adjust atom coordinates on structure clones before saving PDB

frontend/StructureViewerMSA.vue

@@ -25,7 +25,7 @@ import StructureViewerTooltip from './StructureViewerTooltip.vue';
 import StructureViewerToolbar from './StructureViewerToolbar.vue';
 import StructureViewerMixin from './StructureViewerMixin.vue';
 import { mockPDB, makeSubPDB, makeMatrix4, interpolateMatrices, animateMatrix  } from './Utilities.js';
-import { download, PdbWriter, Matrix4, Quaternion, Vector3 } from 'ngl';
+import { download, PdbWriter, Matrix4, Quaternion, Vector3, concatStructures } from 'ngl';
 import { pulchra } from 'pulchra-wasm';
 
 // Mock alignment object from two (MSA-derived) aligned strings
@@ -135,7 +135,17 @@ REMARK    Warning: Non C-alpha atoms may have been re-generated by PULCHRA
 REMARK             if they are not present in the original PDB file.
 `;
             this.stage.eachComponent(comp => {
-                PDB = new PdbWriter(comp.structure, { renumberSerial: false }).getData();
+                let clone = concatStructures("clone", comp.structure)
+                let matrix = new Matrix4();
+                matrix.fromArray(comp.transform.elements);
+                clone.eachAtom(ap => {
+                    let position = new Vector3(ap.x, ap.y, ap.z);
+                    position.applyMatrix4(matrix);
+                    ap.x = position.x;
+                    ap.y = position.y;
+                    ap.z = position.z;
+                });
+                PDB = new PdbWriter(clone, { renumberSerial: false }).getData();
                 PDB = PDB.split('\n').filter(line => line.startsWith("ATOM")).join('\n');
                 let index = parseInt(comp.structure.name.replace("key-", "")); 
                 let name = this.entries[index].name;