molstar 3.0.0-dev.2 → 3.0.0-dev.6

package/lib/commonjs/extensions/mp4-export/controls.js

@@ -124,16 +124,18 @@ var Mp4Controls = /** @class */ (function (_super) {
         });
         this.subscribe((_a = this.plugin.canvas3d) === null || _a === void 0 ? void 0 : _a.resized, function () { return _this.syncInfo(); });
         this.subscribe((_b = this.plugin.helpers.viewportScreenshot) === null || _b === void 0 ? void 0 : _b.events.previewed, function () { return _this.syncInfo(); });
-        this.subscribe(this.plugin.behaviors.state.isBusy, function (b) {
-            var _a, _b, _c;
-            var anim = _this.current;
-            if (!b && anim) {
-                _this.behaviors.canApply.next((_c = (_b = (_a = anim.anim).canApply) === null || _b === void 0 ? void 0 : _b.call(_a, _this.plugin)) !== null && _c !== void 0 ? _c : { canApply: true });
-            }
-        });
+        this.subscribe(this.plugin.behaviors.state.isBusy, function (b) { return _this.updateCanApply(b); });
+        this.subscribe(this.plugin.managers.snapshot.events.changed, function (b) { return _this.updateCanApply(b); });
         this.sync();
         this.syncInfo();
     };
+    Mp4Controls.prototype.updateCanApply = function (b) {
+        var _a, _b, _c;
+        var anim = this.current;
+        if (!b && anim) {
+            this.behaviors.canApply.next((_c = (_b = (_a = anim.anim).canApply) === null || _b === void 0 ? void 0 : _b.call(_a, this.plugin)) !== null && _c !== void 0 ? _c : { canApply: true });
+        }
+    };
     return Mp4Controls;
 }(component_1.PluginComponent));
 exports.Mp4Controls = Mp4Controls;

package/lib/commonjs/extensions/pdbe/structure-quality-report/prop.js

@@ -32,7 +32,7 @@ var StructureQualityReport;
     }
     StructureQualityReport.getEntryUrl = getEntryUrl;
     function isApplicable(model) {
-        return !!model && structure_1.Model.isFromPdbArchive(model);
+        return !!model && structure_1.Model.hasPdbId(model);
     }
     StructureQualityReport.isApplicable = isApplicable;
     StructureQualityReport.Schema = {

package/lib/commonjs/extensions/rcsb/assembly-symmetry/behavior.d.ts

@@ -24,11 +24,14 @@ declare const AssemblySymmetry3D: StateTransformer<PluginStateObject.Molecule.St
     flatShaded: boolean;
     ignoreLight: boolean;
     xrayShaded: boolean;
+    bumpFrequency: number;
+    bumpAmplitude: number;
     alpha: number;
     quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
     material: PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
     }>;
     axesColor: PD.NamedParams<PD.Normalize<{
         colorValue: any;

package/lib/commonjs/extensions/rcsb/assembly-symmetry/prop.js

@@ -53,7 +53,7 @@ var AssemblySymmetry;
     AssemblySymmetry.DefaultServerUrl = 'https://data.rcsb.org/graphql';
     function isApplicable(structure) {
         return (!!structure && structure.models.length === 1 &&
-            structure_1.Model.isFromPdbArchive(structure.models[0]) &&
+            structure_1.Model.hasPdbId(structure.models[0]) &&
             isBiologicalAssembly(structure));
     }
     AssemblySymmetry.isApplicable = isApplicable;

package/lib/commonjs/extensions/rcsb/assembly-symmetry/representation.d.ts

@@ -16,11 +16,14 @@ export declare const AssemblySymmetryParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
     }>>;
     axesColor: PD.Mapped<PD.NamedParams<PD.Normalize<{
         colorValue: Color;

package/lib/commonjs/extensions/rcsb/validation-report/prop.js

@@ -39,7 +39,7 @@ var ValidationReport;
     }
     ValidationReport.getEntryUrl = getEntryUrl;
     function isApplicable(model) {
-        return !!model && model_1.Model.isFromPdbArchive(model);
+        return !!model && model_1.Model.hasPdbId(model);
     }
     ValidationReport.isApplicable = isApplicable;
     function fromXml(xml, model) {

package/lib/commonjs/extensions/rcsb/validation-report/representation.d.ts

@@ -31,11 +31,14 @@ export declare const IntraUnitClashParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
     }>>;
 };
 export declare type IntraUnitClashParams = typeof IntraUnitClashParams;
@@ -60,11 +63,14 @@ export declare const InterUnitClashParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
     }>>;
 };
 export declare type InterUnitClashParams = typeof InterUnitClashParams;
@@ -90,11 +96,14 @@ export declare const ClashesParams: {
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
     }>>;
 };
 export declare type ClashesParams = typeof ClashesParams;
@@ -119,11 +128,14 @@ export declare function getClashesParams(ctx: ThemeRegistryContext, structure: S
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
     }>>;
 };
 export declare type ClashesRepresentation = StructureRepresentation<ClashesParams>;
@@ -149,10 +161,13 @@ export declare const ClashesRepresentationProvider: StructureRepresentationProvi
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
+    bumpFrequency: PD.Numeric;
+    bumpAmplitude: PD.Numeric;
     alpha: PD.Numeric;
     quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
     material: PD.Group<PD.Normalize<{
         metalness: number;
         roughness: number;
+        bumpiness: number;
     }>>;
 }, ValidationReport.Tag.Clashes>;

package/lib/commonjs/mol-canvas3d/canvas3d.d.ts

@@ -67,6 +67,7 @@ export declare const Canvas3DParams: {
         outline: PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
             scale: any;
             threshold: any;
+            color: any;
         }>, "on">;
         antialiasing: PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
             edgeThreshold: any;
@@ -164,6 +165,8 @@ export declare const Canvas3DParams: {
             flipSided: any;
             flatShaded: any;
             xrayShaded: any;
+            bumpFrequency: any;
+            bumpAmplitude: any;
             quality: any;
             material: any;
         }>, "on">;
@@ -215,6 +218,7 @@ export declare const DefaultCanvas3DParams: PD.Values<{
         outline: PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
             scale: any;
             threshold: any;
+            color: any;
         }>, "on">;
         antialiasing: PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
             edgeThreshold: any;
@@ -312,6 +316,8 @@ export declare const DefaultCanvas3DParams: PD.Values<{
             flipSided: any;
             flatShaded: any;
             xrayShaded: any;
+            bumpFrequency: any;
+            bumpAmplitude: any;
             quality: any;
             material: any;
         }>, "on">;

package/lib/commonjs/mol-canvas3d/canvas3d.js

@@ -288,7 +288,13 @@ var Canvas3D;
                     cam = stereoCamera;
                 }
                 if (multi_sample_1.MultiSamplePass.isEnabled(p.multiSample)) {
-                    multiSampleHelper.render(renderer, cam, scene, helper, true, p.transparentBackground, p);
+                    if (!cameraChanged) {
+                        while (!multiSampleHelper.render(renderer, cam, scene, helper, true, p.transparentBackground, p))
+                            ;
+                    }
+                    else {
+                        multiSampleHelper.render(renderer, cam, scene, helper, true, p.transparentBackground, p);
+                    }
                 }
                 else {
                     passes.draw.render(renderer, cam, scene, helper, true, p.transparentBackground, p.postprocessing, p.marking);
@@ -393,7 +399,7 @@ var Canvas3D;
                 return true;
             if (camera.transition.inTransition || nextCameraResetSnapshot)
                 return false;
-            var cameraSphereOverlapsNone = true;
+            var cameraSphereOverlapsNone = true, isEmpty = true;
             geometry_1.Sphere3D.set(cameraSphere, camera.state.target, camera.state.radius);
             // check if any renderable has moved outside of the old bounding sphere
             // and if no renderable is overlapping with the camera sphere
@@ -404,13 +410,14 @@ var Canvas3D;
                 var b = r.values.boundingSphere.ref.value;
                 if (!b.radius)
                     continue;
+                isEmpty = false;
                 var cameraDist = linear_algebra_1.Vec3.distance(cameraSphere.center, b.center);
                 if ((cameraDist > cameraSphere.radius || cameraDist > b.radius || b.radius > camera.state.radiusMax) && !geometry_1.Sphere3D.includes(oldBoundingSphereVisible, b))
                     return true;
                 if (geometry_1.Sphere3D.overlaps(cameraSphere, b))
                     cameraSphereOverlapsNone = false;
             }
-            return cameraSphereOverlapsNone;
+            return cameraSphereOverlapsNone || (!isEmpty && cameraSphere.radius <= 0.1);
         }
         var sceneCommitTimeoutMs = 250;
         function commitScene(isSynchronous) {

package/lib/commonjs/mol-canvas3d/helper/camera-helper.d.ts

@@ -22,10 +22,13 @@ export declare const CameraHelperParams: {
         flipSided: boolean;
         flatShaded: boolean;
         xrayShaded: boolean;
+        bumpFrequency: number;
+        bumpAmplitude: number;
         quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
         material: PD.Normalize<{
             metalness: number;
             roughness: number;
+            bumpiness: number;
         }>;
     }>, "on">>;
 };

package/lib/commonjs/mol-canvas3d/helper/handle-helper.d.ts

@@ -24,10 +24,13 @@ export declare const HandleHelperParams: {
         flipSided: boolean;
         flatShaded: boolean;
         xrayShaded: boolean;
+        bumpFrequency: number;
+        bumpAmplitude: number;
         quality: "auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest";
         material: PD.Normalize<{
             metalness: number;
             roughness: number;
+            bumpiness: number;
         }>;
     }>, "on">>;
 };

package/lib/commonjs/mol-canvas3d/helper/helper.d.ts

@@ -33,6 +33,8 @@ export declare const HelperParams: {
             flipSided: any;
             flatShaded: any;
             xrayShaded: any;
+            bumpFrequency: any;
+            bumpAmplitude: any;
             quality: any;
             material: any;
         }>, "on">;
@@ -62,6 +64,8 @@ export declare const DefaultHelperProps: PD.Values<{
             flipSided: any;
             flatShaded: any;
             xrayShaded: any;
+            bumpFrequency: any;
+            bumpAmplitude: any;
             quality: any;
             material: any;
         }>, "on">;

package/lib/commonjs/mol-canvas3d/passes/image.d.ts

@@ -27,6 +27,7 @@ export declare const ImageParams: {
         outline: PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
             scale: any;
             threshold: any;
+            color: any;
         }>, "on">;
         antialiasing: PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
             edgeThreshold: any;
@@ -58,6 +59,8 @@ export declare const ImageParams: {
             flipSided: any;
             flatShaded: any;
             xrayShaded: any;
+            bumpFrequency: any;
+            bumpAmplitude: any;
             quality: any;
             material: any;
         }>, "on">;

package/lib/commonjs/mol-canvas3d/passes/multi-sample.d.ts

@@ -43,7 +43,8 @@ export declare class MultiSampleHelper {
     private multiSamplePass;
     private sampleIndex;
     update(changed: boolean, props: MultiSampleProps): boolean;
-    render(renderer: Renderer, camera: Camera | StereoCamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, transparentBackground: boolean, props: Props): void;
+    /** Return `true` while more samples are needed */
+    render(renderer: Renderer, camera: Camera | StereoCamera, scene: Scene, helper: Helper, toDrawingBuffer: boolean, transparentBackground: boolean, props: Props): boolean;
     constructor(multiSamplePass: MultiSamplePass);
 }
 export {};

package/lib/commonjs/mol-canvas3d/passes/multi-sample.js

@@ -27,8 +27,8 @@ function getComposeRenderable(ctx, colorTexture) {
     return (0, renderable_1.createComputeRenderable)(renderItem, values);
 }
 exports.MultiSampleParams = {
-    mode: param_definition_1.ParamDefinition.Select('off', [['off', 'Off'], ['on', 'On'], ['temporal', 'Temporal']]),
-    sampleLevel: param_definition_1.ParamDefinition.Numeric(2, { min: 0, max: 5, step: 1 }),
+    mode: param_definition_1.ParamDefinition.Select('temporal', [['off', 'Off'], ['on', 'On'], ['temporal', 'Temporal']]),
+    sampleLevel: param_definition_1.ParamDefinition.Numeric(2, { min: 0, max: 5, step: 1 }, { description: 'Take level^2 samples.' }),
 };
 var MultiSamplePass = /** @class */ (function () {
     function MultiSamplePass(webgl, drawPass) {
@@ -266,8 +266,10 @@ var MultiSampleHelper = /** @class */ (function () {
             this.sampleIndex = -1;
         return props.mode === 'temporal' ? this.sampleIndex !== -2 : false;
     };
+    /** Return `true` while more samples are needed */
     MultiSampleHelper.prototype.render = function (renderer, camera, scene, helper, toDrawingBuffer, transparentBackground, props) {
         this.sampleIndex = this.multiSamplePass.render(this.sampleIndex, renderer, camera, scene, helper, toDrawingBuffer, transparentBackground, props);
+        return this.sampleIndex < 0;
     };
     return MultiSampleHelper;
 }());

package/lib/commonjs/mol-canvas3d/passes/postprocessing.d.ts

@@ -20,6 +20,7 @@ export declare const PostprocessingParams: {
     outline: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
         scale: number;
         threshold: number;
+        color: Color;
     }>, "on">>;
     antialiasing: PD.Mapped<PD.NamedParams<PD.Normalize<unknown>, "off"> | PD.NamedParams<PD.Normalize<{
         edgeThreshold: number;

package/lib/commonjs/mol-canvas3d/passes/postprocessing.js

@@ -68,9 +68,9 @@ function getSamples(vectorSamples, nSamples) {
     }
     return samples;
 }
-var PostprocessingSchema = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, util_1.QuadSchema), { tSsaoDepth: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), tColor: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), tDepth: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), tOutlines: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), uTexSize: (0, schema_1.UniformSpec)('v2'), dOrthographic: (0, schema_1.DefineSpec)('number'), uNear: (0, schema_1.UniformSpec)('f'), uFar: (0, schema_1.UniformSpec)('f'), uFogNear: (0, schema_1.UniformSpec)('f'), uFogFar: (0, schema_1.UniformSpec)('f'), uFogColor: (0, schema_1.UniformSpec)('v3'), uTransparentBackground: (0, schema_1.UniformSpec)('b'), uMaxPossibleViewZDiff: (0, schema_1.UniformSpec)('f'), dOcclusionEnable: (0, schema_1.DefineSpec)('boolean'), dOutlineEnable: (0, schema_1.DefineSpec)('boolean'), dOutlineScale: (0, schema_1.DefineSpec)('number'), uOutlineThreshold: (0, schema_1.UniformSpec)('f') });
+var PostprocessingSchema = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, util_1.QuadSchema), { tSsaoDepth: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), tColor: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), tDepth: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), tOutlines: (0, schema_1.TextureSpec)('texture', 'rgba', 'ubyte', 'nearest'), uTexSize: (0, schema_1.UniformSpec)('v2'), dOrthographic: (0, schema_1.DefineSpec)('number'), uNear: (0, schema_1.UniformSpec)('f'), uFar: (0, schema_1.UniformSpec)('f'), uFogNear: (0, schema_1.UniformSpec)('f'), uFogFar: (0, schema_1.UniformSpec)('f'), uFogColor: (0, schema_1.UniformSpec)('v3'), uOutlineColor: (0, schema_1.UniformSpec)('v3'), uTransparentBackground: (0, schema_1.UniformSpec)('b'), uMaxPossibleViewZDiff: (0, schema_1.UniformSpec)('f'), dOcclusionEnable: (0, schema_1.DefineSpec)('boolean'), dOutlineEnable: (0, schema_1.DefineSpec)('boolean'), dOutlineScale: (0, schema_1.DefineSpec)('number'), uOutlineThreshold: (0, schema_1.UniformSpec)('f') });
 function getPostprocessingRenderable(ctx, colorTexture, depthTexture, outlinesTexture, ssaoDepthTexture) {
-    var values = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, util_1.QuadValues), { tSsaoDepth: mol_util_1.ValueCell.create(ssaoDepthTexture), tColor: mol_util_1.ValueCell.create(colorTexture), tDepth: mol_util_1.ValueCell.create(depthTexture), tOutlines: mol_util_1.ValueCell.create(outlinesTexture), uTexSize: mol_util_1.ValueCell.create(linear_algebra_1.Vec2.create(colorTexture.getWidth(), colorTexture.getHeight())), dOrthographic: mol_util_1.ValueCell.create(0), uNear: mol_util_1.ValueCell.create(1), uFar: mol_util_1.ValueCell.create(10000), uFogNear: mol_util_1.ValueCell.create(10000), uFogFar: mol_util_1.ValueCell.create(10000), uFogColor: mol_util_1.ValueCell.create(linear_algebra_1.Vec3.create(1, 1, 1)), uTransparentBackground: mol_util_1.ValueCell.create(false), uMaxPossibleViewZDiff: mol_util_1.ValueCell.create(0.5), dOcclusionEnable: mol_util_1.ValueCell.create(false), dOutlineEnable: mol_util_1.ValueCell.create(false), dOutlineScale: mol_util_1.ValueCell.create(1), uOutlineThreshold: mol_util_1.ValueCell.create(0.33) });
+    var values = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, util_1.QuadValues), { tSsaoDepth: mol_util_1.ValueCell.create(ssaoDepthTexture), tColor: mol_util_1.ValueCell.create(colorTexture), tDepth: mol_util_1.ValueCell.create(depthTexture), tOutlines: mol_util_1.ValueCell.create(outlinesTexture), uTexSize: mol_util_1.ValueCell.create(linear_algebra_1.Vec2.create(colorTexture.getWidth(), colorTexture.getHeight())), dOrthographic: mol_util_1.ValueCell.create(0), uNear: mol_util_1.ValueCell.create(1), uFar: mol_util_1.ValueCell.create(10000), uFogNear: mol_util_1.ValueCell.create(10000), uFogFar: mol_util_1.ValueCell.create(10000), uFogColor: mol_util_1.ValueCell.create(linear_algebra_1.Vec3.create(1, 1, 1)), uOutlineColor: mol_util_1.ValueCell.create(linear_algebra_1.Vec3.create(0, 0, 0)), uTransparentBackground: mol_util_1.ValueCell.create(false), uMaxPossibleViewZDiff: mol_util_1.ValueCell.create(0.5), dOcclusionEnable: mol_util_1.ValueCell.create(false), dOutlineEnable: mol_util_1.ValueCell.create(false), dOutlineScale: mol_util_1.ValueCell.create(1), uOutlineThreshold: mol_util_1.ValueCell.create(0.33) });
     var schema = (0, tslib_1.__assign)({}, PostprocessingSchema);
     var shaderCode = (0, shader_code_1.ShaderCode)('postprocessing', quad_vert_1.quad_vert, postprocessing_frag_1.postprocessing_frag);
     var renderItem = (0, render_item_1.createComputeRenderItem)(ctx, 'triangles', shaderCode, schema, values);
@@ -90,6 +90,7 @@ exports.PostprocessingParams = {
         on: param_definition_1.ParamDefinition.Group({
             scale: param_definition_1.ParamDefinition.Numeric(1, { min: 1, max: 5, step: 1 }),
             threshold: param_definition_1.ParamDefinition.Numeric(0.33, { min: 0.01, max: 1, step: 0.01 }),
+            color: param_definition_1.ParamDefinition.Color((0, color_1.Color)(0x000000)),
         }),
         off: param_definition_1.ParamDefinition.Group({})
     }, { cycle: true, description: 'Draw outline around 3D objects' }),
@@ -223,6 +224,7 @@ var PostprocessingPass = /** @class */ (function () {
             mol_util_1.ValueCell.updateIfChanged(this.outlinesRenderable.values.uNear, camera.near);
             mol_util_1.ValueCell.updateIfChanged(this.outlinesRenderable.values.uFar, camera.far);
             mol_util_1.ValueCell.updateIfChanged(this.outlinesRenderable.values.uMaxPossibleViewZDiff, maxPossibleViewZDiff);
+            mol_util_1.ValueCell.update(this.renderable.values.uOutlineColor, color_1.Color.toVec3Normalized(this.renderable.values.uOutlineColor.ref.value, props.outline.params.color));
             mol_util_1.ValueCell.updateIfChanged(this.renderable.values.uMaxPossibleViewZDiff, maxPossibleViewZDiff);
             if (this.renderable.values.dOutlineScale.ref.value !== outlineScale) {
                 needsUpdateMain = true;

package/lib/commonjs/mol-geo/geometry/base.d.ts

@@ -46,6 +46,7 @@ export declare namespace BaseGeometry {
         material: PD.Group<PD.Normalize<{
             metalness: number;
             roughness: number;
+            bumpiness: number;
         }>>;
     };
     type Params = typeof Params;
@@ -68,6 +69,7 @@ export declare namespace BaseGeometry {
         drawCount: ValueCell<number, never>;
         uMetalness: ValueCell<number, never>;
         uRoughness: ValueCell<number, never>;
+        uBumpiness: ValueCell<number, never>;
         dLightCount: ValueCell<number, never>;
     };
     function updateValues(values: BaseValues, props: PD.Values<Params>): void;

package/lib/commonjs/mol-geo/geometry/base.js

@@ -99,6 +99,7 @@ var BaseGeometry;
             drawCount: mol_util_1.ValueCell.create(counts.drawCount),
             uMetalness: mol_util_1.ValueCell.create(props.material.metalness),
             uRoughness: mol_util_1.ValueCell.create(props.material.roughness),
+            uBumpiness: mol_util_1.ValueCell.create(props.material.bumpiness),
             dLightCount: mol_util_1.ValueCell.create(1),
         };
     }
@@ -107,6 +108,7 @@ var BaseGeometry;
         mol_util_1.ValueCell.updateIfChanged(values.alpha, props.alpha); // `uAlpha` is set in renderable.render
         mol_util_1.ValueCell.updateIfChanged(values.uMetalness, props.material.metalness);
         mol_util_1.ValueCell.updateIfChanged(values.uRoughness, props.material.roughness);
+        mol_util_1.ValueCell.updateIfChanged(values.uBumpiness, props.material.bumpiness);
     }
     BaseGeometry.updateValues = updateValues;
     function createRenderableState(props) {

package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.d.ts

@@ -43,11 +43,14 @@ export declare namespace Cylinders {
         doubleSided: PD.BooleanParam;
         ignoreLight: PD.BooleanParam;
         xrayShaded: PD.BooleanParam;
+        bumpFrequency: PD.Numeric;
+        bumpAmplitude: PD.Numeric;
         alpha: PD.Numeric;
         quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
         material: PD.Group<PD.Normalize<{
-            metalness: number;
+            metalness: number; /** Number of cylinders */
             roughness: number;
+            bumpiness: number;
         }>>;
     };
     type Params = typeof Params;

package/lib/commonjs/mol-geo/geometry/cylinders/cylinders.js

@@ -110,7 +110,7 @@ var Cylinders;
     }
     Cylinders.transform = transform;
     //
-    Cylinders.Params = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, base_1.BaseGeometry.Params), { sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 3, step: 0.01 }), doubleSided: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.CustomQualityParamInfo), ignoreLight: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), xrayShaded: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory) });
+    Cylinders.Params = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, base_1.BaseGeometry.Params), { sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }), sizeAspectRatio: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 3, step: 0.01 }), doubleSided: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.CustomQualityParamInfo), ignoreLight: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), xrayShaded: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory), bumpAmplitude: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 5, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
     Cylinders.Utils = {
         Params: Cylinders.Params,
         createEmpty: createEmpty,
@@ -156,7 +156,7 @@ var Cylinders;
         var padding = (0, size_data_1.getMaxSize)(size) * props.sizeFactor;
         var invariantBoundingSphere = geometry_1.Sphere3D.clone(cylinders.boundingSphere);
         var boundingSphere = (0, util_2.calculateTransformBoundingSphere)(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
-        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ aMapping: cylinders.mappingBuffer, aGroup: cylinders.groupBuffer, aStart: cylinders.startBuffer, aEnd: cylinders.endBuffer, aScale: cylinders.scaleBuffer, aCap: cylinders.capBuffer, elements: cylinders.indexBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), size), marker), overpaint), transparency), material), clipping), transform), { padding: mol_util_1.ValueCell.create(padding) }), base_1.BaseGeometry.createValues(props, counts)), { uSizeFactor: mol_util_1.ValueCell.create(props.sizeFactor * props.sizeAspectRatio), dDoubleSided: mol_util_1.ValueCell.create(props.doubleSided), dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight), dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded) });
+        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ aMapping: cylinders.mappingBuffer, aGroup: cylinders.groupBuffer, aStart: cylinders.startBuffer, aEnd: cylinders.endBuffer, aScale: cylinders.scaleBuffer, aCap: cylinders.capBuffer, elements: cylinders.indexBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), size), marker), overpaint), transparency), material), clipping), transform), { padding: mol_util_1.ValueCell.create(padding) }), base_1.BaseGeometry.createValues(props, counts)), { uSizeFactor: mol_util_1.ValueCell.create(props.sizeFactor * props.sizeAspectRatio), dDoubleSided: mol_util_1.ValueCell.create(props.doubleSided), dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight), dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded), uBumpFrequency: mol_util_1.ValueCell.create(props.bumpFrequency), uBumpAmplitude: mol_util_1.ValueCell.create(props.bumpAmplitude) });
     }
     function createValuesSimple(cylinders, props, colorValue, sizeValue, transform) {
         var s = base_1.BaseGeometry.createSimple(colorValue, sizeValue, transform);
@@ -169,6 +169,8 @@ var Cylinders;
         mol_util_1.ValueCell.updateIfChanged(values.dDoubleSided, props.doubleSided);
         mol_util_1.ValueCell.updateIfChanged(values.dIgnoreLight, props.ignoreLight);
         mol_util_1.ValueCell.updateIfChanged(values.dXrayShaded, props.xrayShaded);
+        mol_util_1.ValueCell.updateIfChanged(values.uBumpFrequency, props.bumpFrequency);
+        mol_util_1.ValueCell.updateIfChanged(values.uBumpAmplitude, props.bumpAmplitude);
     }
     function updateBoundingSphere(values, cylinders) {
         var invariantBoundingSphere = geometry_1.Sphere3D.clone(cylinders.boundingSphere);

package/lib/commonjs/mol-geo/geometry/direct-volume/direct-volume.d.ts

@@ -76,6 +76,7 @@ export declare namespace DirectVolume {
         material: PD.Group<PD.Normalize<{
             metalness: number;
             roughness: number;
+            bumpiness: number;
         }>>;
     };
     type Params = typeof Params;

package/lib/commonjs/mol-geo/geometry/image/image.d.ts

@@ -37,6 +37,7 @@ declare namespace Image {
         material: PD.Group<PD.Normalize<{
             metalness: number;
             roughness: number;
+            bumpiness: number;
         }>>;
     };
     type Params = typeof Params;

package/lib/commonjs/mol-geo/geometry/lines/lines.d.ts

@@ -44,6 +44,8 @@ export declare namespace Lines {
         material: PD.Group<PD.Normalize<{
             metalness: number;
             roughness: number;
+            /** Number of lines */
+            bumpiness: number;
         }>>;
     };
     type Params = typeof Params;

package/lib/commonjs/mol-geo/geometry/mesh/color-smoothing.js

@@ -306,7 +306,7 @@ function applyMeshSubstanceSmoothing(values, resolution, stride, webgl, colorTex
         colorType: values.dSubstanceType.ref.value,
         boundingSphere: values.boundingSphere.ref.value,
         invariantBoundingSphere: values.invariantBoundingSphere.ref.value,
-        itemSize: 3
+        itemSize: 4
     }, resolution, stride, webgl, colorTexture);
     if (smoothingData.kind === 'volume') {
         mol_util_1.ValueCell.updateIfChanged(values.dSubstanceType, smoothingData.type);

package/lib/commonjs/mol-geo/geometry/mesh/mesh.d.ts

@@ -62,11 +62,14 @@ export declare namespace Mesh {
         flatShaded: PD.BooleanParam;
         ignoreLight: PD.BooleanParam;
         xrayShaded: PD.BooleanParam;
+        bumpFrequency: PD.Numeric;
+        bumpAmplitude: PD.Numeric;
         alpha: PD.Numeric;
         quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
         material: PD.Group<PD.Normalize<{
             metalness: number;
             roughness: number;
+            bumpiness: number;
         }>>;
     };
     type Params = typeof Params;

package/lib/commonjs/mol-geo/geometry/mesh/mesh.js

@@ -554,7 +554,7 @@ var Mesh;
     }
     Mesh.smoothEdges = smoothEdges;
     //
-    Mesh.Params = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, base_1.BaseGeometry.Params), { doubleSided: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.CustomQualityParamInfo), flipSided: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), flatShaded: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), ignoreLight: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), xrayShaded: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory) });
+    Mesh.Params = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, base_1.BaseGeometry.Params), { doubleSided: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.CustomQualityParamInfo), flipSided: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), flatShaded: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), ignoreLight: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), xrayShaded: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory), bumpAmplitude: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 5, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
     Mesh.Utils = {
         Params: Mesh.Params,
         createEmpty: createEmpty,
@@ -596,7 +596,7 @@ var Mesh;
         var counts = { drawCount: mesh.triangleCount * 3, vertexCount: mesh.vertexCount, groupCount: groupCount, instanceCount: instanceCount };
         var invariantBoundingSphere = geometry_1.Sphere3D.clone(mesh.boundingSphere);
         var boundingSphere = (0, util_3.calculateTransformBoundingSphere)(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
-        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ aPosition: mesh.vertexBuffer, aNormal: mesh.normalBuffer, aGroup: mesh.groupBuffer, elements: mesh.indexBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), marker), overpaint), transparency), material), clipping), transform), base_1.BaseGeometry.createValues(props, counts)), { dDoubleSided: mol_util_1.ValueCell.create(props.doubleSided), dFlatShaded: mol_util_1.ValueCell.create(props.flatShaded), dFlipSided: mol_util_1.ValueCell.create(props.flipSided), dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight), dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded), meta: mol_util_1.ValueCell.create(mesh.meta) });
+        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ aPosition: mesh.vertexBuffer, aNormal: mesh.normalBuffer, aGroup: mesh.groupBuffer, elements: mesh.indexBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), marker), overpaint), transparency), material), clipping), transform), base_1.BaseGeometry.createValues(props, counts)), { dDoubleSided: mol_util_1.ValueCell.create(props.doubleSided), dFlatShaded: mol_util_1.ValueCell.create(props.flatShaded), dFlipSided: mol_util_1.ValueCell.create(props.flipSided), dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight), dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded), uBumpFrequency: mol_util_1.ValueCell.create(props.bumpFrequency), uBumpAmplitude: mol_util_1.ValueCell.create(props.bumpAmplitude), meta: mol_util_1.ValueCell.create(mesh.meta) });
     }
     function createValuesSimple(mesh, props, colorValue, sizeValue, transform) {
         var s = base_1.BaseGeometry.createSimple(colorValue, sizeValue, transform);
@@ -610,6 +610,8 @@ var Mesh;
         mol_util_1.ValueCell.updateIfChanged(values.dFlipSided, props.flipSided);
         mol_util_1.ValueCell.updateIfChanged(values.dIgnoreLight, props.ignoreLight);
         mol_util_1.ValueCell.updateIfChanged(values.dXrayShaded, props.xrayShaded);
+        mol_util_1.ValueCell.updateIfChanged(values.uBumpFrequency, props.bumpFrequency);
+        mol_util_1.ValueCell.updateIfChanged(values.uBumpAmplitude, props.bumpAmplitude);
     }
     function updateBoundingSphere(values, mesh) {
         var invariantBoundingSphere = geometry_1.Sphere3D.clone(mesh.boundingSphere);

package/lib/commonjs/mol-geo/geometry/points/points.d.ts

@@ -44,6 +44,7 @@ export declare namespace Points {
         material: PD.Group<PD.Normalize<{
             metalness: number;
             roughness: number;
+            bumpiness: number;
         }>>;
     };
     type Params = typeof Params;

package/lib/commonjs/mol-geo/geometry/spheres/spheres.d.ts

@@ -34,11 +34,14 @@ export declare namespace Spheres {
         doubleSided: PD.BooleanParam;
         ignoreLight: PD.BooleanParam;
         xrayShaded: PD.BooleanParam;
+        bumpFrequency: PD.Numeric;
+        bumpAmplitude: PD.Numeric;
         alpha: PD.Numeric;
         quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
         material: PD.Group<PD.Normalize<{
             metalness: number;
             roughness: number;
+            bumpiness: number;
         }>>;
     };
     type Params = typeof Params;

package/lib/commonjs/mol-geo/geometry/spheres/spheres.js

@@ -91,7 +91,7 @@ var Spheres;
         mol_util_1.ValueCell.update(spheres.groupBuffer, groups);
         return spheres;
     }
-    Spheres.Params = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, base_1.BaseGeometry.Params), { sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }), doubleSided: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.CustomQualityParamInfo), ignoreLight: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), xrayShaded: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory) });
+    Spheres.Params = (0, tslib_1.__assign)((0, tslib_1.__assign)({}, base_1.BaseGeometry.Params), { sizeFactor: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 10, step: 0.1 }), doubleSided: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.CustomQualityParamInfo), ignoreLight: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), xrayShaded: param_definition_1.ParamDefinition.Boolean(false, base_1.BaseGeometry.ShadingCategory), bumpFrequency: param_definition_1.ParamDefinition.Numeric(0, { min: 0, max: 10, step: 0.1 }, base_1.BaseGeometry.ShadingCategory), bumpAmplitude: param_definition_1.ParamDefinition.Numeric(1, { min: 0, max: 5, step: 0.1 }, base_1.BaseGeometry.ShadingCategory) });
     Spheres.Utils = {
         Params: Spheres.Params,
         createEmpty: createEmpty,
@@ -135,7 +135,7 @@ var Spheres;
         var padding = spheres.boundingSphere.radius ? (0, size_data_1.getMaxSize)(size) * props.sizeFactor : 0;
         var invariantBoundingSphere = geometry_1.Sphere3D.expand((0, geometry_1.Sphere3D)(), spheres.boundingSphere, padding);
         var boundingSphere = (0, util_1.calculateTransformBoundingSphere)(invariantBoundingSphere, transform.aTransform.ref.value, instanceCount);
-        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ aPosition: spheres.centerBuffer, aMapping: spheres.mappingBuffer, aGroup: spheres.groupBuffer, elements: spheres.indexBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), size), marker), overpaint), transparency), material), clipping), transform), { padding: mol_util_1.ValueCell.create(padding) }), base_1.BaseGeometry.createValues(props, counts)), { uSizeFactor: mol_util_1.ValueCell.create(props.sizeFactor), dDoubleSided: mol_util_1.ValueCell.create(props.doubleSided), dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight), dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded) });
+        return (0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)((0, tslib_1.__assign)({ aPosition: spheres.centerBuffer, aMapping: spheres.mappingBuffer, aGroup: spheres.groupBuffer, elements: spheres.indexBuffer, boundingSphere: mol_util_1.ValueCell.create(boundingSphere), invariantBoundingSphere: mol_util_1.ValueCell.create(invariantBoundingSphere), uInvariantBoundingSphere: mol_util_1.ValueCell.create(linear_algebra_1.Vec4.ofSphere(invariantBoundingSphere)) }, color), size), marker), overpaint), transparency), material), clipping), transform), { padding: mol_util_1.ValueCell.create(padding) }), base_1.BaseGeometry.createValues(props, counts)), { uSizeFactor: mol_util_1.ValueCell.create(props.sizeFactor), dDoubleSided: mol_util_1.ValueCell.create(props.doubleSided), dIgnoreLight: mol_util_1.ValueCell.create(props.ignoreLight), dXrayShaded: mol_util_1.ValueCell.create(props.xrayShaded), uBumpFrequency: mol_util_1.ValueCell.create(props.bumpFrequency), uBumpAmplitude: mol_util_1.ValueCell.create(props.bumpAmplitude) });
     }
     function createValuesSimple(spheres, props, colorValue, sizeValue, transform) {
         var s = base_1.BaseGeometry.createSimple(colorValue, sizeValue, transform);
@@ -148,6 +148,8 @@ var Spheres;
         mol_util_1.ValueCell.updateIfChanged(values.dDoubleSided, props.doubleSided);
         mol_util_1.ValueCell.updateIfChanged(values.dIgnoreLight, props.ignoreLight);
         mol_util_1.ValueCell.updateIfChanged(values.dXrayShaded, props.xrayShaded);
+        mol_util_1.ValueCell.updateIfChanged(values.uBumpFrequency, props.bumpFrequency);
+        mol_util_1.ValueCell.updateIfChanged(values.uBumpAmplitude, props.bumpAmplitude);
     }
     function updateBoundingSphere(values, spheres) {
         var padding = spheres.boundingSphere.radius

package/lib/commonjs/mol-geo/geometry/substance-data.js

@@ -13,14 +13,14 @@ var texture_1 = require("../../mol-gl/webgl/texture");
 var material_1 = require("../../mol-util/material");
 function applySubstanceMaterial(array, start, end, material) {
     for (var i = start; i < end; ++i) {
-        material_1.Material.toArray(material, array, i * 3);
-        array[i * 3 + 2] = 255;
+        material_1.Material.toArray(material, array, i * 4);
+        array[i * 4 + 3] = 255;
     }
     return true;
 }
 exports.applySubstanceMaterial = applySubstanceMaterial;
 function clearSubstance(array, start, end) {
-    array.fill(0, start * 3, end * 3);
+    array.fill(0, start * 4, end * 4);
     return true;
 }
 exports.clearSubstance = clearSubstance;