fixes

src/mol-geo/representation/structure/visual/polymer-backbone-cylinder.ts

@@ -46,10 +46,12 @@ async function createPolymerBackboneCylinderMesh(ctx: RuntimeContext, unit: Unit
         const residuesIt = Segmentation.transientSegments(residueSegments, elements);
 
         let i = 0
+        let first = true
 
         while (polymerIt.hasNext) {
             const polymerSegment = polymerIt.move();
             residuesIt.setSegment(polymerSegment);
+            first = true
             while (residuesIt.hasNext) {
                 const residueSegment = residuesIt.move();
                 l.element = elements[residueSegment.start];
@@ -70,8 +72,12 @@ async function createPolymerBackboneCylinderMesh(ctx: RuntimeContext, unit: Unit
                 }
                 pos(l.element, curV)
 
-                builder.setId(residueSegment.start)
-                builder.addCylinder(prevV, curV, 1, { radiusTop: 0.2, radiusBottom: 0.2 })
+                if (!first) {
+                    builder.setId(residueSegment.start)
+                    builder.addCylinder(prevV, curV, 1, { radiusTop: 0.2, radiusBottom: 0.2 })
+                } else {
+                    first = false
+                }
 
                 Vec3.copy(prevV, curV)
 

src/mol-geo/representation/structure/visual/util/polymer.ts

@@ -13,14 +13,14 @@ export function getPolymerElementCount(unit: Unit) {
     const { elements } = unit
     const l = Element.Location(unit)
     if (Unit.isAtomic(unit)) {
-        const { chainSegments, residueSegments } = unit.model.atomicHierarchy
-        const chainsIt = Segmentation.transientSegments(chainSegments, elements);
+        const { polymerSegments, residueSegments } = unit.model.atomicHierarchy
+        const polymerIt = Segmentation.transientSegments(polymerSegments, elements);
         const residuesIt = Segmentation.transientSegments(residueSegments, elements);
-        while (chainsIt.hasNext) {
-            residuesIt.setSegment(chainsIt.move());
+        while (polymerIt.hasNext) {
+            residuesIt.setSegment(polymerIt.move());
             while (residuesIt.hasNext) {
-                l.element = elements[residuesIt.move().start];
-                if (StructureProperties.entity.type(l) === 'polymer') count++
+                residuesIt.move();
+                count++
             }
         }
     } else if (Unit.isSpheres(unit)) {

src/mol-model/structure/model/formats/mmcif/atomic.ts

@@ -29,14 +29,12 @@ function findHierarchyOffsets(atom_site: AtomSite) {
 
     for (let i = start + 1; i < end; i++) {
         const newChain = !label_entity_id.areValuesEqual(i - 1, i) || !label_asym_id.areValuesEqual(i - 1, i);
-        // TODO improve???
-        const newPolymer = newChain
-            || label_seq_id.value(i - 1) !== label_seq_id.value(i) - 1;
         const newResidue = newChain
             || !label_seq_id.areValuesEqual(i - 1, i)
             || !auth_seq_id.areValuesEqual(i - 1, i)
             || !pdbx_PDB_ins_code.areValuesEqual(i - 1, i)
             || !label_comp_id.areValuesEqual(i - 1, i);
+        const newPolymer = newResidue && label_seq_id.value(i - 1) !== label_seq_id.value(i) - 1;
 
         if (newResidue) residues[residues.length] = i as Element;
         if (newPolymer) polymers[polymers.length] = i as Element;

src/mol-view/stage.ts

@@ -74,9 +74,10 @@ export class Stage {
         // this.loadPdbid('3pqr') // inter unit bonds
         // this.loadPdbid('4v5a') // ribosome
         // this.loadPdbid('3j3q') // ...
+        this.loadPdbid('3sn6') // ...
         // this.loadMmcifUrl(`../../examples/1cbs_full.bcif`)
 
-        this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000001.cif`)
+        // this.loadMmcifUrl(`../../../test/pdb-dev/PDBDEV_00000001.cif`)
     }
 
     async loadMmcifUrl (url: string) {