icn3d 3.29.8 → 3.29.10

package/icn3d.js

@@ -7378,6 +7378,8 @@ class ClickMenu {
             thisClass.setLogCmd('ig refnum on', true);
             // await ic.refnumCls.showIgRefNum();
             // thisClass.setLogCmd('set annotation ig', true);
+            if(!ic.bAnnoShown) await ic.showAnnoCls.showAnnotations();
+
             let bSelection = true;
             await ic.annotationCls.setAnnoTabIg(bSelection);
 
@@ -7402,6 +7404,7 @@ class ClickMenu {
             thisClass.setLogCmd('ig template ' + template, true);
             let bSelection = true;
             // await ic.refnumCls.showIgRefNum(template);
+            if(!ic.bAnnoShown) await ic.showAnnoCls.showAnnotations();
             await ic.annotationCls.setAnnoTabIg(bSelection, template);
          });
 
@@ -9527,8 +9530,8 @@ class SetMenu {
             //}
 
             //!!!
-            //html += this.getRadio('mn4_clr', 'mn4_clrIgstrand', 'Ig Strand', undefined, undefined, 2);
-            //html += this.getRadio('mn4_clr', 'mn4_clrIgproto', 'Ig Protodomain', undefined, undefined, 2);
+            // html += this.getRadio('mn4_clr', 'mn4_clrIgstrand', 'Ig Strand', undefined, undefined, 2);
+            // html += this.getRadio('mn4_clr', 'mn4_clrIgproto', 'Ig Protodomain', undefined, undefined, 2);
         }
         else {
             //if(!me.cfg.hidelicense) html += this.getRadio('mn4_clr', 'mn1_delphi2', 'DelPhi<br><span style="padding-left:1.5em;">Potential ' + me.htmlCls.licenseStr + '</span>');
@@ -9659,7 +9662,7 @@ class SetMenu {
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelResidues', 'per Residue', undefined, 1, 2);
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelResnum', 'per Residue & Number', undefined, 1, 2);
             //!!!
-            //html += this.getRadio('mn6_addlabel', 'mn6_addlabelRefnum', 'per Reference Number', undefined, 1, 2);
+            // html += this.getRadio('mn6_addlabel', 'mn6_addlabelRefnum', 'per Reference Number', undefined, 1, 2);
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelChains', 'per Chain', undefined, undefined, 2);
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelTermini', 'N- & C-Termini', undefined, 1, 2);
         }
@@ -9757,8 +9760,9 @@ class SetMenu {
             html += this.getLink('mn6_igrefYes', 'Show Ig for Selection', undefined, 2);
             html += this.getLink('mn6_igrefTpl', 'Ig w/ Specified Template', undefined, 2);
             html += this.getLink('mn6_igrefNo', 'Reset Ig Ref. Number', undefined, 2);
-*/
+
             html += this.getMenuSep();
+*/
 
             html += this.getLink('mn6_customref', 'Custom Ref. Number', undefined, 2);
             html += "</ul>";
@@ -14694,6 +14698,14 @@ class Events {
             thisClass.setLogCmd('define igloop sets | chain ' + chainid, true);
         });
 
+        $(document).on("click", ".icn3d-igdomainsets", function(e) { let ic = me.icn3d;
+            e.stopImmediatePropagation();
+            //e.preventDefault();
+            let chainid = $(this).attr('chainid');
+            ic.addTrackCls.defineIgstrand(chainid, 'igdomain');
+            thisClass.setLogCmd('define igdomain sets | chain ' + chainid, true);
+        });
+
         me.myEventCls.onIds("#" + me.pre + "deletesets", "click", function(e) { let ic = me.icn3d;
              ic.definedSetsCls.deleteSelectedSets();
              thisClass.setLogCmd("delete selected sets", true);
@@ -32473,7 +32485,7 @@ class Instancing {
           }
 
           if(ic.mdlImpostor !== undefined) {
-              // after three.js version 128, the cylinder impostor seemed to have a problem in cloning!!!
+              // after three.js version 128, the cylinder impostor seemed to have a problem in cloning
               symmetryMate = ic.mdlImpostor.clone();
               //symmetryMate.applyMatrix(mat);
               this.applyMat(symmetryMate, mat);
@@ -36832,7 +36844,13 @@ class AnnoCddSite {
 
                 if(me.cfg.blast_rep_id != chnid) { // regular
                     for(let i = 0, il = fromArray.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;
+                        if(titleArray) {
+                            emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray[i]) / ic.maxAnnoLength) : Math.round(ic.seqAnnWidth *(fromArray[i] - toArray[i-1] - 1) / ic.maxAnnoLength);
+                        }
+                        else {
+                            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);
+                        }
 
                         html2 += '<div style="display:inline-block; width:' + emptyWidth + 'px;">&nbsp;</div>';
                         html2 += '<div style="display:inline-block; color:white!important; font-weight:bold; background-color:#' + color + '; width:' + Math.round(ic.seqAnnWidth *(toArray[i] - fromArray[i] + 1) / ic.maxAnnoLength) + 'px;" class="icn3d-seqTitle ' + linkStr + '" ' + type + '="' +(index+1).toString() + '" from="' + fromArray + '" to="' + toArray + '" shorttitle="' + title + '" index="' + index + '" setname="' + setname + '" id="' + chnid + '_domain_' + index + '_' + r + '" anno="sequence" chain="' + chnid + '" title="' + fulltitle + '">' + domain + ' </div>';
@@ -38086,7 +38104,7 @@ class AnnoIg {
                 refnumLabel = ic.resid2refnum[residueid];
                 let bHidelabel = false;
 
-                if(refnumLabel) {                        
+                if(refnumLabel) {               
                     refnumStr_ori = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
                     currStrand = refnumLabel.replace(new RegExp(refnumStr_ori,'g'), '');
                     currStrand_ori = currStrand;
@@ -38118,8 +38136,9 @@ class AnnoIg {
 
                         igElem = {};
                         igElem.startPos = i;
-                        igElem.domainid = domainid;
                     }
+
+                    if(domainid) igElem.domainid = domainid;
                 
                     if(bCustom) {
                         if(!refnumStr) {                               
@@ -38177,6 +38196,8 @@ class AnnoIg {
 
         igElem.endPos = prevPos;
         ic.chain2igArray[chnid].push(igElem);
+
+        if(me.bNode) return {html: '', html2: '', html3: ''};
         let titleSpace = 120;
 
         let linkStr = 'icn3d-link icn3d-blue';
@@ -38232,11 +38253,14 @@ class AnnoIg {
         html += '</div>';
         html += '</div>';
 
-        let igArray = ic.chain2igArray[chnid];
+        let igArray = ic.chain2igArray[chnid];      
+        if(igArray.length == 0) return {html: '', html2: '', html3: ''};
         let rangeArray = [], titleArray = [], fullTitleArray = [], domainArray = [];
         for(let i = 0, il = igArray.length; i < il; ++i) {
             let domainid = igArray[i].domainid;
             let info = ic.domainid2info[domainid];
+            if(!info) continue;
+
             let tmscore = info.score;
             let igType = ic.ref2igtype[info.refpdbname];
             titleArray.push(igType + ' (TM:' + parseFloat(tmscore).toFixed(2) + ')');
@@ -38247,6 +38271,7 @@ class AnnoIg {
             range.locs = [{"from":igArray[i].startPos, "to":igArray[i].endPos}];
             rangeArray.push(range);
         }
+        if(titleArray.length == 0) return {html: '', html2: '', html3: ''};
 
         // add tracks for the summary view
         for(let i = 0, il = fromArray.length; i < il; ++i) {
@@ -38256,10 +38281,10 @@ class AnnoIg {
             let colorStr =(atom.color === undefined || atom.color.getHexString() === 'FFFFFF') ? 'DDDDDD' : atom.color.getHexString();
             let color =(atom.color !== undefined) ? colorStr : "CCCCCC";
 
-            let emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray[i] - ic.baseResi[chnid] - 1) / ic.maxAnnoLength) : 
+            let emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray[i]) / ic.maxAnnoLength) : 
                 Math.round(ic.seqAnnWidth *(fromArray[i] - toArray[i-1] - 1) / ic.maxAnnoLength);
             html2 += '<div style="display:inline-block; width:' + emptyWidth + 'px;">&nbsp;</div>';
-            html2 += '<div style="display:inline-block; color:white!important; font-weight:bold; background-color:#' + color + '; width:' + Math.round(ic.seqAnnWidth *(toArray[i] - fromArray[i] + 1) / ic.maxAnnoLength) + 'px;" class="icn3d-seqTitle ' + linkStr + '" ig="0" from="' + fromArray + '" to="' + toArray + '" shorttitle="' + domainArray[i] + '" index="0" setname="' + chnid + '_igs" id="' + chnid + '_igs" anno="sequence" chain="' + chnid + '" title="' + domainArray[i] + '">' + domainArray[i] + ' </div>';
+            html2 += '<div style="display:inline-block; color:white!important; font-weight:bold; background-color:#' + color + '; width:' + Math.round(ic.seqAnnWidth *(toArray[i] - fromArray[i] + 1) / ic.maxAnnoLength) + 'px;" class="icn3d-seqTitle ' + linkStr + '" ig="0" from="' + fromArray + '" to="' + toArray + '" shorttitle="' + domainArray[i] + '" index="0" setname="' + chnid + '_igs" id="' + chnid + '_igs" anno="sequence" chain="' + chnid + '" title="' + domainArray[i] + '">' +  domainArray[i] + ' </div>';
         }
 
         html2 += htmlCnt;
@@ -41583,91 +41608,115 @@ class AddTrack {
         let selectedResidues = {};
         let bUnion = false, bUpdateHighlight = true;
 
-        let strandCnt = 0, loopCnt = 0;
-        let setName, currStrand, prevStrand, prevStrandReal = 'NT', currType, prevType;
-
         // clear selection
         ic.hAtoms = {};
 
-        let bStart = false;
-
-        for(let i = 0, il = ic.chainsSeq[chainid].length; i < il; ++i) {
-            let currResi = ic.chainsSeq[chainid][i].resi;
-            let resid = chainid + '_' + currResi;
+        if(type == 'igdomain') {
+            let igArray = ic.chain2igArray[chainid];
 
-            if(!ic.residues.hasOwnProperty(resid) ) continue;
-          
-            let refnumLabel, refnumStr, refnum;
-            refnumLabel = ic.resid2refnum[resid];
-            if(!refnumLabel) continue;
+            if(igArray && igArray.length > 0) {
+                
+                for(let i = 0, il = igArray.length; i < il; ++i) {
+                    let startPos = igArray[i].startPos;
+                    let endPos = igArray[i].endPos;
+                    let domainid = igArray[i].domainid;
 
-            refnumStr = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
-            currStrand = refnumLabel.replace(refnumStr, '');
-            refnum = parseInt(refnumStr);
+                    selectedResidues = {};
+                    for(let j = parseInt(startPos); j <= parseInt(endPos); ++j) {
+                        let currResi = ic.chainsSeq[chainid][j].resi;
+                        let resid = chainid + '_' + currResi;
+                        selectedResidues[resid] = 1;
+                    }
 
-            if(type == 'iganchor') {
-                if(refnum > 1000 && refnumStr.substr(refnumStr.length - 2, 2) == '50') {
-                    selectedResidues[resid] = 1;
-                }
-            } 
-            else {
-                if(ic.residIgLoop.hasOwnProperty(resid)) {
-                    currType = 'igloop';
+                    let setName = domainid;
+                    ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
                 }
+            }
+        }
+        else {
+            let strandCnt = 0, loopCnt = 0;
+            let setName, currStrand, prevStrand, prevStrandReal = 'NT', currType, prevType;
+
+            let bStart = false;
+
+            for(let i = 0, il = ic.chainsSeq[chainid].length; i < il; ++i) {
+                let currResi = ic.chainsSeq[chainid][i].resi;
+                let resid = chainid + '_' + currResi;
+
+                if(!ic.residues.hasOwnProperty(resid) ) continue;
+            
+                let refnumLabel, refnumStr, refnum;
+                refnumLabel = ic.resid2refnum[resid];
+                if(!refnumLabel) continue;
+
+                refnumStr = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
+                currStrand = refnumLabel.replace(refnumStr, '');
+                refnum = parseInt(refnumStr);
+
+                if(type == 'iganchor') {
+                    if(refnum > 1000 && refnumStr.substr(refnumStr.length - 2, 2) == '50') {
+                        selectedResidues[resid] = 1;
+                    }
+                } 
                 else {
-                    currType = 'igstrand';
-                }
+                    if(ic.residIgLoop.hasOwnProperty(resid)) {
+                        currType = 'igloop';
+                    }
+                    else {
+                        currType = 'igstrand';
+                    }
 
-                if(bStart && currType != prevType && Object.keys(selectedResidues).length > 0) {
-                    if(prevType == 'igstrand') {
-                        ++strandCnt;
-                        setName = 'Strand-' + prevStrand + '-' + chainid + '-' + strandCnt.toString().padStart(3, '0');
-                        setName = setName.replace(/'/g, '`');
-                        if(type == 'igstrand') {
-                            ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
-                            if(!bUnion) bUnion = true;
+                    if(bStart && currType != prevType && Object.keys(selectedResidues).length > 0) {
+                        if(prevType == 'igstrand') {
+                            ++strandCnt;
+                            setName = 'Strand-' + prevStrand + '-' + chainid + '-' + strandCnt.toString().padStart(3, '0');
+                            setName = setName.replace(/'/g, '`');
+                            if(type == 'igstrand') {
+                                ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
+                                if(!bUnion) bUnion = true;
+                            }
+                            prevStrandReal = prevStrand;
                         }
-                        prevStrandReal = prevStrand;
-                    }
-                    else if(prevType == 'igloop') {
-                        ++loopCnt;
-                        setName = 'Loop-' + prevStrandReal + '_' + currStrand + '-' + chainid + '-' + loopCnt.toString().padStart(3, '0');
-                        setName = setName.replace(/'/g, '`');
-                        if(type == 'igloop') {
-                            ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
-                            if(!bUnion) bUnion = true;
+                        else if(prevType == 'igloop') {
+                            ++loopCnt;
+                            setName = 'Loop-' + prevStrandReal + '_' + currStrand + '-' + chainid + '-' + loopCnt.toString().padStart(3, '0');
+                            setName = setName.replace(/'/g, '`');
+                            if(type == 'igloop') {
+                                ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
+                                if(!bUnion) bUnion = true;
+                            }
                         }
-                    }
 
-                    selectedResidues = {};
-                }
+                        selectedResidues = {};
+                    }
 
-                selectedResidues[resid] = 1;
+                    selectedResidues[resid] = 1;
 
-                prevStrand = currStrand;
-                prevType = currType;
+                    prevStrand = currStrand;
+                    prevType = currType;
 
-                bStart = true;
-            }
-        } // for loop
+                    bStart = true;
+                }
+            } // for loop
 
-        if(type == 'iganchor') {
-            setName = 'Anchor-' + chainid;
-            ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
-        }
-        else {
-            if(prevType == 'igstrand') {
-                ++strandCnt;
-                setName = 'Strand-' + prevStrand + '-' + chainid + '-' + strandCnt.toString().padStart(3, '0');
-                setName = setName.replace(/'/g, '`');
-                if(type == 'igstrand') ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
+            if(type == 'iganchor') {
+                setName = 'Anchor-' + chainid;
+                ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
             }
-            else if(prevType == 'igloop') {
-                ++loopCnt;
-                currStrand = 'CT';
-                setName = 'Loop-' + prevStrandReal + '_' + currStrand + '-' + chainid + '-' + loopCnt.toString().padStart(3, '0');
-                setName = setName.replace(/'/g, '`');
-                if(type == 'igloop') ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
+            else {
+                if(prevType == 'igstrand') {
+                    ++strandCnt;
+                    setName = 'Strand-' + prevStrand + '-' + chainid + '-' + strandCnt.toString().padStart(3, '0');
+                    setName = setName.replace(/'/g, '`');
+                    if(type == 'igstrand') ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
+                }
+                else if(prevType == 'igloop') {
+                    ++loopCnt;
+                    currStrand = 'CT';
+                    setName = 'Loop-' + prevStrandReal + '_' + currStrand + '-' + chainid + '-' + loopCnt.toString().padStart(3, '0');
+                    setName = setName.replace(/'/g, '`');
+                    if(type == 'igloop') ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
+                }
             }
         }
     }
@@ -43526,10 +43575,12 @@ class ShowAnno {
                 + this.addButton(chnid, "icn3d-sheetsets", "Sheet Sets", "Define sets for each sheet in this chain and add them to the menu of \"Defined Sets\"", 60, buttonStyle) + "&nbsp;"
                 + this.addButton(chnid, "icn3d-coilsets", "Coil Sets", "Define sets for each coil in this chain and add them to the menu of \"Defined Sets\"", 60, buttonStyle);
 
-                if(ic.bShowRefnum && ic.chainid2refpdbname.hasOwnProperty(chnid) && ic.chainid2refpdbname[chnid].length > 0) {
-                    chainHtml += "&nbsp;&nbsp;&nbsp;" + this.addButton(chnid, "icn3d-iganchorsets", "Ig Anchor Set", "Define the set for all Ig anchors in this chain and add them to the menu of \"Defined Sets\"", 80, buttonStyle) + "&nbsp;" + this.addButton(chnid, "icn3d-igstrandsets", "Ig Strand Sets", "Define sets for each Ig strand in this chain and add them to the menu of \"Defined Sets\"", 80, buttonStyle) + "&nbsp;"
-                    + this.addButton(chnid, "icn3d-igloopsets", "Ig Loop Sets", "Define sets for each Ig loop in this chain and add them to the menu of \"Defined Sets\"", 80, buttonStyle);
-                }
+                // if(ic.bShowRefnum && ic.chainid2refpdbname.hasOwnProperty(chnid) && ic.chainid2refpdbname[chnid].length > 0) {
+                    chainHtml += "&nbsp;&nbsp;&nbsp;" + this.addButton(chnid, "icn3d-iganchorsets", "Ig Anchor Set", "Define the set for all Ig anchors in this chain and add them to the menu of \"Defined Sets\"", 80, buttonStyle) + "&nbsp;" 
+                    + this.addButton(chnid, "icn3d-igstrandsets", "Ig Strand Sets", "Define sets for each Ig strand in this chain and add them to the menu of \"Defined Sets\"", 80, buttonStyle) + "&nbsp;"
+                    + this.addButton(chnid, "icn3d-igloopsets", "Ig Loop Sets", "Define sets for each Ig loop in this chain and add them to the menu of \"Defined Sets\"", 80, buttonStyle) + "&nbsp;"
+                    + this.addButton(chnid, "icn3d-igdomainsets", "Ig Domain Sets", "Define sets for each Ig domain in this chain and add them to the menu of \"Defined Sets\"", 80, buttonStyle);
+                // }
             $("#" + ic.pre + "dl_annotations").append(chainHtml);
             //let itemArray = ['giseq', 'cdd', 'clinvar', 'snp', 'domain', 'site', 'ptm', 'interaction', 'custom', 'ssbond', 'crosslink', 'transmem'];
             let itemArray = ['giseq', 'cdd', 'clinvar', 'snp', 'site', 'ptm', 'ssbond', 'crosslink', 'transmem', 'domain', 'custom', 'interaction', 'ig'];
@@ -60172,6 +60223,7 @@ class ApplyCommand {
           await ic.annotationCls.setAnnoTabIg();
       }
       else if(command == 'ig refnum on') {
+        if(!ic.bAnnoShown) await ic.showAnnoCls.showAnnotations();
         await ic.annotationCls.setAnnoTabIg(true);
     }
       else if(command == 'highlight level up') {
@@ -62661,6 +62713,7 @@ class LoadScript {
           else if(command.indexOf('ig template') == 0 ) { 
             let template = command.substr(command.lastIndexOf(' ') + 1);
             // await ic.refnumCls.showIgRefNum(template);
+            if(!ic.bAnnoShown) await ic.showAnnoCls.showAnnotations();
             await ic.annotationCls.setAnnoTabIg(true, template);
           }
           else if(command.indexOf('set annotation 3ddomain') == 0) { // the command may have "|||{"factor"...
@@ -62864,6 +62917,7 @@ class LoadScript {
                     }
                     else if(lastCommand.indexOf('ig refnum on') == 0) {
                         // await ic.refnumCls.showIgRefNum();
+                        if(!ic.bAnnoShown) await ic.showAnnoCls.showAnnotations();
                         await ic.annotationCls.setAnnoTabIg(true);
                     }
                     else if(lastCommand.indexOf('set annotation 3ddomain') == 0) {
@@ -62990,7 +63044,7 @@ class LoadScript {
         let idNew = '';
         for(let i = 0, il = idArray.length; i < il; ++i) {
           if(!(ic.structures && ic.structures.hasOwnProperty(idArray[i]))) {
-            if(!idNew) idNew += ',';
+            if(idNew) idNew += ',';
             idNew += idArray[i];
           }
         }
@@ -65911,7 +65965,9 @@ class Dssp {
         ic.refpdbHash['1LaminAC_1ifrA_human'] = ['LaminAC_1ifrA_human', 'CD3d_6jxrd_human_Iset'];
         ic.refpdbHash['1CD3g_6jxrg_human_Iset'] = ['CD3g_6jxrg_human_Iset', 'TCRa_6jxrm_human_C1-n2', 'IsdA_2iteA_bacteria'];
         ic.refpdbHash['1CD28_1yjdC_human_V'] = ['CD28_1yjdC_human_V', 'MPT63_1lmiA_bacteria', 'CD3e_6jxrf_human_Iset'];
-        ic.refpdbHash['1CD19_6al5A_human_C2orV-n1'] = ['CD19_6al5A_human_C2orV-n1']; 
+        ic.refpdbHash['1CD19_6al5A_human_C2orV-n1'] = ['CD19_6al5A_human_C2orV-n1'];
+
+        ic.refpdbHash['all_templates'] = ['ASF1A_2iijA_human', 'B2Microglobulin_7phrL_human_C1', 'BArrestin1_4jqiA_rat_n1', 'BTLA_2aw2A_human_Iset', 'C3_2qkiD_human_n1', 'CD19_6al5A_human_C2orV-n1', 'CD28_1yjdC_human_V', 'CD2_1hnfA_human_C2-n2', 'CD2_1hnfA_human_V-n1', 'CD3d_6jxrd_human_Iset', 'CD3e_6jxrf_human_Iset', 'CD3g_6jxrg_human_Iset', 'CD8a_1cd8A_human_V', 'CoAtomerGamma1_1r4xA_human', 'Contactin1_2ee2A_human_FN3-n9', 'Contactin1_3s97C_human_C2-n2', 'CuZnSuperoxideDismutase_1hl5C_human', 'ECadherin_4zt1A_human_n2', 'Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', 'FAB-HEAVY_5esv_C1-n2', 'FAB-HEAVY_5esv_V-n1', 'FAB-LIGHT_5esv_C1-n2', 'FAB-LIGHT_5esv_V-n1', 'GHR_1axiB_human_FN3-n1', 'ICOS_6x4gA_human_V', 'IL6Rb_1bquB_human_FN3-n2', 'IL6Rb_1bquB_human_FN3-n3', 'InsulinR_8guyE_human_FN3-n1', 'InsulinR_8guyE_human_FN3-n2', 'IsdA_2iteA_bacteria', 'JAM1_1nbqA_human_VorIset-n2', 'LAG3_7tzgD_human_C2-n2', 'LAG3_7tzgD_human_V-n1', 'LaminAC_1ifrA_human', 'MHCIa_7phrH_human_C1', 'MPT63_1lmiA_bacteria', 'NaCaExchanger_2fwuA_dog_n2', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'ORF7a_1xakA_virus', 'PD1_4zqkB_human_V', 'PDL1_4z18B_human_V-n1', 'Palladin_2dm3A_human_Iset-n1', 'RBPJ_6py8C_human_Unk-n1', 'RBPJ_6py8C_human_Unk-n2', 'Sidekick2_1wf5A_human_FN3-n7', 'Siglec3_5j0bB_human_C2-n2', 'TCRa_6jxrm_human_C1-n2', 'TCRa_6jxrm_human_V-n1', 'TEAD1_3kysC_human', 'TP34_2o6cA_bacteria', 'TP47_1o75A_bacteria', 'Titin_4uowM_human_Unk-n152', 'VISTA_6oilA_human_V', 'VNAR_1t6vN_shark_V', 'VTCN1_Q7Z7D3_human_V-n2'];
 
         // use known ref structure
         ic.refpdbHash['5ESV_C'] = ['FAB-HEAVY_5esv_V-n1', 'FAB-HEAVY_5esv_C1-n2'];
@@ -65968,9 +66024,9 @@ class Dssp {
 
         ic.ref2igtype['ASF1A_2iijA_human'] = 'IgE';
         ic.ref2igtype['B2Microglobulin_7phrL_human_C1'] = 'IgC1';
-        ic.ref2igtype['BArrestin1_4jqiA_rat_n1'] = 'IgFn3-like';
+        ic.ref2igtype['BArrestin1_4jqiA_rat_n1'] = 'IgFN3-like';
         ic.ref2igtype['BTLA_2aw2A_human_Iset'] = 'IgI';
-        ic.ref2igtype['C3_2qkiD_human_n1'] = 'IgFn3-like';
+        ic.ref2igtype['C3_2qkiD_human_n1'] = 'IgFN3-like';
         ic.ref2igtype['CD19_6al5A_human_C2orV-n1'] = 'other Ig'; //'CD19';
         ic.ref2igtype['CD28_1yjdC_human_V'] = 'IgV';
         ic.ref2igtype['CD2_1hnfA_human_C2-n2'] = 'IgC2';
@@ -65980,7 +66036,7 @@ class Dssp {
         ic.ref2igtype['CD3g_6jxrg_human_Iset'] = 'IgI';
         ic.ref2igtype['CD8a_1cd8A_human_V'] = 'IgV';
         ic.ref2igtype['CoAtomerGamma1_1r4xA_human'] = 'IgE';
-        ic.ref2igtype['Contactin1_2ee2A_human_FN3-n9'] = 'IgFn3';
+        ic.ref2igtype['Contactin1_2ee2A_human_FN3-n9'] = 'IgFN3';
         ic.ref2igtype['Contactin1_3s97C_human_C2-n2'] = 'IgC2';
         ic.ref2igtype['CuZnSuperoxideDismutase_1hl5C_human'] = 'other Ig'; //'SOD';
         ic.ref2igtype['ECadherin_4zt1A_human_n2'] = 'other Ig'; //'Cadherin';
@@ -65989,12 +66045,12 @@ class Dssp {
         ic.ref2igtype['FAB-HEAVY_5esv_V-n1'] = 'IgV';
         ic.ref2igtype['FAB-LIGHT_5esv_C1-n2'] = 'IgC1';
         ic.ref2igtype['FAB-LIGHT_5esv_V-n1'] = 'IgV';
-        ic.ref2igtype['GHR_1axiB_human_FN3-n1'] = 'IgFn3';
+        ic.ref2igtype['GHR_1axiB_human_FN3-n1'] = 'IgFN3';
         ic.ref2igtype['ICOS_6x4gA_human_V'] = 'IgV';
-        ic.ref2igtype['IL6Rb_1bquB_human_FN3-n2'] = 'IgFn3';
-        ic.ref2igtype['IL6Rb_1bquB_human_FN3-n3'] = 'IgFn3';
-        ic.ref2igtype['InsulinR_8guyE_human_FN3-n1'] = 'IgFn3';
-        ic.ref2igtype['InsulinR_8guyE_human_FN3-n2'] = 'IgFn3';
+        ic.ref2igtype['IL6Rb_1bquB_human_FN3-n2'] = 'IgFN3';
+        ic.ref2igtype['IL6Rb_1bquB_human_FN3-n3'] = 'IgFN3';
+        ic.ref2igtype['InsulinR_8guyE_human_FN3-n1'] = 'IgFN3';
+        ic.ref2igtype['InsulinR_8guyE_human_FN3-n2'] = 'IgFN3';
         ic.ref2igtype['IsdA_2iteA_bacteria'] = 'IgE';
         ic.ref2igtype['JAM1_1nbqA_human_VorIset-n2'] = 'IgI';
         ic.ref2igtype['LAG3_7tzgD_human_C2-n2'] = 'IgC2';
@@ -66008,9 +66064,9 @@ class Dssp {
         ic.ref2igtype['PD1_4zqkB_human_V'] = 'IgV';
         ic.ref2igtype['PDL1_4z18B_human_V-n1'] = 'IgV';
         ic.ref2igtype['Palladin_2dm3A_human_Iset-n1'] = 'IgI';
-        ic.ref2igtype['RBPJ_6py8C_human_Unk-n1'] = 'IgFn3-like';
-        ic.ref2igtype['RBPJ_6py8C_human_Unk-n2'] = 'IgFn3-like';
-        ic.ref2igtype['Sidekick2_1wf5A_human_FN3-n7'] = 'IgFn3';
+        ic.ref2igtype['RBPJ_6py8C_human_Unk-n1'] = 'IgFN3-like';
+        ic.ref2igtype['RBPJ_6py8C_human_Unk-n2'] = 'IgFN3-like';
+        ic.ref2igtype['Sidekick2_1wf5A_human_FN3-n7'] = 'IgFN3';
         ic.ref2igtype['Siglec3_5j0bB_human_C2-n2'] = 'IgC2';
         ic.ref2igtype['TCRa_6jxrm_human_C1-n2'] = 'IgC1';
         ic.ref2igtype['TCRa_6jxrm_human_V-n1'] = 'IgV';
@@ -66075,7 +66131,7 @@ class Dssp {
         let thisClass = this;
 
         let struArray = Object.keys(ic.structures);
- 
+
         let ajaxArray = [];
         let domainidpairArray = [];
 
@@ -66094,7 +66150,7 @@ class Dssp {
             for(let j = 0, jl = chainidArray.length; j < jl; ++j) {
                 let chainid = chainidArray[j];
 
-                // for selected atoms only
+                // for selected atoms only, assign ic.resid2domainid[resid]
                 let domainAtomsArray = this.getDomainAtomsArray(chainid, bRerun);
 
                 if(!ic.domainid2refpdbname) ic.domainid2refpdbname = {};
@@ -66111,8 +66167,8 @@ class Dssp {
                     let atomFirst = ic.firstAtomObjCls.getFirstAtomObj(domainAtomsArray[k]);
                     let atomLast = ic.firstAtomObjCls.getLastAtomObj(domainAtomsArray[k]);
                     let resiSum = atomFirst.resi + ':' + atomLast.resi + ':' + Object.keys(domainAtomsArray[k]).length;
-                    //let domainid = chainid + '-' + k + '_' + Object.keys(domainAtomsArray[k]).length; 
-                    let domainid = chainid + ',' + k + '_' + resiSum; 
+                    //let domainid = chainid + '-' + k + '_' + Object.keys(domainAtomsArray[k]).length;
+                    let domainid = chainid + ',' + k + '_' + resiSum;
                     ic.domainid2pdb[domainid] = pdb_target;
 
                     if(!template) {
@@ -66130,7 +66186,7 @@ class Dssp {
                             // let alignAjax = me.getAjaxPostPromise(urlalign, dataObj);
 
                             ajaxArray.push(alignAjax);
-                            
+
                             domainidpairArray.push(domainid + "|" + ic.refpdbArray[index]);
                         }
                     }
@@ -66150,14 +66206,14 @@ class Dssp {
                 // dataArray2 = await allPromise;
 
                 dataArray2 = await this.promiseWithFixedJobs(ajaxArray);
-            
+
                 let bRound1 = true;
-                await thisClass.parseAlignData(dataArray2, domainidpairArray, bRound1);
+                bNoMoreIg = await thisClass.parseAlignData(dataArray2, domainidpairArray, bRound1);
 
                 /// if(ic.deferredRefnum !== undefined) ic.deferredRefnum.resolve();
             }
             else {
-                if(!me.bNode) console.log("Start alignment with the reference culsters " + JSON.stringify(ic.domainid2refpdbname));   
+                if(!me.bNode) console.log("Start alignment with the reference culsters " + JSON.stringify(ic.domainid2refpdbname));
 
                 // start round2
                 let ajaxArray = [];
@@ -66172,36 +66228,36 @@ class Dssp {
                 //let allPromise2 = Promise.allSettled(pdbAjaxArray);
                 //ic.pdbDataArray = await allPromise2;
 
-                ic.pdbDataArray = await this.promiseWithFixedJobs(pdbAjaxArray);
+                let pdbDataArray = await this.promiseWithFixedJobs(pdbAjaxArray);
 
                 for(let domainid in ic.domainid2refpdbname) {
                     ic.domainid2refpdbname[domainid];
                     domainid.substr(0, domainid.indexOf(','));
 
                     let pdb_target = ic.domainid2pdb[domainid];
-                    for(let index = 0, indexl = ic.pdbDataArray.length; index < indexl; ++index) {
+                    for(let index = 0, indexl = pdbDataArray.length; index < indexl; ++index) {
                         let struct2 = ic.defaultPdbId + index;
-                        let pdb_query = ic.pdbDataArray[index].value; //[0];
+                        let pdb_query = pdbDataArray[index].value; //[0];
 
                         let header = 'HEADER                                                        ' + struct2 + '\n';
                         pdb_query = header + pdb_query;
-    
+
                         let dataObj = {'pdb_query': pdb_query, 'pdb_target': pdb_target, "queryid": template};
                         let alignAjax = me.getAjaxPostPromise(urltmalign, dataObj);
                         ajaxArray.push(alignAjax);
-                        
+
                         //domainidpairArray3.push(domainid + "," + refpdbname);
                         domainidpairArray3.push(domainid + "|" + template);
                     }
                 }
-    
+
                 let dataArray3 = [];
                 //let allPromise = Promise.allSettled(ajaxArray);
                 //dataArray3 = await allPromise;
 
                 dataArray3 = await this.promiseWithFixedJobs(ajaxArray);
-    
-                await thisClass.parseAlignData(dataArray3, domainidpairArray3);
+
+                bNoMoreIg = await thisClass.parseAlignData(dataArray3, domainidpairArray3);
             }
 
             return bNoMoreIg;
@@ -66217,8 +66273,8 @@ class Dssp {
             }
             //console.log("Error in aligning with TM-align...");
             return;
-        }        
-        */           
+        }
+        */
     }
 
     getDomainAtomsArray(chainid, bRerunDomain) { let ic = this.icn3d, me = ic.icn3dui;
@@ -66261,21 +66317,22 @@ class Dssp {
         //let result = ic.domain3dCls.c2b_NewSplitChain(ic.chains[chainid]);
         // assign ref numbers to selected residues
         let result = ic.domain3dCls.c2b_NewSplitChain(currAtoms, undefined);
-        let subdomains = result.subdomains;  
+        let subdomains = result.subdomains;
         let pos2resi = result.pos2resi;
 
         if(subdomains.length <= 1) {
             let residueArray = ic.resid2specCls.atoms2residues(Object.keys(currAtoms));
             if(residueArray.length < minResidues) return domainAtomsArray;
-
+/*
             let atomFirst = ic.firstAtomObjCls.getFirstAtomObj(currAtoms);
             let atomLast = ic.firstAtomObjCls.getLastAtomObj(currAtoms);
             let resiSum = atomFirst.resi + ':' + atomLast.resi + ':' + Object.keys(currAtoms).length;
-
+*/
             for(let n = 0, nl = residueArray.length; n < nl; ++n) {
                 let resid = residueArray[n];
-                ic.resid2domainid[resid] = chainid + ',0' + '_' + resiSum; 
-
+/*
+                ic.resid2domainid[resid] = chainid + ',0' + '_' + resiSum;
+*/
                 // clear previous refnum assignment if any
                 // if(!bRerunDomain && ic.resid2refnum && ic.resid2refnum[resid]) {
                 // if(ic.resid2refnum && ic.resid2refnum[resid]) {
@@ -66286,7 +66343,7 @@ class Dssp {
 
             domainAtomsArray.push(currAtoms);
         }
-        else {                 
+        else {
             for(let k = 0, kl = subdomains.length; k < kl; ++k) {
                 let domainAtoms = {};
                 let segArray = subdomains[k];
@@ -66313,7 +66370,7 @@ class Dssp {
                 if(resCnt < minResidues) continue;
 
                 domainAtomsArray.push(domainAtoms);
-
+/*
                 let atomFirst = ic.firstAtomObjCls.getFirstAtomObj(domainAtoms);
                 let atomLast = ic.firstAtomObjCls.getLastAtomObj(domainAtoms);
                 let resiSum = atomFirst.resi + ':' + atomLast.resi + ':' + Object.keys(domainAtoms).length;
@@ -66324,15 +66381,16 @@ class Dssp {
                     for(let n = parseInt(startResi); n <= parseInt(endResi); ++n) {
                         let resid = chainid + '_' + pos2resi[n];
                         //domainAtoms = me.hashUtilsCls.unionHash(domainAtoms, ic.residues[resid]);
-                        ic.resid2domainid[resid] = chainid + ',' + k + '_' + resiSum; 
+                        ic.resid2domainid[resid] = chainid + ',' + k + '_' + resiSum;
                     }
                 }
+*/
             }
         }
 
         return domainAtomsArray;
     }
-    
+
     getTemplateList(domainid) { let ic = this.icn3d; ic.icn3dui;
         let refpdbname = '', score = '', seqid = '', nresAlign = '';
 
@@ -66365,7 +66423,6 @@ class Dssp {
         if(!ic.domainid2ig2imgt) ic.domainid2ig2imgt = {};
 
         let minResidues = 20;
-
         for(let i = 0, il = domainidpairArray.length; i < il; ++i) {
             //let queryData = (me.bNode) ? dataArray[i] : dataArray[i].value; //[0];
             let queryData = (dataArray[i]) ? dataArray[i].value : undefined; //[0];
@@ -66376,7 +66433,7 @@ class Dssp {
             }
 
             if(queryData[0].score === undefined) continue;
-            
+
             //let domainid_index = domainidpairArray[i].split(',');
             //let domainid = domainid_index[0];
             let domainid = domainidpairArray[i].substr(0, domainidpairArray[i].indexOf('|'));
@@ -66397,7 +66454,7 @@ class Dssp {
                     continue;
                 }
             }
-            
+
             if(!bRound1) {
                 if(!me.bNode) console.log("refpdbname " + refpdbname + " TM-score: " + queryData[0].score);
             }
@@ -66460,8 +66517,13 @@ class Dssp {
             }
 
             if(!domainid2segs.hasOwnProperty(domainid) || queryData[0].score >= ic.domainid2score[domainid].split('_')[0]) {
-                ic.domainid2score[domainid] = queryData[0].score + '_' + queryData[0].frac_identical + '_' + queryData[0].num_res ;  
-                ic.domainid2refpdbname[domainid] = refpdbname;
+                ic.domainid2score[domainid] = queryData[0].score + '_' + queryData[0].frac_identical + '_' + queryData[0].num_res ;
+                if(bRound1) {
+                    ic.domainid2refpdbname[domainid] = parseFloat(queryData[0].score) > 0.75 ? refpdbname : 'all_templates';
+                }
+                else {
+                    ic.domainid2refpdbname[domainid] = refpdbname;
+                }
                 domainid2segs[domainid] = queryData[0].segs;
                 ic.domainid2ig2kabat[domainid] = queryData[0].ig2kabat;
                 ic.domainid2ig2imgt[domainid] = queryData[0].ig2imgt;
@@ -66472,10 +66534,17 @@ class Dssp {
     }
 
     async parseAlignData(dataArray, domainidpairArray, bRound1) { let ic = this.icn3d, me = ic.icn3dui;
+        let bNoMoreIg = false;
+
         let domainid2segs = this.parseAlignData_part1(dataArray, domainidpairArray, bRound1);
 
+        if(Object.keys(domainid2segs).length == 0) {
+            bNoMoreIg = true;
+            return bNoMoreIg;
+        }
+
         if(bRound1) {
-            if(!me.bNode) console.log("Start round 2 alignment with the reference culsters " + JSON.stringify(ic.domainid2refpdbname));   
+            if(!me.bNode) console.log("Start round 2 alignment with the reference culsters " + JSON.stringify(ic.domainid2refpdbname));
 
             // start round2
             let ajaxArray = [];
@@ -66493,7 +66562,7 @@ class Dssp {
                     //refpdbname = pdbid;
                     refpdbname = chainid;
 
-                    if(!me.bNode) console.log("Adjusted refpdbname for domainid " + domainid + ": " + refpdbname);   
+                    if(!me.bNode) console.log("Adjusted refpdbname for domainid " + domainid + ": " + refpdbname);
                 }
 
                 if(!ic.refpdbHash[refpdbname]) {
@@ -66511,20 +66580,20 @@ class Dssp {
                 //let allPromise2 = Promise.allSettled(pdbAjaxArray);
                 //ic.pdbDataArray = await allPromise2;
 
-                ic.pdbDataArray = await this.promiseWithFixedJobs(pdbAjaxArray);
+                let pdbDataArray = await this.promiseWithFixedJobs(pdbAjaxArray);
 
                 let pdb_target = ic.domainid2pdb[domainid];
-                for(let index = 0, indexl = ic.pdbDataArray.length; index < indexl; ++index) {
+                for(let index = 0, indexl = pdbDataArray.length; index < indexl; ++index) {
                     let struct2 = ic.defaultPdbId + index;
-                    //let pdb_query = (me.bNode) ? ic.pdbDataArray[index] : ic.pdbDataArray[index].value; //[0];
-                    let pdb_query = ic.pdbDataArray[index].value; //[0];
+                    //let pdb_query = (me.bNode) ? pdbDataArray[index] : pdbDataArray[index].value; //[0];
+                    let pdb_query = pdbDataArray[index].value; //[0];
                     let header = 'HEADER                                                        ' + struct2 + '\n';
                     pdb_query = header + pdb_query;
 
                     let dataObj = {'pdb_query': pdb_query, 'pdb_target': pdb_target, "queryid": ic.refpdbHash[refpdbname][index]};
                     let alignAjax = me.getAjaxPostPromise(urltmalign, dataObj);
                     ajaxArray.push(alignAjax);
-                    
+
                     //domainidpairArray3.push(domainid + "," + refpdbname);
                     domainidpairArray3.push(domainid + "|" + ic.refpdbHash[refpdbname][index]);
                 }
@@ -66537,12 +66606,14 @@ class Dssp {
             dataArray3 = await this.promiseWithFixedJobs(ajaxArray);
 
             await this.parseAlignData(dataArray3, domainidpairArray3, false);
-            
+
             // end of round 2
-            return;
+            return bNoMoreIg;
         }
 
         await this.parseAlignData_part3(domainid2segs);
+
+        return bNoMoreIg;
     }
 
     async parseAlignData_part3(domainid2segs) { let ic = this.icn3d, me = ic.icn3dui;
@@ -66688,7 +66759,7 @@ class Dssp {
             for(let i = 0, il = segArray.length; i < il; ++i) {
                 let seg = segArray[i];
                 if(!seg) continue;
-                
+
                 let qStart = seg.q_start;
                 parseInt(seg.q_start);
                 if(isNaN(seg.q_start)) seg.q_start.substr(seg.q_start.length - 1, 1);
@@ -66729,9 +66800,10 @@ class Dssp {
                     if(currStrand != currStrandFinal) {
                         refnumLabel = this.getLabelFromRefnum(refnum, currStrandFinal);
                     }
-                   
-                    ic.resid2refnum[resid] = refnumLabel;                
+
+                    ic.resid2refnum[resid] = refnumLabel;
                     ic.resid2refnum_ori[resid] = refnumLabel;
+                    ic.resid2domainid[resid] = domainid;
 
                     // final reference numbers will be assign in ic.annoIgCls.showRefNum()
 
@@ -66778,7 +66850,7 @@ class Dssp {
             else {
                 await ic.showAnnoCls.showAnnotations();
             }
-            
+
             ic.annotationCls.setAnnoViewAndDisplay('detailed view');
         }
         else if(!me.bNode) {
@@ -66819,13 +66891,13 @@ class Dssp {
         // loops may have numbers such as 1310, 1410
 
         let refnumLabel;
-        
+
         if(refnum < 1000) refnumLabel = undefined;
         else if(refnum >= 1200 && refnum < 1290) refnumLabel = "A---" + oriRefnum;
         else if(refnum >= 1320 && refnum < 1390) refnumLabel = "A--" + oriRefnum;
         else if(refnum >= 1420 && refnum < 1490) refnumLabel = "A-" + oriRefnum;
-        else if(refnum >= 1520 && refnum < 1590) refnumLabel = "A" + oriRefnum; 
-        else if(refnum >= 1620 && refnum < 1690) refnumLabel = "A+" + oriRefnum; 
+        else if(refnum >= 1520 && refnum < 1590) refnumLabel = "A" + oriRefnum;
+        else if(refnum >= 1620 && refnum < 1690) refnumLabel = "A+" + oriRefnum;
         else if(refnum >= 1820 && refnum < 1890) refnumLabel = "A'" + oriRefnum;
         else if(refnum >= 2000 && refnum < 2900) refnumLabel = "B" + oriRefnum;
         else if(refnum >= 3300 && refnum < 3390) refnumLabel = "C--" + oriRefnum;
@@ -66834,8 +66906,8 @@ class Dssp {
         else if(refnum >= 4000 && refnum < 4900) refnumLabel = "C'" + oriRefnum;
         else if(refnum >= 5000 && refnum < 5900) refnumLabel = "C''" + oriRefnum;
         else if(refnum >= 6000 && refnum < 6900) refnumLabel = "D" + oriRefnum;
-        else if(refnum >= 7500 && refnum < 7590) refnumLabel = "E" + oriRefnum; 
-        else if(refnum >= 7620 && refnum < 7900) refnumLabel = "E+" + oriRefnum; 
+        else if(refnum >= 7500 && refnum < 7590) refnumLabel = "E" + oriRefnum;
+        else if(refnum >= 7620 && refnum < 7900) refnumLabel = "E+" + oriRefnum;
         else if(refnum >= 8000 && refnum < 8900) refnumLabel = "F" + oriRefnum;
         else if(refnum >= 9500 && refnum < 9590) refnumLabel = "G" + oriRefnum;
         else if(refnum >= 9620 && refnum < 9690) refnumLabel = "G+" + oriRefnum;
@@ -66935,22 +67007,22 @@ class Dssp {
                     }
                 }
             }
-    
+
             let resid2refnum = {};
             for(let resid in ic.resid2refnum) {
                 let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
                 if(!atom) continue;
-                
+
                 let resn = me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3));
-        
+
                 let domainid = ic.resid2domainid[resid];
                 let refnumLabel = ic.resid2refnum[resid];
-        
+
                 if(refnumLabel) {
                     let refnumStr_ori = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
                     (ic.domainid2ig2kabat[domainid]) ? ic.domainid2ig2kabat[domainid][refnumStr_ori] : undefined;
                 }
-        
+
                 if(ic.resid2refnum[resid]) {
                     if(ic.residIgLoop.hasOwnProperty(resid)) { // loop
                     resid2refnum[resid + '_' + resn] = ic.resid2refnum[resid] + '_loop';
@@ -66988,21 +67060,22 @@ class Dssp {
                 refData += '}\n';
             }
 */
+
             if(bIgDomain) {
                 refData += '"igs": [\n';
-
                 for(let chnid in ic.chains) {
                     let igArray = ic.chain2igArray[chnid];
 
-                    if(igArray.length > 0) {
+                    if(igArray && igArray.length > 0) {
                         refData += '{"' + chnid + '": {\n';
 
                         for(let i = 0, il = igArray.length; i < il; ++i) {
                             let startPos = igArray[i].startPos;
                             let endPos = igArray[i].endPos;
                             let domainid = igArray[i].domainid;
-
                             let info = ic.domainid2info[domainid];
+                            if(!info) continue;
+
                             refData += '"' + domainid + '": {\n';
 
                             refData += '"refpdbname":"' + info.refpdbname + '", "score":' + info.score + ', "seqid":' + info.seqid + ', "nresAlign":' + info.nresAlign + ', "data": [';
@@ -67030,18 +67103,18 @@ class Dssp {
             for(let resid in ic.resid2refnum) {
             let domainid = ic.resid2domainid[resid];
             let refnumStr, refnumLabel = ic.resid2refnum[resid];
-    
+
             let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
             let resn = me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3));
-    
+
             if(refnumLabel) {
                 let refnumStr_ori = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
                 refnumStr = (ic.domainid2ig2kabat[domainid]) ? ic.domainid2ig2kabat[domainid][refnumStr_ori] : undefined;
             }
-    
+
             resid2kabat[resid + '_' + resn] = refnumStr;
             }
-            
+
             refData += JSON.stringify(resid2kabat);
         }
         // 3. show IMGT ref numbers
@@ -67050,25 +67123,25 @@ class Dssp {
             for(let resid in ic.resid2refnum) {
             let domainid = ic.resid2domainid[resid];
             let refnumStr, refnumLabel = ic.resid2refnum[resid];
-    
+
             let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
             let resn = me.utilsCls.residueName2Abbr(atom.resn.substr(0, 3));
-    
+
             if(refnumLabel) {
                 let refnumStr_ori = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
                 refnumStr = (ic.domainid2ig2imgt[domainid]) ? ic.domainid2ig2imgt[domainid][refnumStr_ori] : undefined;
             }
-    
+
             resid2imgt[resid + '_' + resn] = refnumStr;
             }
-            
+
             refData += JSON.stringify(resid2imgt);
         }
 
 
         if(!me.bNode) {
             let file_pref = Object.keys(me.utilsCls.getHlStructures()).join(',');
-    
+
             ic.saveFileCls.saveFile(file_pref + '_refnum_' + type + '.txt', 'text', [refData]);
         }
         else {
@@ -67086,7 +67159,7 @@ class Dssp {
 
         for(let i = 0, il = parseInt((ajaxArray.length - 1) / n + 1); i < il; ++i) {
             let currAjaxArray = [];
-            if(i == il - 1) { // last one 
+            if(i == il - 1) { // last one
                 currAjaxArray = ajaxArray.slice(i * n, ajaxArray.length);
             }
             else {