tweak cube clamp param

add param to clamp cube values
2026-06-05 14:04:36 +08:00 · 2022-11-08 22:28:47 -08:00 · 2022-11-08 22:17:23 -08:00
104 changed files with 1645 additions and 31327 deletions
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,57 +6,18 @@ Note that since we don't clearly distinguish between a public and private interf

 ## [Unreleased]

-
-## [v3.27.0] - 2022-12-15
-
- Add an `includeTransparent` parameter to hide/show outlines of components that are transparent
- Fix 'once' for animations of systems with many frames
- Better guard against issue (black fringes) with bumpiness in impostors
- Improve impostor shaders
-    - Fix sphere near-clipping with orthographic projection
-    - Fix cylinder near-clipping
-    - Add interior cylinder caps
-    - Add per-pixel object clipping
- Fix `QualityAssessment` assignment bug for structures with different auth vs label sequence numbering
- Refresh `ApplyActionControl`'s param definition when toggling expanded state
- Fix `struct_conn` bond assignment for ions
- Ability to show only polar hydrogens
-
-## [v3.26.0] - 2022-12-04
-
- Support for ``powerPreference`` webgl attribute. Add ``PluginConfig.General.PowerPreference`` and ``power-preference`` Viewer GET param.
- Excluded common protein caps `NME` and `ACE` from the ligand selection query
- Add screen-space shadow post-processing effect
- Add "Structure Molecular Surface" visual
- Add `external-volume` theme (coloring of arbitrary geometries by user-selected volume)
-
-## [v3.25.1] - 2022-11-20
-
- Fix edge-case in `Structure.eachUnitPair` with single-element units
- Fix 'auto' structure-quality for coarse models
-
-## [v3.25.0] - 2022-11-16
-
- Fix handling of gzipped assets (reverts #615)
-
-## [v3.24.0] - 2022-11-13
-
 - Make `PluginContext.initContainer` checkered canvas background optional
- Store URL of downloaded assets to detect zip/gzip based on extension (#615)
- Add optional `operator.key`; can be referenced in `IndexPairBonds`
- Add overpaint/transparency/substance theme strength to representations
- Fix viewport color for transparent background

 ## [v3.23.0] - 2022-10-19

 - Add `PluginContext.initContainer/mount/unmount` methods; these should make it easier to reuse a plugin context with both custom and built-in UI
 - Add `PluginContext.canvas3dInitialized`
 - `createPluginUI` now resolves after the 3d canvas has been initialized
- Change EM Volume Streaming default from `Whole Structure` to `Auto`
+- Change EM Volume Streaming default from `Whote Structure` to `Auto`

 ## [v3.22.0] - 2022-10-17

- Replace `VolumeIsosurfaceParams.pickingGranularity` param with `Volume.PickingGranuality`
+- Replace `VolumeIsosurfaceParams.pickingGranularity` param with `Volume.PickingGranuality` 

 ## [v3.21.0] - 2022-10-17

--- a/examples/long_animation.sdf
+++ b/examples/long_animation.sdf
--- a/package-lock.json
+++ b/package-lock.json
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
  "name": "molstar",
-  "version": "3.27.0",
+  "version": "3.23.0",
  "description": "A comprehensive macromolecular library.",
  "homepage": "https://github.com/molstar/molstar#readme",
  "repository": {
@@ -92,59 +92,57 @@
    "Panagiotis Tourlas <panagiot_tourlov@hotmail.com>",
    "Adam Midlik <midlik@gmail.com>",
    "Koya Sakuma <koya.sakuma.work@gmail.com>",
-    "Gianluca Tomasello <giagitom@gmail.com>",
-    "Jason Pattle <jpattle@exscientia.co.uk>",
-    "David Williams <dwilliams@nobiastx.com>"
+    "Gianluca Tomasello <giagitom@gmail.com>"
  ],
  "license": "MIT",
  "devDependencies": {
    "@graphql-codegen/add": "^3.2.1",
-    "@graphql-codegen/cli": "^2.15.0",
+    "@graphql-codegen/cli": "^2.13.7",
    "@graphql-codegen/time": "^3.2.1",
-    "@graphql-codegen/typescript": "^2.8.3",
+    "@graphql-codegen/typescript": "^2.7.4",
    "@graphql-codegen/typescript-graphql-files-modules": "^2.2.1",
-    "@graphql-codegen/typescript-graphql-request": "^4.5.8",
-    "@graphql-codegen/typescript-operations": "^2.5.8",
+    "@graphql-codegen/typescript-graphql-request": "^4.5.6",
+    "@graphql-codegen/typescript-operations": "^2.5.4",
    "@types/cors": "^2.8.12",
-    "@types/gl": "^6.0.2",
-    "@types/jest": "^29.2.3",
-    "@types/react": "^18.0.26",
-    "@types/react-dom": "^18.0.9",
-    "@typescript-eslint/eslint-plugin": "^5.45.0",
-    "@typescript-eslint/parser": "^5.45.0",
+    "@types/gl": "^4.1.1",
+    "@types/jest": "^29.1.2",
+    "@types/react": "^18.0.21",
+    "@types/react-dom": "^18.0.6",
+    "@typescript-eslint/eslint-plugin": "^5.40.0",
+    "@typescript-eslint/parser": "^5.40.0",
    "benchmark": "^2.1.4",
-    "concurrently": "^7.6.0",
+    "concurrently": "^7.4.0",
    "cpx2": "^4.2.0",
    "crypto-browserify": "^3.12.0",
-    "css-loader": "^6.7.2",
-    "eslint": "^8.29.0",
+    "css-loader": "^6.7.1",
+    "eslint": "^8.25.0",
    "extra-watch-webpack-plugin": "^1.0.3",
    "file-loader": "^6.2.0",
-    "fs-extra": "^11.1.0",
+    "fs-extra": "^10.1.0",
    "graphql": "^16.6.0",
    "http-server": "^14.1.1",
-    "jest": "^29.3.1",
-    "mini-css-extract-plugin": "^2.7.1",
+    "jest": "^29.2.0",
+    "mini-css-extract-plugin": "^2.6.1",
    "path-browserify": "^1.0.1",
    "raw-loader": "^4.0.2",
    "react": "^18.2.0",
    "react-dom": "^18.2.0",
-    "sass": "^1.56.1",
-    "sass-loader": "^13.2.0",
-    "simple-git": "^3.15.1",
+    "sass": "^1.55.0",
+    "sass-loader": "^13.1.0",
+    "simple-git": "^3.14.1",
    "stream-browserify": "^3.0.0",
    "style-loader": "^3.3.1",
    "ts-jest": "^29.0.3",
-    "typescript": "^4.9.3",
-    "webpack": "^5.75.0",
-    "webpack-cli": "^5.0.0"
+    "typescript": "^4.8.4",
+    "webpack": "^5.74.0",
+    "webpack-cli": "^4.10.0"
  },
  "dependencies": {
    "@types/argparse": "^2.0.10",
    "@types/benchmark": "^2.1.2",
    "@types/compression": "1.7.2",
    "@types/express": "^4.17.14",
-    "@types/node": "^16.18.4",
+    "@types/node": "^16.11.66",
    "@types/node-fetch": "^2.6.2",
    "@types/swagger-ui-dist": "3.30.1",
    "argparse": "^2.0.1",
@@ -153,12 +151,12 @@
    "cors": "^2.8.5",
    "express": "^4.18.2",
    "h264-mp4-encoder": "^1.0.12",
-    "immer": "^9.0.16",
+    "immer": "^9.0.15",
    "immutable": "^4.1.0",
    "node-fetch": "^2.6.7",
-    "rxjs": "^7.6.0",
-    "swagger-ui-dist": "^4.15.5",
-    "tslib": "^2.4.1",
+    "rxjs": "^7.5.7",
+    "swagger-ui-dist": "^4.14.3",
+    "tslib": "^2.4.0",
    "util.promisify": "^1.1.1",
    "xhr2": "^0.2.1"
  },
--- a/src/apps/docking-viewer/viewport.tsx
+++ b/src/apps/docking-viewer/viewport.tsx
@@ -31,8 +31,7 @@ function shinyStyle(plugin: PluginContext) {
        postprocessing: {
            ...plugin.canvas3d!.props.postprocessing,
            occlusion: { name: 'off', params: {} },
-            shadow: { name: 'off', params: {} },
-            outline: { name: 'off', params: {} },
+            outline: { name: 'off', params: {} }
        }
    } });
 }
@@ -49,15 +48,13 @@ function occlusionStyle(plugin: PluginContext) {
                blurKernelSize: 15,
                radius: 5,
                samples: 32,
-                resolutionScale: 1,
+                resolutionScale: 1
            } },
            outline: { name: 'on', params: {
                scale: 1.0,
                threshold: 0.33,
                color: Color(0x0000),
-                includeTransparent: true,
-            } },
-            shadow: { name: 'off', params: {} },
+            } }
        }
    } });
 }
--- a/src/apps/viewer/app.ts
+++ b/src/apps/viewer/app.ts
@@ -91,7 +91,6 @@ const DefaultViewerOptions = {
    enableDpoit: PluginConfig.General.EnableDpoit.defaultValue,
    preferWebgl1: PluginConfig.General.PreferWebGl1.defaultValue,
    allowMajorPerformanceCaveat: PluginConfig.General.AllowMajorPerformanceCaveat.defaultValue,
-    powerPreference: PluginConfig.General.PowerPreference.defaultValue,

    viewportShowExpand: PluginConfig.Viewport.ShowExpand.defaultValue,
    viewportShowControls: PluginConfig.Viewport.ShowControls.defaultValue,
@@ -164,7 +163,6 @@ export class Viewer {
                [PluginConfig.General.EnableDpoit, o.enableDpoit],
                [PluginConfig.General.PreferWebGl1, o.preferWebgl1],
                [PluginConfig.General.AllowMajorPerformanceCaveat, o.allowMajorPerformanceCaveat],
-                [PluginConfig.General.PowerPreference, o.powerPreference],
                [PluginConfig.Viewport.ShowExpand, o.viewportShowExpand],
                [PluginConfig.Viewport.ShowControls, o.viewportShowControls],
                [PluginConfig.Viewport.ShowSettings, o.viewportShowSettings],
--- a/src/apps/viewer/index.html
+++ b/src/apps/viewer/index.html
@@ -63,7 +63,6 @@
            var enableDpoit = getParam('enable-dpoit', '[^&]+').trim() === '1';
            var preferWebgl1 = getParam('prefer-webgl1', '[^&]+').trim() === '1' || void 0;
            var allowMajorPerformanceCaveat = getParam('allow-major-performance-caveat', '[^&]+').trim() === '1';
-            var powerPreference = getParam('power-preference', '[^&]+').trim().toLowerCase();

            molstar.Viewer.create('app', {
                layoutShowControls: !hideControls,
@@ -81,7 +80,6 @@
                enableDpoit: enableDpoit ? true : void 0,
                preferWebgl1: preferWebgl1,
                allowMajorPerformanceCaveat: allowMajorPerformanceCaveat,
-                powerPreference: powerPreference || 'high-performance',
            }).then(viewer => {
                var snapshotId = getParam('snapshot-id', '[^&]+').trim();
                if (snapshotId) viewer.setRemoteSnapshot(snapshotId);
--- a/src/examples/lighting/index.ts
+++ b/src/examples/lighting/index.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2022 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>
 */
@@ -25,8 +25,7 @@ const Canvas3DPresets = {
        canvas3d: <Preset>{
            postprocessing: {
                occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15, resolutionScale: 1 } },
-                outline: { name: 'on', params: { scale: 1, threshold: 0.33, color: Color(0x000000), includeTransparent: true, } },
-                shadow: { name: 'off', params: {} },
+                outline: { name: 'on', params: { scale: 1, threshold: 0.33, color: Color(0x000000) } }
            },
            renderer: {
                ambientIntensity: 1.0,
@@ -38,8 +37,7 @@ const Canvas3DPresets = {
        canvas3d: <Preset>{
            postprocessing: {
                occlusion: { name: 'on', params: { samples: 32, radius: 6, bias: 1.4, blurKernelSize: 15, resolutionScale: 1 } },
-                outline: { name: 'off', params: {} },
-                shadow: { name: 'off', params: {} },
+                outline: { name: 'off', params: {} }
            },
            renderer: {
                ambientIntensity: 0.4,
@@ -52,8 +50,7 @@ const Canvas3DPresets = {
        canvas3d: <Preset>{
            postprocessing: {
                occlusion: { name: 'off', params: {} },
-                outline: { name: 'off', params: {} },
-                shadow: { name: 'off', params: {} },
+                outline: { name: 'off', params: {} }
            },
            renderer: {
                ambientIntensity: 0.4,
--- a/src/extensions/cellpack/model.ts
+++ b/src/extensions/cellpack/model.ts
@@ -585,7 +585,7 @@ export const LoadCellPackModel = StateAction.build({
            ... ctx.managers.structure.component.state.options,
            visualQuality: 'custom',
            ignoreLight: true,
-            hydrogens: 'hide-all',
+            showHydrogens: false,
        });
        ctx.canvas3d?.setProps({
            multiSample: { mode: 'off' },
@@ -606,22 +606,12 @@ export const LoadCellPackModel = StateAction.build({
                        resolutionScale: 1,
                    }
                },
-                shadow: {
-                    name: 'on',
-                    params: {
-                        bias: 0.6,
-                        maxDistance: 80,
-                        steps: 3,
-                        tolerance: 1.0,
-                    }
-                },
                outline: {
                    name: 'on',
                    params: {
                        scale: 1,
                        threshold: 0.33,
                        color: ColorNames.black,
-                        includeTransparent: true,
                    }
                }
            }
--- a/src/extensions/model-archive/quality-assessment/prop.ts
+++ b/src/extensions/model-archive/quality-assessment/prop.ts
@@ -2,7 +2,6 @@
 * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author David Sehnal <david.sehnal@gmail.com>
 */

 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
@@ -15,7 +14,6 @@ import { CustomPropSymbol } from '../../../mol-script/language/symbol';
 import { Type } from '../../../mol-script/language/type';
 import { CustomPropertyDescriptor } from '../../../mol-model/custom-property';
 import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
-import { AtomicIndex } from '../../../mol-model/structure/model/properties/atomic';

 export { QualityAssessment };

@@ -73,28 +71,14 @@ namespace QualityAssessment {
            localNames.set(ma_qa_metric.id.value(i), name);
        }

-        const residueKey: AtomicIndex.ResidueLabelKey = {
-            label_entity_id: '',
-            label_asym_id: '',
-            label_seq_id: 0,
-            pdbx_PDB_ins_code: undefined,
-        };
-
        for (let i = 0, il = ma_qa_metric_local._rowCount; i < il; i++) {
            if (model_id.value(i) !== model.modelNum) continue;

            const labelAsymId = label_asym_id.value(i);
            const entityIndex = index.findEntity(labelAsymId);
-
-            residueKey.label_entity_id = model.entities.data.id.value(entityIndex);
-            residueKey.label_asym_id = labelAsymId;
-            residueKey.label_seq_id = label_seq_id.value(i);
-
-            const rI = index.findResidueLabel(residueKey);
-            if (rI >= 0) {
-                const name = localNames.get(metric_id.value(i))!;
-                localMetrics.get(name)!.set(rI, metric_value.value(i));
-            }
+            const rI = index.findResidue(model.entities.data.id.value(entityIndex), labelAsymId, label_seq_id.value(i));
+            const name = localNames.get(metric_id.value(i))!;
+            localMetrics.get(name)!.set(rI, metric_value.value(i));
        }

        return {
--- a/src/extensions/rcsb/graphql/types.ts
+++ b/src/extensions/rcsb/graphql/types.ts
@@ -4,7 +4,7 @@ export type InputMaybe<T> = Maybe<T>;
 export type Exact<T extends { [key: string]: unknown }> = { [K in keyof T]: T[K] };
 export type MakeOptional<T, K extends keyof T> = Omit<T, K> & { [SubKey in K]?: Maybe<T[SubKey]> };
 export type MakeMaybe<T, K extends keyof T> = Omit<T, K> & { [SubKey in K]: Maybe<T[SubKey]> };
-// Generated on 2022-12-03T21:55:37-08:00
+// Generated on 2022-08-20T16:36:05-07:00

 /** All built-in and custom scalars, mapped to their actual values */
 export type Scalars = {
@@ -343,14 +343,6 @@ export type Citation = {
   *
   */
  readonly journal_abbrev?: Maybe<Scalars['String']>;
-  /**
-   * Full name of the cited journal; relevant for journal articles.
-   *
-   * Examples:
-   * Journal of Molecular Biology
-   *
-   */
-  readonly journal_full?: Maybe<Scalars['String']>;
  /**
   * The American Society for Testing and Materials (ASTM) code
   *  assigned to the journal cited (also referred to as the CODEN
@@ -558,7 +550,6 @@ export type CoreBranchedEntityInstance = {
  readonly rcsb_id: Scalars['String'];
  readonly rcsb_latest_revision?: Maybe<RcsbLatestRevision>;
  readonly rcsb_ligand_neighbors?: Maybe<ReadonlyArray<Maybe<RcsbLigandNeighbors>>>;
-  readonly struct_asym?: Maybe<StructAsym>;
 };

 export type CoreChemComp = {
@@ -670,7 +661,6 @@ export type CoreEntry = {
  readonly exptl?: Maybe<ReadonlyArray<Maybe<Exptl>>>;
  readonly exptl_crystal?: Maybe<ReadonlyArray<Maybe<ExptlCrystal>>>;
  readonly exptl_crystal_grow?: Maybe<ReadonlyArray<Maybe<ExptlCrystalGrow>>>;
-  readonly ma_data?: Maybe<ReadonlyArray<Maybe<MaData>>>;
  /** Get all non-polymer (non-solvent) entities for this PDB entry. */
  readonly nonpolymer_entities?: Maybe<ReadonlyArray<Maybe<CoreNonpolymerEntity>>>;
  readonly pdbx_SG_project?: Maybe<ReadonlyArray<Maybe<PdbxSgProject>>>;
@@ -711,7 +701,6 @@ export type CoreEntry = {
  /** The list of content types associated with this entry. */
  readonly rcsb_associated_holdings?: Maybe<CurrentEntry>;
  readonly rcsb_binding_affinity?: Maybe<ReadonlyArray<Maybe<RcsbBindingAffinity>>>;
-  readonly rcsb_comp_model_provenance?: Maybe<RcsbCompModelProvenance>;
  readonly rcsb_entry_container_identifiers: RcsbEntryContainerIdentifiers;
  readonly rcsb_entry_group_membership?: Maybe<ReadonlyArray<Maybe<RcsbEntryGroupMembership>>>;
  readonly rcsb_entry_info: RcsbEntryInfo;
@@ -724,7 +713,6 @@ export type CoreEntry = {
   *
   */
  readonly rcsb_id: Scalars['String'];
-  readonly rcsb_ma_qa_metric_global?: Maybe<ReadonlyArray<Maybe<RcsbMaQaMetricGlobal>>>;
  readonly rcsb_primary_citation?: Maybe<RcsbPrimaryCitation>;
  readonly refine?: Maybe<ReadonlyArray<Maybe<Refine>>>;
  readonly refine_analyze?: Maybe<ReadonlyArray<Maybe<RefineAnalyze>>>;
@@ -798,7 +786,6 @@ export type CoreNonpolymerEntityInstance = {
  readonly rcsb_nonpolymer_instance_validation_score?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerInstanceValidationScore>>>;
  readonly rcsb_nonpolymer_struct_conn?: Maybe<ReadonlyArray<Maybe<RcsbNonpolymerStructConn>>>;
  readonly rcsb_target_neighbors?: Maybe<ReadonlyArray<Maybe<RcsbTargetNeighbors>>>;
-  readonly struct_asym?: Maybe<StructAsym>;
 };

 export type CorePfam = {
@@ -932,7 +919,6 @@ export type CorePolymerEntityInstance = {
  readonly rcsb_polymer_instance_feature?: Maybe<ReadonlyArray<Maybe<RcsbPolymerInstanceFeature>>>;
  readonly rcsb_polymer_instance_feature_summary?: Maybe<ReadonlyArray<Maybe<RcsbPolymerInstanceFeatureSummary>>>;
  readonly rcsb_polymer_struct_conn?: Maybe<ReadonlyArray<Maybe<RcsbPolymerStructConn>>>;
-  readonly struct_asym?: Maybe<StructAsym>;
 };

 export type CorePubmed = {
@@ -1298,9 +1284,9 @@ export type Em2dCrystalEntity = {
  readonly id: Scalars['String'];
  /** pointer to _em_image_processing.id in the EM_IMAGE_PROCESSING category. */
  readonly image_processing_id: Scalars['String'];
-  /** Unit-cell length a in angstroms. */
+  /** Unit-cell length a in Angstroms. */
  readonly length_a?: Maybe<Scalars['Float']>;
-  /** Unit-cell length b in angstroms. */
+  /** Unit-cell length b in Angstroms. */
  readonly length_b?: Maybe<Scalars['Float']>;
  /** Thickness of 2D crystal */
  readonly length_c?: Maybe<Scalars['Float']>;
@@ -1331,11 +1317,11 @@ export type Em3dCrystalEntity = {
  readonly id: Scalars['String'];
  /** pointer to _em_image_processing.id in the EM_IMAGE_PROCESSING category. */
  readonly image_processing_id: Scalars['String'];
-  /** Unit-cell length a in angstroms. */
+  /** Unit-cell length a in Angstroms. */
  readonly length_a?: Maybe<Scalars['Float']>;
-  /** Unit-cell length b in angstroms. */
+  /** Unit-cell length b in Angstroms. */
  readonly length_b?: Maybe<Scalars['Float']>;
-  /** Unit-cell length c in angstroms. */
+  /** Unit-cell length c in Angstroms. */
  readonly length_c?: Maybe<Scalars['Float']>;
  /**
   * Space group name.
@@ -1496,7 +1482,7 @@ export type Em3dReconstruction = {
   */
  readonly refinement_type?: Maybe<Scalars['String']>;
  /**
-   * The final resolution (in angstroms)of the 3D reconstruction.
+   * The final resolution (in Angstroms)of the 3D reconstruction.
   *
   * Examples:
   * null, null
@@ -1572,7 +1558,7 @@ export type EmDiffractionShell = {
   */
  readonly fourier_space_coverage?: Maybe<Scalars['Float']>;
  /**
-   * High resolution limit for this shell (angstroms)
+   * High resolution limit for this shell (Angstroms)
   *
   * Examples:
   * null
@@ -1582,7 +1568,7 @@ export type EmDiffractionShell = {
  /** Unique identifier for the category em_diffraction_shell */
  readonly id: Scalars['String'];
  /**
-   * Low resolution limit for this shell (angstroms)
+   * Low resolution limit for this shell (Angstroms)
   *
   * Examples:
   * null
@@ -1628,7 +1614,7 @@ export type EmDiffractionStats = {
   */
  readonly fourier_space_coverage?: Maybe<Scalars['Float']>;
  /**
-   * High resolution limit of the structure factor data, in angstroms
+   * High resolution limit of the structure factor data, in Angstroms
   *
   * Examples:
   * null
@@ -2012,12 +1998,12 @@ export type EmImaging = {
  /** The magnification indicated by the microscope readout. */
  readonly nominal_magnification?: Maybe<Scalars['Int']>;
  /**
-   * The specimen temperature maximum (kelvin) for the duration
+   * The specimen temperature maximum (degrees Kelvin) for the duration
   *  of imaging.
   */
  readonly recording_temperature_maximum?: Maybe<Scalars['Float']>;
  /**
-   * The specimen temperature minimum (kelvin) for the duration
+   * The specimen temperature minimum (degrees Kelvin) for the duration
   *  of imaging.
   */
  readonly recording_temperature_minimum?: Maybe<Scalars['Float']>;
@@ -2042,7 +2028,7 @@ export type EmImaging = {
  /** Foreign key to the EM_SPECIMEN category */
  readonly specimen_id?: Maybe<Scalars['String']>;
  /**
-   * The mean specimen stage temperature (in kelvin) during imaging
+   * The mean specimen stage temperature (degrees Kelvin) during imaging
   *  in the microscope.
   */
  readonly temperature?: Maybe<Scalars['Float']>;
@@ -2229,7 +2215,7 @@ export type EmStaining = {
 };

 export type EmVitrification = {
-  /** The temperature (in kelvin) of the sample just prior to vitrification. */
+  /** The temperature (in degrees Kelvin) of the sample just prior to vitrification. */
  readonly chamber_temperature?: Maybe<Scalars['Float']>;
  /**
   * This is the name of the cryogen.
@@ -2273,7 +2259,7 @@ export type EmVitrification = {
  /** This data item is a pointer to _em_specimen.id */
  readonly specimen_id: Scalars['String'];
  /**
-   * The vitrification temperature (in kelvin), e.g.,
+   * The vitrification temperature (in degrees Kelvin), e.g.,
   *   temperature of the plunge instrument cryogen bath.
   */
  readonly temp?: Maybe<Scalars['Float']>;
@@ -2378,14 +2364,6 @@ export type EntityPoly = {
   *
   */
  readonly pdbx_seq_one_letter_code_can?: Maybe<Scalars['String']>;
-  /**
-   * Evidence for the assignment of the polymer sequence.
-   *
-   * Allowable values:
-   * depositor provided, derived from coordinates
-   *
-   */
-  readonly pdbx_sequence_evidence_code?: Maybe<Scalars['String']>;
  /**
   * The PDB strand/chain id(s) corresponding to this polymer entity.
   *
@@ -3027,8 +3005,6 @@ export type Entry = {
   *  identifier.
   */
  readonly id: Scalars['String'];
-  /** An identifier for the model collection associated with the entry. */
-  readonly ma_collection_id?: Maybe<Scalars['String']>;
 };

 export type Exptl = {
@@ -3287,29 +3263,6 @@ export type InterfacePartnerFeatureFeaturePositions = {
  readonly values?: Maybe<ReadonlyArray<Maybe<Scalars['Float']>>>;
 };

-export type MaData = {
-  /**
-   * The type of data held in the dataset.
-   *
-   * Allowable values:
-   * coevolution MSA, input structure, model coordinates, other, polymeric template library, spatial restraints, target, target-template alignment, template structure
-   *
-   */
-  readonly content_type?: Maybe<Scalars['String']>;
-  /** Details for other content types. */
-  readonly content_type_other_details?: Maybe<Scalars['String']>;
-  /** A unique identifier for the data. */
-  readonly id: Scalars['Int'];
-  /**
-   * An author-given name for the content held in the dataset.
-   *
-   * Examples:
-   * NMR NOE Distances, Target Template Alignment, Coevolution Data
-   *
-   */
-  readonly name?: Maybe<Scalars['String']>;
-};
-
 export type MethodDetails = {
  /** A description of special aspects of the clustering process */
  readonly description?: Maybe<Scalars['String']>;
@@ -4246,7 +4199,7 @@ export type PdbxNmrExptlSampleConditions = {
   */
  readonly pressure_units?: Maybe<Scalars['String']>;
  /**
-   * The temperature (in kelvin) at which NMR data were
+   * The temperature (in Kelvin) at which NMR data were
   *  collected.
   */
  readonly temperature?: Maybe<Scalars['String']>;
@@ -4500,7 +4453,7 @@ export type PdbxPrdAudit = {
   * An identifier for the wwPDB site creating or modifying the molecule.
   *
   * Allowable values:
-   * BMRB, PDBC, PDBE, PDBJ, RCSB
+   * BMRB, PDBC, PDBJ, PDBe, RCSB
   *
   */
  readonly processing_site?: Maybe<Scalars['String']>;
@@ -6864,7 +6817,7 @@ export type Query = {
  readonly assemblies?: Maybe<ReadonlyArray<Maybe<CoreAssembly>>>;
  /** Get an assembly given the PDB ID and ASSEMBLY ID. Here ASSEMBLY ID is '1', '2', '3', etc. or 'deposited' for deposited coordinates. */
  readonly assembly?: Maybe<CoreAssembly>;
-  /** Get a list of PDB branched entities given a list of ENTITY IDs. Here ENTITY ID is a compound identifier that includes entry_id and entity_id separated by '_', e.g. 1XXX_1. Note that the ENTRY ID part must be upper case. */
+  /** Get a list of PDB branched entities given a list of ENTITY IDs. Here ENTITY ID is a compound identifier that includes entry_id and entity_id separated by '_', e.g. 1XXX_1. */
  readonly branched_entities?: Maybe<ReadonlyArray<Maybe<CoreBranchedEntity>>>;
  /** Get a PDB branched entity, given the PDB ID and ENTITY ID. Here ENTITY ID is a '1', '2', '3', etc. */
  readonly branched_entity?: Maybe<CoreBranchedEntity>;
@@ -6888,9 +6841,9 @@ export type Query = {
  readonly group_provenance?: Maybe<GroupProvenance>;
  /** Get a pairwise polymeric interface given the PDB ID, ASSEMBLY ID and INTERFACE ID. */
  readonly interface?: Maybe<CoreInterface>;
-  /** Get a list of pairwise polymeric interfaces given a list of INTERFACE IDs. Here INTERFACE ID is a compound identifier that includes entry_id, assembly_id and interface_id e.g. 1XXX-1.1. Note that the ENTRY ID part must be upper case. */
+  /** Get a list of pairwise polymeric interfaces given a list of INTERFACE IDs. Here INTERFACE ID is a compound identifier that includes entry_id, assembly_id and interface_id e.g. 1XXX-1.1. */
  readonly interfaces?: Maybe<ReadonlyArray<Maybe<CoreInterface>>>;
-  /** Get a list of PDB non-polymer entities given a list of ENTITY IDs. Here ENTITY ID is a compound identifier that includes entry_id and entity_id separated by '_', e.g. 1XXX_1. Note that the ENTRY ID part must be upper case. */
+  /** Get a list of PDB non-polymer entities given a list of ENTITY IDs. Here ENTITY ID is a compound identifier that includes entry_id and entity_id separated by '_', e.g. 1XXX_1. */
  readonly nonpolymer_entities?: Maybe<ReadonlyArray<Maybe<CoreNonpolymerEntity>>>;
  /** Get a PDB non-polymer entity, given the PDB ID and ENTITY ID. Here ENTITY ID is a '1', '2', '3', etc. */
  readonly nonpolymer_entity?: Maybe<CoreNonpolymerEntity>;
@@ -6898,7 +6851,7 @@ export type Query = {
  readonly nonpolymer_entity_instance?: Maybe<CoreNonpolymerEntityInstance>;
  /** Get a list of PDB non-polymer entity instances (chains), given the list of ENTITY INSTANCE IDs. Here ENTITY INSTANCE ID identifies structural element in the asymmetric unit, e.g. 'A', 'B', etc. */
  readonly nonpolymer_entity_instances?: Maybe<ReadonlyArray<Maybe<CoreNonpolymerEntityInstance>>>;
-  /** Get a list of PDB polymer entities given a list of ENTITY IDs. Here ENTITY ID is a compound identifier that includes entry_id and entity_id separated by '_', e.g. 1XXX_1. Note that the ENTRY ID part must be upper case. */
+  /** Get a list of PDB polymer entities given a list of ENTITY IDs. Here ENTITY ID is a compound identifier that includes entry_id and entity_id separated by '_', e.g. 1XXX_1. */
  readonly polymer_entities?: Maybe<ReadonlyArray<Maybe<CorePolymerEntity>>>;
  /** Get a PDB polymer entity, given the PDB ID and ENTITY ID. Here ENTITY ID is a '1', '2', '3', etc. */
  readonly polymer_entity?: Maybe<CorePolymerEntity>;
@@ -8468,29 +8421,6 @@ export type RcsbClusterMembership = {
  readonly identity?: Maybe<Scalars['Int']>;
 };

-export type RcsbCompModelProvenance = {
-  /**
-   * Entry identifier corresponding to the computed structure model.
-   *
-   * Examples:
-   * AF-P60325-F1, ma-bak-cepc-0019
-   *
-   */
-  readonly entry_id: Scalars['String'];
-  /**
-   * Source database for the computed structure model.
-   *
-   * Allowable values:
-   * AlphaFoldDB, ModelArchive
-   *
-   */
-  readonly source_db?: Maybe<Scalars['String']>;
-  /** Source filename for the computed structure model. */
-  readonly source_filename?: Maybe<Scalars['String']>;
-  /** Source URL for computed structure model file. */
-  readonly source_url?: Maybe<Scalars['String']>;
-};
-
 export type RcsbEntityHostOrganism = {
  /**
   * The beginning polymer sequence position for the polymer section corresponding
@@ -8727,7 +8657,7 @@ export type RcsbEntitySourceOrganism = {
   * A code indicating the provenance of the source organism details for the entity
   *
   * Allowable values:
-   * PDB Primary Data, UniProt
+   * PDB Primary Data
   *
   */
  readonly provenance_source?: Maybe<Scalars['String']>;
@@ -8801,7 +8731,7 @@ export type RcsbEntryContainerIdentifiers = {
   * Entry identifier for the container.
   *
   * Examples:
-   * 4HHB, AF_AFP60325F1, MA_MABAKCEPC0019
+   * 1KIP, 4HHB
   *
   */
  readonly entry_id: Scalars['String'];
@@ -8949,15 +8879,6 @@ export type RcsbEntryInfo = {
   *
   */
  readonly na_polymer_entity_types?: Maybe<Scalars['String']>;
-  /**
-   * This data item identifies secondary structure
-   *  features of nucleic acids in the entry.
-   *
-   * Allowable values:
-   * a-form double helix, b-form double helix, bulge loop, double helix, four-way junction, hairpin loop, internal loop, mismatched base pair, other right-handed double helix, parallel strands, quadruple helix, tetraloop, three-way junction, triple helix, two-way junction, z-form double helix
-   *
-   */
-  readonly ndb_struct_conf_na_feature_combined?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
  /** Bound nonpolymer components in this entry. */
  readonly nonpolymer_bound_components?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
  /** The number of distinct non-polymer entities in the structure entry exclusive of solvent. */
@@ -9034,21 +8955,6 @@ export type RcsbEntryInfo = {
  readonly software_programs_combined?: Maybe<ReadonlyArray<Maybe<Scalars['String']>>>;
  /** The number of distinct solvent entities per deposited structure model. */
  readonly solvent_entity_count?: Maybe<Scalars['Int']>;
-  /**
-   * Indicates if the structure was determined using experimental or computational methods.
-   *
-   * Allowable values:
-   * computational, experimental
-   *
-   */
-  readonly structure_determination_methodology: Scalars['String'];
-  /**
-   * Indicates the priority of the value in _rcsb_entry_info.structure_determination_methodology.
-   *  The lower the number the higher the priority.
-   *  Priority values for "experimental" structures is currently set to 10 and
-   *  the values for "computational" structures is set to 100.
-   */
-  readonly structure_determination_methodology_priority?: Maybe<Scalars['Int']>;
 };

 export type RcsbEntryInfoDiffrnResolutionHigh = {
@@ -9388,49 +9294,6 @@ export type RcsbLigandNeighbors = {
  readonly seq_id?: Maybe<Scalars['Int']>;
 };

-export type RcsbMaQaMetricGlobal = {
-  readonly ma_qa_metric_global?: Maybe<ReadonlyArray<Maybe<RcsbMaQaMetricGlobalMaQaMetricGlobal>>>;
-  /** The model identifier. */
-  readonly model_id: Scalars['Int'];
-};
-
-export type RcsbMaQaMetricGlobalMaQaMetricGlobal = {
-  /**
-   * Description of the global QA metric.
-   *
-   * Examples:
-   * confidence score predicting accuracy according to the CA-only Local Distance Difference Test (lDDT-CA) in [0,100]
-   *
-   */
-  readonly description?: Maybe<Scalars['String']>;
-  /**
-   * Name of the global QA metric.
-   *
-   * Examples:
-   * pLDDT
-   *
-   */
-  readonly name: Scalars['String'];
-  /**
-   * The type of global QA metric.
-   *
-   * Allowable values:
-   * PAE, contact probability, distance, energy, ipTM, normalized score, other, pLDDT, pLDDT all-atom, pLDDT all-atom in [0,1], pLDDT in [0,1], pTM, zscore
-   *
-   */
-  readonly type: Scalars['String'];
-  /** Details for other type of global QA metric. */
-  readonly type_other_details?: Maybe<Scalars['String']>;
-  /**
-   * Value of the global QA metric.
-   *
-   * Examples:
-   * null
-   *
-   */
-  readonly value: Scalars['Float'];
-};
-
 export type RcsbMembraneLineage = {
  /** Hierarchy depth. */
  readonly depth?: Maybe<Scalars['Int']>;
@@ -10469,7 +10332,7 @@ export type RcsbPolymerEntityContainerIdentifiersReferenceSequenceIdentifiers =
   * Source of the reference database assignment
   *
   * Allowable values:
-   * PDB, RCSB, SIFTS, UniProt
+   * PDB, RCSB, SIFTS
   *
   */
  readonly provenance_source?: Maybe<Scalars['String']>;
@@ -10874,7 +10737,7 @@ export type RcsbPolymerInstanceFeature = {
   * A type or category of the feature.
   *
   * Allowable values:
-   * ANGLE_OUTLIER, BEND, BINDING_SITE, BOND_OUTLIER, C-MANNOSYLATION_SITE, CATH, CIS-PEPTIDE, ECOD, HELIX_P, HELX_LH_PP_P, HELX_RH_3T_P, HELX_RH_AL_P, HELX_RH_PI_P, MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY, MA_QA_METRIC_LOCAL_TYPE_DISTANCE, MA_QA_METRIC_LOCAL_TYPE_ENERGY, MA_QA_METRIC_LOCAL_TYPE_IPTM, MA_QA_METRIC_LOCAL_TYPE_NORMALIZED_SCORE, MA_QA_METRIC_LOCAL_TYPE_OTHER, MA_QA_METRIC_LOCAL_TYPE_PAE, MA_QA_METRIC_LOCAL_TYPE_PLDDT, MA_QA_METRIC_LOCAL_TYPE_PLDDT_ALL-ATOM, MA_QA_METRIC_LOCAL_TYPE_PLDDT_ALL-ATOM_[0,1], MA_QA_METRIC_LOCAL_TYPE_PLDDT_[0,1], MA_QA_METRIC_LOCAL_TYPE_PTM, MA_QA_METRIC_LOCAL_TYPE_ZSCORE, MEMBRANE_SEGMENT, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, N-GLYCOSYLATION_SITE, O-GLYCOSYLATION_SITE, RAMACHANDRAN_OUTLIER, ROTAMER_OUTLIER, RSCC_OUTLIER, RSRZ_OUTLIER, S-GLYCOSYLATION_SITE, SABDAB_ANTIBODY_HEAVY_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_TYPE, SCOP, SCOP2B_SUPERFAMILY, SCOP2_FAMILY, SCOP2_SUPERFAMILY, SHEET, STEREO_OUTLIER, STRN, TURN_TY1_P, UNASSIGNED_SEC_STRUCT, UNOBSERVED_ATOM_XYZ, UNOBSERVED_RESIDUE_XYZ, ZERO_OCCUPANCY_ATOM_XYZ, ZERO_OCCUPANCY_RESIDUE_XYZ, ASA
+   * ANGLE_OUTLIER, BINDING_SITE, BOND_OUTLIER, C-MANNOSYLATION_SITE, CATH, CIS-PEPTIDE, ECOD, HELIX_P, MEMBRANE_SEGMENT, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, N-GLYCOSYLATION_SITE, O-GLYCOSYLATION_SITE, RAMACHANDRAN_OUTLIER, ROTAMER_OUTLIER, RSCC_OUTLIER, RSRZ_OUTLIER, S-GLYCOSYLATION_SITE, SABDAB_ANTIBODY_HEAVY_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_TYPE, SCOP, SCOP2B_SUPERFAMILY, SCOP2_FAMILY, SCOP2_SUPERFAMILY, SHEET, STEREO_OUTLIER, UNASSIGNED_SEC_STRUCT, UNOBSERVED_ATOM_XYZ, UNOBSERVED_RESIDUE_XYZ, ZERO_OCCUPANCY_ATOM_XYZ, ZERO_OCCUPANCY_RESIDUE_XYZ, ASA
   *
   */
  readonly type?: Maybe<Scalars['String']>;
@@ -10885,7 +10748,7 @@ export type RcsbPolymerInstanceFeatureAdditionalProperties = {
   * The additional property name.
   *
   * Allowable values:
-   * CATH_DOMAIN_ID, CATH_NAME, ECOD_DOMAIN_ID, ECOD_FAMILY_NAME, MODELCIF_MODEL_ID, OMEGA_ANGLE, PARTNER_ASYM_ID, PARTNER_BOND_DISTANCE, PARTNER_COMP_ID, SCOP2_DOMAIN_ID, SCOP2_FAMILY_ID, SCOP2_FAMILY_NAME, SCOP2_SUPERFAMILY_ID, SCOP2_SUPERFAMILY_NAME, SCOP_DOMAIN_ID, SCOP_NAME, SCOP_SUN_ID, SHEET_SENSE
+   * CATH_DOMAIN_ID, CATH_NAME, ECOD_DOMAIN_ID, ECOD_FAMILY_NAME, OMEGA_ANGLE, PARTNER_ASYM_ID, PARTNER_BOND_DISTANCE, PARTNER_COMP_ID, SCOP2_DOMAIN_ID, SCOP2_FAMILY_ID, SCOP2_FAMILY_NAME, SCOP2_SUPERFAMILY_ID, SCOP2_SUPERFAMILY_NAME, SCOP_DOMAIN_ID, SCOP_NAME, SCOP_SUN_ID, SHEET_SENSE
   *
   */
  readonly name?: Maybe<Scalars['String']>;
@@ -10955,7 +10818,7 @@ export type RcsbPolymerInstanceFeatureSummary = {
   * Type or category of the feature.
   *
   * Allowable values:
-   * ANGLE_OUTLIER, BEND, BINDING_SITE, BOND_OUTLIER, C-MANNOSYLATION_SITE, CATH, CIS-PEPTIDE, ECOD, HELIX_P, HELX_LH_PP_P, HELX_RH_3T_P, HELX_RH_AL_P, HELX_RH_PI_P, MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY, MA_QA_METRIC_LOCAL_TYPE_DISTANCE, MA_QA_METRIC_LOCAL_TYPE_ENERGY, MA_QA_METRIC_LOCAL_TYPE_IPTM, MA_QA_METRIC_LOCAL_TYPE_NORMALIZED_SCORE, MA_QA_METRIC_LOCAL_TYPE_OTHER, MA_QA_METRIC_LOCAL_TYPE_PAE, MA_QA_METRIC_LOCAL_TYPE_PLDDT, MA_QA_METRIC_LOCAL_TYPE_PLDDT_ALL-ATOM, MA_QA_METRIC_LOCAL_TYPE_PLDDT_ALL-ATOM_[0,1], MA_QA_METRIC_LOCAL_TYPE_PLDDT_[0,1], MA_QA_METRIC_LOCAL_TYPE_PTM, MA_QA_METRIC_LOCAL_TYPE_ZSCORE, MEMBRANE_SEGMENT, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, N-GLYCOSYLATION_SITE, O-GLYCOSYLATION_SITE, RAMACHANDRAN_OUTLIER, ROTAMER_OUTLIER, RSCC_OUTLIER, RSRZ_OUTLIER, S-GLYCOSYLATION_SITE, SABDAB_ANTIBODY_HEAVY_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_TYPE, SCOP, SCOP2B_SUPERFAMILY, SCOP2_FAMILY, SCOP2_SUPERFAMILY, SHEET, STEREO_OUTLIER, STRN, TURN_TY1_P, UNASSIGNED_SEC_STRUCT, UNOBSERVED_ATOM_XYZ, UNOBSERVED_RESIDUE_XYZ, ZERO_OCCUPANCY_ATOM_XYZ, ZERO_OCCUPANCY_RESIDUE_XYZ
+   * ANGLE_OUTLIER, BINDING_SITE, BOND_OUTLIER, C-MANNOSYLATION_SITE, CATH, CIS-PEPTIDE, ECOD, HELIX_P, MEMBRANE_SEGMENT, MOGUL_ANGLE_OUTLIER, MOGUL_BOND_OUTLIER, N-GLYCOSYLATION_SITE, O-GLYCOSYLATION_SITE, RAMACHANDRAN_OUTLIER, ROTAMER_OUTLIER, RSCC_OUTLIER, RSRZ_OUTLIER, S-GLYCOSYLATION_SITE, SABDAB_ANTIBODY_HEAVY_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_SUBCLASS, SABDAB_ANTIBODY_LIGHT_CHAIN_TYPE, SAbDab Antibody Heavy Chain Subclass, SAbDab Antibody Light Chain Subclass, SAbDab Antibody Light Chain Type, SCOP, SCOP2 Family, SCOP2 Superfamily, SCOP2B Superfamily, SCOP2B_SUPERFAMILY, SCOP2_FAMILY, SCOP2_SUPERFAMILY, SHEET, STEREO_OUTLIER, UNASSIGNED_SEC_STRUCT, UNOBSERVED_ATOM_XYZ, UNOBSERVED_RESIDUE_XYZ, ZERO_OCCUPANCY_ATOM_XYZ, ZERO_OCCUPANCY_RESIDUE_XYZ
   *
   */
  readonly type?: Maybe<Scalars['String']>;
@@ -13514,11 +13377,6 @@ export type ReflnsShell = {
 };

 export type Software = {
-  /**
-   * This data item is a pointer to _citation.id in the CITATION
-   *  category.
-   */
-  readonly citation_id?: Maybe<Scalars['String']>;
  /**
   * The classification of the program according to its
   *  major function.
@@ -13669,37 +13527,6 @@ export type Struct = {
  readonly title?: Maybe<Scalars['String']>;
 };

-export type StructAsym = {
-  /**
-   * This data item is a pointer to _atom_site.pdbx_PDB_strand_id the
-   *  ATOM_SITE category.
-   *
-   * Examples:
-   * 1ABC
-   *
-   */
-  readonly pdbx_PDB_id?: Maybe<Scalars['String']>;
-  /**
-   * This data item is a pointer to _atom_site.ndb_alias_strand_id the
-   *  ATOM_SITE category.
-   */
-  readonly pdbx_alt_id?: Maybe<Scalars['String']>;
-  /**
-   * This data item gives the order of the structural elements in the
-   *  ATOM_SITE category.
-   */
-  readonly pdbx_order?: Maybe<Scalars['Int']>;
-  /**
-   * This data item describes the general type of the structural elements
-   *  in the ATOM_SITE category.
-   *
-   * Allowable values:
-   * ATOMN, ATOMP, ATOMS, HETAC, HETAD, HETAI, HETAIN, HETAS, HETIC
-   *
-   */
-  readonly pdbx_type?: Maybe<Scalars['String']>;
-};
-
 export type StructKeywords = {
  /**
   * Terms characterizing the macromolecular structure.
--- a/src/mol-canvas3d/canvas3d.ts
+++ b/src/mol-canvas3d/canvas3d.ts
@@ -120,7 +120,6 @@ interface Canvas3DContext {

 namespace Canvas3DContext {
    export const DefaultAttribs = {
-        powerPreference: 'high-performance' as WebGLContextAttributes['powerPreference'],
        failIfMajorPerformanceCaveat: false,
        /** true by default to avoid issues with Safari (Jan 2021) */
        antialias: true,
@@ -141,9 +140,8 @@ namespace Canvas3DContext {

        if (a.enableWboit && a.enableDpoit) throw new Error('Multiple transparency methods not allowed.');

-        const { powerPreference, failIfMajorPerformanceCaveat, antialias, preserveDrawingBuffer, pixelScale, preferWebGl1 } = a;
+        const { failIfMajorPerformanceCaveat, antialias, preserveDrawingBuffer, pixelScale, preferWebGl1 } = a;
        const gl = getGLContext(canvas, {
-            powerPreference,
            failIfMajorPerformanceCaveat,
            antialias,
            preserveDrawingBuffer,
--- a/src/mol-canvas3d/passes/draw.ts
+++ b/src/mol-canvas3d/passes/draw.ts
@@ -142,7 +142,7 @@ export class DrawPass {
        }

        if (PostprocessingPass.isEnabled(postprocessingProps)) {
-            if (PostprocessingPass.isTransparentOutlineEnabled(postprocessingProps)) {
+            if (PostprocessingPass.isOutlineEnabled(postprocessingProps)) {
                this.depthTargetTransparent.bind();
                renderer.clearDepth(true);
                if (scene.opacityAverage < 1) {
@@ -150,7 +150,7 @@ export class DrawPass {
                }
            }

-            this.postprocessing.render(camera, false, transparentBackground, renderer.props.backgroundColor, postprocessingProps, renderer.light);
+            this.postprocessing.render(camera, false, transparentBackground, renderer.props.backgroundColor, postprocessingProps);
        }

        this.depthTextureOpaque.detachFramebuffer(this.colorTarget.framebuffer, 'depth');
@@ -196,7 +196,7 @@ export class DrawPass {
        }

        if (PostprocessingPass.isEnabled(postprocessingProps)) {
-            if (PostprocessingPass.isTransparentOutlineEnabled(postprocessingProps)) {
+            if (PostprocessingPass.isOutlineEnabled(postprocessingProps)) {
                this.depthTargetTransparent.bind();
                renderer.clearDepth(true);
                if (scene.opacityAverage < 1) {
@@ -204,7 +204,7 @@ export class DrawPass {
                }
            }

-            this.postprocessing.render(camera, false, transparentBackground, renderer.props.backgroundColor, postprocessingProps, renderer.light);
+            this.postprocessing.render(camera, false, transparentBackground, renderer.props.backgroundColor, postprocessingProps);
        }

        // render transparent primitives and volumes
@@ -260,7 +260,7 @@ export class DrawPass {
                    this.colorTarget.depthRenderbuffer?.detachFramebuffer(this.postprocessing.target.framebuffer);
                }

-                if (PostprocessingPass.isTransparentOutlineEnabled(postprocessingProps)) {
+                if (PostprocessingPass.isOutlineEnabled(postprocessingProps)) {
                    this.depthTargetTransparent.bind();
                    renderer.clearDepth(true);
                    if (scene.opacityAverage < 1) {
@@ -268,7 +268,7 @@ export class DrawPass {
                    }
                }

-                this.postprocessing.render(camera, false, transparentBackground, renderer.props.backgroundColor, postprocessingProps, renderer.light);
+                this.postprocessing.render(camera, false, transparentBackground, renderer.props.backgroundColor, postprocessingProps);

                if (!this.packedDepth) {
                    this.depthTextureOpaque.attachFramebuffer(this.postprocessing.target.framebuffer, 'depth');
--- a/src/mol-canvas3d/passes/postprocessing.ts
+++ b/src/mol-canvas3d/passes/postprocessing.ts
@@ -3,7 +3,6 @@
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 * @author Áron Samuel Kovács <aron.kovacs@mail.muni.cz>
- * @author Ludovic Autin <ludovic.autin@gmail.com>
 */

 import { CopyRenderable, createCopyRenderable, QuadSchema, QuadValues } from '../../mol-gl/compute/util';
@@ -31,8 +30,6 @@ import { SmaaParams, SmaaPass } from './smaa';
 import { isTimingMode } from '../../mol-util/debug';
 import { BackgroundParams, BackgroundPass } from './background';
 import { AssetManager } from '../../mol-util/assets';
-import { Light } from '../../mol-gl/renderer';
-import { shadows_frag } from '../../mol-gl/shader/shadows.frag';

 const OutlinesSchema = {
    ...QuadSchema,
@@ -45,12 +42,10 @@ const OutlinesSchema = {
    uFar: UniformSpec('f'),

    uMaxPossibleViewZDiff: UniformSpec('f'),
-
-    dTransparentOutline: DefineSpec('boolean'),
 };
 type OutlinesRenderable = ComputeRenderable<Values<typeof OutlinesSchema>>

-function getOutlinesRenderable(ctx: WebGLContext, depthTextureOpaque: Texture, depthTextureTransparent: Texture, transparentOutline: boolean): OutlinesRenderable {
+function getOutlinesRenderable(ctx: WebGLContext, depthTextureOpaque: Texture, depthTextureTransparent: Texture): OutlinesRenderable {
    const width = depthTextureOpaque.getWidth();
    const height = depthTextureOpaque.getHeight();

@@ -65,8 +60,6 @@ function getOutlinesRenderable(ctx: WebGLContext, depthTextureOpaque: Texture, d
        uFar: ValueCell.create(10000),

        uMaxPossibleViewZDiff: ValueCell.create(0.5),
-
-        dTransparentOutline: ValueCell.create(transparentOutline),
    };

    const schema = { ...OutlinesSchema };
@@ -76,64 +69,6 @@ function getOutlinesRenderable(ctx: WebGLContext, depthTextureOpaque: Texture, d
    return createComputeRenderable(renderItem, values);
 }

-const ShadowsSchema = {
-    ...QuadSchema,
-    tDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
-    uTexSize: UniformSpec('v2'),
-
-    uProjection: UniformSpec('m4'),
-    uInvProjection: UniformSpec('m4'),
-    uBounds: UniformSpec('v4'),
-
-    dOrthographic: DefineSpec('number'),
-    uNear: UniformSpec('f'),
-    uFar: UniformSpec('f'),
-
-    dSteps: DefineSpec('number'),
-    uMaxDistance: UniformSpec('f'),
-    uTolerance: UniformSpec('f'),
-    uBias: UniformSpec('f'),
-
-    uLightDirection: UniformSpec('v3[]'),
-    uLightColor: UniformSpec('v3[]'),
-    dLightCount: DefineSpec('number'),
-};
-type ShadowsRenderable = ComputeRenderable<Values<typeof ShadowsSchema>>
-
-function getShadowsRenderable(ctx: WebGLContext, depthTexture: Texture): ShadowsRenderable {
-    const width = depthTexture.getWidth();
-    const height = depthTexture.getHeight();
-
-    const values: Values<typeof ShadowsSchema> = {
-        ...QuadValues,
-        tDepth: ValueCell.create(depthTexture),
-        uTexSize: ValueCell.create(Vec2.create(width, height)),
-
-        uProjection: ValueCell.create(Mat4.identity()),
-        uInvProjection: ValueCell.create(Mat4.identity()),
-        uBounds: ValueCell.create(Vec4()),
-
-        dOrthographic: ValueCell.create(0),
-        uNear: ValueCell.create(1),
-        uFar: ValueCell.create(10000),
-
-        dSteps: ValueCell.create(1),
-        uMaxDistance: ValueCell.create(3.0),
-        uTolerance: ValueCell.create(1.0),
-        uBias: ValueCell.create(0.6),
-
-        uLightDirection: ValueCell.create([]),
-        uLightColor: ValueCell.create([]),
-        dLightCount: ValueCell.create(0),
-    };
-
-    const schema = { ...ShadowsSchema };
-    const shaderCode = ShaderCode('shadows', quad_vert, shadows_frag);
-    const renderItem = createComputeRenderItem(ctx, 'triangles', shaderCode, schema, values);
-
-    return createComputeRenderable(renderItem, values);
-}
-
 const SsaoSchema = {
    ...QuadSchema,
    tDepth: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
@@ -269,7 +204,6 @@ const PostprocessingSchema = {
    tColor: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
    tDepthOpaque: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
    tDepthTransparent: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
-    tShadows: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
    tOutlines: TextureSpec('texture', 'rgba', 'ubyte', 'nearest'),
    uTexSize: UniformSpec('v2'),

@@ -287,25 +221,19 @@ const PostprocessingSchema = {
    dOcclusionEnable: DefineSpec('boolean'),
    uOcclusionOffset: UniformSpec('v2'),

-    dShadowEnable: DefineSpec('boolean'),
-
    dOutlineEnable: DefineSpec('boolean'),
    dOutlineScale: DefineSpec('number'),
    uOutlineThreshold: UniformSpec('f'),
-
-    dTransparentOutline: DefineSpec('boolean'),
 };
 type PostprocessingRenderable = ComputeRenderable<Values<typeof PostprocessingSchema>>

-
-function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, depthTextureOpaque: Texture, depthTextureTransparent: Texture, shadowsTexture: Texture, outlinesTexture: Texture, ssaoDepthTexture: Texture, transparentOutline: boolean): PostprocessingRenderable {
+function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, depthTextureOpaque: Texture, depthTextureTransparent: Texture, outlinesTexture: Texture, ssaoDepthTexture: Texture): PostprocessingRenderable {
    const values: Values<typeof PostprocessingSchema> = {
        ...QuadValues,
        tSsaoDepth: ValueCell.create(ssaoDepthTexture),
        tColor: ValueCell.create(colorTexture),
        tDepthOpaque: ValueCell.create(depthTextureOpaque),
        tDepthTransparent: ValueCell.create(depthTextureTransparent),
-        tShadows: ValueCell.create(shadowsTexture),
        tOutlines: ValueCell.create(outlinesTexture),
        uTexSize: ValueCell.create(Vec2.create(colorTexture.getWidth(), colorTexture.getHeight())),

@@ -323,13 +251,9 @@ function getPostprocessingRenderable(ctx: WebGLContext, colorTexture: Texture, d
        dOcclusionEnable: ValueCell.create(true),
        uOcclusionOffset: ValueCell.create(Vec2.create(0, 0)),

-        dShadowEnable: ValueCell.create(false),
-
        dOutlineEnable: ValueCell.create(false),
        dOutlineScale: ValueCell.create(1),
        uOutlineThreshold: ValueCell.create(0.33),
-
-        dTransparentOutline: ValueCell.create(transparentOutline),
    };

    const schema = { ...PostprocessingSchema };
@@ -350,21 +274,11 @@ export const PostprocessingParams = {
        }),
        off: PD.Group({})
    }, { cycle: true, description: 'Darken occluded crevices with the ambient occlusion effect' }),
-    shadow: PD.MappedStatic('off', {
-        on: PD.Group({
-            steps: PD.Numeric(1, { min: 1, max: 64, step: 1 }),
-            bias: PD.Numeric(0.6, { min: 0.0, max: 1.0, step: 0.01 }),
-            maxDistance: PD.Numeric(3, { min: 0, max: 256, step: 1 }),
-            tolerance: PD.Numeric(1.0, { min: 0.0, max: 10.0, step: 0.1 }),
-        }),
-        off: PD.Group({})
-    }, { cycle: true, description: 'Simplistic shadows' }),
    outline: PD.MappedStatic('off', {
        on: PD.Group({
            scale: PD.Numeric(1, { min: 1, max: 5, step: 1 }),
            threshold: PD.Numeric(0.33, { min: 0.01, max: 1, step: 0.01 }),
            color: PD.Color(Color(0x000000)),
-            includeTransparent: PD.Boolean(true, { description: 'Whether to show outline for transparent objects' }),
        }),
        off: PD.Group({})
    }, { cycle: true, description: 'Draw outline around 3D objects' }),
@@ -375,16 +289,15 @@ export const PostprocessingParams = {
    }, { options: [['fxaa', 'FXAA'], ['smaa', 'SMAA'], ['off', 'Off']], description: 'Smooth pixel edges' }),
    background: PD.Group(BackgroundParams, { isFlat: true }),
 };
-
 export type PostprocessingProps = PD.Values<typeof PostprocessingParams>

 export class PostprocessingPass {
    static isEnabled(props: PostprocessingProps) {
-        return props.occlusion.name === 'on' || props.shadow.name === 'on' || props.outline.name === 'on' || props.background.variant.name !== 'off';
+        return props.occlusion.name === 'on' || props.outline.name === 'on' || props.background.variant.name !== 'off';
    }

-    static isTransparentOutlineEnabled(props: PostprocessingProps) {
-        return props.outline.name === 'on' && props.outline.params.includeTransparent;
+    static isOutlineEnabled(props: PostprocessingProps) {
+        return props.outline.name === 'on';
    }

    readonly target: RenderTarget;
@@ -392,9 +305,6 @@ export class PostprocessingPass {
    private readonly outlinesTarget: RenderTarget;
    private readonly outlinesRenderable: OutlinesRenderable;

-    private readonly shadowsTarget: RenderTarget;
-    private readonly shadowsRenderable: ShadowsRenderable;
-
    private readonly ssaoFramebuffer: Framebuffer;
    private readonly ssaoBlurFirstPassFramebuffer: Framebuffer;
    private readonly ssaoBlurSecondPassFramebuffer: Framebuffer;
@@ -438,10 +348,7 @@ export class PostprocessingPass {
        this.target = webgl.createRenderTarget(width, height, false, 'uint8', 'linear');

        this.outlinesTarget = webgl.createRenderTarget(width, height, false);
-        this.outlinesRenderable = getOutlinesRenderable(webgl, depthTextureOpaque, depthTextureTransparent, true);
-
-        this.shadowsTarget = webgl.createRenderTarget(width, height, false);
-        this.shadowsRenderable = getShadowsRenderable(webgl, depthTextureOpaque);
+        this.outlinesRenderable = getOutlinesRenderable(webgl, depthTextureOpaque, depthTextureTransparent);

        this.ssaoFramebuffer = webgl.resources.framebuffer();
        this.ssaoBlurFirstPassFramebuffer = webgl.resources.framebuffer();
@@ -466,7 +373,7 @@ export class PostprocessingPass {
        this.ssaoRenderable = getSsaoRenderable(webgl, this.downsampleFactor === 1 ? depthTextureOpaque : this.downsampledDepthTarget.texture);
        this.ssaoBlurFirstPassRenderable = getSsaoBlurRenderable(webgl, this.ssaoDepthTexture, 'horizontal');
        this.ssaoBlurSecondPassRenderable = getSsaoBlurRenderable(webgl, this.ssaoDepthBlurProxyTexture, 'vertical');
-        this.renderable = getPostprocessingRenderable(webgl, colorTarget.texture, depthTextureOpaque, depthTextureTransparent, this.shadowsTarget.texture, this.outlinesTarget.texture, this.ssaoDepthTexture, true);
+        this.renderable = getPostprocessingRenderable(webgl, colorTarget.texture, depthTextureOpaque, depthTextureTransparent, this.outlinesTarget.texture, this.ssaoDepthTexture);

        this.background = new BackgroundPass(webgl, assetManager, width, height);
    }
@@ -482,14 +389,12 @@ export class PostprocessingPass {
            const sh = Math.floor(height * this.ssaoScale);
            this.target.setSize(width, height);
            this.outlinesTarget.setSize(width, height);
-            this.shadowsTarget.setSize(width, height);
            this.downsampledDepthTarget.setSize(sw, sh);
            this.ssaoDepthTexture.define(sw, sh);
            this.ssaoDepthBlurProxyTexture.define(sw, sh);

            ValueCell.update(this.renderable.values.uTexSize, Vec2.set(this.renderable.values.uTexSize.ref.value, width, height));
            ValueCell.update(this.outlinesRenderable.values.uTexSize, Vec2.set(this.outlinesRenderable.values.uTexSize.ref.value, width, height));
-            ValueCell.update(this.shadowsRenderable.values.uTexSize, Vec2.set(this.shadowsRenderable.values.uTexSize.ref.value, width, height));
            ValueCell.update(this.downsampleDepthRenderable.values.uTexSize, Vec2.set(this.downsampleDepthRenderable.values.uTexSize.ref.value, sw, sh));
            ValueCell.update(this.ssaoRenderable.values.uTexSize, Vec2.set(this.ssaoRenderable.values.uTexSize.ref.value, sw, sh));
            ValueCell.update(this.ssaoBlurFirstPassRenderable.values.uTexSize, Vec2.set(this.ssaoBlurFirstPassRenderable.values.uTexSize.ref.value, sw, sh));
@@ -499,29 +404,25 @@ export class PostprocessingPass {
        }
    }

-    private updateState(camera: ICamera, transparentBackground: boolean, backgroundColor: Color, props: PostprocessingProps, light: Light) {
-        let needsUpdateShadows = false;
+    private updateState(camera: ICamera, transparentBackground: boolean, backgroundColor: Color, props: PostprocessingProps) {
        let needsUpdateMain = false;
        let needsUpdateSsao = false;
        let needsUpdateSsaoBlur = false;
-        let needsUpdateOutlines = false;

        const orthographic = camera.state.mode === 'orthographic' ? 1 : 0;
        const outlinesEnabled = props.outline.name === 'on';
-        const shadowsEnabled = props.shadow.name === 'on';
        const occlusionEnabled = props.occlusion.name === 'on';

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

-        const [w, h] = this.renderable.values.uTexSize.ref.value;
-        const v = camera.viewport;
-
        if (props.occlusion.name === 'on') {
            ValueCell.update(this.ssaoRenderable.values.uProjection, camera.projection);
            ValueCell.update(this.ssaoRenderable.values.uInvProjection, invProjection);

+            const [w, h] = this.renderable.values.uTexSize.ref.value;
            const b = this.ssaoRenderable.values.uBounds;
+            const v = camera.viewport;
            const s = this.ssaoScale;
            Vec4.set(b.ref.value,
                Math.floor(v.x * s) / (w * s),
@@ -593,41 +494,8 @@ export class PostprocessingPass {
            }
        }

-        if (props.shadow.name === 'on') {
-            ValueCell.update(this.shadowsRenderable.values.uProjection, camera.projection);
-            ValueCell.update(this.shadowsRenderable.values.uInvProjection, invProjection);
-
-            Vec4.set(this.shadowsRenderable.values.uBounds.ref.value,
-                v.x / w,
-                v.y / h,
-                (v.x + v.width) / w,
-                (v.y + v.height) / h
-            );
-            ValueCell.update(this.shadowsRenderable.values.uBounds, this.shadowsRenderable.values.uBounds.ref.value);
-
-            ValueCell.updateIfChanged(this.shadowsRenderable.values.uNear, camera.near);
-            ValueCell.updateIfChanged(this.shadowsRenderable.values.uFar, camera.far);
-            ValueCell.updateIfChanged(this.shadowsRenderable.values.dOrthographic, orthographic);
-
-            ValueCell.updateIfChanged(this.shadowsRenderable.values.uMaxDistance, props.shadow.params.maxDistance);
-            ValueCell.updateIfChanged(this.shadowsRenderable.values.uTolerance, props.shadow.params.tolerance);
-            ValueCell.updateIfChanged(this.shadowsRenderable.values.uBias, props.shadow.params.bias);
-            if (this.shadowsRenderable.values.dSteps.ref.value !== props.shadow.params.steps) {
-                ValueCell.update(this.shadowsRenderable.values.dSteps, props.shadow.params.steps);
-                needsUpdateShadows = true;
-            }
-
-            ValueCell.update(this.shadowsRenderable.values.uLightDirection, light.direction);
-            ValueCell.update(this.shadowsRenderable.values.uLightColor, light.color);
-            if (this.shadowsRenderable.values.dLightCount.ref.value !== light.count) {
-                ValueCell.update(this.shadowsRenderable.values.dLightCount, light.count);
-                needsUpdateShadows = true;
-            }
-        }
-
        if (props.outline.name === 'on') {
-            let { threshold, includeTransparent } = props.outline.params;
-            const transparentOutline = includeTransparent ?? true;
+            let { threshold } = props.outline.params;
            // orthographic needs lower threshold
            if (camera.state.mode === 'orthographic') threshold /= 5;
            const factor = Math.pow(1000, threshold) / 1000;
@@ -638,16 +506,12 @@ export class PostprocessingPass {
            ValueCell.updateIfChanged(this.outlinesRenderable.values.uNear, camera.near);
            ValueCell.updateIfChanged(this.outlinesRenderable.values.uFar, camera.far);
            ValueCell.updateIfChanged(this.outlinesRenderable.values.uMaxPossibleViewZDiff, maxPossibleViewZDiff);
-            if (this.renderable.values.dTransparentOutline.ref.value !== transparentOutline) { needsUpdateOutlines = true; }
-            ValueCell.updateIfChanged(this.outlinesRenderable.values.dTransparentOutline, transparentOutline);

            ValueCell.update(this.renderable.values.uOutlineColor, Color.toVec3Normalized(this.renderable.values.uOutlineColor.ref.value, props.outline.params.color));

            ValueCell.updateIfChanged(this.renderable.values.uMaxPossibleViewZDiff, maxPossibleViewZDiff);
            if (this.renderable.values.dOutlineScale.ref.value !== outlineScale) { needsUpdateMain = true; }
            ValueCell.updateIfChanged(this.renderable.values.dOutlineScale, outlineScale);
-            if (this.renderable.values.dTransparentOutline.ref.value !== transparentOutline) { needsUpdateMain = true; }
-            ValueCell.updateIfChanged(this.renderable.values.dTransparentOutline, transparentOutline);
        }

        ValueCell.updateIfChanged(this.renderable.values.uFar, camera.far);
@@ -658,22 +522,11 @@ export class PostprocessingPass {
        ValueCell.updateIfChanged(this.renderable.values.uTransparentBackground, transparentBackground);
        if (this.renderable.values.dOrthographic.ref.value !== orthographic) { needsUpdateMain = true; }
        ValueCell.updateIfChanged(this.renderable.values.dOrthographic, orthographic);
-
        if (this.renderable.values.dOutlineEnable.ref.value !== outlinesEnabled) { needsUpdateMain = true; }
        ValueCell.updateIfChanged(this.renderable.values.dOutlineEnable, outlinesEnabled);
-        if (this.renderable.values.dShadowEnable.ref.value !== shadowsEnabled) { needsUpdateMain = true; }
-        ValueCell.updateIfChanged(this.renderable.values.dShadowEnable, shadowsEnabled);
        if (this.renderable.values.dOcclusionEnable.ref.value !== occlusionEnabled) { needsUpdateMain = true; }
        ValueCell.updateIfChanged(this.renderable.values.dOcclusionEnable, occlusionEnabled);

-        if (needsUpdateOutlines) {
-            this.outlinesRenderable.update();
-        }
-
-        if (needsUpdateShadows) {
-            this.shadowsRenderable.update();
-        }
-
        if (needsUpdateSsao) {
            this.ssaoRenderable.update();
        }
@@ -711,20 +564,15 @@ export class PostprocessingPass {
        this.transparentBackground = value;
    }

-    render(camera: ICamera, toDrawingBuffer: boolean, transparentBackground: boolean, backgroundColor: Color, props: PostprocessingProps, light: Light) {
+    render(camera: ICamera, toDrawingBuffer: boolean, transparentBackground: boolean, backgroundColor: Color, props: PostprocessingProps) {
        if (isTimingMode) this.webgl.timer.mark('PostprocessingPass.render');
-        this.updateState(camera, transparentBackground, backgroundColor, props, light);
+        this.updateState(camera, transparentBackground, backgroundColor, props);

        if (props.outline.name === 'on') {
            this.outlinesTarget.bind();
            this.outlinesRenderable.render();
        }

-        if (props.shadow.name === 'on') {
-            this.shadowsTarget.bind();
-            this.shadowsRenderable.render();
-        }
-
        // don't render occlusion if offset is given,
        // which will reuse the existing occlusion
        if (props.occlusion.name === 'on' && this.occlusionOffset[0] === 0 && this.occlusionOffset[1] === 0) {
--- a/src/mol-geo/geometry/overpaint-data.ts
+++ b/src/mol-geo/geometry/overpaint-data.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2022 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>
 */
@@ -21,7 +21,6 @@ export type OverpaintData = {
    uOverpaintGridDim: ValueCell<Vec3>,
    uOverpaintGridTransform: ValueCell<Vec4>,
    dOverpaintType: ValueCell<string>,
-    uOverpaintStrength: ValueCell<number>,
 }

 export function applyOverpaintColor(array: Uint8Array, start: number, end: number, color: Color) {
@@ -55,7 +54,6 @@ export function createOverpaint(count: number, type: OverpaintType, overpaintDat
            uOverpaintGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
            uOverpaintGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
            dOverpaintType: ValueCell.create(type),
-            uOverpaintStrength: ValueCell.create(1),
        };
    }
 }
@@ -76,7 +74,6 @@ export function createEmptyOverpaint(overpaintData?: OverpaintData): OverpaintDa
            uOverpaintGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
            uOverpaintGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
            dOverpaintType: ValueCell.create('groupInstance'),
-            uOverpaintStrength: ValueCell.create(1),
        };
    }
 }
--- a/src/mol-geo/geometry/substance-data.ts
+++ b/src/mol-geo/geometry/substance-data.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */
@@ -21,7 +21,6 @@ export type SubstanceData = {
    uSubstanceGridDim: ValueCell<Vec3>,
    uSubstanceGridTransform: ValueCell<Vec4>,
    dSubstanceType: ValueCell<string>,
-    uSubstanceStrength: ValueCell<number>,
 }

 export function applySubstanceMaterial(array: Uint8Array, start: number, end: number, material: Material) {
@@ -55,7 +54,6 @@ export function createSubstance(count: number, type: SubstanceType, substanceDat
            uSubstanceGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
            uSubstanceGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
            dSubstanceType: ValueCell.create(type),
-            uSubstanceStrength: ValueCell.create(1),
        };
    }
 }
@@ -76,7 +74,6 @@ export function createEmptySubstance(substanceData?: SubstanceData): SubstanceDa
            uSubstanceGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
            uSubstanceGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
            dSubstanceType: ValueCell.create('groupInstance'),
-            uSubstanceStrength: ValueCell.create(1),
        };
    }
 }
--- a/src/mol-geo/geometry/texture-mesh/texture-mesh.ts
+++ b/src/mol-geo/geometry/texture-mesh/texture-mesh.ts
@@ -7,7 +7,7 @@
 import { ValueCell } from '../../../mol-util';
 import { Sphere3D } from '../../../mol-math/geometry';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { LocationIterator, PositionLocation } from '../../../mol-geo/util/location-iterator';
+import { LocationIterator } from '../../../mol-geo/util/location-iterator';
 import { TransformData } from '../transform-data';
 import { createColors } from '../color-data';
 import { createMarkers } from '../marker-data';
@@ -20,12 +20,11 @@ import { createEmptyTransparency } from '../transparency-data';
 import { TextureMeshValues } from '../../../mol-gl/renderable/texture-mesh';
 import { calculateTransformBoundingSphere } from '../../../mol-gl/renderable/util';
 import { createNullTexture, Texture } from '../../../mol-gl/webgl/texture';
-import { Vec2, Vec3, Vec4 } from '../../../mol-math/linear-algebra';
+import { Vec2, Vec4 } from '../../../mol-math/linear-algebra';
 import { createEmptyClipping } from '../clipping-data';
 import { NullLocation } from '../../../mol-model/location';
 import { createEmptySubstance } from '../substance-data';
 import { RenderableState } from '../../../mol-gl/renderable';
-import { WebGLContext } from '../../../mol-gl/webgl/context';

 export interface TextureMesh {
    readonly kind: 'texture-mesh',
@@ -44,10 +43,7 @@ export interface TextureMesh {

    readonly boundingSphere: Sphere3D

-    readonly meta: {
-        webgl?: WebGLContext
-        [k: string]: unknown
-    }
+    readonly meta: { [k: string]: unknown }
 }

 export namespace TextureMesh {
@@ -135,42 +131,9 @@ export namespace TextureMesh {
        updateBoundingSphere,
        createRenderableState,
        updateRenderableState,
-        createPositionIterator,
+        createPositionIterator: () => LocationIterator(1, 1, 1, () => NullLocation)
    };

-    const TextureMeshName = 'texture-mesh';
-
-    function createPositionIterator(textureMesh: TextureMesh, transform: TransformData): LocationIterator {
-        const webgl = textureMesh.meta.webgl;
-        if (!webgl) return LocationIterator(1, 1, 1, () => NullLocation);
-
-        if (!webgl.namedFramebuffers[TextureMeshName]) {
-            webgl.namedFramebuffers[TextureMeshName] = webgl.resources.framebuffer();
-        }
-        const framebuffer = webgl.namedFramebuffers[TextureMeshName];
-        const [width, height] = textureMesh.geoTextureDim.ref.value;
-        const vertices = new Float32Array(width * height * 4);
-        framebuffer.bind();
-        textureMesh.vertexTexture.ref.value.attachFramebuffer(framebuffer, 0);
-        webgl.readPixels(0, 0, width, height, vertices);
-
-        const groupCount = textureMesh.vertexCount;
-        const instanceCount = transform.instanceCount.ref.value;
-        const location = PositionLocation();
-        const p = location.position;
-        const v = vertices;
-        const m = transform.aTransform.ref.value;
-        const getLocation = (groupIndex: number, instanceIndex: number) => {
-            if (instanceIndex < 0) {
-                Vec3.fromArray(p, v, groupIndex * 4);
-            } else {
-                Vec3.transformMat4Offset(p, v, m, 0, groupIndex * 4, instanceIndex * 16);
-            }
-            return location;
-        };
-        return LocationIterator(groupCount, instanceCount, 1, getLocation);
-    }
-
    function createValues(textureMesh: TextureMesh, transform: TransformData, locationIt: LocationIterator, theme: Theme, props: PD.Values<Params>): TextureMeshValues {
        const { instanceCount, groupCount } = locationIt;
        const positionIt = Utils.createPositionIterator(textureMesh, transform);
--- a/src/mol-geo/geometry/transparency-data.ts
+++ b/src/mol-geo/geometry/transparency-data.ts
@@ -21,7 +21,6 @@ export type TransparencyData = {
    uTransparencyGridDim: ValueCell<Vec3>,
    uTransparencyGridTransform: ValueCell<Vec4>,
    dTransparencyType: ValueCell<string>,
-    uTransparencyStrength: ValueCell<number>,
 }

 export function applyTransparencyValue(array: Uint8Array, start: number, end: number, value: number) {
@@ -64,7 +63,6 @@ export function createTransparency(count: number, type: TransparencyType, transp
            uTransparencyGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
            uTransparencyGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
            dTransparencyType: ValueCell.create(type),
-            uTransparencyStrength: ValueCell.create(1),
        };
    }
 }
@@ -86,7 +84,6 @@ export function createEmptyTransparency(transparencyData?: TransparencyData): Tr
            uTransparencyGridDim: ValueCell.create(Vec3.create(1, 1, 1)),
            uTransparencyGridTransform: ValueCell.create(Vec4.create(0, 0, 0, 1)),
            dTransparencyType: ValueCell.create('groupInstance'),
-            uTransparencyStrength: ValueCell.create(1),
        };
    }
 }
--- a/src/mol-gl/renderable/schema.ts
+++ b/src/mol-gl/renderable/schema.ts
@@ -229,7 +229,6 @@ export const OverpaintSchema = {
    uOverpaintGridTransform: UniformSpec('v4'),
    tOverpaintGrid: TextureSpec('texture', 'rgba', 'ubyte', 'linear'),
    dOverpaintType: DefineSpec('string', ['instance', 'groupInstance', 'volumeInstance']),
-    uOverpaintStrength: UniformSpec('f', 'material'),
 } as const;
 export type OverpaintSchema = typeof OverpaintSchema
 export type OverpaintValues = Values<OverpaintSchema>
@@ -243,8 +242,7 @@ export const TransparencySchema = {
    uTransparencyGridDim: UniformSpec('v3'),
    uTransparencyGridTransform: UniformSpec('v4'),
    tTransparencyGrid: TextureSpec('texture', 'alpha', 'ubyte', 'linear'),
-    dTransparencyType: DefineSpec('string', ['instance', 'groupInstance', 'volumeInstance']),
-    uTransparencyStrength: UniformSpec('f', 'material'),
+    dTransparencyType: DefineSpec('string', ['instance', 'groupInstance', 'volumeInstance'])
 } as const;
 export type TransparencySchema = typeof TransparencySchema
 export type TransparencyValues = Values<TransparencySchema>
@@ -258,7 +256,6 @@ export const SubstanceSchema = {
    uSubstanceGridTransform: UniformSpec('v4'),
    tSubstanceGrid: TextureSpec('texture', 'rgba', 'ubyte', 'linear'),
    dSubstanceType: DefineSpec('string', ['instance', 'groupInstance', 'volumeInstance']),
-    uSubstanceStrength: UniformSpec('f', 'material'),
 } as const;
 export type SubstanceSchema = typeof SubstanceSchema
 export type SubstanceValues = Values<SubstanceSchema>
--- a/src/mol-gl/renderer.ts
+++ b/src/mol-gl/renderer.ts
@@ -54,7 +54,6 @@ export const enum MarkingType {
 interface Renderer {
    readonly stats: RendererStats
    readonly props: Readonly<RendererProps>
-    readonly light: Readonly<Light>

    clear: (toBackgroundColor: boolean, ignoreTransparentBackground?: boolean) => void
    clearDepth: (packed?: boolean) => void
@@ -104,13 +103,13 @@ export const RendererParams = {
    xrayEdgeFalloff: PD.Numeric(1, { min: 0.0, max: 3.0, step: 0.1 }),

    light: PD.ObjectList({
-        inclination: PD.Numeric(150, { min: 0, max: 180, step: 1 }),
-        azimuth: PD.Numeric(320, { min: 0, max: 360, step: 1 }),
+        inclination: PD.Numeric(180, { min: 0, max: 180, step: 1 }),
+        azimuth: PD.Numeric(0, { min: 0, max: 360, step: 1 }),
        color: PD.Color(Color.fromNormalizedRgb(1.0, 1.0, 1.0)),
        intensity: PD.Numeric(0.6, { min: 0.0, max: 1.0, step: 0.01 }),
    }, o => Color.toHexString(o.color), { defaultValue: [{
-        inclination: 150,
-        azimuth: 320,
+        inclination: 180,
+        azimuth: 0,
        color: Color.fromNormalizedRgb(1.0, 1.0, 1.0),
        intensity: 0.6
    }] }),
@@ -119,7 +118,7 @@ export const RendererParams = {
 };
 export type RendererProps = PD.Values<typeof RendererParams>

-export type Light = {
+type Light = {
    count: number
    direction: number[]
    color: number[]
@@ -828,9 +827,6 @@ namespace Renderer {
                    instancedDrawCount: stats.instancedDrawCount,
                };
            },
-            get light(): Light {
-                return light;
-            },
            dispose: () => {
                // TODO
            }
--- a/src/mol-gl/shader/chunks/apply-light-color.glsl.ts
+++ b/src/mol-gl/shader/chunks/apply-light-color.glsl.ts
@@ -12,7 +12,7 @@ export const apply_light_color = `
    gl_FragColor = material;
 #else
    #ifdef bumpEnabled
-        if (uBumpFrequency > 0.0 && uBumpAmplitude > 0.0 && bumpiness > 0.0) {
+        if (uBumpFrequency > 0.0 && uBumpAmplitude > 0.0) {
            normal = perturbNormal(-vViewPosition, normal, fbm(vModelPosition * uBumpFrequency), (uBumpAmplitude * bumpiness) / uBumpFrequency);
        }
    #endif
--- a/src/mol-gl/shader/chunks/assign-color-varying.glsl.ts
+++ b/src/mol-gl/shader/chunks/assign-color-varying.glsl.ts
@@ -42,7 +42,6 @@ export const assign_color_varying = `
        #else
            vOverpaint.rgb = mix(vColor.rgb, vOverpaint.rgb, vOverpaint.a);
        #endif
-        vOverpaint *= uOverpaintStrength;
    #endif

    #ifdef dSubstance
@@ -59,7 +58,6 @@ export const assign_color_varying = `

        // pre-mix to avoid artifacts due to empty substance
        vSubstance.rgb = mix(vec3(uMetalness, uRoughness, uBumpiness), vSubstance.rgb, vSubstance.a);
-        vSubstance *= uSubstanceStrength;
    #endif
 #elif defined(dRenderVariant_pick)
    #ifdef requiredDrawBuffers
@@ -88,6 +86,5 @@ export const assign_color_varying = `
        vec3 tgridPos = (uTransparencyGridTransform.w * (vModelPosition - uTransparencyGridTransform.xyz)) / uTransparencyGridDim;
        vTransparency = texture3dFrom2dLinear(tTransparencyGrid, tgridPos, uTransparencyGridDim, uTransparencyTexDim).a;
    #endif
-    vTransparency *= uTransparencyStrength;
 #endif
 `;
--- a/src/mol-gl/shader/chunks/clip-instance.glsl.ts
+++ b/src/mol-gl/shader/chunks/clip-instance.glsl.ts
@@ -1,7 +1,12 @@
 export const clip_instance = `
 #if defined(dClipVariant_instance) && dClipObjectCount != 0
+    int flag = 0;
+    #if defined(dClipping)
+        flag = int(floor(vClipping * 255.0 + 0.5));
+    #endif
+
    vec4 mCenter = uModel * aTransform * vec4(uInvariantBoundingSphere.xyz, 1.0);
-    if (clipTest(vec4(mCenter.xyz, uInvariantBoundingSphere.w)))
+    if (clipTest(vec4(mCenter.xyz, uInvariantBoundingSphere.w), flag))
        // move out of [ -w, +w ] to 'discard' in vert shader
        gl_Position.z = 2.0 * gl_Position.w;
 #endif
--- a/src/mol-gl/shader/chunks/clip-pixel.glsl.ts
+++ b/src/mol-gl/shader/chunks/clip-pixel.glsl.ts
@@ -1,6 +1,12 @@
 export const clip_pixel = `
 #if defined(dClipVariant_pixel) && dClipObjectCount != 0
-    if (clipTest(vec4(vModelPosition, 0.0)))
+    #if defined(dClipping)
+        int clippingFlag = int(floor(vClipping * 255.0 + 0.5));
+    #else
+        int clippingFlag = 0;
+    #endif
+
+    if (clipTest(vec4(vModelPosition, 0.0), clippingFlag))
        discard;
 #endif
 `;
--- a/src/mol-gl/shader/chunks/color-vert-params.glsl.ts
+++ b/src/mol-gl/shader/chunks/color-vert-params.glsl.ts
@@ -39,7 +39,6 @@ uniform float uBumpiness;
            uniform vec4 uOverpaintGridTransform;
            uniform sampler2D tOverpaintGrid;
        #endif
-        uniform float uOverpaintStrength;
    #endif

    #ifdef dSubstance
@@ -54,7 +53,6 @@ uniform float uBumpiness;
            uniform vec4 uSubstanceGridTransform;
            uniform sampler2D tSubstanceGrid;
        #endif
-        uniform float uSubstanceStrength;
    #endif
 #elif defined(dRenderVariant_pick)
    #if __VERSION__ == 100 || !defined(dVaryingGroup)
@@ -88,6 +86,5 @@ uniform float uBumpiness;
        uniform vec4 uTransparencyGridTransform;
        uniform sampler2D tTransparencyGrid;
    #endif
-    uniform float uTransparencyStrength;
 #endif
 `;
--- a/src/mol-gl/shader/chunks/common-clip.glsl.ts
+++ b/src/mol-gl/shader/chunks/common-clip.glsl.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Ludovic Autin <autin@scripps.edu>
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -7,45 +7,45 @@

 export const common_clip = `
 #if dClipObjectCount != 0
-    vec3 quaternionTransform(const in vec4 q, const in vec3 v) {
+    vec3 quaternionTransform(vec4 q, vec3 v) {
        vec3 t = 2.0 * cross(q.xyz, v);
        return v + q.w * t + cross(q.xyz, t);
    }

-    vec4 computePlane(const in vec3 normal, const in vec3 inPoint) {
+    vec4 computePlane(vec3 normal, vec3 inPoint) {
        return vec4(normalize(normal), -dot(normal, inPoint));
    }

-    float planeSD(const in vec4 plane, const in vec3 center) {
+    float planeSD(vec4 plane, vec3 center) {
        return -dot(plane.xyz, center - plane.xyz * -plane.w);
    }

-    float sphereSD(const in vec3 position, const in vec4 rotation, const in vec3 size, const in vec3 center) {
+    float sphereSD(vec3 position, vec4 rotation, vec3 size, vec3 center) {
        return (
            length(quaternionTransform(vec4(-rotation.x, -rotation.y, -rotation.z, rotation.w), center - position) / size) - 1.0
        ) * min(min(size.x, size.y), size.z);
    }

-    float cubeSD(const in vec3 position, const in vec4 rotation, const in vec3 size, const in vec3 center) {
+    float cubeSD(vec3 position, vec4 rotation, vec3 size, vec3 center) {
        vec3 d = abs(quaternionTransform(vec4(-rotation.x, -rotation.y, -rotation.z, rotation.w), center - position)) - size;
        return min(max(d.x, max(d.y, d.z)), 0.0) + length(max(d, 0.0));
    }

-    float cylinderSD(const in vec3 position, const in vec4 rotation, const in vec3 size, const in vec3 center) {
+    float cylinderSD(vec3 position, vec4 rotation, vec3 size, vec3 center) {
        vec3 t = quaternionTransform(vec4(-rotation.x, -rotation.y, -rotation.z, rotation.w), center - position);

        vec2 d = abs(vec2(length(t.xz), t.y)) - size.xy;
        return min(max(d.x, d.y), 0.0) + length(max(d, 0.0));
    }

-    float infiniteConeSD(const in vec3 position, const in vec4 rotation, const in vec3 size, const in vec3 center) {
+    float infiniteConeSD(vec3 position, vec4 rotation, vec3 size, vec3 center) {
        vec3 t = quaternionTransform(vec4(-rotation.x, -rotation.y, -rotation.z, rotation.w), center - position);

        float q = length(t.xy);
        return dot(size.xy, vec2(q, t.z));
    }

-    float getSignedDistance(const in vec3 center, const in int type, const in vec3 position, const in vec4 rotation, const in vec3 scale) {
+    float getSignedDistance(vec3 center, int type, vec3 position, vec4 rotation, vec3 scale) {
        if (type == 1) {
            vec3 normal = quaternionTransform(rotation, vec3(0.0, 1.0, 0.0));
            vec4 plane = computePlane(normal, position);
@@ -65,7 +65,7 @@ export const common_clip = `

    #if __VERSION__ == 100
        // 8-bit
-        int bitwiseAnd(const in int a, const in int b) {
+        int bitwiseAnd(int a, int b) {
            int d = 128;
            int result = 0;
            for (int i = 0; i < 8; ++i) {
@@ -78,23 +78,17 @@ export const common_clip = `
            return result;
        }

-        bool hasBit(const in int mask, const in int bit) {
+        bool hasBit(int mask, int bit) {
            return bitwiseAnd(mask, bit) == 0;
        }
    #else
-        bool hasBit(const in int mask, const in int bit) {
+        bool hasBit(int mask, int bit) {
            return (mask & bit) == 0;
        }
    #endif

-    bool clipTest(const in vec4 sphere) {
-        // flag is a bit-flag for clip-objects to ignore (note, object ids start at 1 not 0)
-        #if defined(dClipping)
-            int flag = int(floor(vClipping * 255.0 + 0.5));
-        #else
-            int flag = 0;
-        #endif
-
+    // flag is a bit-flag for clip-objects to ignore (note, object ids start at 1 not 0)
+    bool clipTest(vec4 sphere, int flag) {
        #pragma unroll_loop_start
        for (int i = 0; i < dClipObjectCount; ++i) {
            if (flag == 0 || hasBit(flag, UNROLLED_LOOP_INDEX + 1)) {
--- a/src/mol-gl/shader/cylinders.frag.ts
+++ b/src/mol-gl/shader/cylinders.frag.ts
@@ -33,8 +33,7 @@ uniform mat4 uInvView;
 bool CylinderImpostor(
    in vec3 rayOrigin, in vec3 rayDir,
    in vec3 start, in vec3 end, in float radius,
-    out vec3 cameraNormal, out bool interior,
-    out vec3 modelPosition, out vec3 viewPosition, out float fragmentDepth
+    out vec4 intersection, out bool interior
 ){
    vec3 ba = end - start;
    vec3 oc = rayOrigin - start;
@@ -43,7 +42,7 @@ bool CylinderImpostor(
    float bard = dot(ba, rayDir);
    float baoc = dot(ba, oc);

-    float k2 = baba - bard * bard;
+    float k2 = baba - bard*bard;
    float k1 = baba * dot(oc, rayDir) - baoc * bard;
    float k0 = baba * dot(oc, oc) - baoc * baoc - radius * radius * baba;

@@ -59,14 +58,8 @@ bool CylinderImpostor(
    float y = baoc + t * bard;
    if (y > 0.0 && y < baba) {
        interior = false;
-        cameraNormal = (oc + t * rayDir - ba * y / baba) / radius;
-        modelPosition = rayOrigin + t * rayDir;
-        viewPosition = (uView * vec4(modelPosition, 1.0)).xyz;
-        fragmentDepth = calcDepth(viewPosition);
-        #if defined(dClipVariant_pixel) && dClipObjectCount != 0
-            if (clipTest(vec4(modelPosition, 0.0))) fragmentDepth = -1.0;
-        #endif
-        if (fragmentDepth > 0.0) return true;
+        intersection = vec4(t, (oc + t * rayDir - ba * y / baba) / radius);
+        return true;
    }

    if (topCap && y < 0.0) {
@@ -74,22 +67,16 @@ bool CylinderImpostor(
        t = -baoc / bard;
        if (abs(k1 + k2 * t) < h) {
            interior = false;
-            cameraNormal = -ba / baba;
-            modelPosition = rayOrigin + t * rayDir;
-            viewPosition = (uView * vec4(modelPosition, 1.0)).xyz;
-            fragmentDepth = calcDepth(viewPosition);
-            if (fragmentDepth > 0.0) return true;
+            intersection = vec4(t, ba * sign(y) / baba);
+            return true;
        }
    } else if(bottomCap && y >= 0.0) {
        // bottom cap
        t = (baba - baoc) / bard;
        if (abs(k1 + k2 * t) < h) {
            interior = false;
-            cameraNormal = ba / baba;
-            modelPosition = rayOrigin + t * rayDir;
-            viewPosition = (uView * vec4(modelPosition, 1.0)).xyz;
-            fragmentDepth = calcDepth(viewPosition);
-            if (fragmentDepth > 0.0) return true;
+            intersection = vec4(t, ba * sign(y) / baba);
+            return true;
        }
    }

@@ -100,61 +87,36 @@ bool CylinderImpostor(
        y = baoc + t * bard;
        if (y > 0.0 && y < baba) {
            interior = true;
-            cameraNormal = -(oc + t * rayDir - ba * y / baba) / radius;
-            modelPosition = rayOrigin + t * rayDir;
-            viewPosition = (uView * vec4(modelPosition, 1.0)).xyz;
-            fragmentDepth = calcDepth(viewPosition);
+            intersection = vec4(t, (oc + t * rayDir - ba * y / baba) / radius);
            return true;
        }

-        if (topCap && y < 0.0) {
-            // top cap
-            t = -baoc / bard;
-            if (abs(k1 + k2 * t) < -h) {
-                interior = true;
-                cameraNormal = ba / baba;
-                modelPosition = rayOrigin + t * rayDir;
-                viewPosition = (uView * vec4(modelPosition, 1.0)).xyz;
-                fragmentDepth = calcDepth(viewPosition);
-                if (fragmentDepth > 0.0) return true;
-            }
-        } else if(bottomCap && y >= 0.0) {
-            // bottom cap
-            t = (baba - baoc) / bard;
-            if (abs(k1 + k2 * t) < -h) {
-                interior = true;
-                cameraNormal = -ba / baba;
-                modelPosition = rayOrigin + t * rayDir;
-                viewPosition = (uView * vec4(modelPosition, 1.0)).xyz;
-                fragmentDepth = calcDepth(viewPosition);
-                if (fragmentDepth > 0.0) return true;
-            }
-        }
+        // TODO: handle inside caps???
    }

    return false;
 }

 void main() {
-    vec3 rayOrigin = vModelPosition;
+    #include clip_pixel
+
    vec3 rayDir = mix(normalize(vModelPosition - uCameraPosition), uCameraDir, uIsOrtho);

-    vec3 cameraNormal;
-    vec3 modelPosition;
-    vec3 viewPosition;
-    float fragmentDepth;
-    bool hit = CylinderImpostor(rayOrigin, rayDir, vStart, vEnd, vSize, cameraNormal, interior, modelPosition, viewPosition, fragmentDepth);
+    vec4 intersection;
+    bool interior;
+    bool hit = CylinderImpostor(vModelPosition, rayDir, vStart, vEnd, vSize, intersection, interior);
    if (!hit) discard;

+    vec3 vViewPosition = vModelPosition + intersection.x * rayDir;
+    vViewPosition = (uView * vec4(vViewPosition, 1.0)).xyz;
+    float fragmentDepth = calcDepth(vViewPosition);
+
    if (fragmentDepth < 0.0) discard;
    if (fragmentDepth > 1.0) discard;

    gl_FragDepthEXT = fragmentDepth;

-    vec3 vViewPosition = viewPosition;
-    vec3 vModelPosition = modelPosition;
-
-    #include clip_pixel
+    vec3 vModelPosition = (uInvView * vec4(vViewPosition, 1.0)).xyz;
    #include assign_material_color

    #if defined(dRenderVariant_pick)
@@ -173,7 +135,7 @@ void main() {
        gl_FragColor = material;
    #elif defined(dRenderVariant_color)
        mat3 normalMatrix = transpose3(inverse3(mat3(uView)));
-        vec3 normal = normalize(normalMatrix * -normalize(cameraNormal));
+        vec3 normal = normalize(normalMatrix * -normalize(intersection.yzw));
        #include apply_light_color

        #include apply_interior_color
--- a/src/mol-gl/shader/cylinders.vert.ts
+++ b/src/mol-gl/shader/cylinders.vert.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */
@@ -55,12 +55,7 @@ void main() {
    vec3 camDir = -mix(normalize(vModelPosition - uCameraPosition), uCameraDir, uIsOrtho);
    vec3 dir = vEnd - vStart;
    // ensure cylinder 'dir' is pointing towards the camera
-    if(dot(camDir, dir) < 0.0) {
-        dir = -dir;
-        vec3 tmp = vStart;
-        vStart = vEnd;
-        vEnd = tmp;
-    }
+    if(dot(camDir, dir) < 0.0) dir = -dir;

    vec3 left = cross(camDir, dir);
    vec3 up = cross(left, dir);
@@ -74,9 +69,6 @@ void main() {
    vViewPosition = mvPosition.xyz;
    gl_Position = uProjection * mvPosition;

-    mvPosition.z -= 2.0 * (length(vEnd - vStart) + vSize); // avoid clipping
-    gl_Position.z = (uProjection * mvPosition).z;
-
    #include clip_instance
 }
 `;
--- a/src/mol-gl/shader/direct-volume.frag.ts
+++ b/src/mol-gl/shader/direct-volume.frag.ts
@@ -229,7 +229,7 @@ vec4 raymarch(vec3 startLoc, vec3 step, vec3 rayDir) {

        #if defined(dClipVariant_pixel) && dClipObjectCount != 0
            vec3 vModelPosition = v3m4(unitPos * uGridDim, modelTransform);
-            if (clipTest(vec4(vModelPosition, 0.0))) {
+            if (clipTest(vec4(vModelPosition, 0.0), 0)) {
                prevValue = value;
                pos += step;
                continue;
@@ -270,16 +270,16 @@ vec4 raymarch(vec3 startLoc, vec3 step, vec3 rayDir) {
        #elif defined(dColorType_groupInstance)
            material.rgb = readFromTexture(tColor, vInstance * float(uGroupCount) + group, uColorTexDim).rgb;
        #elif defined(dColorType_vertex)
-            material.rgb = texture3dFrom1dTrilinear(tColor, unitPos, uGridDim, uColorTexDim, 0.0).rgb;
+            material.rgb = texture3dFrom1dTrilinear(tColor, isoPos, uGridDim, uColorTexDim, 0.0).rgb;
        #elif defined(dColorType_vertexInstance)
-            material.rgb = texture3dFrom1dTrilinear(tColor, unitPos, uGridDim, uColorTexDim, vInstance * float(uVertexCount)).rgb;
+            material.rgb = texture3dFrom1dTrilinear(tColor, isoPos, uGridDim, uColorTexDim, vInstance * float(uVertexCount)).rgb;
        #endif

        #ifdef dOverpaint
            #if defined(dOverpaintType_groupInstance)
                overpaint = readFromTexture(tOverpaint, vInstance * float(uGroupCount) + group, uOverpaintTexDim);
            #elif defined(dOverpaintType_vertexInstance)
-                overpaint = texture3dFrom1dTrilinear(tOverpaint, unitPos, uGridDim, uOverpaintTexDim, vInstance * float(uVertexCount));
+                overpaint = texture3dFrom1dTrilinear(tOverpaint, isoPos, uGridDim, uOverpaintTexDim, vInstance * float(uVertexCount));
            #endif

            material.rgb = mix(material.rgb, overpaint.rgb, overpaint.a);
--- a/src/mol-gl/shader/outlines.frag.ts
+++ b/src/mol-gl/shader/outlines.frag.ts
@@ -38,11 +38,7 @@ float getDepthOpaque(const in vec2 coords) {
 }

 float getDepthTransparent(const in vec2 coords) {
-    #ifdef dTransparentOutline
-        return unpackRGBAToDepth(texture2D(tDepthTransparent, coords));
-    #else
-        return 1.0;
-    #endif
+    return unpackRGBAToDepth(texture2D(tDepthTransparent, coords));
 }

 bool isBackground(const in float depth) {
--- a/src/mol-gl/shader/postprocessing.frag.ts
+++ b/src/mol-gl/shader/postprocessing.frag.ts
@@ -14,7 +14,6 @@ uniform sampler2D tSsaoDepth;
 uniform sampler2D tColor;
 uniform sampler2D tDepthOpaque;
 uniform sampler2D tDepthTransparent;
-uniform sampler2D tShadows;
 uniform sampler2D tOutlines;
 uniform vec2 uTexSize;

@@ -51,11 +50,7 @@ float getDepthOpaque(const in vec2 coords) {
 }

 float getDepthTransparent(const in vec2 coords) {
-    #ifdef dTransparentOutline
-        return unpackRGBAToDepth(texture2D(tDepthTransparent, coords));
-    #else
-        return 1.0;
-    #endif
+    return unpackRGBAToDepth(texture2D(tDepthTransparent, coords));
 }

 bool isBackground(const in float depth) {
@@ -125,20 +120,7 @@ void main(void) {
        }
    #endif

-    #ifdef dShadowEnable
-        if (!isBackground(opaqueDepth)) {
-            viewDist = abs(getViewZ(opaqueDepth));
-            fogFactor = smoothstep(uFogNear, uFogFar, viewDist);
-            vec4 shadow = texture2D(tShadows, coords);
-            if (!uTransparentBackground) {
-                color.rgb = mix(mix(vec3(0), uFogColor, fogFactor), color.rgb, shadow.a);
-            } else {
-                color.rgb = mix(vec3(0) * (1.0 - fogFactor), color.rgb, shadow.a);
-            }
-        }
-    #endif
-
-    // outline needs to be handled after occlusion and shadow to keep them clean
+    // outline needs to be handled after occlusion to keep them clean
    #ifdef dOutlineEnable
        float closestTexel;
        float outline = getOutline(coords, opaqueDepth, closestTexel);
--- a/src/mol-gl/shader/shadows.frag.ts
+++ b/src/mol-gl/shader/shadows.frag.ts
@@ -1,131 +0,0 @@
-/**
- * Copyright (c) 2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author Ludovic Autin <ludovic.autin@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
- */
-
-export const shadows_frag = `
-precision highp float;
-precision highp int;
-precision highp sampler2D;
-
-#include common
-
-uniform sampler2D tDepth;
-uniform vec2 uTexSize;
-uniform vec4 uBounds;
-
-uniform float uNear;
-uniform float uFar;
-
-#if dLightCount != 0
-    uniform vec3 uLightDirection[dLightCount];
-    uniform vec3 uLightColor[dLightCount];
-#endif
-
-uniform mat4 uProjection;
-uniform mat4 uInvProjection;
-
-uniform float uMaxDistance;
-uniform float uTolerance;
-uniform float uBias;
-
-bool isBackground(const in float depth) {
-    return depth == 1.0;
-}
-
-bool outsideBounds(const in vec2 p) {
-    return p.x < uBounds.x || p.y < uBounds.y || p.x > uBounds.z || p.y > uBounds.w;
-}
-
-float getViewZ(const in float depth) {
-    #if dOrthographic == 1
-        return orthographicDepthToViewZ(depth, uNear, uFar);
-    #else
-        return perspectiveDepthToViewZ(depth, uNear, uFar);
-    #endif
-}
-
-float getDepth(const in vec2 coords) {
-    #ifdef depthTextureSupport
-        return texture2D(tDepth, coords).r;
-    #else
-        return unpackRGBAToDepth(texture2D(tDepth, coords));
-    #endif
-}
-
-float screenFade(const in vec2 coords) {
-    vec2 c = (coords - uBounds.xy) / (uBounds.zw - uBounds.xy);
-    vec2 fade = max(12.0 * abs(c - 0.5) - 5.0, vec2(0.0));
-    return saturate(1.0 - dot(fade, fade));
-}
-
-// based on https://panoskarabelas.com/posts/screen_space_shadows/
-float screenSpaceShadow(const in vec3 position, const in vec3 lightDirection, const in float stepLength) {
-    // Ray position and direction (in view-space)
-    vec3 rayPos = position;
-    vec3 rayDir = -lightDirection;
-
-    // Compute ray step
-    vec3 rayStep = rayDir * stepLength;
-
-    // Ray march towards the light
-    float occlusion = 0.0;
-    vec4 rayCoords = vec4(0.0);
-    for (int i = 0; i < dSteps; ++i) {
-        // Step the ray
-        rayPos += rayStep;
-
-        rayCoords = uProjection * vec4(rayPos, 1.0);
-        rayCoords.xyz = (rayCoords.xyz / rayCoords.w) * 0.5 + 0.5;
-
-        if (outsideBounds(rayCoords.xy))
-            return 1.0;
-
-        // Compute the difference between the ray's and the camera's depth
-        float depth = getDepth(rayCoords.xy);
-        float viewZ = getViewZ(depth);
-        float zDelta = rayPos.z - viewZ;
-
-        if (zDelta < uTolerance) {
-            occlusion = 1.0;
-
-            // Fade out as we approach the edges of the screen
-            occlusion *= screenFade(rayCoords.xy);
-
-            break;
-        }
-    }
-
-    return 1.0 - (uBias * occlusion);
-}
-
-void main(void) {
-    vec2 invTexSize = 1.0 / uTexSize;
-    vec2 selfCoords = gl_FragCoord.xy * invTexSize;
-
-    float selfDepth = getDepth(selfCoords);
-
-    if (isBackground(selfDepth)) {
-        gl_FragColor = vec4(0.0);
-        return;
-    }
-
-    vec3 selfViewPos = screenSpaceToViewSpace(vec3(selfCoords, selfDepth), uInvProjection);
-    float stepLength = uMaxDistance / float(dSteps);
-
-    float o = 1.0;
-    #if dLightCount != 0
-        float sh[dLightCount];
-        #pragma unroll_loop_start
-        for (int i = 0; i < dLightCount; ++i) {
-            sh[i] = screenSpaceShadow(selfViewPos, uLightDirection[i], stepLength);
-            o = min(o, sh[i]);
-        }
-        #pragma unroll_loop_end
-    #endif
-
-    gl_FragColor = vec4(o);
-}
-`;
--- a/src/mol-gl/shader/spheres.frag.ts
+++ b/src/mol-gl/shader/spheres.frag.ts
@@ -23,8 +23,12 @@ varying float vRadiusSq;
 varying vec3 vPoint;
 varying vec3 vPointViewPosition;

-bool SphereImpostor(out vec3 modelPos, out vec3 cameraPos, out vec3 cameraNormal, out bool interior, out float fragmentDepth, out bool clipped){
+vec3 cameraPos;
+vec3 cameraNormal;
+
+bool Impostor(out vec3 cameraPos, out vec3 cameraNormal){
    vec3 cameraSpherePos = -vPointViewPosition;
+    cameraSpherePos.z += vRadius;

    vec3 rayOrigin = mix(vec3(0.0, 0.0, 0.0), vPoint, uIsOrtho);
    vec3 rayDirection = mix(normalize(vPoint), vec3(0.0, 0.0, 1.0), uIsOrtho);
@@ -33,61 +37,50 @@ bool SphereImpostor(out vec3 modelPos, out vec3 cameraPos, out vec3 cameraNormal
    float B = dot(rayDirection, cameraSphereDir);
    float det = B * B + vRadiusSq - dot(cameraSphereDir, cameraSphereDir);

-    if (det < 0.0) return false;
-
-    float sqrtDet = sqrt(det);
-    float posT = mix(B + sqrtDet, B - sqrtDet, uIsOrtho);
-    float negT = mix(B - sqrtDet, B + sqrtDet, uIsOrtho);
-
-    cameraPos = rayDirection * negT + rayOrigin;
-    modelPos = (uInvView * vec4(cameraPos, 1.0)).xyz;
-    fragmentDepth = calcDepth(cameraPos);
-
-    #if defined(dClipVariant_pixel) && dClipObjectCount != 0
-        if (clipTest(vec4(modelPos, 0.0))) {
-            clipped = true;
-            fragmentDepth = -1.0;
-        }
-    #endif
-
-    if (fragmentDepth > 0.0) {
-        cameraNormal = normalize(cameraPos - cameraSpherePos);
-        interior = false;
-        return true;
-    } else if (uDoubleSided) {
-        cameraPos = rayDirection * posT + rayOrigin;
-        modelPos = (uInvView * vec4(cameraPos, 1.0)).xyz;
-        fragmentDepth = calcDepth(cameraPos);
-        cameraNormal = -normalize(cameraPos - cameraSpherePos);
-        interior = true;
-        return true;
+    if (det < 0.0){
+        discard;
+        return false;
    }

-    return false;
+    float sqrtDet = sqrt(det);
+    float posT = mix(B + sqrtDet, B + sqrtDet, uIsOrtho);
+    float negT = mix(B - sqrtDet, sqrtDet - B, uIsOrtho);
+
+    cameraPos = rayDirection * negT + rayOrigin;
+
+    if (calcDepth(cameraPos) <= 0.0) {
+        cameraPos = rayDirection * posT + rayOrigin;
+        interior = true;
+    } else {
+        interior = false;
+    }
+
+    cameraNormal = normalize(cameraPos - cameraSpherePos);
+    cameraNormal *= float(!interior) * 2.0 - 1.0;
+
+    return !interior;
 }

 void main(void){
-    vec3 modelPos;
-    vec3 cameraPos;
-    vec3 cameraNormal;
-    float fragmentDepth;
-    bool clipped = false;
-    bool hit = SphereImpostor(modelPos, cameraPos, cameraNormal, interior, fragmentDepth, clipped);
-    if (!hit) discard;
+    #include clip_pixel
+
+    bool flag = Impostor(cameraPos, cameraNormal);
+    if (!uDoubleSided) {
+        if (interior) discard;
+    }
+
+    vec3 vViewPosition = cameraPos;
+    float fragmentDepth = calcDepth(vViewPosition);
+    if (!flag && fragmentDepth >= 0.0) {
+        fragmentDepth = 0.0 + (0.0000001 / vRadius);
+    }

    if (fragmentDepth < 0.0) discard;
    if (fragmentDepth > 1.0) discard;

-    vec3 vViewPosition = cameraPos;
-    vec3 vModelPosition = modelPos;
-
-    if (interior && !clipped) {
-        fragmentDepth = 0.0 + (0.0000001 / vRadius);
-    }
-
    gl_FragDepthEXT = fragmentDepth;

-    #include clip_pixel
+    vec3 vModelPosition = (uInvView * vec4(vViewPosition, 1.0)).xyz;
    #include assign_material_color

    #if defined(dRenderVariant_pick)
--- a/src/mol-gl/shader/spheres.vert.ts
+++ b/src/mol-gl/shader/spheres.vert.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */
@@ -85,6 +85,7 @@ void main(void){

    vec4 position4 = vec4(aPosition, 1.0);
    vec4 mvPosition = uModelView * aTransform * position4;
+    mvPosition.z -= vRadius; // avoid clipping, added again in fragment shader

    gl_Position = uProjection * vec4(mvPosition.xyz, 1.0);
    quadraticProjection(size, aPosition);
@@ -96,9 +97,6 @@ void main(void){

    vModelPosition = (uModel * aTransform * position4).xyz; // for clipping in frag shader

-    mvPosition.z -= 2.0 * vRadius; // avoid clipping
-    gl_Position.z = (uProjection * vec4(mvPosition.xyz, 1.0)).z;
-
    #include clip_instance
 }
 `;
--- a/src/mol-gl/webgl/compat.ts
+++ b/src/mol-gl/webgl/compat.ts
@@ -19,9 +19,6 @@ export function isWebGL2(gl: any): gl is WebGL2RenderingContext {
    return typeof WebGL2RenderingContext !== 'undefined' && gl instanceof WebGL2RenderingContext;
 }

-/**
- * See https://registry.khronos.org/webgl/extensions/ANGLE_instanced_arrays/
- */
 export interface COMPAT_instanced_arrays {
    drawArraysInstanced(mode: number, first: number, count: number, primcount: number): void;
    drawElementsInstanced(mode: number, count: number, type: number, offset: number, primcount: number): void;
@@ -49,9 +46,6 @@ export function getInstancedArrays(gl: GLRenderingContext): COMPAT_instanced_arr
    }
 }

-/**
- * See https://registry.khronos.org/webgl/extensions/OES_standard_derivatives/
- */
 export interface COMPAT_standard_derivatives {
    readonly FRAGMENT_SHADER_DERIVATIVE_HINT: number;
 }
@@ -66,9 +60,6 @@ export function getStandardDerivatives(gl: GLRenderingContext): COMPAT_standard_
    }
 }

-/**
- * See https://registry.khronos.org/webgl/extensions/OES_element_index_uint/
- */
 export interface COMPAT_element_index_uint {
 }

@@ -76,9 +67,6 @@ export function getElementIndexUint(gl: GLRenderingContext): COMPAT_element_inde
    return isWebGL2(gl) ? {} : gl.getExtension('OES_element_index_uint');
 }

-/**
- * See https://registry.khronos.org/webgl/extensions/OES_vertex_array_object/
- */
 export interface COMPAT_vertex_array_object {
    readonly VERTEX_ARRAY_BINDING: number;
    bindVertexArray(arrayObject: WebGLVertexArrayObject | null): void;
@@ -144,9 +132,6 @@ export function getTextureHalfFloatLinear(gl: GLRenderingContext): COMPAT_textur
    return gl.getExtension('OES_texture_half_float_linear');
 }

-/**
- * See https://registry.khronos.org/webgl/extensions/EXT_blend_minmax/
- */
 export interface COMPAT_blend_minmax {
    readonly MIN: number
    readonly MAX: number
@@ -162,9 +147,6 @@ export function getBlendMinMax(gl: GLRenderingContext): COMPAT_blend_minmax | nu
    }
 }

-/**
- * See https://registry.khronos.org/webgl/extensions/EXT_frag_depth/
- */
 export interface COMPAT_frag_depth {
 }

@@ -214,9 +196,6 @@ export function getColorBufferHalfFloat(gl: GLRenderingContext): COMPAT_color_bu
    }
 }

-/**
- * See https://registry.khronos.org/webgl/extensions/WEBGL_draw_buffers/
- */
 export interface COMPAT_draw_buffers {
    drawBuffers(buffers: number[]): void;
    readonly COLOR_ATTACHMENT0: number;
@@ -289,73 +268,6 @@ export function getDrawBuffers(gl: GLRenderingContext): COMPAT_draw_buffers | nu
    }
 }

-/**
- * See https://registry.khronos.org/webgl/extensions/OES_draw_buffers_indexed/
- */
-export interface COMPAT_draw_buffers_indexed {
-    /**
-     * Enables blending for an individual draw buffer.
-     *
-     * @param target must be BLEND.
-     * @param index is an integer i specifying the draw buffer associated with the symbolic constant DRAW_BUFFERi.
-     */
-    enablei: (target: number, index: number) => void;
-    /**
-     * Disables  blending for an individual draw buffer.
-     *
-     * @param target must be BLEND.
-     * @param index is an integer i specifying the draw buffer associated with the symbolic constant DRAW_BUFFERi.
-     */
-    disablei: (buf: number, mode: number) => void;
-    /**
-     * The buf argument is an integer i that indicates that the blend equations should be modified for DRAW_BUFFERi.
-     *
-     * mode accepts the same tokens as mode in blendEquation.
-     */
-    blendEquationi: (target: number, index: number) => void;
-    /**
-     * The buf argument is an integer i that indicates that the blend equations should be modified for DRAW_BUFFERi.
-     *
-     * modeRGB and modeAlpha accept the same tokens as modeRGB and modeAlpha in blendEquationSeparate.
-     */
-    blendEquationSeparatei: (buf: number, modeRGB: number, modeAlpha: number) => void;
-    /**
-     * The buf argument is an integer i that indicates that the blend functions should be modified for DRAW_BUFFERi.
-     *
-     * src and dst accept the same tokens as src and dst in blendFunc.
-     */
-    blendFunci: (buf: number, src: number, dst: number) => void;
-    /**
-     * The buf argument is an integer i that indicates that the blend functions should be modified for DRAW_BUFFERi.
-     *
-     * srcRGB, dstRGB, srcAlpha, and dstAlpha accept the same tokens as srcRGB, dstRGB, srcAlpha, and dstAlpha parameters in blendEquationSeparate.
-     */
-    blendFuncSeparatei: (buf: number, srcRGB: number, dstRGB: number, srcAlpha: number, dstAlpha: number) => void;
-    /**
-     * The buf argument is an integer i that indicates that the write mask should be modified for DRAW_BUFFERi.
-     *
-     * r, g, b, and a indicate whether R, G, B, or A values, respectively, are written or not (a value of TRUE means that the corresponding value is written).
-     */
-    colorMaski: (buf: number, r: boolean, g: boolean, b: boolean, a: boolean) => void;
-}
-
-export function getDrawBuffersIndexed(gl: GLRenderingContext): COMPAT_draw_buffers_indexed | null {
-    const ext = gl.getExtension('OES_draw_buffers_indexed');
-    if (ext === null) return null;
-    return {
-        enablei: ext.enableiOES.bind(ext),
-        disablei: ext.disableiOES.bind(ext),
-        blendEquationi: ext.blendEquationiOES.bind(ext),
-        blendEquationSeparatei: ext.blendEquationSeparateiOES.bind(ext),
-        blendFunci: ext.blendFunciOES.bind(ext),
-        blendFuncSeparatei: ext.blendFuncSeparateiOES.bind(ext),
-        colorMaski: ext.colorMaskiOES.bind(ext),
-    };
-}
-
-/**
- * See https://registry.khronos.org/webgl/extensions/EXT_shader_texture_lod/
- */
 export interface COMPAT_shader_texture_lod {
 }

@@ -363,9 +275,6 @@ export function getShaderTextureLod(gl: GLRenderingContext): COMPAT_shader_textu
    return isWebGL2(gl) ? {} : gl.getExtension('EXT_shader_texture_lod');
 }

-/**
- * See https://registry.khronos.org/webgl/extensions/WEBGL_depth_texture/
- */
 export interface COMPAT_depth_texture {
    readonly UNSIGNED_INT_24_8: number;
 }
@@ -384,9 +293,6 @@ export function getDepthTexture(gl: GLRenderingContext): COMPAT_depth_texture |
    }
 }

-/**
- * See https://registry.khronos.org/webgl/extensions/EXT_sRGB/
- */
 export interface COMPAT_sRGB {
    readonly FRAMEBUFFER_ATTACHMENT_COLOR_ENCODING: number;
    readonly SRGB8_ALPHA8: number;
@@ -414,9 +320,6 @@ export function getSRGB(gl: GLRenderingContext): COMPAT_sRGB | null {
    }
 }

-/**
- * See https://registry.khronos.org/webgl/extensions/EXT_disjoint_timer_query/ and https://registry.khronos.org/webgl/extensions/EXT_disjoint_timer_query_webgl2/
- */
 export interface COMPAT_disjoint_timer_query {
    /** A GLint indicating the number of bits used to hold the query result for the given target. */
    QUERY_COUNTER_BITS: number
@@ -498,31 +401,6 @@ export function getDisjointTimerQuery(gl: GLRenderingContext): COMPAT_disjoint_t
    }
 }

-/**
- * See https://registry.khronos.org/webgl/extensions/KHR_parallel_shader_compile/
- */
-export interface COMPAT_parallel_shader_compile {
-    readonly COMPLETION_STATUS: number;
-}
-
-export function getParallelShaderCompile(gl: GLRenderingContext): COMPAT_parallel_shader_compile | null {
-    const ext = gl.getExtension('KHR_parallel_shader_compile');
-    if (ext === null) return null;
-    return {
-        COMPLETION_STATUS: ext.COMPLETION_STATUS_KHR,
-    };
-}
-
-/**
- * See https://registry.khronos.org/webgl/extensions/OES_fbo_render_mipmap/
- */
-export interface COMPAT_fboRenderMipmap {
-}
-
-export function getFboRenderMipmap(gl: GLRenderingContext): COMPAT_fboRenderMipmap | null {
-    return isWebGL2(gl) ? {} : gl.getExtension('OES_fbo_render_mipmap');
-}
-
 export function getNoNonInstancedActiveAttribs(gl: GLRenderingContext): boolean {
    if (!isWebGL2(gl)) return false;

--- a/src/mol-gl/webgl/extensions.ts
+++ b/src/mol-gl/webgl/extensions.ts
@@ -4,14 +4,14 @@
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */

-import { GLRenderingContext, COMPAT_instanced_arrays, COMPAT_standard_derivatives, COMPAT_vertex_array_object, getInstancedArrays, getStandardDerivatives, COMPAT_element_index_uint, getElementIndexUint, COMPAT_texture_float, getTextureFloat, COMPAT_texture_float_linear, getTextureFloatLinear, COMPAT_blend_minmax, getBlendMinMax, getFragDepth, COMPAT_frag_depth, COMPAT_color_buffer_float, getColorBufferFloat, COMPAT_draw_buffers, getDrawBuffers, getShaderTextureLod, COMPAT_shader_texture_lod, getDepthTexture, COMPAT_depth_texture, COMPAT_sRGB, getSRGB, getTextureHalfFloat, getTextureHalfFloatLinear, COMPAT_texture_half_float, COMPAT_texture_half_float_linear, COMPAT_color_buffer_half_float, getColorBufferHalfFloat, getVertexArrayObject, getDisjointTimerQuery, COMPAT_disjoint_timer_query, getNoNonInstancedActiveAttribs, getDrawBuffersIndexed, COMPAT_draw_buffers_indexed, getParallelShaderCompile, COMPAT_parallel_shader_compile, getFboRenderMipmap, COMPAT_fboRenderMipmap } from './compat';
+import { GLRenderingContext, COMPAT_instanced_arrays, COMPAT_standard_derivatives, COMPAT_vertex_array_object, getInstancedArrays, getStandardDerivatives, COMPAT_element_index_uint, getElementIndexUint, COMPAT_texture_float, getTextureFloat, COMPAT_texture_float_linear, getTextureFloatLinear, COMPAT_blend_minmax, getBlendMinMax, getFragDepth, COMPAT_frag_depth, COMPAT_color_buffer_float, getColorBufferFloat, COMPAT_draw_buffers, getDrawBuffers, getShaderTextureLod, COMPAT_shader_texture_lod, getDepthTexture, COMPAT_depth_texture, COMPAT_sRGB, getSRGB, getTextureHalfFloat, getTextureHalfFloatLinear, COMPAT_texture_half_float, COMPAT_texture_half_float_linear, COMPAT_color_buffer_half_float, getColorBufferHalfFloat, getVertexArrayObject, getDisjointTimerQuery, COMPAT_disjoint_timer_query, getNoNonInstancedActiveAttribs } from './compat';
 import { isDebugMode } from '../../mol-util/debug';

 export type WebGLExtensions = {
    instancedArrays: COMPAT_instanced_arrays
    elementIndexUint: COMPAT_element_index_uint
-    standardDerivatives: COMPAT_standard_derivatives

+    standardDerivatives: COMPAT_standard_derivatives | null
    textureFloat: COMPAT_texture_float | null
    textureFloatLinear: COMPAT_texture_float_linear | null
    textureHalfFloat: COMPAT_texture_half_float | null
@@ -23,12 +23,9 @@ export type WebGLExtensions = {
    colorBufferFloat: COMPAT_color_buffer_float | null
    colorBufferHalfFloat: COMPAT_color_buffer_half_float | null
    drawBuffers: COMPAT_draw_buffers | null
-    drawBuffersIndexed: COMPAT_draw_buffers_indexed | null
    shaderTextureLod: COMPAT_shader_texture_lod | null
    sRGB: COMPAT_sRGB | null
    disjointTimerQuery: COMPAT_disjoint_timer_query | null
-    parallelShaderCompile: COMPAT_parallel_shader_compile | null
-    fboRenderMipmap: COMPAT_fboRenderMipmap | null

    noNonInstancedActiveAttribs: boolean
 }
@@ -97,10 +94,6 @@ export function createExtensions(gl: GLRenderingContext): WebGLExtensions {
    if (isDebugMode && drawBuffers === null) {
        console.log('Could not find support for "draw_buffers"');
    }
-    const drawBuffersIndexed = getDrawBuffersIndexed(gl);
-    if (isDebugMode && drawBuffersIndexed === null) {
-        console.log('Could not find support for "draw_buffers_indexed"');
-    }
    const shaderTextureLod = getShaderTextureLod(gl);
    if (isDebugMode && shaderTextureLod === null) {
        console.log('Could not find support for "shader_texture_lod"');
@@ -113,39 +106,28 @@ export function createExtensions(gl: GLRenderingContext): WebGLExtensions {
    if (isDebugMode && disjointTimerQuery === null) {
        console.log('Could not find support for "disjoint_timer_query"');
    }
-    const parallelShaderCompile = getParallelShaderCompile(gl);
-    if (isDebugMode && parallelShaderCompile === null) {
-        console.log('Could not find support for "parallel_shader_compile"');
-    }
-    const fboRenderMipmap = getFboRenderMipmap(gl);
-    if (isDebugMode && fboRenderMipmap === null) {
-        console.log('Could not find support for "fbo_render_mipmap"');
-    }

    const noNonInstancedActiveAttribs = getNoNonInstancedActiveAttribs(gl);

    return {
        instancedArrays,
        standardDerivatives,
-        elementIndexUint,
-
        textureFloat,
        textureFloatLinear,
        textureHalfFloat,
        textureHalfFloatLinear,
+        elementIndexUint,
        depthTexture,
+
        blendMinMax,
        vertexArrayObject,
        fragDepth,
        colorBufferFloat,
        colorBufferHalfFloat,
        drawBuffers,
-        drawBuffersIndexed,
        shaderTextureLod,
        sRGB,
        disjointTimerQuery,
-        parallelShaderCompile,
-        fboRenderMipmap,

        noNonInstancedActiveAttribs,
    };
--- a/src/mol-io/reader/cif/schema/bird.ts
+++ b/src/mol-io/reader/cif/schema/bird.ts
@@ -1,7 +1,7 @@
 /**
 * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.363, IHM 1.17, MA 1.4.3.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.362, IHM 1.17, MA 1.4.3.
 *
 * @author molstar/ciftools package
 */
--- a/src/mol-io/reader/cif/schema/ccd.ts
+++ b/src/mol-io/reader/cif/schema/ccd.ts
@@ -1,7 +1,7 @@
 /**
 * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.363, IHM 1.17, MA 1.4.3.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.362, IHM 1.17, MA 1.4.3.
 *
 * @author molstar/ciftools package
 */
--- a/src/mol-io/reader/cif/schema/mmcif.ts
+++ b/src/mol-io/reader/cif/schema/mmcif.ts
@@ -1,7 +1,7 @@
 /**
 * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.363, IHM 1.17, MA 1.4.3.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.362, IHM 1.17, MA 1.4.3.
 *
 * @author molstar/ciftools package
 */
--- a/src/mol-math/geometry/symmetry-operator.ts
+++ b/src/mol-math/geometry/symmetry-operator.ts
@@ -1,11 +1,11 @@
 /**
- * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
- * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */

 import { lerp as scalar_lerp } from '../../mol-math/interpolate';
+import { defaults } from '../../mol-util';
 import { Mat3 } from '../linear-algebra/3d/mat3';
 import { Mat4 } from '../linear-algebra/3d/mat4';
 import { Quat } from '../linear-algebra/3d/quat';
@@ -29,13 +29,11 @@ interface SymmetryOperator {
    readonly hkl: Vec3,
    /** spacegroup symmetry operator index, -1 if not applicable */
    readonly spgrOp: number,
-    /** unique (external) key, -1 if not available */
-    readonly key: number,

    readonly matrix: Mat4,
-    /** cache the inverse of the transform */
+    // cache the inverse of the transform
    readonly inverse: Mat4,
-    /** optimize the identity case */
+    // optimize the identity case
    readonly isIdentity: boolean,

    /**
@@ -53,20 +51,19 @@ namespace SymmetryOperator {

    export const RotationTranslationEpsilon = 0.005;

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

    function isSymmetryOperator(x: any): x is SymmetryOperator {
--- a/src/mol-model-formats/structure/property/bonds/index-pair.ts
+++ b/src/mol-model-formats/structure/property/bonds/index-pair.ts
@@ -14,8 +14,6 @@ import { ElementIndex } from '../../../../mol-model/structure';

 export type IndexPairsProps = {
    readonly key: ArrayLike<number>
-    readonly operatorA: ArrayLike<number>
-    readonly operatorB: ArrayLike<number>
    readonly order: ArrayLike<number>
    readonly distance: ArrayLike<number>
    readonly flag: ArrayLike<BondType.Flag>
@@ -26,22 +24,18 @@ export type IndexPairBonds = { bonds: IndexPairs, maxDistance: number }
 function getGraph(indexA: ArrayLike<ElementIndex>, indexB: ArrayLike<ElementIndex>, props: Partial<IndexPairsProps>, count: number): IndexPairs {
    const builder = new IntAdjacencyGraph.EdgeBuilder(count, indexA, indexB);
    const key = new Int32Array(builder.slotCount);
-    const operatorA = new Array(builder.slotCount);
-    const operatorB = new Array(builder.slotCount);
    const order = new Int8Array(builder.slotCount);
    const distance = new Array(builder.slotCount);
    const flag = new Array(builder.slotCount);
    for (let i = 0, _i = builder.edgeCount; i < _i; i++) {
        builder.addNextEdge();
        builder.assignProperty(key, props.key ? props.key[i] : -1);
-        builder.assignProperty(operatorA, props.operatorA ? props.operatorA[i] : -1);
-        builder.assignProperty(operatorB, props.operatorB ? props.operatorB[i] : -1);
        builder.assignProperty(order, props.order ? props.order[i] : 1);
        builder.assignProperty(distance, props.distance ? props.distance[i] : -1);
        builder.assignProperty(flag, props.flag ? props.flag[i] : BondType.Flag.Covalent);
    }

-    return builder.createGraph({ key, operatorA, operatorB, order, distance, flag });
+    return builder.createGraph({ key, order, distance, flag });
 }

 export namespace IndexPairBonds {
@@ -56,10 +50,6 @@ export namespace IndexPairBonds {
            indexA: Column<number>,
            indexB: Column<number>,
            key?: Column<number>,
-            /** Operator key for indexA. Used in bond computation. */
-            operatorA?: Column<number>,
-            /** Operator key for indexB. Used in bond computation. */
-            operatorB?: Column<number>,
            order?: Column<number>,
            /**
             * Useful for bonds in periodic cells. That is, only bonds within the given
@@ -93,30 +83,12 @@ export namespace IndexPairBonds {
        const indexA = pairs.indexA.toArray() as ArrayLike<ElementIndex>;
        const indexB = pairs.indexB.toArray() as ArrayLike<ElementIndex>;
        const key = pairs.key && pairs.key.toArray();
-        const operatorA = pairs.operatorA && pairs.operatorA.toArray();
-        const operatorB = pairs.operatorB && pairs.operatorB.toArray();
        const order = pairs.order && pairs.order.toArray();
        const distance = pairs.distance && pairs.distance.toArray();
        const flag = pairs.flag && pairs.flag.toArray();
        return {
-            bonds: getGraph(indexA, indexB, { key, operatorA, operatorB, order, distance, flag }, count),
+            bonds: getGraph(indexA, indexB, { key, order, distance, flag }, count),
            maxDistance: p.maxDistance
        };
    }
-
-    /** Like `getEdgeIndex` but taking `edgeProps.operatorA` and `edgeProps.operatorB` into account */
-    export function getEdgeIndexForOperators(bonds: IndexPairs, i: ElementIndex, j: ElementIndex, opI: number, opJ: number): number {
-        let a, b, opA, opB;
-        if (i < j) {
-            a = i; b = j;
-            opA = opI; opB = opJ;
-        } else {
-            a = j; b = i;
-            opA = opJ; opB = opI;
-        }
-        for (let t = bonds.offset[a], _t = bonds.offset[a + 1]; t < _t; t++) {
-            if (bonds.b[t] === b && bonds.edgeProps.operatorA[t] === opA && bonds.edgeProps.operatorB[t] === opB) return t;
-        }
-        return -1;
-    }
 }
--- a/src/mol-model-formats/volume/cube.ts
+++ b/src/mol-model-formats/volume/cube.ts
@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */

 import { CubeFile } from '../../mol-io/reader/cube/parser';
@@ -11,8 +12,9 @@ import { Task } from '../../mol-task';
 import { arrayMax, arrayMean, arrayMin, arrayRms } from '../../mol-util/array';
 import { ModelFormat } from '../format';
 import { CustomProperties } from '../../mol-model/custom-property';
+import { clamp } from '../../mol-math/interpolate';

-export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number, label?: string, entryId?: string }): Task<Volume> {
+export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number, label?: string, entryId?: string, clamp?: { min: number, max: number } }): Task<Volume> {
    return Task.create<Volume>('Create Volume', async () => {
        const { header, values: sourceValues } = source;
        const space = Tensor.Space(header.dim, [0, 1, 2], Float64Array);
@@ -24,6 +26,7 @@ export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number,
            // get every nth value from the source values
            const [h, k, l] = header.dim;
            const nth = (params?.dataIndex || 0) + 1;
+            const { min, max } = params?.clamp || { min: -Infinity, max: Infinity };

            let o = 0, s = 0;

@@ -31,7 +34,7 @@ export function volumeFromCube(source: CubeFile, params?: { dataIndex?: number,
            for (let u = 0; u < h; u++) {
                for (let v = 0; v < k; v++) {
                    for (let w = 0; w < l; w++) {
-                        values[o++] = sourceValues[s];
+                        values[o++] = clamp(sourceValues[s], min, max);
                        s += nth;
                    }
                }
--- a/src/mol-model/sequence/alignment/sequence.ts
+++ b/src/mol-model/sequence/alignment/sequence.ts
@@ -22,7 +22,7 @@ namespace AlignSequences {
        score: number
    }

-    export function createSeqIdIndicesMap(element: StructureElement.Loci.Element) {
+    function createSeqIdIndicesMap(element: StructureElement.Loci.Element) {
        const seqIds = new Map<number, StructureElement.UnitIndex[]>();
        if (Unit.isAtomic(element.unit)) {
            const { label_seq_id } = element.unit.model.atomicHierarchy.residues;
@@ -94,7 +94,7 @@ namespace AlignSequences {
    }
 }

-export function entityKey(unit: Unit) {
+function entityKey(unit: Unit) {
    switch (unit.kind) {
        case Unit.Kind.Atomic:
            return unit.model.atomicHierarchy.index.getEntityFromChain(unit.chainIndex[unit.elements[0]]);
@@ -105,6 +105,6 @@ export function entityKey(unit: Unit) {
    }
 }

-export function getSequence(unit: Unit) {
+function getSequence(unit: Unit) {
    return unit.model.sequence.byEntityKey[entityKey(unit)].sequence;
 }
--- a/src/mol-model/structure/model/properties/atomic/hierarchy.ts
+++ b/src/mol-model/structure/model/properties/atomic/hierarchy.ts
@@ -166,14 +166,6 @@ export interface AtomicIndex {
    findResidue(key: AtomicIndex.ResidueKey): ResidueIndex,
    findResidue(label_entity_id: string, label_asym_id: string, auth_seq_id: number, pdbx_PDB_ins_code?: string): ResidueIndex,

-
-    /**
-     * Index of the 1st occurence of this residue using "all-label" address.
-     * Doesn't work for "ligands" as they don't have a label seq id assigned.
-     * @returns index or -1 if not present.
-     */
-    findResidueLabel(key: AtomicIndex.ResidueLabelKey): ResidueIndex,
-
    /**
     * Index of the 1st occurence of this residue.
     * @param key.pdbx_PDB_ins_code Empty string for undefined
--- a/src/mol-model/structure/model/properties/utils/atomic-index.ts
+++ b/src/mol-model/structure/model/properties/utils/atomic-index.ts
@@ -124,14 +124,6 @@ class Index implements AtomicIndex {
        return rm.has(id) ? rm.get(id)! : -1 as ResidueIndex;
    }

-    findResidueLabel(key: AtomicIndex.ResidueLabelKey): ResidueIndex {
-        const cI = this.findChainLabel(key);
-        if (cI < 0) return -1 as ResidueIndex;
-        const rm = this.map.chain_index_label_seq_id.get(cI)!;
-        const id = getResidueId(key.label_seq_id, key.pdbx_PDB_ins_code || '');
-        return rm.has(id) ? rm.get(id)! : -1 as ResidueIndex;
-    }
-
    findResidueAuth(key: AtomicIndex.ResidueAuthKey): ResidueIndex {
        const cI = this.findChainAuth(key);
        if (cI < 0) return -1 as ResidueIndex;
--- a/src/mol-model/structure/model/types.ts
+++ b/src/mol-model/structure/model/types.ts
@@ -285,10 +285,6 @@ export const AminoAcidNamesD = new Set([
 ]);
 export const AminoAcidNames = SetUtils.unionMany(AminoAcidNamesL, AminoAcidNamesD);

-export const CommonProteinCaps = new Set([
-    'NME', 'ACE'
-]);
-
 export const RnaBaseNames = new Set([
    'A', 'C', 'T', 'G', 'I', 'U',
    'N' // unknown RNA base from CCD
--- a/src/mol-model/structure/model/types/saccharides.ts
+++ b/src/mol-model/structure/model/types/saccharides.ts
--- a/src/mol-model/structure/query/context.ts
+++ b/src/mol-model/structure/query/context.ts
@@ -155,6 +155,6 @@ class QueryContextBondInfo<U extends Unit = Unit> {
    }

    get length() {
-        return StructureElement.Location.distance(this.a, this.b);
+        return StructureElement.Location.distance(this.a, this. b);
    }
 }
--- a/src/mol-model/structure/structure/properties.ts
+++ b/src/mol-model/structure/structure/properties.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2022 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>
@@ -173,7 +173,6 @@ const unit = {
    multiChain: p(l => Unit.Traits.is(l.unit.traits, Unit.Trait.MultiChain)),
    object_primitive: p(l => l.unit.objectPrimitive),
    operator_name: p(l => l.unit.conformation.operator.name),
-    operator_key: p(l => l.unit.conformation.operator.key),
    model_index: p(l => l.unit.model.modelNum),
    model_label: p(l => l.unit.model.label),
    model_entry_id: p(l => l.unit.model.entryId),
--- a/src/mol-model/structure/structure/structure.ts
+++ b/src/mol-model/structure/structure/structure.ts
@@ -1224,7 +1224,7 @@ namespace Structure {
            const closeUnits = lookup.findUnitIndices(imageCenter[0], imageCenter[1], imageCenter[2], bs.radius + maxRadius);
            for (let i = 0; i < closeUnits.count; i++) {
                const other = structure.units[closeUnits.indices[i]];
-                if (other.elements.length > 3 && !Box3D.overlaps(bbox, other.boundary.box)) continue;
+                if (!Box3D.overlaps(bbox, other.boundary.box)) continue;
                if (!validUnit(other) || unit.id >= other.id || !validUnitPair(unit, other)) continue;

                if (other.elements.length >= unit.elements.length) callback(unit, other);
--- a/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/inter-compute.ts
@@ -71,8 +71,6 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
    const testDistanceSq = (bRadius + maxRadius) * (bRadius + maxRadius);

    builder.startUnitPair(unitA.id, unitB.id);
-    const opKeyA = unitA.conformation.operator.key;
-    const opKeyB = unitB.conformation.operator.key;

    for (let _aI = 0 as StructureElement.UnitIndex; _aI < atomCount; _aI++) {
        const aI = atomsA[_aI];
@@ -82,7 +80,7 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput

        if (!props.forceCompute && indexPairs) {
            const { maxDistance } = indexPairs;
-            const { offset, b, edgeProps: { order, distance, flag, key, operatorA, operatorB } } = indexPairs.bonds;
+            const { offset, b, edgeProps: { order, distance, flag, key } } = indexPairs.bonds;

            const srcA = sourceIndex.value(aI);
            const aeI = getElementIdx(type_symbolA.value(aI));
@@ -92,11 +90,6 @@ function findPairBonds(unitA: Unit.Atomic, unitB: Unit.Atomic, props: BondComput
                const _bI = SortedArray.indexOf(unitB.elements, bI) as StructureElement.UnitIndex;
                if (_bI < 0) continue;

-                const opA = operatorA[i];
-                const opB = operatorB[i];
-                if ((opA >= 0 && opA !== opKeyA && opA !== opKeyB) ||
-                    (opB >= 0 && opB !== opKeyB && opB !== opKeyA)) continue;
-
                const beI = getElementIdx(type_symbolA.value(bI));

                const d = distance[i];
@@ -249,29 +242,13 @@ function computeInterUnitBonds(structure: Structure, props?: Partial<InterBondCo
                (!Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== MoleculeType.Water) &&
                (!Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== MoleculeType.Water)
            );
-
-            const sameModel = a.model === b.model;
-            const notIonA = (!Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== MoleculeType.Ion) || (sameModel && hasStructConnRecord(a));
-            const notIonB = (!Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== MoleculeType.Ion) || (sameModel && hasStructConnRecord(b));
-            const notIon = notIonA && notIonB;
+            const notIon = (
+                (!Unit.isAtomic(a) || mtA[a.residueIndex[a.elements[0]]] !== MoleculeType.Ion) &&
+                (!Unit.isAtomic(b) || mtB[b.residueIndex[b.elements[0]]] !== MoleculeType.Ion)
+            );
            return Structure.validUnitPair(s, a, b) && (notWater || !p.ignoreWater) && (notIon || !p.ignoreIon);
        }),
    });
 }

-function hasStructConnRecord(unit: Unit) {
-    if (!Unit.isAtomic(unit)) return false;
-
-    const elements = unit.elements;
-    const structConn = StructConn.Provider.get(unit.model);
-    if (structConn) {
-        for (let i = 0, _i = elements.length; i < _i; i++) {
-            if (structConn.byAtomIndex.get(elements[i])) {
-                return true;
-            }
-        }
-    }
-    return false;
-}
-
 export { computeInterUnitBonds };
--- a/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
+++ b/src/mol-model/structure/structure/unit/bonds/intra-compute.ts
@@ -55,7 +55,7 @@ function findIndexPairBonds(unit: Unit.Atomic) {
    const { type_symbol } = unit.model.atomicHierarchy.atoms;
    const atomCount = unit.elements.length;
    const { maxDistance } = indexPairs;
-    const { offset, b, edgeProps: { order, distance, flag, key, operatorA, operatorB } } = indexPairs.bonds;
+    const { offset, b, edgeProps: { order, distance, flag, key } } = indexPairs.bonds;

    const { atomSourceIndex: sourceIndex } = unit.model.atomicHierarchy;
    const { invertedIndex } = Model.getInvertedAtomSourceIndex(unit.model);
@@ -66,8 +66,6 @@ function findIndexPairBonds(unit: Unit.Atomic) {
    const orders: number[] = [];
    const keys: number[] = [];

-    const opKey = unit.conformation.operator.key;
-
    for (let _aI = 0 as StructureElement.UnitIndex; _aI < atomCount; _aI++) {
        const aI = atoms[_aI];
        const aeI = getElementIdx(type_symbol.value(aI));
@@ -82,10 +80,6 @@ function findIndexPairBonds(unit: Unit.Atomic) {
            const _bI = SortedArray.indexOf(unit.elements, bI) as StructureElement.UnitIndex;
            if (_bI < 0) continue;

-            const opA = operatorA[i];
-            const opB = operatorB[i];
-            if ((opA >= 0 && opA !== opKey) || (opB >= 0 && opB !== opKey)) continue;
-
            const beI = getElementIdx(type_symbol.value(bI));

            const d = distance[i];
--- a/src/mol-model/structure/structure/util/superposition.ts
+++ b/src/mol-model/structure/structure/util/superposition.ts
@@ -64,7 +64,7 @@ export function alignAndSuperpose(xs: StructureElement.Loci[]): AlignAndSuperpos
    return ret;
 }

-export function getPositionTable(xs: StructureElement.Loci, n: number): MinimizeRmsd.Positions {
+function getPositionTable(xs: StructureElement.Loci, n: number): MinimizeRmsd.Positions {
    const ret = MinimizeRmsd.Positions.empty(n);
    let o = 0;
    for (const u of xs.elements) {
--- a/src/mol-plugin-state/animation/built-in/model-index.ts
+++ b/src/mol-plugin-state/animation/built-in/model-index.ts
@@ -124,11 +124,6 @@ export const AnimateModelIndex = PluginStateAnimation.create({
                        ? params.duration.params.durationInS * 1000
                        : Math.ceil(1000 * traj.data.frameCount / params.duration.params.targetFps);

-                    if (params.mode.name === 'once' && t.current >= durationInMs) {
-                        isEnd = true;
-                        return { modelIndex: traj.data.frameCount - 1 };
-                    }
-
                    let phase: number = (t.current % durationInMs) / durationInMs;
                    if (params.mode.name === 'loop') {
                        if (params.mode.params.direction === 'backward') {
@@ -140,6 +135,7 @@ export const AnimateModelIndex = PluginStateAnimation.create({
                    }

                    const modelIndex = Math.min(Math.floor(traj.data.frameCount * phase), traj.data.frameCount - 1);
+                    isEnd = isEnd || modelIndex === traj.data.frameCount - 1;
                    return { modelIndex };
                }
            });
--- a/src/mol-plugin-state/builder/structure/representation-preset.ts
+++ b/src/mol-plugin-state/builder/structure/representation-preset.ts
@@ -37,7 +37,6 @@ export namespace StructureRepresentationPresetProvider {

    export const CommonParams = {
        ignoreHydrogens: PD.Optional(PD.Boolean(false)),
-        onlyPolarHydrogens: PD.Optional(PD.Boolean(false)),
        ignoreLight: PD.Optional(PD.Boolean(false)),
        quality: PD.Optional(PD.Select<VisualQuality>('auto', VisualQualityOptions)),
        theme: PD.Optional(PD.Group({
@@ -71,13 +70,11 @@ export namespace StructureRepresentationPresetProvider {
        const builder = plugin.builders.structure.representation;
        const typeParams = {
            quality: plugin.managers.structure.component.state.options.visualQuality,
-            ignoreHydrogens: plugin.managers.structure.component.state.options.hydrogens === 'hide-all',
-            onlyPolarHydrogens: plugin.managers.structure.component.state.options.hydrogens === 'only-polar',
+            ignoreHydrogens: !plugin.managers.structure.component.state.options.showHydrogens,
            ignoreLight: plugin.managers.structure.component.state.options.ignoreLight,
        };
        if (params.quality && params.quality !== 'auto') typeParams.quality = params.quality;
        if (params.ignoreHydrogens !== void 0) typeParams.ignoreHydrogens = !!params.ignoreHydrogens;
-        if (params.onlyPolarHydrogens !== void 0) typeParams.onlyPolarHydrogens = !!params.onlyPolarHydrogens;
        if (params.ignoreLight !== void 0) typeParams.ignoreLight = !!params.ignoreLight;
        const color: ColorTheme.BuiltIn | undefined = params.theme?.globalName ? params.theme?.globalName : void 0;
        const ballAndStickColor: ColorTheme.BuiltInParams<'element-symbol'> = params.theme?.carbonColor !== undefined
--- a/src/mol-plugin-state/helpers/structure-selection-query.ts
+++ b/src/mol-plugin-state/helpers/structure-selection-query.ts
@@ -7,7 +7,7 @@

 import { CustomProperty } from '../../mol-model-props/common/custom-property';
 import { QueryContext, Structure, StructureQuery, StructureSelection, StructureProperties, StructureElement } from '../../mol-model/structure';
-import { BondType, NucleicBackboneAtoms, ProteinBackboneAtoms, SecondaryStructureType, AminoAcidNamesL, RnaBaseNames, DnaBaseNames, WaterNames, ElementSymbol, PolymerNames, CommonProteinCaps } from '../../mol-model/structure/model/types';
+import { BondType, NucleicBackboneAtoms, ProteinBackboneAtoms, SecondaryStructureType, AminoAcidNamesL, RnaBaseNames, DnaBaseNames, WaterNames, ElementSymbol, PolymerNames } from '../../mol-model/structure/model/types';
 import { PluginContext } from '../../mol-plugin/context';
 import { MolScriptBuilder as MS } from '../../mol-script/language/builder';
 import { Expression } from '../../mol-script/language/expression';
@@ -350,23 +350,14 @@ const ligand = StructureSelectionQuery('Ligand', MS.struct.modifier.union([
                ])
            ]),
        ]),
-        by: MS.struct.combinator.merge([
-            MS.struct.modifier.union([
-                MS.struct.generator.atomGroups({
-                    'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
-                    'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
-                    'residue-test': MS.core.set.has([
-                        MS.set(...SetUtils.toArray(PolymerNames)), MS.ammp('label_comp_id')
-                    ])
-                }),
-            ]),
+        by: MS.struct.modifier.union([
            MS.struct.generator.atomGroups({
+                'entity-test': MS.core.rel.eq([MS.ammp('entityType'), 'polymer']),
                'chain-test': MS.core.rel.eq([MS.ammp('objectPrimitive'), 'atomistic']),
                'residue-test': MS.core.set.has([
-                    MS.set(...SetUtils.toArray(CommonProteinCaps)),
-                    MS.ammp('label_comp_id'),
-                ]),
-            }),
+                    MS.set(...SetUtils.toArray(PolymerNames)), MS.ammp('label_comp_id')
+                ])
+            })
        ])
    })
 ]), { category: StructureSelectionCategory.Type });
--- a/src/mol-plugin-state/manager/structure/component.ts
+++ b/src/mol-plugin-state/manager/structure/component.ts
@@ -70,8 +70,7 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
        return this.plugin.dataTransaction(async () => {
            await update.commit();
            await this.plugin.state.updateBehavior(StructureFocusRepresentation, p => {
-                p.ignoreHydrogens = options.hydrogens === 'hide-all';
-                p.onlyPolarHydrogens = options.hydrogens === 'only-polar';
+                p.ignoreHydrogens = !options.showHydrogens;
                p.ignoreLight = options.ignoreLight;
                p.material = options.materialStyle;
                p.clip = options.clipObjects;
@@ -81,17 +80,15 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
    }

    private updateReprParams(update: StateBuilder.Root, component: StructureComponentRef) {
-        const { hydrogens, visualQuality: quality, ignoreLight, materialStyle: material, clipObjects: clip } = this.state.options;
-        const ignoreHydrogens = hydrogens === 'hide-all';
-        const onlyPolarHydrogens = hydrogens === 'only-polar';
+        const { showHydrogens, visualQuality: quality, ignoreLight, materialStyle: material, clipObjects: clip } = this.state.options;
+        const ignoreHydrogens = !showHydrogens;
        for (const r of component.representations) {
            if (r.cell.transform.transformer !== StructureRepresentation3D) continue;

            const params = r.cell.transform.params as StateTransformer.Params<StructureRepresentation3D>;
-            if (!!params.type.params.ignoreHydrogens !== ignoreHydrogens || !!params.type.params.onlyPolarHydrogens !== onlyPolarHydrogens || params.type.params.quality !== quality || params.type.params.ignoreLight !== ignoreLight || !shallowEqual(params.type.params.material, material) || !PD.areEqual(Clip.Params, params.type.params.clip, clip)) {
+            if (!!params.type.params.ignoreHydrogens !== ignoreHydrogens || params.type.params.quality !== quality || params.type.params.ignoreLight !== ignoreLight || !shallowEqual(params.type.params.material, material) || !PD.areEqual(Clip.Params, params.type.params.clip, clip)) {
                update.to(r.cell).update(old => {
                    old.type.params.ignoreHydrogens = ignoreHydrogens;
-                    old.type.params.onlyPolarHydrogens = onlyPolarHydrogens;
                    old.type.params.quality = quality;
                    old.type.params.ignoreLight = ignoreLight;
                    old.type.params.material = material;
@@ -314,10 +311,9 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
    addRepresentation(components: ReadonlyArray<StructureComponentRef>, type: string) {
        if (components.length === 0) return;

-        const { hydrogens, visualQuality: quality, ignoreLight, materialStyle: material, clipObjects: clip } = this.state.options;
-        const ignoreHydrogens = hydrogens === 'hide-all';
-        const onlyPolarHydrogens = hydrogens === 'only-polar';
-        const typeParams = { ignoreHydrogens, onlyPolarHydrogens, quality, ignoreLight, material, clip };
+        const { showHydrogens, visualQuality: quality, ignoreLight, materialStyle: material, clipObjects: clip } = this.state.options;
+        const ignoreHydrogens = !showHydrogens;
+        const typeParams = { ignoreHydrogens, quality, ignoreLight, material, clip };

        return this.plugin.dataTransaction(async () => {
            for (const component of components) {
@@ -352,10 +348,9 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone
            const xs = structures || this.currentStructures;
            if (xs.length === 0) return;

-            const { hydrogens, visualQuality: quality, ignoreLight, materialStyle: material, clipObjects: clip } = this.state.options;
-            const ignoreHydrogens = hydrogens === 'hide-all';
-            const onlyPolarHydrogens = hydrogens === 'only-polar';
-            const typeParams = { ignoreHydrogens, onlyPolarHydrogens, quality, ignoreLight, material, clip };
+            const { showHydrogens, visualQuality: quality, ignoreLight, materialStyle: material, clipObjects: clip } = this.state.options;
+            const ignoreHydrogens = !showHydrogens;
+            const typeParams = { ignoreHydrogens, quality, ignoreLight, material, clip };

            const componentKey = UUID.create22();
            for (const s of xs) {
@@ -463,13 +458,9 @@ class StructureComponentManager extends StatefulPluginComponent<StructureCompone

 namespace StructureComponentManager {
    export const OptionsParams = {
-        hydrogens: PD.Select(
-            'all',
-            [['all', 'Show All'], ['hide-all', 'Hide All'], ['only-polar', 'Only Polar']] as const,
-            { description: 'Determine display of hydrogen atoms in representations' }
-        ),
+        showHydrogens: PD.Boolean(true, { description: 'Toggle display of hydrogen atoms in representations' }),
        visualQuality: PD.Select('auto', VisualQualityOptions, { description: 'Control the visual/rendering quality of representations' }),
-        ignoreLight: PD.Boolean(false, { description: 'Ignore light for stylized rendering of representations' }),
+        ignoreLight: PD.Boolean(false, { description: 'Ignore light for stylized rendering of representtions' }),
        materialStyle: Material.getParam(),
        clipObjects: PD.Group(Clip.Params),
        interactions: PD.Group(InteractionsProvider.defaultParams, { label: 'Non-covalent Interactions' }),
--- a/src/mol-plugin-state/transforms/representation.ts
+++ b/src/mol-plugin-state/transforms/representation.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2022 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>
@@ -43,7 +43,6 @@ import { Box3D } from '../../mol-math/geometry';
 import { PlaneParams, PlaneRepresentation } from '../../mol-repr/shape/loci/plane';
 import { Substance } from '../../mol-theme/substance';
 import { Material } from '../../mol-util/material';
-import { lerp } from '../../mol-math/interpolate';

 export { StructureRepresentation3D };
 export { ExplodeStructureRepresentation3D };
@@ -57,7 +56,6 @@ export { SubstanceStructureRepresentation3DFromScript };
 export { SubstanceStructureRepresentation3DFromBundle };
 export { ClippingStructureRepresentation3DFromScript };
 export { ClippingStructureRepresentation3DFromBundle };
-export { ThemeStrengthRepresentation3D };
 export { VolumeRepresentation3D };

 type StructureRepresentation3D = typeof StructureRepresentation3D
@@ -747,62 +745,6 @@ const ClippingStructureRepresentation3DFromBundle = PluginStateTransform.BuiltIn
    }
 });

-type ThemeStrengthRepresentation3D = typeof ThemeStrengthRepresentation3D
-const ThemeStrengthRepresentation3D = PluginStateTransform.BuiltIn({
-    name: 'theme-strength-representation-3d',
-    display: 'Theme Strength 3D Representation',
-    from: SO.Molecule.Structure.Representation3D,
-    to: SO.Molecule.Structure.Representation3DState,
-    params: () => ({
-        overpaintStrength: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
-        transparencyStrength: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
-        substanceStrength: PD.Numeric(1, { min: 0, max: 1, step: 0.01 }),
-    })
-})({
-    canAutoUpdate() {
-        return true;
-    },
-    apply({ a, params }) {
-        return new SO.Molecule.Structure.Representation3DState({
-            state: {
-                themeStrength: {
-                    overpaint: params.overpaintStrength,
-                    transparency: params.transparencyStrength,
-                    substance: params.substanceStrength
-                },
-            },
-            initialState: {
-                themeStrength: { overpaint: 1, transparency: 1, substance: 1 },
-            },
-            info: { },
-            repr: a.data.repr
-        }, { label: 'Theme Strength', description: `${params.overpaintStrength.toFixed(2)}, ${params.transparencyStrength.toFixed(2)}, ${params.substanceStrength.toFixed(2)}` });
-    },
-    update({ a, b, newParams, oldParams }) {
-        if (newParams.overpaintStrength === b.data.state.themeStrength?.overpaint &&
-            newParams.transparencyStrength === b.data.state.themeStrength?.transparency &&
-            newParams.substanceStrength === b.data.state.themeStrength?.substance
-        ) return StateTransformer.UpdateResult.Unchanged;
-
-        b.data.state.themeStrength = {
-            overpaint: newParams.overpaintStrength,
-            transparency: newParams.transparencyStrength,
-            substance: newParams.substanceStrength,
-        };
-        b.data.repr = a.data.repr;
-        b.label = 'Theme Strength';
-        b.description = `${newParams.overpaintStrength.toFixed(2)}, ${newParams.transparencyStrength.toFixed(2)}, ${newParams.substanceStrength.toFixed(2)}`;
-        return StateTransformer.UpdateResult.Updated;
-    },
-    interpolate(src, tar, t) {
-        return {
-            overpaintStrength: lerp(src.overpaintStrength, tar.overpaintStrength, t),
-            transparencyStrength: lerp(src.transparencyStrength, tar.transparencyStrength, t),
-            substanceStrength: lerp(src.substanceStrength, tar.substanceStrength, t),
-        };
-    }
-});
-
 //

 export namespace VolumeRepresentation3DHelpers {
--- a/src/mol-plugin-state/transforms/volume.ts
+++ b/src/mol-plugin-state/transforms/volume.ts
@@ -88,12 +88,24 @@ const VolumeFromCube = PluginStateTransform.BuiltIn({
        return {
            dataIndex,
            entryId: PD.Text(''),
+            clamp: PD.MappedStatic('off', {
+                'off': PD.EmptyGroup(),
+                'on': PD.Group({
+                    min: PD.Numeric(-1024),
+                    max: PD.Numeric(1024),
+                })
+            }, { cycle: true })
        };
    }
 })({
    apply({ a, params }) {
        return Task.create('Create volume from Cube', async ctx => {
-            const volume = await volumeFromCube(a.data, { ...params, label: a.data.name || a.label }).runInContext(ctx);
+            const volume = await volumeFromCube(a.data, {
+                dataIndex: params.dataIndex,
+                label: a.data.name || a.label,
+                entryId: params.entryId,
+                clamp: params.clamp.name === 'on' ? params.clamp.params : undefined,
+            }).runInContext(ctx);
            const props = { label: volume.label || 'Volume', description: `Volume ${a.data.header.dim[0]}\u00D7${a.data.header.dim[1]}\u00D7${a.data.header.dim[2]}` };
            return new SO.Volume.Data(volume, props);
        });
--- a/src/mol-plugin-ui/controls/parameters.tsx
+++ b/src/mol-plugin-ui/controls/parameters.tsx
@@ -18,7 +18,7 @@ import { getPrecision } from '../../mol-util/number';
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { ParamMapping } from '../../mol-util/param-mapping';
 import { camelCaseToWords } from '../../mol-util/string';
-import { PluginReactContext, PluginUIComponent } from '../base';
+import { PluginUIComponent } from '../base';
 import { PluginUIContext } from '../context';
 import { ActionMenu } from './action-menu';
 import { ColorOptions, ColorValueOption, CombinedColorControl } from './color';
@@ -505,12 +505,10 @@ export class ValueRefControl extends React.PureComponent<ParamProps<PD.ValueRef<

    toggle = () => this.setState({ showOptions: !this.state.showOptions });

-    private get items() {
-        return ActionMenu.createItemsFromSelectOptions(this.props.param.getOptions(this.context));
-    }
+    items = memoizeLatest((param: PD.ValueRef) => ActionMenu.createItemsFromSelectOptions(param.getOptions()));

    renderControl() {
-        const items = this.items;
+        const items = this.items(this.props.param);
        const current = this.props.value.ref ? ActionMenu.findItem(items, this.props.value.ref) : void 0;
        const label = current
            ? current.label
@@ -523,7 +521,7 @@ export class ValueRefControl extends React.PureComponent<ParamProps<PD.ValueRef<
    renderAddOn() {
        if (!this.state.showOptions) return null;

-        const items = this.items;
+        const items = this.items(this.props.param);
        const current = ActionMenu.findItem(items, this.props.value.ref);

        return <ActionMenu items={items} current={current} onSelect={this.onSelect} />;
@@ -541,7 +539,6 @@ export class ValueRefControl extends React.PureComponent<ParamProps<PD.ValueRef<
        });
    }
 }
-ValueRefControl.contextType = PluginReactContext;

 export class IntervalControl extends React.PureComponent<ParamProps<PD.Interval>, { isExpanded: boolean }> {
    state = { isExpanded: false };
--- a/src/mol-plugin-ui/sequence.tsx
+++ b/src/mol-plugin-ui/sequence.tsx
@@ -29,7 +29,7 @@ const MaxDisplaySequenceLength = 5000;
 const MaxSelectOptionsCount = 1000;
 const MaxSequenceWrappersCount = 30;

-export function opKey(l: StructureElement.Location) {
+function opKey(l: StructureElement.Location) {
    const ids = SP.unit.pdbx_struct_oper_list_ids(l);
    const ncs = SP.unit.struct_ncs_oper_id(l);
    const hkl = SP.unit.hkl(l);
@@ -37,12 +37,12 @@ export function opKey(l: StructureElement.Location) {
    return `${ids.sort().join(',')}|${ncs}|${hkl}|${spgrOp}`;
 }

-export function splitModelEntityId(modelEntityId: string) {
+function splitModelEntityId(modelEntityId: string) {
    const [modelIdx, entityId] = modelEntityId.split('|');
    return [parseInt(modelIdx), entityId];
 }

-export function getSequenceWrapper(state: { structure: Structure, modelEntityId: string, chainGroupId: number, operatorKey: string }, structureSelection: StructureSelectionManager): SequenceWrapper.Any | string {
+function getSequenceWrapper(state: { structure: Structure, modelEntityId: string, chainGroupId: number, operatorKey: string }, structureSelection: StructureSelectionManager): SequenceWrapper.Any | string {
    const { structure, modelEntityId, chainGroupId, operatorKey } = state;
    const l = StructureElement.Location.create(structure);
    const [modelIdx, entityId] = splitModelEntityId(modelEntityId);
@@ -97,7 +97,7 @@ export function getSequenceWrapper(state: { structure: Structure, modelEntityId:
    }
 }

-export function getModelEntityOptions(structure: Structure, polymersOnly = false): [string, string][] {
+function getModelEntityOptions(structure: Structure, polymersOnly = false): [string, string][] {
    const options: [string, string][] = [];
    const l = StructureElement.Location.create(structure);
    const seen = new Set<string>();
@@ -131,7 +131,7 @@ export function getModelEntityOptions(structure: Structure, polymersOnly = false
    return options;
 }

-export function getChainOptions(structure: Structure, modelEntityId: string): [number, string][] {
+function getChainOptions(structure: Structure, modelEntityId: string): [number, string][] {
    const options: [number, string][] = [];
    const l = StructureElement.Location.create(structure);
    const seen = new Set<number>();
@@ -161,7 +161,7 @@ export function getChainOptions(structure: Structure, modelEntityId: string): [n
    return options;
 }

-export function getOperatorOptions(structure: Structure, modelEntityId: string, chainGroupId: number): [string, string][] {
+function getOperatorOptions(structure: Structure, modelEntityId: string, chainGroupId: number): [string, string][] {
    const options: [string, string][] = [];
    const l = StructureElement.Location.create(structure);
    const seen = new Set<string>();
@@ -189,7 +189,7 @@ export function getOperatorOptions(structure: Structure, modelEntityId: string,
    return options;
 }

-export function getStructureOptions(state: State) {
+function getStructureOptions(state: State) {
    const options: [string, string][] = [];
    const all: Structure[] = [];

--- a/src/mol-plugin-ui/sequence/sequence.tsx
+++ b/src/mol-plugin-ui/sequence/sequence.tsx
@@ -27,21 +27,21 @@ const MaxSequenceNumberSize = 5;

 // TODO: this is somewhat inefficient and should be done using a canvas.
 export class Sequence<P extends SequenceProps> extends PluginUIComponent<P> {
-    protected parentDiv = React.createRef<HTMLDivElement>();
-    protected lastMouseOverSeqIdx = -1;
-    protected highlightQueue = new Subject<{ seqIdx: number, buttons: number, button: number, modifiers: ModifiersKeys }>();
+    private parentDiv = React.createRef<HTMLDivElement>();
+    private lastMouseOverSeqIdx = -1;
+    private highlightQueue = new Subject<{ seqIdx: number, buttons: number, button: number, modifiers: ModifiersKeys }>();

-    protected lociHighlightProvider = (loci: Representation.Loci, action: MarkerAction) => {
+    private lociHighlightProvider = (loci: Representation.Loci, action: MarkerAction) => {
        const changed = this.props.sequenceWrapper.markResidue(loci.loci, action);
        if (changed) this.updateMarker();
    };

-    protected lociSelectionProvider = (loci: Representation.Loci, action: MarkerAction) => {
+    private lociSelectionProvider = (loci: Representation.Loci, action: MarkerAction) => {
        const changed = this.props.sequenceWrapper.markResidue(loci.loci, action);
        if (changed) this.updateMarker();
    };

-    protected get sequenceNumberPeriod() {
+    private get sequenceNumberPeriod() {
        if (this.props.sequenceNumberPeriod !== undefined) {
            return this.props.sequenceNumberPeriod as number;
        }
@@ -104,7 +104,7 @@ export class Sequence<P extends SequenceProps> extends PluginUIComponent<P> {
        e.preventDefault();
    };

-    protected mouseDownLoci: StructureElement.Loci | undefined = undefined;
+    private mouseDownLoci: StructureElement.Loci | undefined = undefined;

    mouseDown = (e: React.MouseEvent) => {
        e.stopPropagation();
@@ -148,7 +148,7 @@ export class Sequence<P extends SequenceProps> extends PluginUIComponent<P> {
        this.mouseDownLoci = undefined;
    };

-    protected getBackgroundColor(marker: number) {
+    private getBackgroundColor(marker: number) {
        // TODO: make marker color configurable
        if (typeof marker === 'undefined') console.error('unexpected marker value');
        return marker === 0
@@ -158,17 +158,17 @@ export class Sequence<P extends SequenceProps> extends PluginUIComponent<P> {
                : 'rgb(255, 102, 153)'; // highlighted
    }

-    protected getResidueClass(seqIdx: number, label: string) {
+    private getResidueClass(seqIdx: number, label: string) {
        return label.length > 1
            ? this.props.sequenceWrapper.residueClass(seqIdx) + (seqIdx === 0 ? ' msp-sequence-residue-long-begin' : ' msp-sequence-residue-long')
            : this.props.sequenceWrapper.residueClass(seqIdx);
    }

-    protected residue(seqIdx: number, label: string, marker: number) {
+    private residue(seqIdx: number, label: string, marker: number) {
        return <span key={seqIdx} data-seqid={seqIdx} style={{ backgroundColor: this.getBackgroundColor(marker) }} className={this.getResidueClass(seqIdx, label)}>{`\u200b${label}\u200b`}</span>;
    }

-    protected getSequenceNumberClass(seqIdx: number, seqNum: string, label: string) {
+    private getSequenceNumberClass(seqIdx: number, seqNum: string, label: string) {
        const classList = ['msp-sequence-number'];
        if (seqNum.startsWith('-')) {
            if (label.length > 1 && seqIdx > 0) classList.push('msp-sequence-number-long-negative');
@@ -179,8 +179,8 @@ export class Sequence<P extends SequenceProps> extends PluginUIComponent<P> {
        return classList.join(' ');
    }

-    protected location = StructureElement.Location.create(void 0);
-    protected getSequenceNumber(seqIdx: number) {
+    private location = StructureElement.Location.create(void 0);
+    private getSequenceNumber(seqIdx: number) {
        let seqNum = '';
        const loci = this.props.sequenceWrapper.getLoci(seqIdx);
        const l = StructureElement.Loci.getFirstLocation(loci, this.location);
@@ -196,16 +196,16 @@ export class Sequence<P extends SequenceProps> extends PluginUIComponent<P> {
        return seqNum;
    }

-    protected padSeqNum(n: string) {
+    private padSeqNum(n: string) {
        if (n.length < MaxSequenceNumberSize) return n + new Array(MaxSequenceNumberSize - n.length + 1).join('\u00A0');
        return n;
    }
-    protected getSequenceNumberSpan(seqIdx: number, label: string) {
+    private getSequenceNumberSpan(seqIdx: number, label: string) {
        const seqNum = this.getSequenceNumber(seqIdx);
        return <span key={`marker-${seqIdx}`} className={this.getSequenceNumberClass(seqIdx, seqNum, label)}>{this.padSeqNum(seqNum)}</span>;
    }

-    protected updateMarker() {
+    private updateMarker() {
        if (!this.parentDiv.current) return;
        const xs = this.parentDiv.current.children;
        const { markerArray } = this.props.sequenceWrapper;
--- a/src/mol-plugin-ui/skin/base/components/viewport.scss
+++ b/src/mol-plugin-ui/skin/base/components/viewport.scss
@@ -4,7 +4,7 @@
    top: 0;
    right: 0;
    bottom: 0;
-    background: $default-background;
+    background: black;

    .msp-btn-link {
        background: rgba(0,0,0,0.2);
--- a/src/mol-plugin-ui/state/apply-action.tsx
+++ b/src/mol-plugin-ui/state/apply-action.tsx
@@ -28,8 +28,7 @@ namespace ApplyActionControl {
        params: any,
        error?: string,
        busy: boolean,
-        isInitial: boolean,
-        isCollapsed?: boolean,
+        isInitial: boolean
    }
 }

@@ -41,7 +40,7 @@ class ApplyActionControl extends TransformControlBase<ApplyActionControl.Props,
            ref: this.props.nodeRef
        });
    }
-    getInfo() { return this._getInfo(this.props.nodeRef, this.props.state.transforms.get(this.props.nodeRef).version, this.state?.isCollapsed); }
+    getInfo() { return this._getInfo(this.props.nodeRef, this.props.state.transforms.get(this.props.nodeRef).version); }
    getTransformerId() { return this.props.state.transforms.get(this.props.nodeRef).transformer.id; }
    getHeader() { return this.props.hideHeader ? 'none' : this.props.action.definition.display; }
    canApply() { return !this.state.error && !this.state.busy; }
@@ -50,9 +49,9 @@ class ApplyActionControl extends TransformControlBase<ApplyActionControl.Props,
    isUpdate() { return false; }
    getSourceAndTarget() { return { a: this.props.state.cells.get(this.props.nodeRef)!.obj }; }

-    private _getInfo = memoizeLatest((t: StateTransform.Ref, v: string, collapsed?: boolean) => StateTransformParameters.infoFromAction(this.plugin, this.props.state, this.props.action, this.props.nodeRef));
+    private _getInfo = memoizeLatest((t: StateTransform.Ref, v: string) => StateTransformParameters.infoFromAction(this.plugin, this.props.state, this.props.action, this.props.nodeRef));

-    state: ApplyActionControl.ComponentState = { plugin: this.plugin, ref: this.props.nodeRef, version: this.props.state.transforms.get(this.props.nodeRef).version, error: void 0, isInitial: true, params: this.getInfo().initialValues, busy: false, isCollapsed: this.props.initiallyCollapsed };
+    state = { plugin: this.plugin, ref: this.props.nodeRef, version: this.props.state.transforms.get(this.props.nodeRef).version, error: void 0, isInitial: true, params: this.getInfo().initialValues, busy: false, isCollapsed: this.props.initiallyCollapsed };

    static getDerivedStateFromProps(props: ApplyActionControl.Props, state: ApplyActionControl.ComponentState) {
        const version = props.state.transforms.get(props.nodeRef).version;
--- a/src/mol-plugin-ui/structure/quick-styles.tsx
+++ b/src/mol-plugin-ui/structure/quick-styles.tsx
@@ -56,13 +56,12 @@ export class QuickStyles extends PurePluginUIComponent {
                postprocessing: {
                    outline: {
                        name: 'on',
-                        params: { scale: 1, color: Color(0x000000), threshold: 0.25, includeTransparent: true }
+                        params: { scale: 1, color: Color(0x000000), threshold: 0.25 }
                    },
                    occlusion: {
                        name: 'on',
                        params: { bias: 0.8, blurKernelSize: 15, radius: 5, samples: 32, resolutionScale: 1 }
                    },
-                    shadow: { name: 'off', params: {} },
                }
            });
        }
@@ -79,7 +78,7 @@ export class QuickStyles extends PurePluginUIComponent {
                        name: 'on',
                        params: pp.outline.name === 'on'
                            ? pp.outline.params
-                            : { scale: 1, color: Color(0x000000), threshold: 0.33, includeTransparent: true }
+                            : { scale: 1, color: Color(0x000000), threshold: 0.33 }
                    },
                    occlusion: {
                        name: 'on',
@@ -87,7 +86,6 @@ export class QuickStyles extends PurePluginUIComponent {
                            ? pp.occlusion.params
                            : { bias: 0.8, blurKernelSize: 15, radius: 5, samples: 32, resolutionScale: 1 }
                    },
-                    shadow: { name: 'off', params: {} },
                }
            });
        }
--- a/src/mol-plugin-ui/structure/superposition.tsx
+++ b/src/mol-plugin-ui/structure/superposition.tsx
@@ -65,7 +65,7 @@ type SuperpositionControlsState = {
    options: StructureSuperpositionOptions
 }

-export interface LociEntry {
+interface LociEntry {
    loci: StructureElement.Loci,
    label: string,
    cell: StateObjectCell<PluginStateObject.Molecule.Structure>
--- a/src/mol-plugin-ui/viewport/simple-settings.tsx
+++ b/src/mol-plugin-ui/viewport/simple-settings.tsx
@@ -59,7 +59,6 @@ const SimpleSettingsParams = {
    }, { pivot: 'color' }),
    lighting: PD.Group({
        occlusion: Canvas3DParams.postprocessing.params.occlusion,
-        shadow: Canvas3DParams.postprocessing.params.shadow,
        outline: Canvas3DParams.postprocessing.params.outline,
        fog: Canvas3DParams.cameraFog,
    }, { isFlat: true }),
@@ -115,7 +114,6 @@ const SimpleSettingsMapping = ParamMapping({
            },
            lighting: {
                occlusion: canvas.postprocessing.occlusion,
-                shadow: canvas.postprocessing.shadow,
                outline: canvas.postprocessing.outline,
                fog: canvas.cameraFog,
            },
@@ -131,7 +129,6 @@ const SimpleSettingsMapping = ParamMapping({
        canvas.transparentBackground = s.background.transparent;
        canvas.renderer.backgroundColor = s.background.color;
        canvas.postprocessing.occlusion = s.lighting.occlusion;
-        canvas.postprocessing.shadow = s.lighting.shadow;
        canvas.postprocessing.outline = s.lighting.outline;
        canvas.postprocessing.background = s.background.style;
        canvas.cameraFog = s.lighting.fog;
--- a/src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts
+++ b/src/mol-plugin/behavior/dynamic/selection/structure-focus-representation.ts
@@ -52,7 +52,6 @@ const StructureFocusRepresentationParams = (plugin: PluginContext) => {
        components: PD.MultiSelect(FocusComponents, PD.arrayToOptions(FocusComponents)),
        excludeTargetFromSurroundings: PD.Boolean(false, { label: 'Exclude Target', description: 'Exclude the focus "target" from the surroudings component.' }),
        ignoreHydrogens: PD.Boolean(false),
-        onlyPolarHydrogens: PD.Boolean(false),
        ignoreLight: PD.Boolean(false),
        material: Material.getParam(),
        clip: PD.Group(Clip.Params),
@@ -81,7 +80,7 @@ class StructureFocusRepresentationBehavior extends PluginBehavior.WithSubscriber
            ...reprParams,
            type: {
                name: reprParams.type.name,
-                params: { ...reprParams.type.params, ignoreHydrogens: this.params.ignoreHydrogens, onlyPolarHydrogens: this.params.onlyPolarHydrogens, ignoreLight: this.params.ignoreLight, material: this.params.material, clip: this.params.clip }
+                params: { ...reprParams.type.params, ignoreHydrogens: this.params.ignoreHydrogens, ignoreLight: this.params.ignoreLight, material: this.params.material, clip: this.params.clip }
            }
        };
    }
--- a/src/mol-plugin/config.ts
+++ b/src/mol-plugin/config.ts
@@ -37,7 +37,6 @@ export const PluginConfig = {
        // TODO: check back in a few weeks to see if it was fixed
        PreferWebGl1: item('plugin-config.prefer-webgl1', PluginFeatureDetection.preferWebGl1),
        AllowMajorPerformanceCaveat: item('plugin-config.allow-major-performance-caveat', false),
-        PowerPreference: item<WebGLContextAttributes['powerPreference']>('plugin-config.power-preference', 'high-performance'),
    },
    State: {
        DefaultServer: item('plugin-state.server', 'https://webchem.ncbr.muni.cz/molstar-state'),
--- a/src/mol-plugin/context.ts
+++ b/src/mol-plugin/context.ts
@@ -267,8 +267,7 @@ export class PluginContext {
                const enableDpoit = this.config.get(PluginConfig.General.EnableDpoit) || false;
                const preferWebGl1 = this.config.get(PluginConfig.General.PreferWebGl1) || false;
                const failIfMajorPerformanceCaveat = !(this.config.get(PluginConfig.General.AllowMajorPerformanceCaveat) ?? false);
-                const powerPreference = this.config.get(PluginConfig.General.PowerPreference) || 'high-performance';
-                (this.canvas3dContext as Canvas3DContext) = Canvas3DContext.fromCanvas(canvas, this.managers.asset, { antialias, preserveDrawingBuffer, pixelScale, pickScale, pickPadding, enableWboit, enableDpoit, preferWebGl1, failIfMajorPerformanceCaveat, powerPreference });
+                (this.canvas3dContext as Canvas3DContext) = Canvas3DContext.fromCanvas(canvas, this.managers.asset, { antialias, preserveDrawingBuffer, pixelScale, pickScale, pickPadding, enableWboit, enableDpoit, preferWebGl1, failIfMajorPerformanceCaveat });
            }
            (this.canvas3d as Canvas3D) = Canvas3D.create(this.canvas3dContext!);
            this.canvas3dInit.next(true);
--- a/src/mol-plugin/spec.ts
+++ b/src/mol-plugin/spec.ts
@@ -104,7 +104,6 @@ export const DefaultPluginSpec = (): PluginSpec => ({
        PluginSpec.Action(StateTransforms.Representation.TransparencyStructureRepresentation3DFromScript),
        PluginSpec.Action(StateTransforms.Representation.ClippingStructureRepresentation3DFromScript),
        PluginSpec.Action(StateTransforms.Representation.SubstanceStructureRepresentation3DFromScript),
-        PluginSpec.Action(StateTransforms.Representation.ThemeStrengthRepresentation3D),

        PluginSpec.Action(AssignColorVolume),
        PluginSpec.Action(StateTransforms.Volume.VolumeFromCcp4),
--- a/src/mol-repr/representation.ts
+++ b/src/mol-repr/representation.ts
@@ -140,7 +140,7 @@ export class RepresentationRegistry<D, S extends Representation.State> {
 //

 export { Representation };
-interface Representation<D, P extends PD.Params = PD.Params, S extends Representation.State = Representation.State> {
+interface Representation<D, P extends PD.Params = {}, S extends Representation.State = Representation.State> {
    readonly label: string
    readonly updated: Subject<number>
    /** Number of addressable groups in all visuals of the representation */
@@ -191,8 +191,6 @@ namespace Representation {
        substance: Substance
        /** Bit mask of per group clipping applied to the representation's renderobjects */
        clipping: Clipping
-        /** Strength of the representations overpaint, transparency, substance*/
-        themeStrength: { overpaint: number, transparency: number, substance: number }
        /** Controls if the representation's renderobjects are synced automatically with GPU or not */
        syncManually: boolean
        /** A transformation applied to the representation's renderobjects */
@@ -201,20 +199,7 @@ namespace Representation {
        markerActions: MarkerActions
    }
    export function createState(): State {
-        return {
-            visible: true,
-            alphaFactor: 1,
-            pickable: true,
-            colorOnly: false,
-            syncManually: false,
-            transform: Mat4.identity(),
-            overpaint: Overpaint.Empty,
-            transparency: Transparency.Empty,
-            substance: Substance.Empty,
-            clipping: Clipping.Empty,
-            themeStrength: { overpaint: 1, transparency: 1, substance: 1 },
-            markerActions: MarkerActions.All
-        };
+        return { visible: true, alphaFactor: 1, pickable: true, colorOnly: false, syncManually: false, transform: Mat4.identity(), overpaint: Overpaint.Empty, transparency: Transparency.Empty, substance: Substance.Empty, clipping: Clipping.Empty, markerActions: MarkerActions.All };
    }
    export function updateState(state: State, update: Partial<State>) {
        if (update.visible !== undefined) state.visible = update.visible;
@@ -225,7 +210,6 @@ namespace Representation {
        if (update.transparency !== undefined) state.transparency = update.transparency;
        if (update.substance !== undefined) state.substance = update.substance;
        if (update.clipping !== undefined) state.clipping = update.clipping;
-        if (update.themeStrength !== undefined) state.themeStrength = update.themeStrength;
        if (update.syncManually !== undefined) state.syncManually = update.syncManually;
        if (update.transform !== undefined) Mat4.copy(state.transform, update.transform);
        if (update.markerActions !== undefined) state.markerActions = update.markerActions;
@@ -236,7 +220,7 @@ namespace Representation {
    }
    export const StateBuilder: StateBuilder<State> = { create: createState, update: updateState };

-    export type Any<P extends PD.Params = PD.Params, S extends State = State> = Representation<any, P, S>
+    export type Any = Representation<any, any, any>
    export const Empty: Any = {
        label: '', groupCount: 0, renderObjects: [], geometryVersion: -1, props: {}, params: {}, updated: new Subject(), state: createState(), theme: Theme.createEmpty(),
        createOrUpdate: () => Task.constant('', undefined),
@@ -248,7 +232,7 @@ namespace Representation {
        destroy: () => {}
    };

-    export type Def<D, P extends PD.Params = PD.Params, S extends State = State> = { [k: string]: RepresentationFactory<D, P, S> }
+    export type Def<D, P extends PD.Params = {}, S extends State = State> = { [k: string]: RepresentationFactory<D, P, S> }

    export class GeometryState {
        private curr = new Set<number>();
@@ -272,7 +256,7 @@ namespace Representation {
        }
    }

-    export function createMulti<D, P extends PD.Params = PD.Params, S extends State = State>(label: string, ctx: RepresentationContext, getParams: RepresentationParamsGetter<D, P>, stateBuilder: StateBuilder<S>, reprDefs: Def<D, P>): Representation<D, P, S> {
+    export function createMulti<D, P extends PD.Params = {}, S extends State = State>(label: string, ctx: RepresentationContext, getParams: RepresentationParamsGetter<D, P>, stateBuilder: StateBuilder<S>, reprDefs: Def<D, P>): Representation<D, P, S> {
        let version = 0;
        const updated = new Subject<number>();
        const geometryState = new GeometryState();
@@ -448,7 +432,6 @@ namespace Representation {
                if (state.substance !== undefined) {
                    // TODO
                }
-                if (state.themeStrength !== undefined) Visual.setThemeStrength(renderObject, state.themeStrength);
                if (state.transform !== undefined) Visual.setTransform(renderObject, state.transform);

                Representation.updateState(currentState, state);
--- a/src/mol-repr/structure/complex-representation.ts
+++ b/src/mol-repr/structure/complex-representation.ts
@@ -127,7 +127,6 @@ export function ComplexRepresentation<P extends StructureParams>(label: string,
            const remappedClipping = Clipping.remap(state.clipping, _structure);
            visual.setClipping(remappedClipping);
        }
-        if (state.themeStrength !== undefined && visual) visual.setThemeStrength(state.themeStrength);
        if (state.transform !== undefined && visual) visual.setTransform(state.transform);
        if (state.unitTransforms !== undefined && visual) {
            // Since ComplexVisuals always renders geometries between units, the application
--- a/src/mol-repr/structure/complex-visual.ts
+++ b/src/mol-repr/structure/complex-visual.ts
@@ -299,9 +299,6 @@ export function ComplexVisual<G extends Geometry, P extends StructureParams & Ge
        setClipping(clipping: Clipping) {
            Visual.setClipping(renderObject, clipping, lociApply, true);
        },
-        setThemeStrength(strength: { overpaint: number, transparency: number, substance: number }) {
-            Visual.setThemeStrength(renderObject, strength);
-        },
        destroy() {
            dispose?.(geometry);
            if (renderObject) {
--- a/src/mol-repr/structure/representation/molecular-surface.ts
+++ b/src/mol-repr/structure/representation/molecular-surface.ts
@@ -1,13 +1,13 @@
 /**
- * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */

-import { MolecularSurfaceMeshVisual, MolecularSurfaceMeshParams, StructureMolecularSurfaceMeshVisual } from '../visual/molecular-surface-mesh';
+import { MolecularSurfaceMeshVisual, MolecularSurfaceMeshParams } from '../visual/molecular-surface-mesh';
 import { UnitsRepresentation } from '../units-representation';
 import { ParamDefinition as PD } from '../../../mol-util/param-definition';
-import { ComplexRepresentation, StructureRepresentation, StructureRepresentationProvider, StructureRepresentationStateBuilder } from '../representation';
+import { StructureRepresentation, StructureRepresentationProvider, StructureRepresentationStateBuilder } from '../representation';
 import { Representation, RepresentationParamsGetter, RepresentationContext } from '../../../mol-repr/representation';
 import { ThemeRegistryContext } from '../../../mol-theme/theme';
 import { Structure } from '../../../mol-model/structure';
@@ -16,7 +16,6 @@ import { BaseGeometry } from '../../../mol-geo/geometry/base';

 const MolecularSurfaceVisuals = {
    'molecular-surface-mesh': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, MolecularSurfaceMeshParams>) => UnitsRepresentation('Molecular surface mesh', ctx, getParams, MolecularSurfaceMeshVisual),
-    'structure-molecular-surface-mesh': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, MolecularSurfaceMeshParams>) => ComplexRepresentation('Structure Molecular surface mesh', ctx, getParams, StructureMolecularSurfaceMeshVisual),
    'molecular-surface-wireframe': (ctx: RepresentationContext, getParams: RepresentationParamsGetter<Structure, MolecularSurfaceWireframeParams>) => UnitsRepresentation('Molecular surface wireframe', ctx, getParams, MolecularSurfaceWireframeVisual),
 };

--- a/src/mol-repr/structure/units-representation.ts
+++ b/src/mol-repr/structure/units-representation.ts
@@ -222,7 +222,7 @@ export function UnitsRepresentation<P extends StructureParams>(label: string, ct
    }

    function setVisualState(visual: UnitsVisual<P>, group: Unit.SymmetryGroup, state: Partial<StructureRepresentationState>) {
-        const { visible, alphaFactor, pickable, overpaint, transparency, substance, clipping, themeStrength, transform, unitTransforms } = state;
+        const { visible, alphaFactor, pickable, overpaint, transparency, substance, clipping, transform, unitTransforms } = state;

        if (visible !== undefined) visual.setVisibility(visible);
        if (alphaFactor !== undefined) visual.setAlphaFactor(alphaFactor);
@@ -231,7 +231,6 @@ export function UnitsRepresentation<P extends StructureParams>(label: string, ct
        if (transparency !== undefined) visual.setTransparency(transparency, webgl);
        if (substance !== undefined) visual.setSubstance(substance, webgl);
        if (clipping !== undefined) visual.setClipping(clipping);
-        if (themeStrength !== undefined) visual.setThemeStrength(themeStrength);
        if (transform !== undefined) visual.setTransform(transform);
        if (unitTransforms !== undefined) {
            if (unitTransforms) {
@@ -244,7 +243,7 @@ export function UnitsRepresentation<P extends StructureParams>(label: string, ct
    }

    function setState(state: Partial<StructureRepresentationState>) {
-        const { visible, alphaFactor, pickable, overpaint, transparency, substance, clipping, themeStrength, transform, unitTransforms, syncManually, markerActions } = state;
+        const { visible, alphaFactor, pickable, overpaint, transparency, substance, clipping, transform, unitTransforms, syncManually, markerActions } = state;
        const newState: Partial<StructureRepresentationState> = {};

        if (visible !== _state.visible) newState.visible = visible;
@@ -262,7 +261,6 @@ export function UnitsRepresentation<P extends StructureParams>(label: string, ct
        if (clipping !== undefined && _structure) {
            newState.clipping = Clipping.remap(clipping, _structure);
        }
-        if (themeStrength !== undefined) newState.themeStrength = themeStrength;
        if (transform !== undefined && !Mat4.areEqual(transform, _state.transform, EPSILON)) {
            newState.transform = transform;
        }
--- a/src/mol-repr/structure/units-visual.ts
+++ b/src/mol-repr/structure/units-visual.ts
@@ -381,9 +381,6 @@ export function UnitsVisual<G extends Geometry, P extends StructureParams & Geom
        setClipping(clipping: Clipping) {
            Visual.setClipping(renderObject, clipping, lociApply, true);
        },
-        setThemeStrength(strength: { overpaint: number, transparency: number, substance: number }) {
-            Visual.setThemeStrength(renderObject, strength);
-        },
        destroy() {
            dispose?.(geometry);
            if (renderObject) {
--- a/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts
+++ b/src/mol-repr/structure/visual/bond-inter-unit-cylinder.ts
@@ -222,7 +222,6 @@ export function InterUnitBondCylinderImpostorVisual(materialId: number): Complex
                newProps.linkScale !== currentProps.linkScale ||
                newProps.linkSpacing !== currentProps.linkSpacing ||
                newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
-                newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens ||
                newProps.linkCap !== currentProps.linkCap ||
                newProps.aromaticScale !== currentProps.aromaticScale ||
                newProps.aromaticSpacing !== currentProps.aromaticSpacing ||
@@ -265,7 +264,6 @@ export function InterUnitBondCylinderMeshVisual(materialId: number): ComplexVisu
                newProps.linkScale !== currentProps.linkScale ||
                newProps.linkSpacing !== currentProps.linkSpacing ||
                newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
-                newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens ||
                newProps.linkCap !== currentProps.linkCap ||
                newProps.aromaticScale !== currentProps.aromaticScale ||
                newProps.aromaticSpacing !== currentProps.aromaticSpacing ||
--- a/src/mol-repr/structure/visual/bond-inter-unit-line.ts
+++ b/src/mol-repr/structure/visual/bond-inter-unit-line.ts
@@ -138,7 +138,6 @@ export function InterUnitBondLineVisual(materialId: number): ComplexVisual<Inter
                newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
                newProps.dashCount !== currentProps.dashCount ||
                newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
-                newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens ||
                !arrayEqual(newProps.includeTypes, currentProps.includeTypes) ||
                !arrayEqual(newProps.excludeTypes, currentProps.excludeTypes) ||
                newProps.multipleBonds !== currentProps.multipleBonds
--- a/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
+++ b/src/mol-repr/structure/visual/bond-intra-unit-cylinder.ts
@@ -239,7 +239,6 @@ export function IntraUnitBondCylinderImpostorVisual(materialId: number): UnitsVi
                newProps.linkScale !== currentProps.linkScale ||
                newProps.linkSpacing !== currentProps.linkSpacing ||
                newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
-                newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens ||
                newProps.linkCap !== currentProps.linkCap ||
                newProps.aromaticScale !== currentProps.aromaticScale ||
                newProps.aromaticSpacing !== currentProps.aromaticSpacing ||
@@ -287,7 +286,6 @@ export function IntraUnitBondCylinderMeshVisual(materialId: number): UnitsVisual
                newProps.linkScale !== currentProps.linkScale ||
                newProps.linkSpacing !== currentProps.linkSpacing ||
                newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
-                newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens ||
                newProps.linkCap !== currentProps.linkCap ||
                newProps.aromaticScale !== currentProps.aromaticScale ||
                newProps.aromaticSpacing !== currentProps.aromaticSpacing ||
--- a/src/mol-repr/structure/visual/bond-intra-unit-line.ts
+++ b/src/mol-repr/structure/visual/bond-intra-unit-line.ts
@@ -164,7 +164,6 @@ export function IntraUnitBondLineVisual(materialId: number): UnitsVisual<IntraUn
                newProps.aromaticDashCount !== currentProps.aromaticDashCount ||
                newProps.dashCount !== currentProps.dashCount ||
                newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
-                newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens ||
                !arrayEqual(newProps.includeTypes, currentProps.includeTypes) ||
                !arrayEqual(newProps.excludeTypes, currentProps.excludeTypes) ||
                newProps.aromaticBonds !== currentProps.aromaticBonds ||
--- a/src/mol-repr/structure/visual/element-cross.ts
+++ b/src/mol-repr/structure/visual/element-cross.ts
@@ -27,7 +27,6 @@ export const ElementCrossParams = {
    ...UnitsLinesParams,
    lineSizeAttenuation: PD.Boolean(false),
    ignoreHydrogens: PD.Boolean(false),
-    onlyPolarHydrogens: PD.Boolean(false),
    traceOnly: PD.Boolean(false),
    crosses: PD.Select('lone', PD.arrayToOptions(['lone', 'all'] as const)),
    crossSize: PD.Numeric(0.35, { min: 0, max: 2, step: 0.01 }),
@@ -86,7 +85,6 @@ export function ElementCrossVisual(materialId: number): UnitsVisual<ElementCross
        setUpdateState: (state: VisualUpdateState, newProps: PD.Values<ElementCrossParams>, currentProps: PD.Values<ElementCrossParams>) => {
            state.createGeometry = (
                newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
-                newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens ||
                newProps.traceOnly !== currentProps.traceOnly ||
                newProps.crosses !== currentProps.crosses ||
                newProps.crossSize !== currentProps.crossSize
--- a/src/mol-repr/structure/visual/element-point.ts
+++ b/src/mol-repr/structure/visual/element-point.ts
@@ -23,7 +23,6 @@ export const ElementPointParams = {
    ...UnitsPointsParams,
    pointSizeAttenuation: PD.Boolean(false),
    ignoreHydrogens: PD.Boolean(false),
-    onlyPolarHydrogens: PD.Boolean(false),
    traceOnly: PD.Boolean(false),
 };
 export type ElementPointParams = typeof ElementPointParams
@@ -90,7 +89,6 @@ export function ElementPointVisual(materialId: number): UnitsVisual<ElementPoint
        setUpdateState: (state: VisualUpdateState, newProps: PD.Values<ElementPointParams>, currentProps: PD.Values<ElementPointParams>) => {
            state.createGeometry = (
                newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
-                newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens ||
                newProps.traceOnly !== currentProps.traceOnly
            );
        }
--- a/src/mol-repr/structure/visual/element-sphere.ts
+++ b/src/mol-repr/structure/visual/element-sphere.ts
@@ -20,7 +20,6 @@ export const ElementSphereParams = {
    sizeFactor: PD.Numeric(1, { min: 0, max: 10, step: 0.1 }),
    detail: PD.Numeric(0, { min: 0, max: 3, step: 1 }, BaseGeometry.CustomQualityParamInfo),
    ignoreHydrogens: PD.Boolean(false),
-    onlyPolarHydrogens: PD.Boolean(false),
    traceOnly: PD.Boolean(false),
    tryUseImpostor: PD.Boolean(true),
 };
@@ -42,7 +41,6 @@ export function ElementSphereImpostorVisual(materialId: number): UnitsVisual<Ele
        setUpdateState: (state: VisualUpdateState, newProps: PD.Values<ElementSphereParams>, currentProps: PD.Values<ElementSphereParams>) => {
            state.createGeometry = (
                newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
-                newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens ||
                newProps.traceOnly !== currentProps.traceOnly
            );
        },
@@ -64,7 +62,6 @@ export function ElementSphereMeshVisual(materialId: number): UnitsVisual<Element
                newProps.sizeFactor !== currentProps.sizeFactor ||
                newProps.detail !== currentProps.detail ||
                newProps.ignoreHydrogens !== currentProps.ignoreHydrogens ||
-                newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens ||
                newProps.traceOnly !== currentProps.traceOnly
            );
        },
--- a/src/mol-repr/structure/visual/gaussian-density-volume.ts
+++ b/src/mol-repr/structure/visual/gaussian-density-volume.ts
@@ -43,7 +43,6 @@ export const GaussianDensityVolumeParams = {
    ...ComplexDirectVolumeParams,
    ...GaussianDensityParams,
    ignoreHydrogens: PD.Boolean(false),
-    onlyPolarHydrogens: PD.Boolean(false),
    includeParent: PD.Boolean(false, { isHidden: true }),
 };
 export type GaussianDensityVolumeParams = typeof GaussianDensityVolumeParams
@@ -60,7 +59,6 @@ export function GaussianDensityVolumeVisual(materialId: number): ComplexVisual<G
            if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true;
            if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true;
            if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true;
-            if (newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens) state.createGeometry = true;
            if (newProps.traceOnly !== currentProps.traceOnly) state.createGeometry = true;
            if (newProps.includeParent !== currentProps.includeParent) state.createGeometry = true;
        },
@@ -101,7 +99,6 @@ export const UnitsGaussianDensityVolumeParams = {
    ...UnitsDirectVolumeParams,
    ...GaussianDensityParams,
    ignoreHydrogens: PD.Boolean(false),
-    onlyPolarHydrogens: PD.Boolean(false),
    includeParent: PD.Boolean(false, { isHidden: true }),
 };
 export type UnitsGaussianDensityVolumeParams = typeof UnitsGaussianDensityVolumeParams
@@ -118,7 +115,6 @@ export function UnitsGaussianDensityVolumeVisual(materialId: number): UnitsVisua
            if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true;
            if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true;
            if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true;
-            if (newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens) state.createGeometry = true;
            if (newProps.traceOnly !== currentProps.traceOnly) state.createGeometry = true;
            if (newProps.includeParent !== currentProps.includeParent) state.createGeometry = true;
        },
--- a/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
+++ b/src/mol-repr/structure/visual/gaussian-surface-mesh.ts
@@ -34,7 +34,6 @@ const SharedParams = {
    ...GaussianDensityParams,
    ...ColorSmoothingParams,
    ignoreHydrogens: PD.Boolean(false),
-    onlyPolarHydrogens: PD.Boolean(false),
    tryUseGpu: PD.Boolean(true),
    includeParent: PD.Boolean(false, { isHidden: true }),
 };
@@ -128,7 +127,6 @@ export function GaussianSurfaceMeshVisual(materialId: number): UnitsVisual<Gauss
            if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true;
            if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true;
            if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true;
-            if (newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens) state.createGeometry = true;
            if (newProps.traceOnly !== currentProps.traceOnly) state.createGeometry = true;
            if (newProps.includeParent !== currentProps.includeParent) state.createGeometry = true;
            if (newProps.smoothColors.name !== currentProps.smoothColors.name) {
@@ -195,7 +193,6 @@ export function StructureGaussianSurfaceMeshVisual(materialId: number): ComplexV
            if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true;
            if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true;
            if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true;
-            if (newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens) state.createGeometry = true;
            if (newProps.traceOnly !== currentProps.traceOnly) state.createGeometry = true;
            if (newProps.smoothColors.name !== currentProps.smoothColors.name) {
                state.updateColor = true;
@@ -250,7 +247,6 @@ async function createGaussianSurfaceTextureMesh(ctx: VisualContext, unit: Unit,
    const boundingSphere = Sphere3D.expand(Sphere3D(), unit.boundary.sphere, densityTextureData.maxRadius);
    const surface = TextureMesh.create(gv.vertexCount, groupCount, gv.vertexTexture, gv.groupTexture, gv.normalTexture, boundingSphere, textureMesh);
    (surface.meta as GaussianSurfaceMeta).resolution = densityTextureData.resolution;
-    surface.meta.webgl = ctx.webgl;

    return surface;
 }
@@ -267,7 +263,6 @@ export function GaussianSurfaceTextureMeshVisual(materialId: number): UnitsVisua
            if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true;
            if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true;
            if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true;
-            if (newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens) state.createGeometry = true;
            if (newProps.traceOnly !== currentProps.traceOnly) state.createGeometry = true;
            if (newProps.includeParent !== currentProps.includeParent) state.createGeometry = true;
            if (newProps.smoothColors.name !== currentProps.smoothColors.name) {
@@ -326,7 +321,6 @@ async function createStructureGaussianSurfaceTextureMesh(ctx: VisualContext, str
    const boundingSphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, densityTextureData.maxRadius);
    const surface = TextureMesh.create(gv.vertexCount, groupCount, gv.vertexTexture, gv.groupTexture, gv.normalTexture, boundingSphere, textureMesh);
    (surface.meta as GaussianSurfaceMeta).resolution = densityTextureData.resolution;
-    surface.meta.webgl = ctx.webgl;

    return surface;
 }
@@ -343,7 +337,6 @@ export function StructureGaussianSurfaceTextureMeshVisual(materialId: number): C
            if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true;
            if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true;
            if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true;
-            if (newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens) state.createGeometry = true;
            if (newProps.traceOnly !== currentProps.traceOnly) state.createGeometry = true;
            if (newProps.includeParent !== currentProps.includeParent) state.createGeometry = true;
            if (newProps.smoothColors.name !== currentProps.smoothColors.name) {
--- a/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
+++ b/src/mol-repr/structure/visual/gaussian-surface-wireframe.ts
@@ -41,7 +41,6 @@ export const GaussianWireframeParams = {
    sizeFactor: PD.Numeric(3, { min: 0, max: 10, step: 0.1 }),
    lineSizeAttenuation: PD.Boolean(false),
    ignoreHydrogens: PD.Boolean(false),
-    onlyPolarHydrogens: PD.Boolean(false),
    includeParent: PD.Boolean(false, { isHidden: true }),
 };
 export type GaussianWireframeParams = typeof GaussianWireframeParams
@@ -58,7 +57,6 @@ export function GaussianWireframeVisual(materialId: number): UnitsVisual<Gaussia
            if (newProps.radiusOffset !== currentProps.radiusOffset) state.createGeometry = true;
            if (newProps.smoothness !== currentProps.smoothness) state.createGeometry = true;
            if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true;
-            if (newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens) state.createGeometry = true;
            if (newProps.traceOnly !== currentProps.traceOnly) state.createGeometry = true;
            if (newProps.includeParent !== currentProps.includeParent) state.createGeometry = true;
        }
--- a/src/mol-repr/structure/visual/molecular-surface-mesh.ts
+++ b/src/mol-repr/structure/visual/molecular-surface-mesh.ts
@@ -11,9 +11,9 @@ import { VisualContext } from '../../visual';
 import { Unit, Structure } from '../../../mol-model/structure';
 import { Theme } from '../../../mol-theme/theme';
 import { Mesh } from '../../../mol-geo/geometry/mesh/mesh';
-import { computeStructureMolecularSurface, computeUnitMolecularSurface } from './util/molecular-surface';
+import { computeUnitMolecularSurface } from './util/molecular-surface';
 import { computeMarchingCubesMesh } from '../../../mol-geo/util/marching-cubes/algorithm';
-import { ElementIterator, getElementLoci, eachElement, getSerialElementLoci, eachSerialElement } from './util/element';
+import { ElementIterator, getElementLoci, eachElement } from './util/element';
 import { VisualUpdateState } from '../../util';
 import { CommonSurfaceParams } from './util/common';
 import { Sphere3D } from '../../../mol-math/geometry';
@@ -23,7 +23,6 @@ import { WebGLContext } from '../../../mol-gl/webgl/context';
 import { applyMeshColorSmoothing } from '../../../mol-geo/geometry/mesh/color-smoothing';
 import { ColorSmoothingParams, getColorSmoothingProps } from '../../../mol-geo/geometry/base';
 import { ValueCell } from '../../../mol-util';
-import { ComplexMeshVisual, ComplexVisual } from '../complex-visual';

 export const MolecularSurfaceMeshParams = {
    ...UnitsMeshParams,
@@ -83,76 +82,6 @@ export function MolecularSurfaceMeshVisual(materialId: number): UnitsVisual<Mole
            if (newProps.probeRadius !== currentProps.probeRadius) state.createGeometry = true;
            if (newProps.probePositions !== currentProps.probePositions) state.createGeometry = true;
            if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true;
-            if (newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens) state.createGeometry = true;
-            if (newProps.traceOnly !== currentProps.traceOnly) state.createGeometry = true;
-            if (newProps.includeParent !== currentProps.includeParent) state.createGeometry = true;
-
-            if (newProps.smoothColors.name !== currentProps.smoothColors.name) {
-                state.updateColor = true;
-            } else if (newProps.smoothColors.name === 'on' && currentProps.smoothColors.name === 'on') {
-                if (newProps.smoothColors.params.resolutionFactor !== currentProps.smoothColors.params.resolutionFactor) state.updateColor = true;
-                if (newProps.smoothColors.params.sampleStride !== currentProps.smoothColors.params.sampleStride) state.updateColor = true;
-            }
-        },
-        processValues: (values: MeshValues, geometry: Mesh, props: PD.Values<MolecularSurfaceMeshParams>, theme: Theme, webgl?: WebGLContext) => {
-            const { resolution, colorTexture } = geometry.meta as MolecularSurfaceMeta;
-            const csp = getColorSmoothingProps(props.smoothColors, theme.color.preferSmoothing, resolution);
-            if (csp) {
-                applyMeshColorSmoothing(values, csp.resolution, csp.stride, webgl, colorTexture);
-                (geometry.meta as MolecularSurfaceMeta).colorTexture = values.tColorGrid.ref.value;
-            }
-        },
-        dispose: (geometry: Mesh) => {
-            (geometry.meta as MolecularSurfaceMeta).colorTexture?.destroy();
-        }
-    }, materialId);
-}
-
-//
-
-async function createStructureMolecularSurfaceMesh(ctx: VisualContext, structure: Structure, theme: Theme, props: MolecularSurfaceMeshProps, mesh?: Mesh): Promise<Mesh> {
-    const { transform, field, idField, resolution, maxRadius } = await computeStructureMolecularSurface(structure, theme.size, props).runInContext(ctx.runtime);
-
-    const params = {
-        isoLevel: props.probeRadius,
-        scalarField: field,
-        idField
-    };
-    const surface = await computeMarchingCubesMesh(params, mesh).runAsChild(ctx.runtime);
-
-    if (props.includeParent) {
-        const iterations = Math.ceil(2 / props.resolution);
-        Mesh.smoothEdges(surface, { iterations, maxNewEdgeLength: Math.sqrt(2) });
-    }
-
-    Mesh.transform(surface, transform);
-    if (ctx.webgl && !ctx.webgl.isWebGL2) {
-        Mesh.uniformTriangleGroup(surface);
-        ValueCell.updateIfChanged(surface.varyingGroup, false);
-    } else {
-        ValueCell.updateIfChanged(surface.varyingGroup, true);
-    }
-
-    const sphere = Sphere3D.expand(Sphere3D(), structure.boundary.sphere, maxRadius);
-    surface.setBoundingSphere(sphere);
-    (surface.meta as MolecularSurfaceMeta).resolution = resolution;
-
-    return surface;
-}
-
-export function StructureMolecularSurfaceMeshVisual(materialId: number): ComplexVisual<MolecularSurfaceMeshParams> {
-    return ComplexMeshVisual<MolecularSurfaceMeshParams>({
-        defaultProps: PD.getDefaultValues(MolecularSurfaceMeshParams),
-        createGeometry: createStructureMolecularSurfaceMesh,
-        createLocationIterator: ElementIterator.fromStructure,
-        getLoci: getSerialElementLoci,
-        eachLocation: eachSerialElement,
-        setUpdateState: (state: VisualUpdateState, newProps: PD.Values<MolecularSurfaceMeshParams>, currentProps: PD.Values<MolecularSurfaceMeshParams>) => {
-            if (newProps.resolution !== currentProps.resolution) state.createGeometry = true;
-            if (newProps.probeRadius !== currentProps.probeRadius) state.createGeometry = true;
-            if (newProps.probePositions !== currentProps.probePositions) state.createGeometry = true;
-            if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true;
-            if (newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens) state.createGeometry = true;
            if (newProps.traceOnly !== currentProps.traceOnly) state.createGeometry = true;
            if (newProps.includeParent !== currentProps.includeParent) state.createGeometry = true;

--- a/src/mol-repr/structure/visual/molecular-surface-wireframe.ts
+++ b/src/mol-repr/structure/visual/molecular-surface-wireframe.ts
@@ -57,7 +57,6 @@ export function MolecularSurfaceWireframeVisual(materialId: number): UnitsVisual
            if (newProps.probeRadius !== currentProps.probeRadius) state.createGeometry = true;
            if (newProps.probePositions !== currentProps.probePositions) state.createGeometry = true;
            if (newProps.ignoreHydrogens !== currentProps.ignoreHydrogens) state.createGeometry = true;
-            if (newProps.onlyPolarHydrogens !== currentProps.onlyPolarHydrogens) state.createGeometry = true;
            if (newProps.includeParent !== currentProps.includeParent) state.createGeometry = true;
        }
    }, materialId);
--- a/src/mol-repr/structure/visual/util/bond.ts
+++ b/src/mol-repr/structure/visual/util/bond.ts
@@ -2,7 +2,6 @@
 * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author David Sehnal <david.sehnal@gmail.com>
 */

 import { BondType } from '../../../../mol-model/structure/model/types';
@@ -15,13 +14,11 @@ import { PickingId } from '../../../../mol-geo/geometry/picking';
 import { EmptyLoci, Loci } from '../../../../mol-model/loci';
 import { Interval, OrderedSet, SortedArray } from '../../../../mol-data/int';
 import { isH, isHydrogen, StructureGroup } from './common';
-import { hasPolarNeighbour } from '../../../../mol-model-props/computed/chemistry/functional-group';

 export const BondParams = {
    includeTypes: PD.MultiSelect(ObjectKeys(BondType.Names), PD.objectToOptions(BondType.Names)),
    excludeTypes: PD.MultiSelect([] as BondType.Names[], PD.objectToOptions(BondType.Names)),
    ignoreHydrogens: PD.Boolean(false),
-    onlyPolarHydrogens: PD.Boolean(false),
    aromaticBonds: PD.Boolean(true, { description: 'Display aromatic bonds with dashes' }),
    multipleBonds: PD.Select('symmetric', PD.arrayToOptions(['off', 'symmetric', 'offset'] as const)),
 };
@@ -54,7 +51,7 @@ export function makeIntraBondIgnoreTest(structure: Structure, unit: Unit.Atomic,
    const { a, b, edgeProps } = bonds;
    const { flags: _flags } = edgeProps;

-    const { ignoreHydrogens, onlyPolarHydrogens, includeTypes, excludeTypes } = props;
+    const { ignoreHydrogens, includeTypes, excludeTypes } = props;

    const include = BondType.fromNames(includeTypes);
    const exclude = BondType.fromNames(excludeTypes);
@@ -64,31 +61,14 @@ export function makeIntraBondIgnoreTest(structure: Structure, unit: Unit.Atomic,
    const childUnit = child?.unitMap.get(unit.id);
    if (child && !childUnit) throw new Error('expected childUnit to exist if child exists');

-    if (allBondTypes && !onlyPolarHydrogens && !ignoreHydrogens && !child) return;
+    if (allBondTypes && !ignoreHydrogens && !child) return;

    return (edgeIndex: number) => {
-        const aI = a[edgeIndex];
-        const bI = b[edgeIndex];
-
-        if ((!!childUnit && !SortedArray.has(childUnit.elements, elements[aI]))) {
-            return true;
-        }
-
-        if (!allBondTypes && ignoreBondType(include, exclude, _flags[edgeIndex])) {
-            return true;
-        }
-
-        if (!ignoreHydrogens && !onlyPolarHydrogens) return false;
-        if (isH(atomicNumber, elements[aI])) {
-            if (ignoreHydrogens) return true;
-            if (onlyPolarHydrogens && !hasPolarNeighbour(structure, unit, aI)) return true;
-        }
-        if (isH(atomicNumber, elements[bI])) {
-            if (ignoreHydrogens) return true;
-            if (onlyPolarHydrogens && !hasPolarNeighbour(structure, unit, bI)) return true;
-        }
-
-        return false;
+        return (
+            (!!childUnit && !SortedArray.has(childUnit.elements, elements[a[edgeIndex]])) ||
+            (ignoreHydrogens && (isH(atomicNumber, elements[a[edgeIndex]]) || isH(atomicNumber, elements[b[edgeIndex]]))) ||
+            (!allBondTypes && ignoreBondType(include, exclude, _flags[edgeIndex]))
+        );
    };
 }

@@ -96,7 +76,7 @@ export function makeInterBondIgnoreTest(structure: Structure, props: BondProps):
    const bonds = structure.interUnitBonds;
    const { edges } = bonds;

-    const { ignoreHydrogens, onlyPolarHydrogens, includeTypes, excludeTypes } = props;
+    const { ignoreHydrogens, includeTypes, excludeTypes } = props;

    const include = BondType.fromNames(includeTypes);
    const exclude = BondType.fromNames(excludeTypes);
@@ -104,7 +84,7 @@ export function makeInterBondIgnoreTest(structure: Structure, props: BondProps):

    const { child } = structure;

-    if (allBondTypes && !onlyPolarHydrogens && !ignoreHydrogens && !child) return;
+    if (allBondTypes && !ignoreHydrogens && !child) return;

    return (edgeIndex: number) => {
        if (child) {
@@ -124,18 +104,6 @@ export function makeInterBondIgnoreTest(structure: Structure, props: BondProps):
            if (isHydrogen(uA, uA.elements[b.indexA]) || isHydrogen(uB, uB.elements[b.indexB])) return true;
        }

-        if (onlyPolarHydrogens) {
-            const b = edges[edgeIndex];
-            const uA = structure.unitMap.get(b.unitA);
-            if (isHydrogen(uA, uA.elements[b.indexA]) && !hasPolarNeighbour(structure, uA as Unit.Atomic, b.indexA)) {
-                return true;
-            }
-            const uB = structure.unitMap.get(b.unitB);
-            if (isHydrogen(uB, uB.elements[b.indexB]) && !hasPolarNeighbour(structure, uB as Unit.Atomic, b.indexB)) {
-                return true;
-            }
-        }
-
        if (!allBondTypes) {
            if (ignoreBondType(include, exclude, edges[edgeIndex].props.flag)) return true;
        }
--- a/src/mol-repr/structure/visual/util/common.ts
+++ b/src/mol-repr/structure/visual/util/common.ts
@@ -2,7 +2,6 @@
 * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
- * @author David Sehnal <david.sehnal@gmail.com>
 */

 import { Unit, Structure, ElementIndex, StructureElement, ResidueIndex } from '../../../../mol-model/structure';
@@ -17,7 +16,6 @@ import { AssignableArrayLike } from '../../../../mol-util/type-helpers';
 import { getBoundary } from '../../../../mol-math/geometry/boundary';
 import { Box3D } from '../../../../mol-math/geometry';
 import { SizeTheme } from '../../../../mol-theme/size';
-import { hasPolarNeighbour } from '../../../../mol-model-props/computed/chemistry/functional-group';

 /** Return a Loci for the elements of a whole residue the elementIndex belongs to. */
 export function getResidueLoci(structure: Structure, unit: Unit.Atomic, elementIndex: ElementIndex): Loci {
@@ -141,7 +139,6 @@ export function getConformation(unit: Unit) {

 export const CommonSurfaceParams = {
    ignoreHydrogens: PD.Boolean(false, { description: 'Whether or not to include hydrogen atoms in the surface calculation.' }),
-    onlyPolarHydrogens: PD.Boolean(false, { description: 'Whether or not to include polar hydrogen atoms in the surface calculation.' }),
    traceOnly: PD.Boolean(false, { description: 'Whether or not to only use trace atoms in the surface calculation.' }),
    includeParent: PD.Boolean(false, { description: 'Include elements of the parent structure in surface calculation to get a surface patch of the current structure.' }),
 };
@@ -154,7 +151,7 @@ function squaredDistance(x: number, y: number, z: number, center: Vec3) {
 }

 /** marks `indices` for filtering/ignoring in `id` when not in `elements` */
-function filterUnitId(id: AssignableArrayLike<number>, elements: SortedArray, indices: SortedArray) {
+function filterId(id: AssignableArrayLike<number>, elements: SortedArray, indices: SortedArray) {
    let start = 0;
    const end = elements.length;
    for (let i = 0, il = indices.length; i < il; ++i) {
@@ -169,28 +166,26 @@ function filterUnitId(id: AssignableArrayLike<number>, elements: SortedArray, in
 }

 export function getUnitConformationAndRadius(structure: Structure, unit: Unit, sizeTheme: SizeTheme<any>, props: CommonSurfaceProps) {
-    const { ignoreHydrogens, onlyPolarHydrogens, traceOnly, includeParent } = props;
+    const { ignoreHydrogens, traceOnly, includeParent } = props;
    const rootUnit = includeParent ? structure.root.unitMap.get(unit.id) : unit;
-    const differentRoot = includeParent && rootUnit !== unit;

    const { x, y, z } = getConformation(rootUnit);
    const { elements } = rootUnit;
    const { center, radius: sphereRadius } = unit.boundary.sphere;
-    const extraRadius = (4 + 1.5) * 2; // TODO should be twice (the max vdW/sphere radius plus the probe radius)
+    const extraRadius = (2 + 1.5) * 2; // TODO should be twice (the max vdW/sphere radius plus the probe radius)
    const radiusSq = (sphereRadius + extraRadius) * (sphereRadius + extraRadius);

    let indices: SortedArray<ElementIndex>;
    let id: AssignableArrayLike<number>;

-    if (ignoreHydrogens || onlyPolarHydrogens || traceOnly || differentRoot) {
-        const _indices: number[] = [];
-        const _id: number[] = [];
+    if (ignoreHydrogens || traceOnly || (includeParent && rootUnit !== unit)) {
+        const _indices = [];
+        const _id = [];
        for (let i = 0, il = elements.length; i < il; ++i) {
            const eI = elements[i];
            if (ignoreHydrogens && isHydrogen(rootUnit, eI)) continue;
-            if (onlyPolarHydrogens && isHydrogen(rootUnit, eI) && Unit.isAtomic(rootUnit) && !hasPolarNeighbour(structure, rootUnit, SortedArray.indexOf(rootUnit.elements, eI) as StructureElement.UnitIndex)) continue;
            if (traceOnly && !isTrace(rootUnit, eI)) continue;
-            if (differentRoot && squaredDistance(x[eI], y[eI], z[eI], center) > radiusSq) continue;
+            if (includeParent && squaredDistance(x[eI], y[eI], z[eI], center) > radiusSq) continue;

            _indices.push(eI);
            _id.push(i);
@@ -203,11 +198,11 @@ export function getUnitConformationAndRadius(structure: Structure, unit: Unit, s
    }

    if (includeParent && rootUnit !== unit) {
-        filterUnitId(id, unit.elements, indices);
+        filterId(id, unit.elements, indices);
    }

    const position = { indices, x, y, z, id };
-    const boundary = differentRoot ? getBoundary(position) : unit.boundary;
+    const boundary = unit === rootUnit ? unit.boundary : getBoundary(position);

    const l = StructureElement.Location.create(structure, rootUnit);
    const radius = (index: number) => {
@@ -218,68 +213,43 @@ export function getUnitConformationAndRadius(structure: Structure, unit: Unit, s
    return { position, boundary, radius };
 }

-export function getStructureConformationAndRadius(structure: Structure, sizeTheme: SizeTheme<any>, props: CommonSurfaceProps) {
-    const { ignoreHydrogens, onlyPolarHydrogens, traceOnly, includeParent } = props;
-    const differentRoot = includeParent && !!structure.parent;
-    const l = StructureElement.Location.create(structure.root);
-
-    const { center, radius: sphereRadius } = structure.boundary.sphere;
-    const extraRadius = (4 + 1.5) * 2; // TODO should be twice (the max vdW/sphere radius plus the probe radius)
-    const radiusSq = (sphereRadius + extraRadius) * (sphereRadius + extraRadius);
+export function getStructureConformationAndRadius(structure: Structure, sizeTheme: SizeTheme<any>, ignoreHydrogens: boolean, traceOnly: boolean) {
+    const l = StructureElement.Location.create(structure);

    let xs: ArrayLike<number>;
    let ys: ArrayLike<number>;
    let zs: ArrayLike<number>;
    let rs: ArrayLike<number>;
-    let id: AssignableArrayLike<number>;
-    let indices: OrderedSet<number>;
-
-    if (ignoreHydrogens || onlyPolarHydrogens || traceOnly || differentRoot) {
-        const { getSerialIndex } = structure.serialMapping;
-        const units = differentRoot ? structure.root.units : structure.units;
+    let id: ArrayLike<number>;

+    if (ignoreHydrogens || traceOnly) {
        const _xs: number[] = [];
        const _ys: number[] = [];
        const _zs: number[] = [];
        const _rs: number[] = [];
        const _id: number[] = [];
-        for (let i = 0, il = units.length; i < il; ++i) {
-            const unit = units[i];
+        for (let i = 0, m = 0, il = structure.units.length; i < il; ++i) {
+            const unit = structure.units[i];
            const { elements } = unit;
            const { x, y, z } = unit.conformation;
-            const childUnit = structure.unitMap.get(unit.id);

            l.unit = unit;
            for (let j = 0, jl = elements.length; j < jl; ++j) {
                const eI = elements[j];
                if (ignoreHydrogens && isHydrogen(unit, eI)) continue;
-                if (onlyPolarHydrogens && isHydrogen(unit, eI) && Unit.isAtomic(unit) && !hasPolarNeighbour(structure, unit, SortedArray.indexOf(unit.elements, eI) as StructureElement.UnitIndex)) continue;
                if (traceOnly && !isTrace(unit, eI)) continue;

-                const _x = x(eI), _y = y(eI), _z = z(eI);
-                if (differentRoot && squaredDistance(_x, _y, _z, center) > radiusSq) continue;
-
-                _xs.push(_x);
-                _ys.push(_y);
-                _zs.push(_z);
+                _xs.push(x(eI));
+                _ys.push(y(eI));
+                _zs.push(z(eI));
                l.element = eI;
                _rs.push(sizeTheme.size(l));
-
-                if (differentRoot) {
-                    const idx = childUnit ? SortedArray.indexOf(childUnit.elements, eI) : -1;
-                    if (idx === -1) {
-                        _id.push(-2); // mark for filtering/ignoring when not in `elements`
-                    } else {
-                        _id.push(getSerialIndex(childUnit, eI));
-                    }
-                } else {
-                    _id.push(getSerialIndex(unit, eI));
-                }
+                _id.push(m + j);
            }
+            m += elements.length;
        }
        xs = _xs, ys = _ys, zs = _zs, rs = _rs;
        id = _id;
-        indices = OrderedSet.ofRange(0, id.length);
    } else {
        const { elementCount } = structure;
        const _xs = new Float32Array(elementCount);
@@ -305,14 +275,12 @@ export function getStructureConformationAndRadius(structure: Structure, sizeThem
        }
        xs = _xs, ys = _ys, zs = _zs, rs = _rs;
        id = fillSerial(new Uint32Array(elementCount));
-        indices = OrderedSet.ofRange(0, id.length);
    }

-    const position = { indices, x: xs, y: ys, z: zs, id };
-    const boundary = differentRoot ? getBoundary(position) : structure.boundary;
+    const position = { indices: OrderedSet.ofRange(0, id.length), x: xs, y: ys, z: zs, id };
    const radius = (index: number) => rs[index];

-    return { position, boundary, radius };
+    return { position, radius };
 }

 const _H = AtomicNumbers['H'];
--- a/src/mol-repr/structure/visual/util/element.ts
+++ b/src/mol-repr/structure/visual/util/element.ts
@@ -21,14 +21,12 @@ import { Spheres } from '../../../../mol-geo/geometry/spheres/spheres';
 import { SpheresBuilder } from '../../../../mol-geo/geometry/spheres/spheres-builder';
 import { isTrace, isH, StructureGroup } from './common';
 import { Sphere3D } from '../../../../mol-math/geometry';
-import { hasPolarNeighbour } from '../../../../mol-model-props/computed/chemistry/functional-group';

 // avoiding namespace lookup improved performance in Chrome (Aug 2020)
 const v3add = Vec3.add;

 type ElementProps = {
    ignoreHydrogens: boolean,
-    onlyPolarHydrogens: boolean,
    traceOnly: boolean,
 }

@@ -38,7 +36,7 @@ export type ElementSphereMeshProps = {
 } & ElementProps

 export function makeElementIgnoreTest(structure: Structure, unit: Unit, props: ElementProps): undefined | ((i: ElementIndex) => boolean) {
-    const { ignoreHydrogens, onlyPolarHydrogens, traceOnly } = props;
+    const { ignoreHydrogens, traceOnly } = props;

    const { atomicNumber } = unit.model.atomicHierarchy.derived.atom;
    const isCoarse = Unit.isCoarse(unit);
@@ -47,26 +45,14 @@ export function makeElementIgnoreTest(structure: Structure, unit: Unit, props: E
    const childUnit = child?.unitMap.get(unit.id);
    if (child && !childUnit) throw new Error('expected childUnit to exist if child exists');

-    if (!child && !ignoreHydrogens && !traceOnly && !onlyPolarHydrogens) return;
+    if (!child && !ignoreHydrogens && !traceOnly) return;

    return (element: ElementIndex) => {
-        if (!!childUnit && !SortedArray.has(childUnit.elements, element)) {
-            return true;
-        }
-
-        if (traceOnly && !isTrace(unit, element)) {
-            return true;
-        }
-
-        if (isCoarse) return false;
-
-        if (!isH(atomicNumber, element)) return false;
-        if (ignoreHydrogens) return true;
-        if (onlyPolarHydrogens) {
-            return !hasPolarNeighbour(structure, unit, SortedArray.indexOf(unit.elements, element) as StructureElement.UnitIndex);
-        }
-
-        return false;
+        return (
+            (!!childUnit && !SortedArray.has(childUnit.elements, element)) ||
+            (!isCoarse && ignoreHydrogens && isH(atomicNumber, element)) ||
+            (traceOnly && !isTrace(unit, element))
+        );
    };
 }

--- a/src/mol-repr/structure/visual/util/gaussian.ts
+++ b/src/mol-repr/structure/visual/util/gaussian.ts
@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2022 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>
 */
@@ -34,51 +34,56 @@ export function getTextureMaxCells(webgl: WebGLContext, structure?: Structure) {
 //

 export function computeUnitGaussianDensity(structure: Structure, unit: Unit, sizeTheme: SizeTheme<any>, props: GaussianDensityProps) {
-    const { position, boundary, radius } = getUnitConformationAndRadius(structure, unit, sizeTheme, props);
-    const p = ensureReasonableResolution(boundary.box, props);
+    const { box } = unit.lookup3d.boundary;
+    const p = ensureReasonableResolution(box, props);
+    const { position, radius } = getUnitConformationAndRadius(structure, unit, sizeTheme, p);
    return Task.create('Gaussian Density', async ctx => {
-        return await GaussianDensityCPU(ctx, position, boundary.box, radius, p);
+        return await GaussianDensityCPU(ctx, position, box, radius, p);
    });
 }

 export function computeUnitGaussianDensityTexture(structure: Structure, unit: Unit, sizeTheme: SizeTheme<any>, props: GaussianDensityProps, webgl: WebGLContext, texture?: Texture) {
-    const { position, boundary, radius } = getUnitConformationAndRadius(structure, unit, sizeTheme, props);
-    const p = ensureReasonableResolution(boundary.box, props, getTextureMaxCells(webgl, structure));
+    const { box } = unit.lookup3d.boundary;
+    const p = ensureReasonableResolution(box, props, getTextureMaxCells(webgl, structure));
+    const { position, radius } = getUnitConformationAndRadius(structure, unit, sizeTheme, p);
    return Task.create('Gaussian Density', async ctx => {
-        return GaussianDensityTexture(webgl, position, boundary.box, radius, p, texture);
+        return GaussianDensityTexture(webgl, position, box, radius, p, texture);
    });
 }

 export function computeUnitGaussianDensityTexture2d(structure: Structure, unit: Unit, sizeTheme: SizeTheme<any>, powerOfTwo: boolean, props: GaussianDensityProps, webgl: WebGLContext, texture?: Texture) {
-    const { position, boundary, radius } = getUnitConformationAndRadius(structure, unit, sizeTheme, props);
-    const p = ensureReasonableResolution(boundary.box, props, getTextureMaxCells(webgl, structure));
+    const { box } = unit.lookup3d.boundary;
+    const p = ensureReasonableResolution(box, props, getTextureMaxCells(webgl, structure));
+    const { position, radius } = getUnitConformationAndRadius(structure, unit, sizeTheme, p);
    return Task.create('Gaussian Density', async ctx => {
-        return GaussianDensityTexture2d(webgl, position, boundary.box, radius, powerOfTwo, p, texture);
+        return GaussianDensityTexture2d(webgl, position, box, radius, powerOfTwo, p, texture);
    });
 }

 //

 export function computeStructureGaussianDensity(structure: Structure, sizeTheme: SizeTheme<any>, props: GaussianDensityProps) {
-    const { position, boundary, radius } = getStructureConformationAndRadius(structure, sizeTheme, props);
-    const p = ensureReasonableResolution(boundary.box, props);
+    const { box } = structure.lookup3d.boundary;
+    const p = ensureReasonableResolution(box, props);
+    const { position, radius } = getStructureConformationAndRadius(structure, sizeTheme, props.ignoreHydrogens, props.traceOnly);
    return Task.create('Gaussian Density', async ctx => {
-        return await GaussianDensityCPU(ctx, position, boundary.box, radius, p);
+        return await GaussianDensityCPU(ctx, position, box, radius, p);
    });
 }

 export function computeStructureGaussianDensityTexture(structure: Structure, sizeTheme: SizeTheme<any>, props: GaussianDensityProps, webgl: WebGLContext, texture?: Texture) {
-    const { position, boundary, radius } = getStructureConformationAndRadius(structure, sizeTheme, props);
-    const p = ensureReasonableResolution(boundary.box, props);
+    const { box } = structure.lookup3d.boundary;
+    const p = ensureReasonableResolution(box, props, getTextureMaxCells(webgl));
+    const { position, radius } = getStructureConformationAndRadius(structure, sizeTheme, props.ignoreHydrogens, props.traceOnly);
    return Task.create('Gaussian Density', async ctx => {
-        return GaussianDensityTexture(webgl, position, boundary.box, radius, p, texture);
+        return GaussianDensityTexture(webgl, position, box, radius, p, texture);
    });
 }

 export function computeStructureGaussianDensityTexture2d(structure: Structure, sizeTheme: SizeTheme<any>, powerOfTwo: boolean, props: GaussianDensityProps, webgl: WebGLContext, texture?: Texture) {
    const { box } = structure.lookup3d.boundary;
-    const { position, boundary, radius } = getStructureConformationAndRadius(structure, sizeTheme, props);
-    const p = ensureReasonableResolution(boundary.box, props);
+    const p = ensureReasonableResolution(box, props, getTextureMaxCells(webgl));
+    const { position, radius } = getStructureConformationAndRadius(structure, sizeTheme, props.ignoreHydrogens, props.traceOnly);
    return Task.create('Gaussian Density', async ctx => {
        return GaussianDensityTexture2d(webgl, position, box, radius, powerOfTwo, p, texture);
    });
--- a/src/mol-repr/structure/visual/util/molecular-surface.ts
+++ b/src/mol-repr/structure/visual/util/molecular-surface.ts
@@ -1,12 +1,12 @@
 /**
- * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
 *
 * @author Alexander Rose <alexander.rose@weirdbyte.de>
 */

 import { Unit, Structure } from '../../../../mol-model/structure';
 import { Task, RuntimeContext } from '../../../../mol-task';
-import { getUnitConformationAndRadius, CommonSurfaceProps, ensureReasonableResolution, getStructureConformationAndRadius } from './common';
+import { getUnitConformationAndRadius, CommonSurfaceProps, ensureReasonableResolution } from './common';
 import { PositionData, DensityData, Box3D } from '../../../../mol-math/geometry';
 import { MolecularSurfaceCalculationProps, calcMolecularSurface } from '../../../../mol-math/geometry/molecular-surface';
 import { OrderedSet } from '../../../../mol-data/int';
@@ -15,7 +15,7 @@ import { SizeTheme } from '../../../../mol-theme/size';

 export type MolecularSurfaceProps = MolecularSurfaceCalculationProps & CommonSurfaceProps

-function getUnitPositionDataAndMaxRadius(structure: Structure, unit: Unit, sizeTheme: SizeTheme<any>, props: MolecularSurfaceProps) {
+function getPositionDataAndMaxRadius(structure: Structure, unit: Unit, sizeTheme: SizeTheme<any>, props: MolecularSurfaceProps) {
    const { probeRadius } = props;
    const { position, boundary, radius } = getUnitConformationAndRadius(structure, unit, sizeTheme, props);
    const { indices } = position;
@@ -34,38 +34,11 @@ function getUnitPositionDataAndMaxRadius(structure: Structure, unit: Unit, sizeT
 }

 export function computeUnitMolecularSurface(structure: Structure, unit: Unit, sizeTheme: SizeTheme<any>, props: MolecularSurfaceProps) {
-    const { position, boundary, maxRadius } = getUnitPositionDataAndMaxRadius(structure, unit, sizeTheme, props);
-    const p = ensureReasonableResolution(boundary.box, props);
+    const { box } = unit.lookup3d.boundary;
+    const p = ensureReasonableResolution(box, props);
+    const { position, boundary, maxRadius } = getPositionDataAndMaxRadius(structure, unit, sizeTheme, p);
    return Task.create('Molecular Surface', async ctx => {
-        return await MolecularSurface(ctx, position, boundary, maxRadius, boundary.box, p);
-    });
-}
-
-//
-
-function getStructurePositionDataAndMaxRadius(structure: Structure, sizeTheme: SizeTheme<any>, props: MolecularSurfaceProps) {
-    const { probeRadius } = props;
-    const { position, boundary, radius } = getStructureConformationAndRadius(structure, sizeTheme, props);
-    const { indices } = position;
-    const n = OrderedSet.size(indices);
-    const radii = new Float32Array(OrderedSet.end(indices));
-
-    let maxRadius = 0;
-    for (let i = 0; i < n; ++i) {
-        const j = OrderedSet.getAt(indices, i);
-        const r = radius(j);
-        if (maxRadius < r) maxRadius = r;
-        radii[j] = r + probeRadius;
-    }
-
-    return { position: { ...position, radius: radii }, boundary, maxRadius };
-}
-
-export function computeStructureMolecularSurface(structure: Structure, sizeTheme: SizeTheme<any>, props: MolecularSurfaceProps) {
-    const { position, boundary, maxRadius } = getStructurePositionDataAndMaxRadius(structure, sizeTheme, props);
-    const p = ensureReasonableResolution(boundary.box, props);
-    return Task.create('Molecular Surface', async ctx => {
-        return await MolecularSurface(ctx, position, boundary, maxRadius, boundary.box, p);
+        return await MolecularSurface(ctx, position, boundary, maxRadius, box, p);
    });
 }

--- a/src/mol-repr/util.ts
+++ b/src/mol-repr/util.ts
@@ -75,7 +75,7 @@ export type QualityThresholds = typeof DefaultQualityThresholds
 export function getStructureQuality(structure: Structure, tresholds: Partial<QualityThresholds> = {}): VisualQuality {
    const t = { ...DefaultQualityThresholds, ...tresholds };
    let score = structure.elementCount * t.elementCountFactor;
-    if (structure.isCoarseGrained || structure.isCoarse) score *= t.coarseGrainedFactor;
+    if (structure.isCoarseGrained) score *= t.coarseGrainedFactor;
    if (score > t.lowestElementCount) {
        return 'lowest';
    } else if (score > t.lowerElementCount) {
--- a/src/mol-repr/visual.ts
+++ b/src/mol-repr/visual.ts
@@ -55,7 +55,6 @@ interface Visual<D, P extends PD.Params> {
    setTransparency: (transparency: Transparency, webgl?: WebGLContext) => void
    setSubstance: (substance: Substance, webgl?: WebGLContext) => void
    setClipping: (clipping: Clipping) => void
-    setThemeStrength: (strength: { overpaint: number, transparency: number, substance: number }) => void
    destroy: () => void
    mustRecreate?: (data: D, props: PD.Values<P>, webgl?: WebGLContext) => boolean
 }
@@ -350,14 +349,6 @@ namespace Visual {
        ValueCell.updateIfChanged(dClipping, clipping.layers.length > 0);
    }

-    export function setThemeStrength(renderObject: GraphicsRenderObject | undefined, strength: { overpaint: number, transparency: number, substance: number }) {
-        if (renderObject) {
-            ValueCell.updateIfChanged(renderObject.values.uOverpaintStrength, strength.overpaint);
-            ValueCell.updateIfChanged(renderObject.values.uTransparencyStrength, strength.transparency);
-            ValueCell.updateIfChanged(renderObject.values.uSubstanceStrength, strength.substance);
-        }
-    }
-
    export function setTransform(renderObject: GraphicsRenderObject | undefined, transform?: Mat4, instanceTransforms?: Float32Array | null) {
        if (!renderObject || (!transform && !instanceTransforms)) return;

--- a/src/mol-repr/volume/isosurface.ts
+++ b/src/mol-repr/volume/isosurface.ts
@@ -201,7 +201,6 @@ async function createVolumeIsosurfaceTextureMesh(ctx: VisualContext, volume: Vol

    const groupCount = volume.grid.cells.data.length;
    const surface = TextureMesh.create(gv.vertexCount, groupCount, gv.vertexTexture, gv.groupTexture, gv.normalTexture, Volume.getBoundingSphere(volume), textureMesh);
-    surface.meta.webgl = ctx.webgl;

    return surface;
 }
--- a/src/mol-repr/volume/representation.ts
+++ b/src/mol-repr/volume/representation.ts
@@ -252,9 +252,6 @@ export function VolumeVisual<G extends Geometry, P extends VolumeParams & Geomet
        setClipping(clipping: Clipping) {
            return Visual.setClipping(renderObject, clipping, lociApply, true);
        },
-        setThemeStrength(strength: { overpaint: number, transparency: number, substance: number }) {
-            Visual.setThemeStrength(renderObject, strength);
-        },
        destroy() {
            dispose?.(geometry);
            if (renderObject) {
--- a/src/mol-script/language/symbol-table/structure-query.ts
+++ b/src/mol-script/language/symbol-table/structure-query.ts
@@ -273,7 +273,6 @@ const atomProperty = {

        sourceIndex: atomProp(Type.Num, 'Index of the atom/element in the input file.'),
        operatorName: atomProp(Type.Str, 'Name of the symmetry operator applied to this element.'),
-        operatorKey: atomProp(Type.Num, 'Key of the symmetry operator applied to this element.'),
        modelIndex: atomProp(Type.Num, 'Index of the model in the input file.'),
        modelLabel: atomProp(Type.Str, 'Label/header of the model in the input file.')
    },
--- a/src/mol-script/runtime/query/table.ts
+++ b/src/mol-script/runtime/query/table.ts
@@ -299,7 +299,6 @@ const symbols = [
    D(MolScript.structureQuery.atomProperty.core.z, atomProp(StructureProperties.atom.z)),
    D(MolScript.structureQuery.atomProperty.core.sourceIndex, atomProp(StructureProperties.atom.sourceIndex)),
    D(MolScript.structureQuery.atomProperty.core.operatorName, atomProp(StructureProperties.unit.operator_name)),
-    D(MolScript.structureQuery.atomProperty.core.operatorKey, atomProp(StructureProperties.unit.operator_key)),
    D(MolScript.structureQuery.atomProperty.core.modelIndex, atomProp(StructureProperties.unit.model_index)),
    D(MolScript.structureQuery.atomProperty.core.modelLabel, atomProp(StructureProperties.unit.model_label)),
    D(MolScript.structureQuery.atomProperty.core.atomKey, (ctx, xs) => {
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
Alexander Rose	3667092327	tweak cube clamp param	2022-11-08 22:28:47 -08:00
Alexander Rose	842824057b	add param to clamp cube values	2022-11-08 22:17:23 -08:00