D } from '../../../mol-math/geometry';
 import { Vec2, Vec4, Vec3 } from '../../../mol-math/linear-algebra';
 import { Theme } from '../../../mol-theme/theme';
@@ -113,7 +113,10 @@ namespace Image {
    }

    export function createEmpty(image?: Image): Image {
-        return {} as Image; // TODO
+        const imageTexture = createTextureImage(0, 4, Uint8Array);
+        const corners = image ? image.cornerBuffer.ref.value : new Float32Array(8 * 3);
+        const groupTexture = createTextureImage(0, 4, Uint8Array);
+        return create(imageTexture, corners, groupTexture, image);
    }

    export const Params = {
--- a/src/mol-geo/geometry/lines/lines.ts
+++ b/src/mol-geo/geometry/lines/lines.ts
@@ -6,7 +6,7 @@

 import { ValueCell } from '../../../mol-util';
 import { Mat4, Vec3, Vec4 } from '../../../mol-math/linear-algebra';
-import { transformPositionArray, GroupMapping, createGroupMapping} from '../../util';
+import { transformPositionArray, GroupMapping, createGroupMapping } from '../../util';
 import { GeometryUtils } from '../geometry';
 import { createColors } from '../color-data';
 import { createMarkers } from '../marker-data';
@@ -164,7 +164,7 @@ export namespace Lines {

    export const Params = {
        ...BaseGeometry.Params,
-        sizeFactor: PD.Numeric(1.5, { min: 0, max: 10, step: 0.1 }),
+        sizeFactor: PD.Numeric(3, { min: 0, max: 10, step: 0.1 }),
        lineSizeAttenuation: PD.Boolean(false),
    };
    export type Params = typeof Params
--- a/src/mol-geo/geometry/marker-data.ts
+++ b/src/mol-geo/geometry/marker-data.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */
@@ -9,20 +9,75 @@ import { Vec2 } from '../../mol-math/linear-algebra';
 import { TextureImage, createTextureImage } from '../../mol-gl/renderable/util';

 export type MarkerData = {
+    uMarker: ValueCell<number>,
    tMarker: ValueCell<TextureImage<Uint8Array>>
    uMarkerTexDim: ValueCell<Vec2>
+    dMarkerType: ValueCell<string>,
+    markerAverage: ValueCell<number>
+    markerStatus: ValueCell<number>
+}
+
+const MarkerCountLut = new Uint8Array(0x0303 + 1);
+MarkerCountLut[0x0001] = 1;
+MarkerCountLut[0x0002] = 1;
+MarkerCountLut[0x0003] = 1;
+MarkerCountLut[0x0100] = 1;
+MarkerCountLut[0x0200] = 1;
+MarkerCountLut[0x0300] = 1;
+MarkerCountLut[0x0101] = 2;
+MarkerCountLut[0x0201] = 2;
+MarkerCountLut[0x0301] = 2;
+MarkerCountLut[0x0102] = 2;
+MarkerCountLut[0x0202] = 2;
+MarkerCountLut[0x0302] = 2;
+MarkerCountLut[0x0103] = 2;
+MarkerCountLut[0x0203] = 2;
+MarkerCountLut[0x0303] = 2;
+
+/**
+ * Calculates the average number of entries that have any marker flag set.
+ *
+ * For alternative implementations and performance tests see
+ * `src\perf-tests\markers-average.ts`.
+ */
+export function getMarkersAverage(array: Uint8Array, count: number): number {
+    if (count === 0) return 0;
+
+    const view = new Uint32Array(array.buffer, 0, array.buffer.byteLength >> 2);
+    const viewEnd = (count - 4) >> 2;
+    const backStart = 4 * viewEnd;
+
+    let sum = 0;
+    for (let i = 0; i < viewEnd; ++i) {
+        const v = view[i];
+        sum += MarkerCountLut[v & 0xFFFF] + MarkerCountLut[v >> 16];
+    }
+    for (let i = backStart; i < count; ++i) {
+        sum += array[i] && 1;
+    }
+    return sum / count;
 }

 export function createMarkers(count: number, markerData?: MarkerData): MarkerData {
    const markers = createTextureImage(Math.max(1, count), 1, Uint8Array, markerData && markerData.tMarker.ref.value.array);
+    const average = getMarkersAverage(markers.array, count);
+    const status = average === 0 ? 0 : -1;
    if (markerData) {
+        ValueCell.updateIfChanged(markerData.uMarker, 0);
        ValueCell.update(markerData.tMarker, markers);
        ValueCell.update(markerData.uMarkerTexDim, Vec2.create(markers.width, markers.height));
+        ValueCell.updateIfChanged(markerData.dMarkerType, status === -1 ? 'groupInstance' : 'uniform');
+        ValueCell.updateIfChanged(markerData.markerAverage, average);
+        ValueCell.updateIfChanged(markerData.markerStatus, status);
        return markerData;
    } else {
        return {
+            uMarker: ValueCell.create(0),
            tMarker: ValueCell.create(markers),
            uMarkerTexDim: ValueCell.create(Vec2.create(markers.width, markers.height)),
+            markerAverage: ValueCell.create(average),
+            markerStatus: ValueCell.create(status),
+            dMarkerType: ValueCell.create('uniform'),
        };
    }
 }
@@ -30,13 +85,21 @@ export function createMarkers(count: number, markerData?: MarkerData): MarkerDat
 const emptyMarkerTexture = { array: new Uint8Array(1), width: 1, height: 1 };
 export function createEmptyMarkers(markerData?: MarkerData): MarkerData {
    if (markerData) {
+        ValueCell.updateIfChanged(markerData.uMarker, 0);
        ValueCell.update(markerData.tMarker, emptyMarkerTexture);
        ValueCell.update(markerData.uMarkerTexDim, Vec2.create(1, 1));
+        ValueCell.updateIfChanged(markerData.dMarkerType, 'uniform');
+        ValueCell.updateIfChanged(markerData.markerAverage, 0);
+        ValueCell.updateIfChanged(markerData.markerStatus, 0);
        return markerData;
    } else {
        return {
+            uMarker: ValueCell.create(0),
            tMarker: ValueCell.create(emptyMarkerTexture),
            uMarkerTexDim: ValueCell.create(Vec2.create(1, 1)),
+            markerAverage: ValueCell.create(0),
+            markerStatus: ValueCell.create(0),
+            dMarkerType: ValueCell.create('uniform'),
        };
    }
 }
--- a/src/mol-geo/geometry/mesh/builder/ribbon.ts
+++ b/src/mol-geo/geometry/mesh/builder/ribbon.ts
@@ -36,7 +36,7 @@ const torsionVector = Vec3();
 export function addRibbon(state: MeshBuilder.State, controlPoints: ArrayLike<number>, normalVectors: ArrayLike<number>, binormalVectors: ArrayLike<number>, linearSegments: number, widthValues: ArrayLike<number>, heightValues: ArrayLike<number>, arrowHeight: number) {
    const { currentGroup, vertices, normals, indices, groups } = state;

-    let vertexCount = vertices.elementCount;
+    const vertexCount = vertices.elementCount;
    let offsetLength = 0;

    if (arrowHeight > 0) {
--- a/src/mol-geo/geometry/mesh/builder/sheet.ts
+++ b/src/mol-geo/geometry/mesh/builder/sheet.ts
@@ -85,7 +85,7 @@ function addCap(offset: number, state: MeshBuilder.State, controlPoints: ArrayLi
 export function addSheet(state: MeshBuilder.State, controlPoints: ArrayLike<number>, normalVectors: ArrayLike<number>, binormalVectors: ArrayLike<number>, linearSegments: number, widthValues: ArrayLike<number>, heightValues: ArrayLike<number>, arrowHeight: number, startCap: boolean, endCap: boolean) {
    const { currentGroup, vertices, normals, indices, groups } = state;

-    let vertexCount = vertices.elementCount;
+    const vertexCount = vertices.elementCount;
    let offsetLength = 0;

    if (arrowHeight > 0) {
--- a/src/mol-geo/geometry/mesh/color-smoothing.ts
+++ b/src/mol-geo/geometry/mesh/color-smoothing.ts
@@ -39,7 +39,7 @@ export function calcMeshColorSmoothing(input: ColorSmoothingInput, resolution: n
    Vec3.add(gridDim, gridDim, Vec3.create(2, 2, 2));
    const { min } = box;

-    const [ xn, yn ] = gridDim;
+    const [xn, yn] = gridDim;
    const { width, height } = getVolumeTexture2dLayout(gridDim);
    // console.log({ width, height, dim });

@@ -104,7 +104,7 @@ export function calcMeshColorSmoothing(input: ColorSmoothingInput, resolution: n
                        const d = Math.sqrt(dx * dx + dy * dy + dz * dz);
                        if (d > p) continue;

-                        let s = p - d;
+                        const s = p - d;
                        const index = getIndex(xi, yi, zi);
                        data[index] += r * s;
                        data[index + 1] += g * s;
--- a/src/mol-geo/geometry/mesh/mesh-builder.ts
+++ b/src/mol-geo/geometry/mesh/mesh-builder.ts
@@ -61,8 +61,8 @@ export namespace MeshBuilder {

        v3triangleNormal(tmpV, a, b, c);
        for (let i = 0; i < 3; ++i) {
-            caAdd3(normals, tmpV[0], tmpV[1], tmpV[2]);  // normal
-            caAdd(groups, currentGroup);  // group
+            caAdd3(normals, tmpV[0], tmpV[1], tmpV[2]); // normal
+            caAdd(groups, currentGroup); // group
        }
        caAdd3(indices, offset, offset + 1, offset + 2);
    }
@@ -152,7 +152,7 @@ export namespace MeshBuilder {
        });
    }

-    export function getMesh (state: State): Mesh {
+    export function getMesh(state: State): Mesh {
        const { vertices, normals, indices, groups, mesh } = state;
        const vb = ChunkedArray.compact(vertices, true) as Float32Array;
        const ib = ChunkedArray.compact(indices, true) as Uint32Array;
--- a/src/mol-geo/geometry/mesh/mesh.ts
+++ b/src/mol-geo/geometry/mesh/mesh.ts
@@ -8,13 +8,13 @@
 import { ValueCell } from '../../../mol-util';
 import { Vec3, Mat4, Mat3, Vec4 } from '../../../mol-math/linear-algebra';
 import { Sphere3D } from '../../../mol-math/geometry';
-import { transformPositionArray, transformDirectionArray, computeIndexedVertexNormals, GroupMapping, createGroupMapping} from '../../util';
+import { transformPositionArray, transformDirectionArray, computeIndexedVertexNormals, GroupMapping, createGroupMapping } from '../../util';
 import { GeometryUtils } from '../geometry';
 import { createMarkers } from '../marker-data';
 import { TransformData } from '../transform-data';
 import { LocationIterator, PositionLocation } from '../../util/location-iterator';
 import { createColors } from '../color-data';
-import { ChunkedArray, hashFnv32a } from '../../../mol-data/util';
+import { ChunkedArray, hashFnv32a, invertCantorPairing, sortedCantorPairing } from '../../../mol-data/util';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
 import { calculateInvariantBoundingSphere, calculateTransformBoundingSphere } from '../../../mol-gl/renderable/util';
 import { Theme } from '../../../mol-theme/theme';
@@ -25,6 +25,8 @@ import { createEmptyOverpaint } from '../overpaint-data';
 import { createEmptyTransparency } from '../transparency-data';
 import { createEmptyClipping } from '../clipping-data';
 import { RenderableState } from '../../../mol-gl/renderable';
+import { arraySetAdd } from '../../../mol-util/array';
+import { degToRad } from '../../../mol-math/misc';

 export interface Mesh {
    readonly kind: 'mesh',
@@ -332,10 +334,10 @@ export namespace Mesh {
        mesh.vertexCount = newVertexCount;
        mesh.triangleCount = newTriangleCount;

-        ValueCell.update(vertexBuffer, newVb) as ValueCell<Float32Array>;
-        ValueCell.update(groupBuffer, newGb) as ValueCell<Float32Array>;
-        ValueCell.update(indexBuffer, newIb) as ValueCell<Uint32Array>;
-        ValueCell.update(normalBuffer, newNb) as ValueCell<Float32Array>;
+        ValueCell.update(vertexBuffer, newVb);
+        ValueCell.update(groupBuffer, newGb);
+        ValueCell.update(indexBuffer, newIb);
+        ValueCell.update(normalBuffer, newNb);

        // keep some original data, e.g., for geometry export
        (mesh.meta.originalData as OriginalData) = { indexBuffer: ib, vertexCount, triangleCount };
@@ -345,6 +347,276 @@ export namespace Mesh {

    //

+    function getNeighboursMap(mesh: Mesh) {
+        const { vertexCount, triangleCount } = mesh;
+        const elements = mesh.indexBuffer.ref.value;
+
+        const neighboursMap: number[][] = [];
+        for (let i = 0; i < vertexCount; ++i) {
+            neighboursMap[i] = [];
+        }
+
+        for (let i = 0; i < triangleCount; ++i) {
+            const v1 = elements[i * 3];
+            const v2 = elements[i * 3 + 1];
+            const v3 = elements[i * 3 + 2];
+            arraySetAdd(neighboursMap[v1], v2);
+            arraySetAdd(neighboursMap[v1], v3);
+            arraySetAdd(neighboursMap[v2], v1);
+            arraySetAdd(neighboursMap[v2], v3);
+            arraySetAdd(neighboursMap[v3], v1);
+            arraySetAdd(neighboursMap[v3], v2);
+        }
+        return neighboursMap;
+    }
+
+    function getEdgeCounts(mesh: Mesh) {
+        const { triangleCount } = mesh;
+        const elements = mesh.indexBuffer.ref.value;
+
+        const edgeCounts = new Map<number, number>();
+        const add = (a: number, b: number) => {
+            const z = sortedCantorPairing(a, b);
+            const c = edgeCounts.get(z) || 0;
+            edgeCounts.set(z, c + 1);
+        };
+
+        for (let i = 0; i < triangleCount; ++i) {
+            const a = elements[i * 3];
+            const b = elements[i * 3 + 1];
+            const c = elements[i * 3 + 2];
+            add(a, b); add(a, c); add(b, c);
+        }
+        return edgeCounts;
+    }
+
+    function getBorderVertices(edgeCounts: Map<number, number>) {
+        const borderVertices = new Set<number>();
+        const pair: [number, number] = [0, 0];
+        edgeCounts.forEach((c, z) => {
+            if (c === 1) {
+                invertCantorPairing(pair, z);
+                borderVertices.add(pair[0]);
+                borderVertices.add(pair[1]);
+            }
+        });
+
+        return borderVertices;
+    }
+
+    function getBorderNeighboursMap(neighboursMap: number[][], borderVertices: Set<number>, edgeCounts: Map<number, number>) {
+        const borderNeighboursMap = new Map<number, number[]>();
+        const add = (v: number, nb: number) => {
+            if (borderNeighboursMap.has(v)) arraySetAdd(borderNeighboursMap.get(v)!, nb);
+            else borderNeighboursMap.set(v, [nb]);
+        };
+
+        borderVertices.forEach(v => {
+            const neighbours = neighboursMap[v];
+            for (const nb of neighbours) {
+                if (borderVertices.has(nb) && edgeCounts.get(sortedCantorPairing(v, nb)) === 1) {
+                    add(v, nb);
+                }
+            }
+        });
+
+        return borderNeighboursMap;
+    }
+
+    function trimEdges(mesh: Mesh, neighboursMap: number[][]) {
+        const { indexBuffer, triangleCount } = mesh;
+        const ib = indexBuffer.ref.value;
+
+        // new
+        const index = ChunkedArray.create(Uint32Array, 3, 1024, triangleCount);
+
+        let newTriangleCount = 0;
+        for (let i = 0; i < triangleCount; ++i) {
+            const a = ib[i * 3];
+            const b = ib[i * 3 + 1];
+            const c = ib[i * 3 + 2];
+            if (neighboursMap[a].length === 2 ||
+                neighboursMap[b].length === 2 ||
+                neighboursMap[c].length === 2) continue;
+
+            ChunkedArray.add3(index, a, b, c);
+            newTriangleCount += 1;
+        }
+
+        const newIb = ChunkedArray.compact(index);
+        mesh.triangleCount = newTriangleCount;
+        ValueCell.update(indexBuffer, newIb);
+
+        return mesh;
+    }
+
+    function fillEdges(mesh: Mesh, neighboursMap: number[][], borderNeighboursMap: Map<number, number[]>, maxLengthSquared: number) {
+        const { vertexBuffer, indexBuffer, normalBuffer, triangleCount } = mesh;
+        const vb = vertexBuffer.ref.value;
+        const ib = indexBuffer.ref.value;
+        const nb = normalBuffer.ref.value;
+
+        // new
+        const index = ChunkedArray.create(Uint32Array, 3, 1024, triangleCount);
+
+        let newTriangleCount = 0;
+        for (let i = 0; i < triangleCount; ++i) {
+            ChunkedArray.add3(index, ib[i * 3], ib[i * 3 + 1], ib[i * 3 + 2]);
+            newTriangleCount += 1;
+        }
+
+        const vA = Vec3();
+        const vB = Vec3();
+        const vC = Vec3();
+        const vD = Vec3();
+        const vAB = Vec3();
+        const vAC = Vec3();
+        const vAD = Vec3();
+        const vABC = Vec3();
+
+        const vAN = Vec3();
+        const vN = Vec3();
+
+        const AngleThreshold = degToRad(120);
+        const added = new Set<number>();
+
+        const indices = Array.from(borderNeighboursMap.keys())
+            .filter(v => borderNeighboursMap.get(v)!.length < 2)
+            .map(v => {
+                const bnd = borderNeighboursMap.get(v)!;
+
+                Vec3.fromArray(vA, vb, v * 3);
+                Vec3.fromArray(vB, vb, bnd[0] * 3);
+                Vec3.fromArray(vC, vb, bnd[1] * 3);
+                Vec3.sub(vAB, vB, vA);
+                Vec3.sub(vAC, vC, vA);
+
+                return [v, Vec3.angle(vAB, vAC)];
+            });
+
+        // start with the smallest angle
+        indices.sort(([, a], [, b]) => a - b);
+
+        for (const [v, angle] of indices) {
+            if (added.has(v) || angle > AngleThreshold) continue;
+
+            const nbs = borderNeighboursMap.get(v)!;
+            if (neighboursMap[nbs[0]].includes(nbs[1]) &&
+                !borderNeighboursMap.get(nbs[0])?.includes(nbs[1])
+            ) continue;
+
+            Vec3.fromArray(vA, vb, v * 3);
+            Vec3.fromArray(vB, vb, nbs[0] * 3);
+            Vec3.fromArray(vC, vb, nbs[1] * 3);
+            Vec3.sub(vAB, vB, vA);
+            Vec3.sub(vAC, vC, vA);
+            Vec3.add(vABC, vAB, vAC);
+
+            if (Vec3.squaredDistance(vA, vB) >= maxLengthSquared) continue;
+
+            let add = false;
+            for (const nb of neighboursMap[v]) {
+                if (nbs.includes(nb)) continue;
+
+                Vec3.fromArray(vD, vb, nb * 3);
+                Vec3.sub(vAD, vD, vA);
+                if (Vec3.dot(vABC, vAD) < 0) {
+                    add = true;
+                    break;
+                }
+            }
+            if (!add) continue;
+
+            Vec3.fromArray(vAN, nb, v * 3);
+            Vec3.triangleNormal(vN, vA, vB, vC);
+            if (Vec3.dot(vN, vAN) > 0) {
+                ChunkedArray.add3(index, v, nbs[0], nbs[1]);
+            } else {
+                ChunkedArray.add3(index, nbs[1], nbs[0], v);
+            }
+            added.add(v); added.add(nbs[0]); added.add(nbs[1]);
+            newTriangleCount += 1;
+        }
+
+        const newIb = ChunkedArray.compact(index);
+        mesh.triangleCount = newTriangleCount;
+        ValueCell.update(indexBuffer, newIb);
+
+        return mesh;
+    }
+
+    function laplacianEdgeSmoothing(mesh: Mesh, borderNeighboursMap: Map<number, number[]>, options: { iterations: number, lambda: number }) {
+        const { iterations, lambda } = options;
+
+        const a = Vec3();
+        const b = Vec3();
+        const c = Vec3();
+        const t = Vec3();
+
+        const mu = -lambda;
+
+        let dst = new Float32Array(mesh.vertexBuffer.ref.value.length);
+
+        const step = (f: number) => {
+            const pos = mesh.vertexBuffer.ref.value;
+            dst.set(pos);
+
+            borderNeighboursMap.forEach((nbs, v) => {
+                if (nbs.length !== 2) return;
+
+                Vec3.fromArray(a, pos, v * 3);
+                Vec3.fromArray(b, pos, nbs[0] * 3);
+                Vec3.fromArray(c, pos, nbs[1] * 3);
+
+                const wab = 1 / Vec3.distance(a, b);
+                const wac = 1 / Vec3.distance(a, c);
+                Vec3.scale(b, b, wab);
+                Vec3.scale(c, c, wac);
+
+                Vec3.add(t, b, c);
+                Vec3.scale(t, t, 1 / (wab + wac));
+                Vec3.sub(t, t, a);
+
+                Vec3.scale(t, t, f);
+                Vec3.add(t, a, t);
+
+                Vec3.toArray(t, dst, v * 3);
+            });
+
+            const tmp = mesh.vertexBuffer.ref.value;
+            ValueCell.update(mesh.vertexBuffer, dst);
+            dst = tmp;
+        };
+
+        for (let k = 0; k < iterations; ++k) {
+            step(lambda);
+            step(mu);
+        }
+    }
+
+    export function smoothEdges(mesh: Mesh, options: { iterations: number, maxNewEdgeLength: number }) {
+        trimEdges(mesh, getNeighboursMap(mesh));
+
+        for (let k = 0; k < 10; ++k) {
+            const oldTriangleCount = mesh.triangleCount;
+            const edgeCounts = getEdgeCounts(mesh);
+            const neighboursMap = getNeighboursMap(mesh);
+            const borderVertices = getBorderVertices(edgeCounts);
+            const borderNeighboursMap = getBorderNeighboursMap(neighboursMap, borderVertices, edgeCounts);
+            fillEdges(mesh, neighboursMap, borderNeighboursMap, options.maxNewEdgeLength * options.maxNewEdgeLength);
+            if (mesh.triangleCount === oldTriangleCount) break;
+        }
+
+        const edgeCounts = getEdgeCounts(mesh);
+        const neighboursMap = getNeighboursMap(mesh);
+        const borderVertices = getBorderVertices(edgeCounts);
+        const borderNeighboursMap = getBorderNeighboursMap(neighboursMap, borderVertices, edgeCounts);
+        laplacianEdgeSmoothing(mesh, borderNeighboursMap, { iterations: options.iterations, lambda: 0.5 });
+        return mesh;
+    }
+
+    //
+
    export const Params = {
        ...BaseGeometry.Params,
        doubleSided: PD.Boolean(false, BaseGeometry.CustomQualityParamInfo),
--- a/src/mol-geo/geometry/points/points.ts
+++ b/src/mol-geo/geometry/points/points.ts
@@ -1,12 +1,12 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */

 import { ValueCell } from '../../../mol-util';
 import { Mat4, Vec3, Vec4 } from '../../../mol-math/linear-algebra';
-import { transformPositionArray, GroupMapping, createGroupMapping} from '../../util';
+import { transformPositionArray, GroupMapping, createGroupMapping } from '../../util';
 import { GeometryUtils } from '../geometry';
 import { createColors } from '../color-data';
 import { createMarkers } from '../marker-data';
@@ -117,12 +117,19 @@ export namespace Points {

    //

+    export const StyleTypes = {
+        'square': 'Square',
+        'circle': 'Circle',
+        'fuzzy': 'Fuzzy',
+    };
+    export type StyleTypes = keyof typeof StyleTypes;
+    export const StyleTypeNames = Object.keys(StyleTypes) as StyleTypes[];
+
    export const Params = {
        ...BaseGeometry.Params,
-        sizeFactor: PD.Numeric(1.5, { min: 0, max: 10, step: 0.1 }),
+        sizeFactor: PD.Numeric(3, { min: 0, max: 10, step: 0.1 }),
        pointSizeAttenuation: PD.Boolean(false),
-        pointFilledCircle: PD.Boolean(false),
-        pointEdgeBleach: PD.Numeric(0.2, { min: 0, max: 1, step: 0.05 }),
+        pointStyle: PD.Select('square', PD.objectToOptions(StyleTypes)),
    };
    export type Params = typeof Params

@@ -189,8 +196,7 @@ export namespace Points {
            ...BaseGeometry.createValues(props, counts),
            uSizeFactor: ValueCell.create(props.sizeFactor),
            dPointSizeAttenuation: ValueCell.create(props.pointSizeAttenuation),
-            dPointFilledCircle: ValueCell.create(props.pointFilledCircle),
-            uPointEdgeBleach: ValueCell.create(props.pointEdgeBleach),
+            dPointStyle: ValueCell.create(props.pointStyle),
        };
    }

@@ -204,8 +210,7 @@ export namespace Points {
        BaseGeometry.updateValues(values, props);
        ValueCell.updateIfChanged(values.uSizeFactor, props.sizeFactor);
        ValueCell.updateIfChanged(values.dPointSizeAttenuation, props.pointSizeAttenuation);
-        ValueCell.updateIfChanged(values.dPointFilledCircle, props.pointFilledCircle);
-        ValueCell.updateIfChanged(values.uPointEdgeBleach, props.pointEdgeBleach);
+        ValueCell.updateIfChanged(values.dPointStyle, props.pointStyle);
    }

    function updateBoundingSphere(values: PointsValues, points: Points) {
@@ -229,10 +234,7 @@ export namespace Points {

    function updateRenderableState(state: RenderableState, props: PD.Values<Params>) {
        BaseGeometry.updateRenderableState(state, props);
-        state.opaque = state.opaque && (
-            !props.pointFilledCircle ||
-            (props.pointFilledCircle && props.pointEdgeBleach === 0)
-        );
+        state.opaque = state.opaque && props.pointStyle !== 'fuzzy';
        state.writeDepth = state.opaque;
    }
 }
--- a/src/mol-geo/geometry/size-data.ts
+++ b/src/mol-geo/geometry/size-data.ts
@@ -98,7 +98,7 @@ export function createTextureSize(sizes: TextureImage<Uint8Array>, type: SizeTyp

 /** Creates size texture with size for each instance/unit */
 export function createInstanceSize(locationIt: LocationIterator, sizeFn: LocationSize, sizeData?: SizeData): SizeData {
-    const { instanceCount} = locationIt;
+    const { instanceCount } = locationIt;
    const sizes = createTextureImage(Math.max(1, instanceCount), 3, Uint8Array, sizeData && sizeData.tSize.ref.value.array);
    locationIt.reset();
    while (locationIt.hasNext && !locationIt.isNextNewInstance) {
--- a/src/mol-geo/geometry/text/font-atlas.ts
+++ b/src/mol-geo/geometry/text/font-atlas.ts
@@ -10,7 +10,7 @@ import { createTextureImage, TextureImage } from '../../../mol-gl/renderable/uti

 const TextAtlasCache: { [k: string]: FontAtlas } = {};

-export function getFontAtlas (props: Partial<FontAtlasProps>) {
+export function getFontAtlas(props: Partial<FontAtlasProps>) {
    const hash = JSON.stringify(props);
    if (TextAtlasCache[hash] === undefined) {
        TextAtlasCache[hash] = new FontAtlas(props);
@@ -69,7 +69,7 @@ export class FontAtlas {
    private readonly maxWidth: number
    private readonly middle: number

-    constructor (props: Partial<FontAtlasProps> = {}) {
+    constructor(props: Partial<FontAtlasProps> = {}) {
        const p = { ...PD.getDefaultValues(FontAtlasParams), ...props };
        this.props = p;

@@ -110,7 +110,7 @@ export class FontAtlas {
        this.placeholder = this.get(String.fromCharCode(0xFFFD));
    }

-    get (char: string) {
+    get(char: string) {
        if (this.mapped[char] === undefined) {
            this.draw(char);

@@ -144,7 +144,7 @@ export class FontAtlas {
        return this.mapped[char];
    }

-    draw (char: string) {
+    draw(char: string) {
        const h = this.lineHeight;
        const ctx = this.scratchContext;
        const data = this.scratchData;
--- a/src/mol-geo/geometry/text/text-builder.ts
+++ b/src/mol-geo/geometry/text/text-builder.ts
@@ -69,7 +69,7 @@ export namespace TextBuilder {
                } else if (attachment.startsWith('middle')) {
                    yShift = bHeight / 2;
                } else {
-                    yShift = 0;  // "bottom"
+                    yShift = 0; // "bottom"
                }
                // horizontal
                if (attachment.endsWith('right')) {
@@ -77,7 +77,7 @@ export namespace TextBuilder {
                } else if (attachment.endsWith('center')) {
                    xShift = bWidth / 2;
                } else {
-                    xShift = 0;  // "left"
+                    xShift = 0; // "left"
                }

                if (tether) {
--- a/src/mol-geo/geometry/texture-mesh/color-smoothing.ts
+++ b/src/mol-geo/geometry/texture-mesh/color-smoothing.ts
@@ -259,7 +259,7 @@ export function calcTextureMeshColorSmoothing(input: ColorSmoothingInput, resolu
    Vec3.add(gridDim, gridDim, Vec3.create(2, 2, 2));
    const { min } = box;

-    const [ dx, dy, dz ] = gridDim;
+    const [dx, dy, dz] = gridDim;
    const { texDimX: width, texDimY: height, texCols } = getTexture2dSize(gridDim);
    // console.log({ width, height, texCols, dim, resolution });

--- a/src/mol-geo/geometry/texture-mesh/texture-mesh.ts
+++ b/src/mol-geo/geometry/texture-mesh/texture-mesh.ts
@@ -19,7 +19,7 @@ import { createEmptyOverpaint } from '../overpaint-data';
 import { createEmptyTransparency } from '../transparency-data';
 import { TextureMeshValues } from '../../../mol-gl/renderable/texture-mesh';
 import { calculateTransformBoundingSphere } from '../../../mol-gl/renderable/util';
-import { Texture } from '../../../mol-gl/webgl/texture';
+import { createNullTexture, Texture } from '../../../mol-gl/webgl/texture';
 import { Vec2, Vec4 } from '../../../mol-math/linear-algebra';
 import { createEmptyClipping } from '../clipping-data';
 import { NullLocation } from '../../../mol-model/location';
@@ -97,7 +97,11 @@ export namespace TextureMesh {
    }

    export function createEmpty(textureMesh?: TextureMesh): TextureMesh {
-        return {} as TextureMesh; // TODO
+        const vt = textureMesh ? textureMesh.vertexTexture.ref.value : createNullTexture();
+        const gt = textureMesh ? textureMesh.groupTexture.ref.value : createNullTexture();
+        const nt = textureMesh ? textureMesh.normalTexture.ref.value : createNullTexture();
+        const bs = textureMesh ? textureMesh.boundingSphere : Sphere3D();
+        return create(0, 0, vt, gt, nt, bs, textureMesh);
    }

    export const Params = {
--- a/src/mol-geo/geometry/transform-data.ts
+++ b/src/mol-geo/geometry/transform-data.ts
@@ -60,11 +60,8 @@ export function createTransform(transformArray: Float32Array, instanceCount: num
        ValueCell.update(transformData.aInstance, fillSerial(aInstance, instanceCount));

        ValueCell.update(transformData.hasReflection, hasReflection);
-
-        updateTransformData(transformData);
-        return transformData;
    } else {
-        return {
+        transformData = {
            aTransform: ValueCell.create(new Float32Array(instanceCount * 16)),
            matrix: ValueCell.create(Mat4.identity()),
            transform: ValueCell.create(new Float32Array(transformArray)),
@@ -75,6 +72,9 @@ export function createTransform(transformArray: Float32Array, instanceCount: num
            hasReflection: ValueCell.create(hasReflection),
        };
    }
+
+    updateTransformData(transformData);
+    return transformData;
 }

 const identityTransform = new Float32Array(16);
--- a/src/mol-geo/primitive/box.ts
+++ b/src/mol-geo/primitive/box.ts
@@ -73,18 +73,18 @@ let boxCage: Cage;
 export function BoxCage() {
    if (!boxCage) {
        boxCage = createCage([
-            0.5,  0.5, -0.5, // bottom
-            -0.5,  0.5, -0.5,
+            0.5, 0.5, -0.5, // bottom
+            -0.5, 0.5, -0.5,
            -0.5, -0.5, -0.5,
            0.5, -0.5, -0.5,
-            0.5,  0.5, 0.5,  // top
-            -0.5,  0.5, 0.5,
+            0.5, 0.5, 0.5, // top
+            -0.5, 0.5, 0.5,
            -0.5, -0.5, 0.5,
            0.5, -0.5, 0.5
        ], [
-            0, 4,  1, 5,  2, 6,  3, 7, // sides
-            0, 1,  1, 2,  2, 3,  3, 0,  // bottom base
-            4, 5,  5, 6,  6, 7,  7, 4   // top base
+            0, 4, 1, 5, 2, 6, 3, 7, // sides
+            0, 1, 1, 2, 2, 3, 3, 0, // bottom base
+            4, 5, 5, 6, 6, 7, 7, 4 // top base
        ]);
    }
    return boxCage;
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
dsehnal	2ebb0a35fd	2.3.6	2021-11-08 18:57:06 +01:00
dsehnal	64aaa92d45	changelog	2021-11-08 18:54:52 +01:00
dsehnal	4baf391efe	prefer webgl1 in safari 15.1 - WebGL2 is broken there for Mol* shaders - It works again in Safari 15.4 tech preview	2021-11-08 18:50:16 +01:00
David Sehnal	5afdcff6a5	Merge pull request #273 from molstar/shader-tests add basic unit tests for graphics shaders	2021-11-08 18:40:51 +01:00
dsehnal	339c397860	package lock	2021-11-08 18:30:52 +01:00
dsehnal	a58cbd31ef	Merge branch 'master' of https://github.com/molstar/molstar into shader-tests	2021-11-08 18:30:30 +01:00
David Sehnal	d232b01cf9	Merge pull request #283 from MadCatX/improve-measurements-ux Improve measurements user experience	2021-11-08 17:12:37 +01:00
Michal Malý	ec95270854	Use the entire element to trigger highlighting of loci from additionsHistory	2021-11-08 15:46:07 +01:00
Michal Malý	78cc0d960f	Show the order of locis to be used for measurements in 3D view	2021-11-08 15:46:02 +01:00
Alexander Rose	7f39cf0f37	add missing updateFocusRepr to atomicDetail preset - fixes #280	2021-11-02 22:10:35 -07:00
Alexander Rose	4592510a95	linting fix	2021-10-30 21:50:15 -07:00
Alexander Rose	46d5442dc5	Merge pull request #252 from corredD/forkdev binary model loading support and latest mycoplasma model.	2021-10-30 17:11:27 -07:00
Alexander Rose	271cff4aba	changelog	2021-10-30 17:09:35 -07:00
Alexander Rose	94fd5a97d6	Merge branch 'master' of https://github.com/molstar/molstar into pr/corredD/252	2021-10-30 16:53:35 -07:00
Alexander Rose	28678e2f80	Merge pull request #270 from molstar/measurements Additional measurement controls	2021-10-30 16:52:32 -07:00
Alexander Rose	406307a432	add radiusScale param to orientation measurement	2021-10-30 16:48:47 -07:00
Alexander Rose	56345b5096	Merge branch 'master' of https://github.com/molstar/molstar into measurements	2021-10-30 16:31:12 -07:00
Alexander Rose	3fcc42ee0e	fix, proper EmptyRepresentationProvider	2021-10-30 16:26:37 -07:00
Alexander Rose	b903677f8a	gh action, add npm run build	2021-10-30 16:12:42 -07:00
Alexander Rose	ef4b632a07	update package-lock	2021-10-30 16:05:24 -07:00
Alexander Rose	e9d485ca85	gh action, use npm ci	2021-10-30 16:01:09 -07:00
Alexander Rose	a149fa5929	gh action	2021-10-30 15:53:58 -07:00
Alexander Rose	bb3dde585b	gh action	2021-10-30 15:46:23 -07:00
Alexander Rose	cd6bbeaa86	gh action	2021-10-30 15:44:06 -07:00
Alexander Rose	e3d24dae4b	gh action	2021-10-30 15:43:05 -07:00
Alexander Rose	687a814a62	gh action - update eslint - add jest	2021-10-30 15:02:25 -07:00
Alexander Rose	8f2e99dc51	improve shader tests - made gl package optional - skip test if gl package not available	2021-10-30 14:52:11 -07:00
Alexander Rose	568be030c3	Merge branch 'master' of https://github.com/molstar/molstar into shader-tests	2021-10-30 14:45:19 -07:00
Alexander Rose	97c3ab8b5a	changelog	2021-10-30 14:44:27 -07:00
Alexander Rose	5db646d139	fix marker highlight color overriding select color	2021-10-30 14:43:57 -07:00
Alexander Rose	340f8f1af3	add additional aromatic bond visual params	2021-10-30 14:42:17 -07:00
dsehnal	4484a4452c	2.3.5	2021-10-19 18:22:50 +02:00
dsehnal	65b654a0a2	fix index pair bonds order assignment	2021-10-19 18:20:54 +02:00
dsehnal	a8e0c13b0e	fix sequence viewer for PDB files with COMPND record and multichain entities	2021-10-17 13:21:57 +02:00
dsehnal	41d67eb642	2.3.4	2021-10-12 19:05:48 +02:00
dsehnal	c76c8335d1	changelog	2021-10-12 19:03:37 +02:00
dsehnal	42528b7be5	fix argparse config	2021-10-12 19:01:23 +02:00
Alexander Rose	b371f8c11c	Merge branch 'master' of https://github.com/molstar/molstar into shader-tests	2021-10-03 15:24:02 -07:00
Alexander Rose	3d651b40f0	use node 14 in lint action	2021-10-03 15:12:58 -07:00
Alexander Rose	895a13fc0d	Merge branch 'master' into shader-tests	2021-10-03 14:36:23 -07:00
Alexander Rose	c94acff82e	update packages	2021-10-03 11:12:24 -07:00
Alexander Rose	2f9ac711d1	add basic unit tests for graphics shaders - compile using `gl` package	2021-10-03 10:52:58 -07:00
Alexander Rose	93b9953f6d	add missing createEmpty* geo utils - direct-volume - image - texture-mesh	2021-10-03 10:43:56 -07:00
Alexander Rose	dcaf6f8927	add multipleBonds param to bond visuals	2021-10-02 15:44:17 -07:00
Alexander Rose	d96eb404e1	add elements crosses visual	2021-10-02 15:09:13 -07:00
Alexander Rose	07322819f0	Merge pull request #271 from molstar/pick-atom Picking improvements	2021-10-02 13:41:25 -07:00
Alexander Rose	9be686686d	add pickPadding config option	2021-10-02 09:34:56 -07:00
Alexander Rose	3df539c9e1	Merge branch 'master' of https://github.com/molstar/molstar into pick-atom	2021-10-02 09:30:07 -07:00
dsehnal	903f06bab6	2.3.3	2021-10-01 17:56:26 +02:00
dsehnal	13f2810f90	fix direct volume shader	2021-10-01 17:54:33 +02:00
dsehnal	ee8cae16d2	2.3.2	2021-10-01 17:12:42 +02:00
dsehnal	feaf6f7fd4	(temporarily) prefer webgl1 on iOS	2021-10-01 17:10:49 +02:00
dsehnal	04775a2e44	2.3.1	2021-09-28 16:13:51 +02:00
dsehnal	bec9fec755	chem_comp_bond and struct_conn to mmcif exporter + fix argparse config for Model/Volume servers	2021-09-28 16:12:01 +02:00
Alexander Rose	e840059a38	pick improvements - ensure lines & points are at least 1 pixel big - look around center pixel in a spiral for hits	2021-09-26 17:20:16 -07:00
Alexander Rose	1bd0339dec	add points visual to line repr	2021-09-26 17:13:49 -07:00
Alexander Rose	d0eaf2f71e	Merge branch 'master' of https://github.com/molstar/molstar into pick-atom	2021-09-26 13:41:23 -07:00
Alexander Rose	c7edf40afe	add markerPriority param to renderer	2021-09-26 13:31:41 -07:00
Alexander Rose	b44962eb2f	lint: add semi-spacing rule	2021-09-26 13:14:32 -07:00
Alexander Rose	254c9efbf5	improve/fix implicit atom picking	2021-09-26 13:06:56 -07:00
Alexander Rose	73e9aed98c	add preferAtoms param to Select/Highlight behaviors	2021-09-26 12:58:29 -07:00
Alexander Rose	6e60d9713a	fix bond atoms not added in selection manager	2021-09-26 12:53:53 -07:00
Alexander Rose	ef0593b1e2	add pixel-scale & pick-scale GET params to Viewer	2021-09-26 12:43:57 -07:00
Alexander Rose	7831fa8b33	fix: pickScale not considered in line/point shader	2021-09-26 12:39:44 -07:00
dsehnal	c64851492c	applyMarkerAction take 2	2021-09-21 18:38:05 +02:00
dsehnal	4a2e93e265	fix applyMarkerAction edge case	2021-09-21 10:15:29 +02:00
Alexander Rose	d4bb1a6e93	wip: prefer to pick atoms close to ends over bonds	2021-09-19 16:24:45 -07:00
Alexander Rose	55de0aba69	fix point repr & shader	2021-09-19 16:00:40 -07:00
Alexander Rose	ecfa7b5a99	fix currentTheme not set in Representation.createMulti	2021-09-19 15:45:08 -07:00
dsehnal	bee3dc4595	fix double bonds from sctruct_conn records	2021-09-19 17:40:38 +02:00
Alexander Rose	787ca47825	fix line shader not accounting for aspect ratio - also remove uViewportHeight in favor of uViewport	2021-09-18 23:13:00 -07:00
Alexander Rose	b06c134b61	add additional measurement controls - orientation (box, axes, ellipsoid) - plane (best fit)	2021-09-18 22:39:40 -07:00
Alexander Rose	3436d03468	add helpers to work with many locis - StructureElement.Loci.getPrincipalAxesMany - structureElementLociLabelMany	2021-09-18 22:13:22 -07:00
Alexander Rose	58df6f3b85	formating	2021-09-18 22:12:08 -07:00
Alexander Rose	6fab6ce1f2	add map-provider GET param to Viewer app	2021-09-18 16:52:35 -07:00
Alexander Rose	9fd95f1a11	handle missing occupancy column - treat as occ 1	2021-09-18 16:47:52 -07:00
Alexander Rose	69fe0901e2	add CharmmSaccharideNames	2021-09-18 16:37:39 -07:00
Alexander Rose	ffaf008dce	limit max display counts in sequence panel - MaxSelectOptionsCount - MaxSequenceWrappersCount - workaround for cellpack models	2021-09-18 16:30:14 -07:00
ludovic autin	eb196a41b5	change variables names to avoid confusion with other types. Added the xrayshading for the compartment geometry	2021-09-14 11:25:15 -07:00
ludovic autin	35baaaf594	support for compartment PLY file.	2021-09-13 11:46:27 -07:00
Alexander Rose	0fc305aaea	fix linting issues	2021-09-12 23:32:55 -07:00
Alexander Rose	bf67546a61	Merge branch 'master' of https://github.com/molstar/molstar into pr/corredD/252	2021-09-12 23:30:26 -07:00
Alexander Rose	8c417ef35c	lint: add space-before-blocks rule	2021-09-12 23:23:03 -07:00
Alexander Rose	01691f3050	lint: add keyword-spacing rule	2021-09-12 23:20:59 -07:00
Alexander Rose	128abf3090	lint: add no-multi-spaces rule	2021-09-12 23:13:44 -07:00
Alexander Rose	0c0e995256	lint: add no-multi-spaces rule	2021-09-12 23:11:29 -07:00
Alexander Rose	4090498f92	lint: add func-call-spacing rule	2021-09-12 23:03:35 -07:00
Alexander Rose	24677d6931	lint: add space-before-function-paren rule	2021-09-12 22:57:48 -07:00
Alexander Rose	80d54afdd0	Merge branch 'master' into forkdev	2021-09-12 20:16:00 -07:00
Alexander Rose	908fff8041	lint: add prefer-const rule	2021-09-12 20:02:53 -07:00
Alexander Rose	aa1eb90f66	lint: add computed-property-spacing rule	2021-09-12 19:41:13 -07:00
Alexander Rose	1d21787e7e	lint: add space-in-parens rule	2021-09-12 19:37:26 -07:00
Alexander Rose	42409a2bc7	lint: add array-bracket-spacing rule	2021-09-12 19:32:54 -07:00
Alexander Rose	b31302ba3a	lint: add object-curly-spacing rule	2021-09-12 18:45:32 -07:00
Alexander Rose	3840b0041b	lint: add key-spacing rule	2021-09-12 18:38:45 -07:00
Alexander Rose	cc68f8311d	lint: add no-throw-literal rule	2021-09-12 16:22:43 -07:00
Alexander Rose	3400c8e94a	update coreCif dictionary	2021-09-12 16:19:23 -07:00
Alexander Rose	61c47c517b	update mmcif schema types and derived data	2021-09-12 15:06:54 -07:00
Alexander Rose	76674917ca	update rscb graphql schema types	2021-09-12 15:04:49 -07:00
Alexander Rose	b835eb8de7	update packages	2021-09-12 13:39:00 -07:00
Alexander Rose	2a74dfcf46	factor out membrane sphere handling	2021-09-12 10:26:10 -07:00
Alexander Rose	b0f447adde	fix cellpack results file asset handling	2021-09-12 10:17:37 -07:00
Alexander Rose	3f0d476e94	Merge pull request #266 from JonStargaryen/master ANVIL: add TMDET amino acid classification and reference	2021-09-10 22:41:01 -07:00
Sebastian Bittrich	9423d56d36	lint	2021-09-09 16:16:49 -07:00
Sebastian Bittrich	0f03fe99d6	ANVIL: fix for 6y1z	2021-09-09 16:02:39 -07:00
Sebastian Bittrich	556d5bb003	ANVIL: add TMDET ref and option	2021-09-09 09:06:51 -07:00
dsehnal	8e3ea6943f	updated packages & tsc	2021-09-07 14:10:10 +02:00
Alexander Rose	599cfc1b1c	2.3.0	2021-09-06 15:33:03 -07:00
Alexander Rose	84eccb5019	changelog	2021-09-06 15:29:44 -07:00
Alexander Rose	2dd07bb0e3	improved getMarkersAverage performance - use lut - add performance tests	2021-09-04 15:12:35 -07:00
Alexander Rose	f404d23280	take include/exclude flags into account when displaying aromatic bonds - this allows to show aromatic rings only when explicitely given	2021-09-04 14:56:40 -07:00
Alexander Rose	8b7333b470	avoid unnecessary draw calls/ui updates when marking - fix wrong type narrowing of Loci.isEmpty	2021-09-04 14:48:09 -07:00
ludovic autin	b8628ccff1	Merge branch 'master' of https://github.com/molstar/molstar into forkdev	2021-09-01 09:55:13 -07:00
Alexander Rose	7d26567d40	Merge pull request #258 from molstar/marking Add optional marking pass	2021-08-31 21:18:23 -07:00
Alexander Rose	8f6dbf2192	asorted performance tweaks	2021-08-31 21:14:02 -07:00
Alexander Rose	db350ddfd3	loci/marking performance improvements - use Interval for ranges instead of SortedArray - pre-check if loci overlaps with unit visual	2021-08-30 22:43:01 -07:00
Alexander Rose	c0144d826c	SortedArray: add .isRange, improve .areEqual	2021-08-30 22:33:09 -07:00
Alexander Rose	de3e819b80	fix uMarker not being updated	2021-08-30 22:29:35 -07:00
Alexander Rose	bbf96567b1	handle clipping/fog for marking edges	2021-08-29 22:14:11 -07:00
Alexander Rose	c9a3254bd6	fix partial marker average calculation	2021-08-29 21:25:41 -07:00
Alexander Rose	bad6d030f1	marker-data improvements - add uniform marker type - check if a loci is superset of a visual - special case to improve reversing the previous mark	2021-08-29 10:44:09 -07:00
Alexander Rose	e1ad67a059	StructureElement.Loci improvements - early return in .isEmpty - ensure Interval is used when possible in .extendToAllInstances	2021-08-29 10:35:05 -07:00
ludovic autin	4c30057edf	I am trying to get the binary asset to get cached. But still can't save a working session.	2021-08-27 16:14:43 -07:00
ludovic autin	53a4826274	Merge branch 'master' of https://github.com/molstar/molstar into forkdev	2021-08-27 14:55:22 -07:00
dsehnal	8d3ac92989	2.2.3	2021-08-25 17:40:28 +02:00
dsehnal	d6eb334d12	changelog	2021-08-25 17:38:28 +02:00
Alexander Rose	c62f19623c	add optional marking pass - outlines visible and hidden parts of highlighted/selected groups - add highlightStrength/selectStrength renderer params	2021-08-22 12:08:15 -07:00
Alexander Rose	77139afe7f	tweak Interval.size	2021-08-21 14:00:51 -07:00
Alexander Rose	54476ad85e	improve print texture debug helpers	2021-08-21 13:59:38 -07:00
Alexander Rose	6dd876232d	avoid superfluous calls to Loci.isWholeStructure	2021-08-21 13:51:40 -07:00
Alexander Rose	ae2314d76c	fix camera/bounding helper not showing up	2021-08-21 13:48:56 -07:00
David Sehnal	6667509745	Merge pull request #257 from JonStargaryen/master ANVIL: improve prediction for 3pqr	2021-08-21 20:22:38 +02:00
JonStargaryen	5c871a5aae	ANVIL: increase number of sphere points to 175	2021-08-20 12:43:24 -07:00
ludovic autin	393fc99ed2	moved the model loading in model.ts and get the info from the recipe dictionary ( result file and lipids file ) if available. Fix the dates and some const / let variable defintion	2021-08-16 12:35:51 -07:00
ludovic autin	7c5dff1c8b	Merge remote-tracking branch 'upstream/master' into forkdev	2021-08-16 11:55:09 -07:00
Alexander Rose	2482ef92af	Improved StructureElement.Loci.size performance - inlined code - important for marking large cellpack models	2021-08-15 14:42:49 -07:00
Alexander Rose	db59303a84	Merge pull request #244 from molstar/meshproc Mesh processing: border smoothing	2021-08-14 19:36:23 -07:00
Alexander Rose	fe700953ff	Merge branch 'master' into meshproc	2021-08-14 19:32:06 -07:00
Alexander Rose	047946e41c	remove superfluous type casts	2021-08-14 19:30:16 -07:00
ludovic autin	ce3f13431d	endianess test with IsNativeEndianLittle	2021-08-13 10:58:25 -07:00
ludovic autin	df54766ab2	lower-case icosahedron	2021-08-12 10:48:27 -07:00
ludovic autin	94233fbcd9	eslint error fix	2021-08-11 11:07:34 -07:00
ludovic autin	d044496eaa	fix eslint errors	2021-08-11 11:04:08 -07:00
ludovic autin	ca825d720e	binary model loading support, latest mycoplasma model.	2021-08-11 10:44:44 -07:00
dsehnal	2fe43eda2b	Merge branch 'master' of https://github.com/molstar/molstar into meshproc	2021-08-09 20:33:57 +02:00
dsehnal	45fc0c61af	Mesh.smoothEdges options	2021-08-09 20:32:40 +02:00
dsehnal	7e7993f5ba	improve fillEdges in mesh edge smoothing - sort boundary vertices - limit the length added edges	2021-08-09 20:22:13 +02:00
Alexander Rose	3e9de449c8	cleanup	2021-08-07 19:45:47 -07:00
Alexander Rose	0132c7ef5e	Merge branch 'master' of https://github.com/molstar/molstar into meshproc	2021-08-07 19:42:41 -07:00
Alexander Rose	aa2222c086	remove clipSphere option & param cleanup - clip objects are better - includeParent option not useful for gaussian-surface visuals	2021-08-07 19:20:51 -07:00
Alexander Rose	f892917e1c	Merge branch 'master' of https://github.com/molstar/molstar into meshproc	2021-08-01 14:04:50 -07:00
Alexander Rose	f011025f16	changelog	2021-07-31 23:22:11 -07:00
Alexander Rose	9e44cd83fa	add clipSphere param to molecular-surface mesh	2021-07-31 23:21:57 -07:00
Alexander Rose	e0e45b64ac	optimize invertCantorPairing	2021-07-31 23:15:33 -07:00
Alexander Rose	f10b152252	Merge branch 'master' of https://github.com/molstar/molstar into meshproc	2021-07-31 14:42:18 -07:00
Alexander Rose	b983df7eb5	mesh edge smoothing	2021-07-25 20:26:17 -07:00