diff --git a/src/mol-geo/util/marching-cubes/algorithm.ts b/src/mol-geo/util/marching-cubes/algorithm.ts
index 2e4b5e4de34d41391f715b98775320accbea1bb0..2c79d5ae95be1eadbaab65278651b20c1d97c4d9 100644
--- a/src/mol-geo/util/marching-cubes/algorithm.ts
+++ b/src/mol-geo/util/marching-cubes/algorithm.ts
@@ -196,11 +196,16 @@ class MarchingCubesState {
const n1y = sfg(sf, hi, Math.max(0, hj - 1), hk) - sfg(sf, hi, Math.min(this.nY - 1, hj + 1), hk);
const n1z = sfg(sf, hi, hj, Math.max(0, hk - 1)) - sfg(sf, hi, hj, Math.min(this.nZ - 1, hk + 1));
- this.builder.addNormal(
- n0x + t * (n0x - n1x),
- n0y + t * (n0y - n1y),
- n0z + t * (n0z - n1z)
- );
+ const nx = n0x + t * (n0x - n1x);
+ const ny = n0y + t * (n0y - n1y);
+ const nz = n0z + t * (n0z - n1z);
+
+ // ensure normal-direction is the same for negative and positive iso-levels
+ if (this.isoLevel >= 0) {
+ this.builder.addNormal(nx, ny, nz);
+ } else {
+ this.builder.addNormal(-nx, -ny, -nz);
+ }
return id;
}
@@ -255,7 +260,13 @@ class MarchingCubesState {
const triInfo = TriTable[tableIndex];
for (let t = 0; t < triInfo.length; t += 3) {
- this.builder.addTriangle(this.vertList, triInfo[t], triInfo[t + 1], triInfo[t + 2], edgeFilter);
+ const l = triInfo[t], m = triInfo[t + 1], n = triInfo[t + 2];
+ // ensure winding-order is the same for negative and positive iso-levels
+ if (this.isoLevel >= 0) {
+ this.builder.addTriangle(this.vertList, l, m, n, edgeFilter);
+ } else {
+ this.builder.addTriangle(this.vertList, n, m, l, edgeFilter);
+ }
}
}
}
\ No newline at end of file
diff --git a/src/mol-model-formats/structure/pdb/assembly.ts b/src/mol-model-formats/structure/pdb/assembly.ts
index 64f2ac42c5a4e0cab8efb9e0874f382bd2fcc224..2bd23d554bcdad13da0bec063d9c5e4cb4b86f83 100644
--- a/src/mol-model-formats/structure/pdb/assembly.ts
+++ b/src/mol-model-formats/structure/pdb/assembly.ts
@@ -59,13 +59,13 @@ export function parseRemark350(lines: Tokens, lineStart: number, lineEnd: number
const assemblies: PdbAssembly[] = [];
// Read the assemblies
- let current: PdbAssembly, group: PdbAssembly['groups'][0], matrix: Mat4, operId = 1;
+ let current: PdbAssembly, group: PdbAssembly['groups'][0], matrix: Mat4, operId = 1, asmId = 1;
const getLine = (n: number) => lines.data.substring(lines.indices[2 * n], lines.indices[2 * n + 1]);
for (let i = lineStart; i < lineEnd; i++) {
let line = getLine(i);
if (line.substr(11, 12) === 'BIOMOLECULE:') {
const id = line.substr(23).trim();
- let details: string = `Biomolecule ` + id;
+ let details = `Biomolecule ${id}`;
line = getLine(i + 1);
if (line.substr(11, 30) !== 'APPLY THE FOLLOWING TO CHAINS:') {
i++;
@@ -100,6 +100,23 @@ export function parseRemark350(lines: Tokens, lineStart: number, lineEnd: number
const c = chainList[j].trim();
if (c) group!.chains.push(c);
}
+ } else if (line.substr(11, 33) === 'APPLYING THE FOLLOWING TO CHAINS:') {
+ // variant in older PDB format version
+ current = PdbAssembly(`${asmId}`, `Biomolecule ${asmId}`);
+ assemblies.push(current);
+ asmId += 1;
+
+ group = { chains: [], operators: [] };
+ current!.groups.push(group);
+
+ i++;
+ line = getLine(i);
+
+ const chainList = line.substr(11, 69).split(',');
+ for (let j = 0, jl = chainList.length; j < jl; ++j) {
+ const c = chainList[j].trim();
+ if (c) group!.chains.push(c);
+ }
}
}
diff --git a/src/mol-model/structure/model/model.ts b/src/mol-model/structure/model/model.ts
index 859375f5f0f3042446f45cc059348d8312615f59..2d4a95177e551e1fc1e2dfc9cafc257772287e5c 100644
--- a/src/mol-model/structure/model/model.ts
+++ b/src/mol-model/structure/model/model.ts
@@ -25,6 +25,7 @@ import { MmcifFormat } from '../../../mol-model-formats/structure/mmcif';
import { ChainIndex } from './indexing';
import { SymmetryOperator } from '../../../mol-math/geometry';
import { ModelSymmetry } from '../../../mol-model-formats/structure/property/symmetry';
+import { Column } from '../../../mol-data/db';
/**
* Interface to the "source data" of the molecule.
@@ -233,18 +234,24 @@ export namespace Model {
}
export function hasDensityMap(model: Model): boolean {
+ if (!MmcifFormat.is(model.sourceData)) return false;
+ return hasXrayMap(model) || hasEmMap(model);
+ }
+
+ export function probablyHasDensityMap(model: Model): boolean {
if (!MmcifFormat.is(model.sourceData)) return false;
const { db } = model.sourceData.data;
- return (
- hasXrayMap(model) || hasEmMap(model) || (
- // check if from pdb archive but missing relevant meta data
- isFromPdbArchive(model) &&
- !db.pdbx_database_related.db_name.isDefined &&
- !db.pdbx_database_status.status_code_sf.isDefined && (
- !db.exptl.method.isDefined ||
- isFromXray(model) ||
- isFromEm(model)
- )
+ return hasDensityMap(model) || (
+ // check if from pdb archive but missing relevant meta data
+ isFromPdbArchive(model) && (
+ !db.exptl.method.isDefined ||
+ (isFromXray(model) && (
+ !db.pdbx_database_status.status_code_sf.isDefined ||
+ db.pdbx_database_status.status_code_sf.valueKind(0) === Column.ValueKind.Unknown
+ )) ||
+ (isFromEm(model) && (
+ !db.pdbx_database_related.db_name.isDefined
+ ))
)
);
}
diff --git a/src/mol-plugin-state/formats/volume.ts b/src/mol-plugin-state/formats/volume.ts
index 914a7eed1671103d52227cfa1ab0fd7d2a9b6c4a..a89920a3684e7ea0c7fc7cb3b322cfd0166de140 100644
--- a/src/mol-plugin-state/formats/volume.ts
+++ b/src/mol-plugin-state/formats/volume.ts
@@ -181,7 +181,7 @@ export const DscifProvider = DataFormatProvider({
export const BuiltInVolumeFormats = [
['ccp4', Ccp4Provider] as const,
- ['dns6', Dsn6Provider] as const,
+ ['dsn6', Dsn6Provider] as const,
['cube', CubeProvider] as const,
['dx', DxProvider] as const,
['dscif', DscifProvider] as const,
diff --git a/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts b/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts
index fd1bd1db6354d8b83e6c8b0c272981e1434e7eef..99c01876329954d0d043927e15d41e5f24b0b1a6 100644
--- a/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts
+++ b/src/mol-plugin/behavior/dynamic/volume-streaming/transformers.ts
@@ -54,7 +54,7 @@ export const InitVolumeStreaming = StateAction.build({
isApplicable: (a, _, plugin: PluginContext) => {
const canStreamTest = plugin.config.get(PluginConfig.VolumeStreaming.CanStream);
if (canStreamTest) return canStreamTest(a.data, plugin);
- return a.data.models.length === 1 && Model.hasDensityMap(a.data.models[0]);
+ return a.data.models.length === 1 && Model.probablyHasDensityMap(a.data.models[0]);
}
})(({ ref, state, params }, plugin: PluginContext) => Task.create('Volume Streaming', async taskCtx => {
const entries: InfoEntryProps[] = [];
diff --git a/src/mol-plugin/config.ts b/src/mol-plugin/config.ts
index f63b5dc835d748fad98c0fd5f7f8bc61dbbbb525..52a83c6093a2aa88a39263b30dec7706ce0f1917 100644
--- a/src/mol-plugin/config.ts
+++ b/src/mol-plugin/config.ts
@@ -28,9 +28,7 @@ export const PluginConfig = {
VolumeStreaming: {
DefaultServer: item('volume-streaming.server', 'https://ds.litemol.org'),
CanStream: item('volume-streaming.can-stream', (s: Structure, plugin: PluginContext) => {
- return s.models.length === 1 && (Model.hasDensityMap(s.models[0])
- // the following test is to include e.g. 'updated' files from PDBe
- || (!Model.isFromPdbArchive(s.models[0]) && s.models[0].entryId.length === 4));
+ return s.models.length === 1 && Model.probablyHasDensityMap(s.models[0]);
}),
EmdbHeaderServer: item('volume-streaming.emdb-header-server', 'https://ftp.wwpdb.org/pub/emdb/structures'),
},