icn3d 3.31.9 → 3.31.11

package/icn3d.js

@@ -9062,9 +9062,9 @@ class ClickMenu {
         });
        
         me.myEventCls.onIds("#" + me.pre + "mn1_collection", "click", function (e) { me.icn3d; //e.preventDefault();
-         me.htmlCls.dialogCls.openDlg('dl_collection', 'Please input the collection file');
-       });
-
+           me.htmlCls.dialogCls.openDlg("dl_selectCollections", "Select Collections");
+        });
+       
         me.myEventCls.onIds("#" + me.pre + "mn1_dsn6", "click", function(e) { me.icn3d; //e.preventDefault();
            me.htmlCls.dialogCls.openDlg('dl_dsn6', 'Please input the map file to display electron density map');
         });
@@ -14131,18 +14131,18 @@ class SetDialog {
         html += me.htmlCls.buttonStr + "reload_selectionfile' style='margin-top: 6px;'>Load</button>";
         html += "</div>";
 
-        html += me.htmlCls.divStr + "dl_collection' class='" + dialogClass + "'>";
-        html += this.addNotebookTitle('dl_collection', 'Please input the collection file');
+        html += me.htmlCls.divStr + "dl_selectCollections' class='" + dialogClass + "'>";
+        html += me.htmlCls.divStr + "dl_collectionsMenu'>";
+        html += '<b>Collection File</b>: <div style="width:20px; margin-top:6px; display:inline-block;"><span id="' + me.pre + 'dl_collection_file_expand" class="ui-icon ui-icon-plus icn3d-expand icn3d-link" style="display:none; width:15px;" title="Expand"></span><span id="' + me.pre + 'dl_collection_file_shrink" class="ui-icon ui-icon-minus icn3d-shrink icn3d-link" style="width:15px;" title="Shrink"></span></div><br>';
+        html += me.htmlCls.divStr + "dl_collection_file' style=''>";
         html += "You can load a collection of structures via a file. Here is <a href='https://github.com/ncbi/icn3d/blob/master/example/collection.json' target='_blank'>one example file</a><br><br>";
         html += "Collection file: " + me.htmlCls.inputFileStr + "id='" + me.pre + "collectionfile'><br/>";
         html += me.htmlCls.buttonStr + "reload_collectionfile' style='margin-top: 6px;'>Load</button>";
         html += "</div>";
-
-        html += me.htmlCls.divStr + "dl_selectCollections' class='" + dialogClass + "'>";
-        html += me.htmlCls.divStr + "dl_collectionsMenu'>";
-        html += "<b>Structures:</b> <br/>";
-        html += "<select id='" +  me.pre + "collections_menu' multiple size='6' style='min-width:130px;'>";
-        html += "</select>";
+        html += "</div>";
+        html += '<br/><b>Structures</b>: <div style="width:20px; margin-top:6px; display:inline-block;"><span id="' + me.pre + 'dl_collection_structures_expand" class="ui-icon ui-icon-plus icn3d-expand icn3d-link" style="width:15px;" title="Expand"></span><span id="' + me.pre + 'dl_collection_structures_shrink" class="ui-icon ui-icon-minus icn3d-shrink icn3d-link" style="display:none; width:15px;" title="Shrink"></span></div><br>';
+        html += me.htmlCls.divStr + "dl_collection_structures' style='display: none'>";
+        html += "<select id='" + me.pre + "collections_menu'multiple size='6' style='min-width:300px;'></select>";
         html += "</div>";
         html += "</div>";
 
@@ -16505,17 +16505,13 @@ class Events {
                 ic.resizeCanvasCls.closeDialogs();
             }
             me.htmlCls.setHtmlCls.fileSupport();
-            let reader = new FileReader();
-            reader.onload = async function (e) {
+                let reader = new FileReader();
+                
+                reader.onload = async function (e) {
                 let dataStr = JSON.parse(e.target.result);
                 let collection = [dataStr["structures"].map(({ id }) => id), dataStr["structures"].map(({ title }) => title)];
                 let collectionHtml = ic.selectCollectionsCls.setAtomMenu(collection[0], collection[1]);
-                let bNoDuplicate = true;
-                await ic.chainalignParserCls.downloadMmdbAf(collection[0][0], undefined, undefined, bNoDuplicate);
-    
-                ic.opts["color"] = "structure";
-                ic.setColorCls.setColorByOptions(ic.opts, ic.dAtoms);
-    
+
                 $("#" + ic.pre + "collections_menu").html(collectionHtml);
                 ic.selectCollectionsCls.clickStructure();
     
@@ -16526,8 +16522,27 @@ class Events {
                     $("#" + me.pre + "collectionfile").val(),
                 false
                 );
+                
             };
             reader.readAsText(file);
+            
+            if (Object.keys(me.utilsCls.getStructures(ic.dAtoms))){
+                $("#" + me.pre + "dl_collection_file").hide();
+                $("#" + me.pre + "dl_collection_structures").show();
+                $("#" + me.pre + "dl_collection_file_expand").show();
+                $("#" + me.pre + "dl_collection_file_shrink").hide();
+                $("#" + me.pre + "dl_collection_structures_expand").hide();
+                $("#" + me.pre + "dl_collection_structures_shrink").show();
+
+            } else {
+                $("#" + me.pre + "dl_collection_file").show();
+                $("#" + me.pre + "dl_collection_structures").hide();
+                $("#" + me.pre + "dl_collection_file_expand").hide();
+                $("#" + me.pre + "dl_collection_file_shrink").hide();
+                $("#" + me.pre + "dl_collection_structures_expand").show();
+                $("#" + me.pre + "dl_collection_structures_shrink").hide();
+            }
+              
             me.htmlCls.dialogCls.openDlg("dl_selectCollections", "Select Collections");
             }
         });
@@ -40865,8 +40880,10 @@ class AnnoIg {
     }
 
     showRefNum(giSeq, chnid, kabat_or_imgt, bCustom) {  let ic = this.icn3d; ic.icn3dui;
-        let bResult = ic.chainid2igtrack[chnid];
-        if(!bResult) return {html: '', html2: '', html3: ''};
+        if(ic.chainid2igtrack) {
+            let bResult = ic.chainid2igtrack[chnid];
+            if(!bResult) return {html: '', html2: '', html3: ''};
+        }
 
         let html = this.getIgAnnoHtml(chnid, giSeq, bCustom, kabat_or_imgt);
 
@@ -40933,12 +40950,13 @@ class AnnoIg {
         ic.chain2igArray[chnid] = [];
         this.setChain2igArray(chnid, giSeq, bCustom);
 
-
         // remove Igs without BCEF strands one more time
         let igArray = ic.chain2igArray[chnid];    
 
         for(let i = 0, il = igArray.length; i < il; ++i) {
             let domainid = igArray[i].domainid;
+
+            if(!ic.domainid2info) continue;
             let info = ic.domainid2info[domainid];
             if(!info) continue;
 
@@ -41006,7 +41024,6 @@ class AnnoIg {
             }
         }
 
-
         // reset ic.chain2igArray
         ic.chain2igArray[chnid] = [];
         this.setChain2igArray(chnid, giSeq, bCustom);
@@ -41025,7 +41042,7 @@ class AnnoIg {
             //    htmlIg += '<span></span>';
             //}
             //else {
-                refnumLabel = ic.resid2refnum[residueid];
+                refnumLabel = (bCustom) ? ic.chainsMapping[chnid][residueid] : ic.resid2refnum[residueid];
                 let bHidelabel = false;
 
                 if(refnumLabel) {              
@@ -41150,9 +41167,14 @@ class AnnoIg {
         html3 += htmlTmp + '<br>';
         html += htmlTmp + '<span class="icn3d-seqLine">';
 
+        if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGap(ic.seqStartLen[chnid], '-');
+ 
         html += htmlIg;
 
-        html += htmlCnt;
+        if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGap(ic.seqEndLen[chnid], '-');
+        
+        if(!bCustom) html += htmlCnt;
+
         html += '</span>';
         html += '<br>';
         html += '</div>';
@@ -41166,6 +41188,8 @@ class AnnoIg {
 
         for(let i = 0, il = igArray.length; i < il; ++i) {
             let domainid = igArray[i].domainid;
+            if(!ic.domainid2info) continue;
+
             let info = ic.domainid2info[domainid];
             if(!info) continue;
 
@@ -41194,6 +41218,8 @@ class AnnoIg {
             html2 += htmlTitle; 
             html2 += htmlCnt + '<span class="icn3d-seqLine">';
 
+            if(ic.seqStartLen && ic.seqStartLen[chnid]) html2 += ic.showSeqCls.insertMulGapOverview(chnid, ic.seqStartLen[chnid]);
+
             let prevDomainindex, color;
             for(let i = 0, il = fromArray.length; i < il; ++i) {
                 let resi = ic.ParserUtilsCls.getResi(chnid, fromArray[i]);
@@ -41625,7 +41651,7 @@ class AnnoDomain {
 
             if(ic.seqStartLen && ic.seqStartLen[chnid]) html2 += ic.showSeqCls.insertMulGapOverview(chnid, ic.seqStartLen[chnid]);
 
-            if(me.cfg.blast_rep_id != chnid) { // regular
+            if(me.cfg.blast_rep_id != chnid) { // regular             
                 for(let i = 0, il = posFromArray.length; i < il; ++i) {
                     // let emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray[i] - ic.baseResi[chnid] - 1) / ic.maxAnnoLength) : Math.round(ic.seqAnnWidth *(fromArray[i] - toArray[i-1] - 1) / ic.maxAnnoLength);
                     let emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(posFromArray[i]) / ic.maxAnnoLength) : Math.round(ic.seqAnnWidth *(posFromArray[i] - posToArray[i-1] - 1) / ic.maxAnnoLength);
@@ -41634,7 +41660,7 @@ class AnnoDomain {
                     html2 += '<div style="display:inline-block; color:white!important; font-weight:bold; background-color:#' + color + '; width:' + Math.round(ic.seqAnnWidth *(posToArray[i] - posFromArray[i] + 1) / ic.maxAnnoLength) + 'px;" class="icn3d-seqTitle icn3d-link icn3d-blue" 3ddomain="' +(index+1).toString() + '" from="' + posFromArray + '" to="' + posToArray + '" shorttitle="' + title + '" index="' + index + '" setname="' + chnid + '_3d_domain_' +(index+1).toString() + '" id="' + chnid + '_3d_domain_' + index + '" anno="sequence" chain="' + chnid + '" title="' + fulltitle + '">3D domain ' +(index+1).toString() + '</div>';
                 }
             }
-            else { // with potential gaps
+            else { // with potential gaps 
                 let fromArray2 = [], toArray2 = [];
                 for(let i = 0, il = fromArray.length; i < il; ++i) {
                     fromArray2.push(fromArray[i]);
@@ -46938,6 +46964,7 @@ class ShowAnno {
                   // the missing residues at the end of the seq will be filled up in the API showNewTrack()
                   let nGap = 0;
                   ic.alnChainsSeq[chnid] = [];
+
                   //let offset =(ic.chainid2offset[chnid]) ? ic.chainid2offset[chnid] : 0;                
                   for(let i = 0, il = targetSeq.length; i < il; ++i) {
                       //text += ic.showSeqCls.insertGap(chnid, i, '-', true);
@@ -47557,6 +47584,7 @@ class ShowSeq {
                 let bCustom = true;
                 let result = ic.annoIgCls.showRefNum(giSeq, chnid, undefined, bCustom);
                 html += result.html;
+                // html2 += result.html2;
                 html3 += result.html3;
             }
         }
@@ -57030,8 +57058,9 @@ class RealignParser {
       }
 
       // If rmsd from vastsrv is too large, realign the chains
-      //if(me.cfg.chainalign && !me.cfg.usepdbnum && me.cfg.resdef && rmsd > 5) {   
-      if(!me.cfg.usepdbnum && me.cfg.resdef && rmsd > 5) {     
+      //if(me.cfg.chainalign && !me.cfg.usepdbnum && me.cfg.resdef && rmsd > 5) {  
+      // redo algnment only for VAST serv page 
+      if(!me.cfg.usepdbnum && me.cfg.resdef && rmsd > 5) {    
         console.log("RMSD from VAST is larger than 5. Realign the chains with TM-align."); 
         //let nameArray = me.cfg.chainalign.split(',');
         let nameArray = Object.keys(chainidHash);
@@ -60993,13 +61022,15 @@ class SetSeqAlign {
         ic.alnChains = {};
         ic.alnChains[chainid1] = {};      
 
-        let resi2range_t = {}; // accumulative aligned residues in the template chain
+        let resid2range_t = {}; // accumulative aligned residues in the template chain
         // start and end of MSA
         let start_t = 9999, end_t = -1;
 
         let baseResi = ic.chainsSeq[chainid1][0].resi - 1;
+
         for(let index = 1, indexl = chainidArray.length; index < indexl; ++index) { 
             let chainIndex = index - 1;
+            chainidArray[index];
             if(!ic.qt_start_end[chainIndex]) continue;
 
             for(let i = 0, il = ic.qt_start_end[chainIndex].length; i < il; ++i) {
@@ -61010,11 +61041,12 @@ class SetSeqAlign {
                 //     end1 = ic.qt_start_end[chainIndex][i].t_end;
                 // }
                 // else {
+                    //ic.qt_start_end is zero-based
                     start1 = parseInt(ic.qt_start_end[chainIndex][i].t_start) - 1;
                     end1 = parseInt(ic.qt_start_end[chainIndex][i].t_end) - 1;
                 // }
                 for(let j = start1; j <= end1; ++j) {
-                    let resi;
+                    let resi, resid;
 
                     // if(me.cfg.aligntool == 'tmalign') { // tmalign: just one residue in this for loop
                     //     resi = ic.qt_start_end[chainIndex][i].t_start;
@@ -61026,53 +61058,56 @@ class SetSeqAlign {
                             resiPos = j - baseResi;
                         }
                         else {
-                            resiPos = (bRealign) ? j : j - baseResi;
+                            // resiPos = (bRealign) ? j : j - baseResi;
+                            resiPos = j;
                         }
                         resi = ic.ParserUtilsCls.getResi(chainidArray[0], resiPos);
+                        resid = chainidArray[0] + '_' + resi;
                     // }
 
-                    resi2range_t[resi] = 1;
+                    resid2range_t[resid] = 1;
                     if(j < start_t) start_t = j;
                     if(j > end_t) end_t = j;
                 }
             }
         }
-        
+
         // TM-align should use "start1 = ic.qt_start_end[chainIndex][i].t_start - 1", but the rest are the same as ""bRealign"
         if(me.cfg.aligntool == 'tmalign') bRealign = true; // real residue numbers are stored
 
-        let resi2rangeArray = Object.keys(resi2range_t);
-        resi2rangeArray.sort(function(a, b) {
-            return parseInt(a) - parseInt(b);
+        let resid2rangeArray = Object.keys(resid2range_t);
+        resid2rangeArray.sort(function(a, b) {
+            return parseInt(a.split('_')[2]) - parseInt(b.split('_')[2]);
         });
 
         // assign range to each resi
-        let prevResi = -999, start = 0, end = 0, resiArray = [], prevEnd = 0;
-        for(let i = 0, il = resi2rangeArray.length; i < il; ++i) {
-            let resi = resi2rangeArray[i];
+        let prevResi = -999, start = 0, end = 0, residArray = [], prevEnd = 0;
+        for(let i = 0, il = resid2rangeArray.length; i < il; ++i) {
+            let resid = resid2rangeArray[i];
+            let resi = resid.split('_')[2];
             
             if(i == 0) {
                 start = resi;
             }
             else if(i > 0 && ic.resid2ncbi[resi] != ic.resid2ncbi[prevResi] + 1 && ic.resid2ncbi[resi] != ic.resid2ncbi[prevResi]) { // new start
                 end = prevResi;
-                for(let j = 0, jl = resiArray.length; j < jl; ++j) {
-                    resi2range_t[resiArray[j]] = {resiStart: start, resiEnd: end, prevResiEnd: prevEnd};
+                for(let j = 0, jl = residArray.length; j < jl; ++j) {
+                    resid2range_t[residArray[j]] = {resiStart: start, resiEnd: end, prevResiEnd: prevEnd};
                 }
 
-                resiArray = [];
+                residArray = [];
                 start = resi;
                 prevEnd = end;
             }
 
-            resiArray.push(resi);
+            residArray.push(resid);
 
             prevResi = resi;
         }
 
         end = prevResi;
-        for(let j = 0, jl = resiArray.length; j < jl; ++j) {
-            resi2range_t[resiArray[j]] = {resiStart: start, resiEnd: end, prevResiEnd: prevEnd};
+        for(let j = 0, jl = residArray.length; j < jl; ++j) {
+            resid2range_t[residArray[j]] = {resiStart: start, resiEnd: end, prevResiEnd: prevEnd};
         }
 
         for(let i = 0, il = chainidArray.length; i < il; ++i) { 
@@ -61086,6 +61121,7 @@ class SetSeqAlign {
         // fill the template ic.alnChainsSeq[chainid1]
         for(let j = 0, jl = ic.chainsSeq[chainid1].length; j < jl; ++j) { 
             let resi = ic.chainsSeq[chainid1][j].resi;
+            let resid = chainid1 + '_' + resi;
 
             let jAdjusted = (me.cfg.aligntool != 'tmalign') ? j : j + baseResi;
 
@@ -61099,15 +61135,15 @@ class SetSeqAlign {
             resObject.mmdbid = chainid1.substr(0, pos);
             resObject.chain = chainid1.substr(pos+1);
             resObject.resi = resi;
-            resObject.resn = (resi2range_t[resi]) ? ic.chainsSeq[chainid1][j].name.toUpperCase() : ic.chainsSeq[chainid1][j].name.toLowerCase();
-            resObject.aligned = (resi2range_t[resi]) ? true : false;
-            resObject.color = (resi2range_t[resi]) ? '#FF0000' : me.htmlCls.GREYC; // color by identity
-            resObject.color2 = (resi2range_t[resi]) ? '#FF0000' : me.htmlCls.GREYC; // color by conservation
-            resObject.class = (resi2range_t[resi]) ? 'icn3d-align' : 'icn3d-nalign';
+            resObject.resn = (resid2range_t[resid]) ? ic.chainsSeq[chainid1][j].name.toUpperCase() : ic.chainsSeq[chainid1][j].name.toLowerCase();
+            resObject.aligned = (resid2range_t[resid]) ? true : false;
+            resObject.color = (resid2range_t[resid]) ? '#FF0000' : me.htmlCls.GREYC; // color by identity
+            resObject.color2 = (resid2range_t[resid]) ? '#FF0000' : me.htmlCls.GREYC; // color by conservation
+            resObject.class = (resid2range_t[resid]) ? 'icn3d-align' : 'icn3d-nalign';
     
             ic.alnChainsSeq[chainid1].push(resObject);
 
-            if(resi2range_t[resi]) {
+            if(resid2range_t[resid]) {
                 $.extend(ic.alnChains[chainid1], ic.residues[chainid1 + '_' + resObject.resi] );
                 hAtoms = me.hashUtilsCls.unionHash(hAtoms, ic.residues[chainid1 + '_' + resObject.resi]);
             }
@@ -61119,7 +61155,7 @@ class SetSeqAlign {
         for(let arrayIndex = 0, arrayIndexl = index_alignLen.length; arrayIndex < arrayIndexl; ++arrayIndex) { 
             let index = index_alignLen[arrayIndex].index;
             alignedChainIndice.push(index);
-            let hAtomsTmp = this.mergeTwoSeqForAll(chainidArray, index, alignedChainIndice, resi2range_t, start_t, end_t, bRealign);
+            let hAtomsTmp = this.mergeTwoSeqForAll(chainidArray, index, alignedChainIndice, resid2range_t, start_t, end_t, bRealign);
 
             hAtoms = me.hashUtilsCls.unionHash(hAtoms, hAtomsTmp);
         }      
@@ -61292,7 +61328,7 @@ class SetSeqAlign {
         return {"pos1": result1.pos, "pos2": result2.pos};
     }
 
-    mergeTwoSeqForAll(chainidArray, index, alignedChainIndice, resi2range_t, start_t, end_t, bRealign) { let ic = this.icn3d, me = ic.icn3dui;
+    mergeTwoSeqForAll(chainidArray, index, alignedChainIndice, resid2range_t, start_t, end_t, bRealign) { let ic = this.icn3d, me = ic.icn3dui;
         let hAtoms = {};
 
         let chainid = chainidArray[index];
@@ -61381,7 +61417,7 @@ class SetSeqAlign {
                 start1Pos = start1;
                 end1Pos = end1;
             }
-            //let range = resi2range_t[resiStart1];
+            //let range = resid2range_t[chainid1 + '_' + resiStart1];
   
             // if the mapping does not start from start_t, add gaps to the query seq
             if(i == 0) {
@@ -66849,70 +66885,181 @@ class SelectCollections {
     return html;
   }
 
+  reset() {
+    let ic = this.icn3d;
+
+    ic.atoms = {};
+
+    ic.proteins = {};
+    ic.nucleotides = {};
+    ic.chemicals = {};
+    ic.ions = {};
+    ic.water = {};
+
+    ic.structures = {};
+    ic.chains = {};
+    ic.chainsSeq = {};
+    ic.residues = {};
+
+    ic.defNames2Atoms = {};
+    ic.defNames2Residues = {};
+
+    ic.ssbondpnts = {};
+
+    ic.bShowHighlight = false;
+    ic.bResetSets = true;
+  }
+
+  dictionaryDifference(dict1, dict2) {
+      const difference = {};
+
+      for (let key in dict2) {
+          if (!(key in dict1)) {
+              difference[key] = dict2[key];
+          }
+      }
+
+      return difference;
+    }
+
   clickStructure() {
     let ic = this.icn3d,
       me = ic.icn3dui;
     let thisClass = this;
 
+    if (ic.allData == undefined) {
+      ic.allData = {};
+      ic.allData['all'] = {
+        'atoms': {},
+        'proteins': {},
+        'nucleotides': {},
+        'chemicals': {},
+        'ions': {},
+        'water': {},
+        'structures': {}, // getSSExpandedAtoms
+        'ssbondpnts': {},
+        'residues': {}, // getSSExpandedAtoms
+        'chains': {},
+        'chainsSeq': {}, //Sequences and Annotation
+        'defNames2Atoms': {},
+        'defNames2Residues': {}
+      };
+      ic.allData['prev'] = {};
+    }
+
     //me.myEventCls.onIds("#" + ic.pre + "atomsCustom", "change", function(e) { let  ic = thisClass.icn3d;
     $("#" + ic.pre + "collections_menu").change(async function (e) {
       let ic = thisClass.icn3d;
-      //    ic.init()
+
       let nameArray = $(this).val();
       let nameStructure = $(this).find("option:selected").text();
 
       ic.nameArray = nameArray;
       if (nameArray !== null) {
-        ic.bShowHighlight = false;
+        // let chainIdHash = {};
+
         let bNoDuplicate = true;
-        await ic.chainalignParserCls.downloadMmdbAf(nameArray.toString(), undefined, undefined, bNoDuplicate);
+        thisClass.reset();
+        for (const name of nameArray) {
+          if (!(name in ic.allData)) {
+            ic.allData['prev'] = JSON.parse(JSON.stringify(ic.allData['all']));//me.hashUtilsCls.cloneHash(ic.allData['all']);
 
-        ic.dAtoms = {};
-        ic.hAtoms = {};
-        //  ic.ssbondpnts = {};
-        let chainIdHash = {};
-
-        for (const name in nameArray) {
-          for (const key in ic.chains) {
-            if (key.includes(nameArray[name])) {
-              chainIdHash[key] = 1;
-              if (ic.chains.hasOwnProperty(key)) {
-                const innerDict = ic.chains[key];
-                for (const innerKey in innerDict) {
-                  if (innerDict.hasOwnProperty(innerKey)) {
-                    ic.dAtoms[innerKey] = innerDict[innerKey];
-                    ic.hAtoms[innerKey] = innerDict[innerKey];
-                  }
-                }
-              }
-            }
+            ic.atoms = ic.allData['all']['atoms'];
+            
+            ic.proteins = ic.allData['all']['proteins'];
+            ic.nucleotides = ic.allData['all']['nucleotides'];
+            ic.chemicals = ic.allData['all']['chemicals'];
+            ic.ions = ic.allData['all']['ions'];
+            ic.water = ic.allData['all']['water'];
+  
+            ic.structures = ic.allData['all']['structures'];
+            ic.ssbondpnts = ic.allData['all']['ssbondpnts'];
+            ic.residues = ic.allData['all']['residues'];
+            ic.chains = ic.allData['all']['chains'];
+            ic.chainsSeq = ic.allData['all']['chainsSeq'];
+            ic.defalls2Atoms = ic.allData['all']['defalls2Atoms'];
+            ic.defalls2Residues = ic.allData['all']['defalls2Residues'];
+            await ic.chainalignParserCls.downloadMmdbAf(name, undefined, undefined, bNoDuplicate).then(() => {
+              ic.allData['all'] = {
+                'atoms': ic.atoms,
+                'proteins': ic.proteins,
+                'nucleotides': ic.nucleotides,
+                'chemicals': ic.chemicals,
+                'ions': ic.ions,
+                'water': ic.water,
+                'structures': ic.structures, // getSSExpandedAtoms
+                'ssbondpnts': ic.ssbondpnts,
+                'residues': ic.residues, // getSSExpandedAtoms
+                'chains': ic.chains,
+                'chainsSeq': ic.chainsSeq, //Sequences and Annotation
+                'defNames2Atoms': ic.defNames2Atoms,
+                'defNames2Residues': ic.defNames2Residues
+              };
+
+              ic.allData[name] = {
+                'atoms': thisClass.dictionaryDifference(ic.allData['prev']['atoms'], ic.atoms),
+                'proteins': thisClass.dictionaryDifference(ic.allData['prev']['proteins'], ic.proteins),
+                'nucleotides': thisClass.dictionaryDifference(ic.allData['prev']['nucleotides'], ic.nucleotides),
+                'chemicals': thisClass.dictionaryDifference(ic.allData['prev']['chemicals'], ic.chemicals),
+                'ions': thisClass.dictionaryDifference(ic.allData['prev']['ions'], ic.ions),
+                'water': thisClass.dictionaryDifference(ic.allData['prev']['water'], ic.water),
+                'structures': thisClass.dictionaryDifference(ic.allData['prev']['structures'], ic.structures), // getSSExpandedAtoms
+                'ssbondpnts': thisClass.dictionaryDifference(ic.allData['prev']['ssbondpnts'], ic.ssbondpnts),
+                'residues': thisClass.dictionaryDifference(ic.allData['prev']['residues'], ic.residues), // getSSExpandedAtoms
+                'chains': thisClass.dictionaryDifference(ic.allData['prev']['chains'], ic.chains),
+                'chainsSeq': thisClass.dictionaryDifference(ic.allData['prev']['chainsSeq'], ic.chainsSeq), //Sequences and Annotation
+                'defNames2Atoms': thisClass.dictionaryDifference(ic.allData['prev']['defNames2Atoms'], ic.defNames2Atoms),
+                'defNames2Residues': thisClass.dictionaryDifference(ic.allData['prev']['defNames2Residues'], ic.defNames2Residues)
+              };
+
+              // ic.atoms = Object.assign(ic.atoms, ic.atomsTemp);
+              thisClass.reset();
+            });
           }
         }
+        for (const name of nameArray) {
+            ic.atoms = Object.assign(ic.atoms, ic.allData[name]['atoms']);
+            
+            ic.proteins = Object.assign(ic.proteins, ic.allData[name]['proteins']);
+            ic.nucleotides = Object.assign(ic.nucleotides, ic.allData[name]['nucleotides']);
+            ic.chemicals = Object.assign(ic.chemicals, ic.allData[name]['chemicals']);
+            ic.ions = Object.assign(ic.ions, ic.allData[name]['ions']);
+            ic.water = Object.assign(ic.water, ic.allData[name]['water']);
+
+            ic.structures = Object.assign(ic.structures, ic.allData[name]['structures']);
+            ic.ssbondpnts = Object.assign(ic.ssbondpnts, ic.allData[name]['ssbondpnts']);
+            ic.residues = Object.assign(ic.residues, ic.allData[name]['residues']);
+            ic.chains = Object.assign(ic.chains, ic.allData[name]['chains']);
+            ic.chainsSeq = Object.assign(ic.chainsSeq, ic.allData[name]['chainsSeq']);
+            ic.defNames2Atoms = Object.assign(ic.defNames2Atoms, ic.allData[name]['defNames2Atoms']);
+            ic.defNames2Residues = Object.assign(ic.defNames2Residues, ic.allData[name]['defNames2Residues']);
+            ic.dAtoms = me.hashUtilsCls.cloneHash(ic.atoms);
+            ic.hAtoms = me.hashUtilsCls.cloneHash(ic.atoms);
+          }
+          
+        ic.opts["color"] = "structure";
+        ic.setStyleCls.setAtomStyleByOptions();
+        ic.setColorCls.setColorByOptions(ic.opts, ic.atoms);
 
         ic.transformCls.zoominSelection();
         ic.definedSetsCls.showSets();
 
-        await ic.drawCls.draw();
-        ic.saveFileCls.showTitle();
-
         ic.bResetAnno = true;
         if(ic.bAnnoShown) {
-          // show annotations just fo the displayed atoms
-          // await ic.showAnnoCls.showAnnotations(ic.dAtoms);
           await ic.showAnnoCls.showAnnotations();
 
           ic.hlUpdateCls.updateHlAll(nameArray);
           // show selected chains in annotation window
           ic.annotationCls.showAnnoSelectedChains();
         }
-        
+
+        await ic.drawCls.draw();
+        ic.saveFileCls.showTitle();
+
         me.htmlCls.clickMenuCls.setLogCmd(
           "select structure " + "[" + nameStructure + "]",
           true
         );
-        ic.bSelectResidue = false;
-
-        ic.bShowHighlight = true; // reset
       }
     });
 
@@ -67467,7 +67614,10 @@ class LoadScript {
         let idArray = id.split(',');
         let idNew = '';
         for(let i = 0, il = idArray.length; i < il; ++i) {
-          if(!(ic.structures && ic.structures.hasOwnProperty(idArray[i]))) {
+          if(!(ic.structures && (ic.structures.hasOwnProperty(idArray[i]) 
+              || ic.structures.hasOwnProperty(idArray[i].toLowerCase()) 
+              || ic.structures.hasOwnProperty(idArray[i].toUpperCase())
+              ) )) {
             if(idNew) idNew += ',';
             idNew += idArray[i];
           }
@@ -71492,7 +71642,12 @@ class Dssp {
     }
 
     rmStrandFromRefnumlabel(refnumLabel) { let ic = this.icn3d; ic.icn3dui;
-        return (!refnumLabel) ? refnumLabel : refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').replace(/\+/g, '').replace(/\-/g, '').substr(1); // C', C''
+        if(refnumLabel && isNaN(refnumLabel.substr(0,1))) {
+            return (!refnumLabel) ? refnumLabel : refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').replace(/\+/g, '').replace(/\-/g, '').substr(1); // C', C''
+        }
+        else { // custom ref numbers
+            return refnumLabel;
+        }
     }
 
     exportRefnum(type, bNoArraySymbol) { let ic = this.icn3d, me = ic.icn3dui;
@@ -71540,25 +71695,15 @@ class Dssp {
                 }
             }
 
-            // let bIgDomain = (ic.domainid2info && Object.keys(ic.domainid2info).length > 0) ? 1 : 0;
-            let stru2bIgDomain = {};
-            for(let domainid in ic.domainid2info) {
-                let stru = domainid.split('_')[0];
-                stru2bIgDomain[stru] = 1;
-            }
-
         // if(bIgDomain) {
             for(let structure in ic.structures) {
-                let bIgDomain = stru2bIgDomain.hasOwnProperty(structure) ? 1 : 0;
-
-                refData += '{"' + structure + '": {"Ig domain" : ' + bIgDomain + ', "igs": [\n';
-
+                let refDataTmp = '';
                 for(let m = 0, ml = ic.structures[structure].length; ic.bShowRefnum && m < ml; ++m) {
                     let chnid = ic.structures[structure][m]; 
                     let igArray = ic.chain2igArray[chnid];
 
                     if(igArray && igArray.length > 0) {
-                        refData += '{"' + chnid + '": {\n';
+                        refDataTmp += '{"' + chnid + '": {\n';
 
                         for(let i = 0, il = igArray.length; i < il; ++i) {
                             let startPosArray = igArray[i].startPosArray;
@@ -71567,26 +71712,32 @@ class Dssp {
                             let info = ic.domainid2info[domainid];
                             if(!info) continue;
 
-                            refData += '"' + domainid + '": {\n';
+                            refDataTmp += '"' + domainid + '": {\n';
 
-                            refData += '"refpdbname":"' + info.refpdbname + '", "score":' + info.score + ', "seqid":' + info.seqid + ', "nresAlign":' + info.nresAlign + ', "data": [';
+                            refDataTmp += '"refpdbname":"' + info.refpdbname + '", "score":' + info.score + ', "seqid":' + info.seqid + ', "nresAlign":' + info.nresAlign + ', "data": [';
                             for(let j = 0, jl = startPosArray.length; j < jl; ++j) {
                                 let startPos = startPosArray[j];
                                 let endPos = endPosArray[j];
                                 for(let k = startPos; k <= endPos; ++k) {
                                     const resid = chnid + '_' + ic.chainsSeq[chnid][k].resi + '_' + ic.chainsSeq[chnid][k].name;
-                                    refData += '{"' + resid + '": "' + resid2refnum[resid] + '"},\n';
+                                    refDataTmp += '{"' + resid + '": "' + resid2refnum[resid] + '"},\n';
                                 }
                             }
-                            refData += '],\n';
+                            refDataTmp += '],\n';
 
-                            refData += '},\n';
+                            refDataTmp += '},\n';
                         }
 
-                        refData += '}},\n';
+                        refDataTmp += '}},\n';
                     }
                 }
 
+                let bIgDomain = (refDataTmp) ? 1 : 0;
+
+                refData += '{"' + structure + '": {"Ig domain" : ' + bIgDomain + ', "igs": [\n';
+
+                refData += refDataTmp;
+
                 refData += ']}},\n';
             }
         // }
@@ -71951,7 +72102,7 @@ class Dssp {
             let strandTmp = strandArray[i].strand;
 
             if(strandTmp != 'G' && strandArray[i].endRefnum - strandArray[i].startRefnum + 1 < 3) { // remove the strand
-                if(i != il - 1) { // modify 
+                if(strandArray[i + 1]) { // modify 
                     strandArray[i + 1].loopResCnt += strandArray[i].loopResCnt + parseInt(strandArray[i].endResi) - parseInt(strandArray[i].startResi) + 1;
                 }
                 
@@ -80337,7 +80488,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.31.2';
+    this.REVISION = '3.31.3';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;