icn3d 3.25.11 → 3.25.13

package/icn3d.module.js

@@ -7136,19 +7136,19 @@ class ClickMenu {
         });
 
         me.myEventCls.onIds("#" + me.pre + "mn1_link_bind", "click", function(e) { let ic = me.icn3d; e.preventDefault();
-           url = "https://www.ncbi.nlm.nih.gov/pccompound?LinkName=pccompound_structure&from_uid=" + ic.inputid;
+           let url = "https://www.ncbi.nlm.nih.gov/pccompound?LinkName=pccompound_structure&from_uid=" + ic.inputid;
            thisClass.setLogCmd("link to 3D protein structures bound to CID " + ic.inputid + ": " + url, false);
            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
            window.open(url, urlTarget);
         });
 
         me.myEventCls.onIds("#" + me.pre + "mn1_link_vast", "click", function(e) { let ic = me.icn3d; e.preventDefault();
-           if(ic.inputid === undefined) {
-                   url = "https://www.ncbi.nlm.nih.gov/pccompound?term=" + ic.molTitle;
-                   thisClass.setLogCmd("link to compounds " + ic.molTitle + ": " + url, false);
+         let url;  
+         if(ic.inputid === undefined) {
+               url = "https://www.ncbi.nlm.nih.gov/pccompound?term=" + ic.molTitle;
+               thisClass.setLogCmd("link to compounds " + ic.molTitle + ": " + url, false);
            }
            else {
-               let url;
                if(me.cfg.cid !== undefined) {
                        url = "https://www.ncbi.nlm.nih.gov/pccompound?LinkName=pccompound_pccompound_3d&from_uid=" + ic.inputid;
                        thisClass.setLogCmd("link to compounds with structure similar to CID " + ic.inputid + ": " + url, false);
@@ -7172,8 +7172,8 @@ class ClickMenu {
         });
 
         me.myEventCls.onIds("#" + me.pre + "mn1_link_pubmed", "click", function(e) { let ic = me.icn3d; e.preventDefault();
+           let url;
            if(ic.inputid === undefined) {
-               let url;
                url = "https://www.ncbi.nlm.nih.gov/pubmed/?term=" + ic.molTitle;
                thisClass.setLogCmd("link to literature about " + ic.molTitle + ": " + url, false);
                let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
@@ -7181,7 +7181,6 @@ class ClickMenu {
            }
            else if(ic.pmid) {
                let idArray = ic.pmid.toString().split('_');
-               let url;
                if(idArray.length === 1) {
                    url = "https://www.ncbi.nlm.nih.gov/pubmed/" + ic.pmid;
                    thisClass.setLogCmd("link to PubMed ID " + ic.pmid + ": " + url, false);
@@ -7195,7 +7194,6 @@ class ClickMenu {
            }
            else if(isNaN(ic.inputid)) {
                let idArray = ic.inputid.toString().split('_');
-               let url;
                if(idArray.length === 1) {
                    url = "https://www.ncbi.nlm.nih.gov/pubmed/?term=" + ic.inputid;
                    thisClass.setLogCmd("link to literature about PDB " + ic.inputid + ": " + url, false);
@@ -11909,11 +11907,11 @@ class SetDialog {
         
         html += "<div>4. " + me.htmlCls.buttonStr + "applyhbonds'>3D Display Interactions</button></div><br>";
 
-        html += "<div style='text-indent:1.1em'>" + me.htmlCls.buttonStr + "hbondWindow'>Highlight Interactions in Table</button><span style='margin-left:30px; font-wieght:bold'>Sort Interactions on</span>: " + me.htmlCls.buttonStr + "sortSet1'> Set 1</button>" + me.htmlCls.buttonStr + "sortSet2' style='margin-left:20px'>Set 2</button></div><br>";
+        html += "<div style='text-indent:1.1em'>" + me.htmlCls.buttonStr + "hbondWindow'>Highlight Interactions in Table</button><span style='margin-left:30px; font-wieght:bold'>Sort Interactions on</span>: " + me.htmlCls.buttonStr + "sortSet1'> Set 1</button>" + me.htmlCls.buttonStr + "sortSet2' style='margin-left:12px'>Set 2</button></div><br>";
 
-        html += "<div style='text-indent:1.1em'>" + me.htmlCls.buttonStr + "hbondLineGraph'>2D Interaction Network</button> to show interactions between two lines of residue nodes</div><br>";
+        html += "<div style='text-indent:1.1em'>" + me.htmlCls.buttonStr + "hbondLineGraph'>2D Interaction Network</button> " + me.htmlCls.buttonStr + "hbondLineGraph2' style='margin-left:12px'>2D Network with Reference Numbers</button> to show two lines of residue nodes</div><br>";
 
-        html += "<div style='text-indent:1.1em'>" + me.htmlCls.buttonStr + "hbondScatterplot'>2D Interaction Map</button> to show interactions as map</div><br>";
+        html += "<div style='text-indent:1.1em'>" + me.htmlCls.buttonStr + "hbondScatterplot'>2D Interaction Map</button> " + me.htmlCls.buttonStr + "hbondScatterplot2' style='margin-left:12px'>2D Map with Reference Numbers</button> to show map</div><br>";
 
         tmpStr = ': </td><td><input style="margin-left:-12px" type="text" id="';
 
@@ -12681,7 +12679,7 @@ class Events {
     async searchSeq() { let me = this.icn3dui, ic = me.icn3d, thisClass = this;
        let select = $("#" + me.pre + "search_seq").val();
        if(isNaN(select) && select.indexOf('$') == -1 && select.indexOf('.') == -1 && select.indexOf(':') == -1 
-       && select.indexOf('%') == -1 && select.indexOf('@') == -1) {
+       && select.indexOf('@') == -1) {
            select = ':' + select;
        }
        let commandname = select.replace(/\s+/g, '_');
@@ -14326,11 +14324,29 @@ class Events {
         me.myEventCls.onIds("#" + me.pre + "hbondLineGraph", "click", async function(e) { let ic = me.icn3d;
            e.preventDefault();
            
+           ic.bShownRefnum = false;
+           thisClass.setLogCmd("hide ref number", true);
            await ic.showInterCls.showInteractions('linegraph');
         });
+        me.myEventCls.onIds("#" + me.pre + "hbondLineGraph2", "click", async function(e) { let ic = me.icn3d;
+            e.preventDefault();
+            
+            ic.bShownRefnum = true;
+            thisClass.setLogCmd("show ref number", true);
+            await ic.showInterCls.showInteractions('linegraph');
+        });
         me.myEventCls.onIds("#" + me.pre + "hbondScatterplot", "click", async function(e) { let ic = me.icn3d;
+            e.preventDefault();
+            
+            ic.bShownRefnum = false;
+            thisClass.setLogCmd("hide ref number", true);
+            await ic.showInterCls.showInteractions('scatterplot');
+        });
+        me.myEventCls.onIds("#" + me.pre + "hbondScatterplot2", "click", async function(e) { let ic = me.icn3d;
            e.preventDefault();
            
+           ic.bShownRefnum = true;
+           thisClass.setLogCmd("show ref number", true);
            await ic.showInterCls.showInteractions('scatterplot');
         });
         // select residues
@@ -15117,6 +15133,22 @@ class Events {
           thisClass.setLogCmd('define coil sets | chain ' + chainid, true);
         });
 
+        $(document).on("click", ".icn3d-igstrandsets", function(e) { let ic = me.icn3d;
+            e.stopImmediatePropagation();
+            //e.preventDefault();
+            let chainid = $(this).attr('chainid');
+            ic.addTrackCls.defineIgstrand(chainid, 'igstrand');
+            thisClass.setLogCmd('define igstrand sets | chain ' + chainid, true);
+        });
+
+        $(document).on("click", ".icn3d-igloopsets", function(e) { let ic = me.icn3d;
+            e.stopImmediatePropagation();
+            //e.preventDefault();
+            let chainid = $(this).attr('chainid');
+            ic.addTrackCls.defineIgstrand(chainid, 'igloop');
+            thisClass.setLogCmd('define igloop 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);
@@ -35588,7 +35620,7 @@ class SetColor {
                             //     color = me.parasCls.thr(me.htmlCls.GREYB);
                             // }
                             // else {
-                                let refnumStr = refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').replace(/\+/g, '').replace(/\-/g, '').substr(1); // C', C''
+                                let refnumStr = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
                                 let currStrand = refnumLabel.replace(new RegExp(refnumStr,'g'), '');
                                 color = ic.showSeqCls.getRefnumColor(currStrand);
 
@@ -35624,7 +35656,7 @@ class SetColor {
                                 color = me.parasCls.thr(me.htmlCls.GREYB);
                             }
                             else {
-                                let refnumStr = refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').replace(/\+/g, '').replace(/\-/g, '').substr(1); // C', C''
+                                let refnumStr = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
                                 let currStrand = refnumLabel.replace(new RegExp(refnumStr,'g'), '');
                                 color = ic.showSeqCls.getProtodomainColor(currStrand);
 
@@ -40752,7 +40784,7 @@ class AddTrack {
                     ++helixCnt;
 
                     if(Object.keys(selectedResidues).length > 0) {
-                        setName = currName + 'H' + helixCnt + ')';
+                        setName = currName + 'H' + helixCnt.toString().padStart(2, '0') + ')';
                         if(type == 'coil') {
                             ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
                             if(!bUnion) bUnion = true;
@@ -40763,13 +40795,13 @@ class AddTrack {
 
                 //zero =(index < 10) ? '0' : '';
                 //currName = chainid + zero + index + '_H' + helixCnt;
-                currName = chainid + '_H' + helixCnt;
+                currName = chainid + '_H' + helixCnt.toString().padStart(2, '0');
                 selectedResidues[residueid] = 1;
 
                 if(atom.ssend) {
                     //zero =(index < 9) ? '0' : '';
                     //prevName = chainid + zero +(index+1) + '_L(H' + helixCnt;
-                    prevName = chainid + '_C(H' + helixCnt;
+                    prevName = chainid + '_C(H' + helixCnt.toString().padStart(2, '0');
                     if(type == 'helix') {
                         ic.selectionCls.selectResidueList(selectedResidues, currName, currName, bUnion, bUpdateHighlight);
                         if(!bUnion) bUnion = true;
@@ -40782,7 +40814,7 @@ class AddTrack {
                     ++sheetCnt;
 
                     if(Object.keys(selectedResidues).length > 0) {
-                        setName = currName + 'S' + sheetCnt + ')';
+                        setName = currName + 'S' + sheetCnt.toString().padStart(2, '0') + ')';
                         if(type == 'coil') {
                             ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
                             if(!bUnion) bUnion = true;
@@ -40793,13 +40825,13 @@ class AddTrack {
 
                 //zero =(index < 10) ? '0' : '';
                 //currName = chainid + zero + index + '_S' + sheetCnt;
-                currName = chainid + '_S' + sheetCnt;
+                currName = chainid + '_S' + sheetCnt.toString().padStart(2, '0');
                 selectedResidues[residueid] = 1;
 
                 if(atom.ssend) {
                     //zero =(index < 9) ? '0' : '';
                     //prevName = chainid + zero +(index+1) + '_L(S' + sheetCnt;
-                    prevName = chainid + '_C(S' + sheetCnt;
+                    prevName = chainid + '_C(S' + sheetCnt.toString().padStart(2, '0');
                     if(type == 'sheet') {
                         ic.selectionCls.selectResidueList(selectedResidues, currName, currName, bUnion, bUpdateHighlight);
                         if(!bUnion) bUnion = true;
@@ -40822,6 +40854,90 @@ class AddTrack {
         }
     }
 
+    // type: igstrand, igloop
+    defineIgstrand(chainid, type) { let ic = this.icn3d, me = ic.icn3dui;       
+        if(!$('#' + ic.pre + 'dl_definedsets').hasClass('ui-dialog-content') || !$('#' + ic.pre + 'dl_definedsets').dialog( 'isOpen' )) {
+            me.htmlCls.dialogCls.openDlg('dl_definedsets', 'Select sets');
+            $("#" + ic.pre + "atomsCustom").resizable();
+        }
+
+        let selectedResidues = {};
+        let bUnion = false, bUpdateHighlight = true;
+
+        let strandCnt = 0, loopCnt = 0;
+        let setName, currStrand, prevStrand, prevStrandReal, 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(!ic.residues.hasOwnProperty(resid) ) continue;
+          
+            let refnumLabel, refnumStr;
+            refnumLabel = ic.resid2refnum[resid];
+            if(!refnumLabel) continue;
+
+            refnumStr = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
+            currStrand = refnumLabel.replace(refnumStr, '');
+
+            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;
+                    }
+                    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;
+                    }
+                }
+
+                selectedResidues = {};
+            }
+
+            selectedResidues[resid] = 1;
+
+            prevStrand = currStrand;
+            prevType = currType;
+
+            bStart = true;
+        } // for loop
+
+        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;
+            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);
+        }
+    }
+
     simplifyText(text) { let ic = this.icn3d; ic.icn3dui;
         let out = ''; // 1-based text positions
         let bFoundText = false;
@@ -41831,6 +41947,11 @@ class ShowAnno {
                 chainHtml += this.addButton(chnid, "icn3d-helixsets", "Helix Sets", "Define sets for each helix in this chain and add them to the menu of \"Defined Sets\"", 60, buttonStyle) + "&nbsp;"
                 + 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)) {
+                    chainHtml += "&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);
+                }
             $("#" + 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'];
@@ -41889,7 +42010,7 @@ class ShowAnno {
             }
             catch(err) {
                 thisClass.enableHlSeq();
-                if(!me.bNode) console.log( "No data were found for the protein " + chnidBaseArray + "..." );
+                if(!me.bNode) console.log( "No sequence data were found for the protein " + chnidBaseArray + "..." );
                 for(let chnid in ic.protein_chainid) {
                     let chnidBase = ic.protein_chainid[chnid];
                     ic.showSeqCls.setAlternativeSeq(chnid, chnidBase);
@@ -42015,7 +42136,7 @@ class ShowAnno {
                 }
             }
             else {
-                if(!me.bNode) console.log( "No data were found for the chain " + chnid + "..." );
+                if(!me.bNode) console.log( "No sequence data were found for the chain " + chnid + "..." );
                 ic.showSeqCls.setAlternativeSeq(chnid, chnidBase);
             }
                      
@@ -42724,7 +42845,7 @@ class ShowSeq {
                 html += '</div>';
                 html3 += '</div></div>';
             }         
-            else if(ic.bShowRefnum && ic.chainid2index.hasOwnProperty(chnid)) {              
+            else if(ic.bShowRefnum && ic.chainid2refpdbname.hasOwnProperty(chnid)) {              
                 let result = this.showRefNum(giSeq, chnid);
                 html += result.html;
                 html3 += result.html3;
@@ -42767,10 +42888,10 @@ class ShowSeq {
         let html = '', html3 = '';
 
         let chainList = '';
-        if(!ic.chainid2index[chnid]) return {html: html, html3: html3};
+        if(!ic.chainid2refpdbname[chnid]) return {html: html, html3: html3};
 
-        for(let i = 0, il = ic.chainid2index[chnid].length; i < il; ++i) {
-            chainList += ic.refpdbArray[ic.chainid2index[chnid][i]] + " ";
+        for(let i = 0, il = ic.chainid2refpdbname[chnid].length; i < il; ++i) {
+            chainList += ic.chainid2refpdbname[chnid][i] + " ";
         }
 
         let refStruTitle = (chainList) ? "based on " + chainList : "";
@@ -42831,13 +42952,23 @@ class ShowSeq {
 
         // sometimes one chain may have several Ig domains,set an index for each IgDomain
         let index = 1, bStart = false;
-        
+
+        if(!bCustom && !kabat_or_imgt) {     
+            // reset ic.residIgLoop for the current selection, which could be the second round of ref num assignment
+            let residHash = ic.firstAtomObjCls.getResiduesFromAtoms(ic.hAtoms);
+            for(let resid in residHash) {
+                // not in loop any more if you assign ref numbers multiple times
+                delete ic.residIgLoop[resid];
+            }
+        }
+
         // 1. get the range of each strand excluding loops
         let strandArray = [], strandHash = {}, strandCnt = 0, resCnt = 0, resCntBfAnchor = 0, resCntAtAnchor = 0;
         if(!bCustom && !kabat_or_imgt) {
             for(let i = 0, il = giSeq.length; i < il; ++i, ++resCnt, ++resCntBfAnchor, ++resCntAtAnchor) {
                 let currResi = ic.ParserUtilsCls.getResi(chnid, i);
                 let residueid = chnid + '_' + currResi;
+
                 refnumLabel = ic.resid2refnum[residueid];
 
                 let firstChar = (refnumLabel) ? refnumLabel.substr(0,1) : ' ';
@@ -42851,7 +42982,7 @@ class ShowSeq {
                 }
 
                 if(refnumLabel) {                        
-                    refnumStr_ori = refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').replace(/\+/g, '').replace(/\-/g, '').substr(1); // C', C''
+                    refnumStr_ori = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
                     currStrand = refnumLabel.replace(new RegExp(refnumStr_ori,'g'), '');
                     refnumStr_ori.substr(0, 1);
 
@@ -42959,7 +43090,7 @@ class ShowSeq {
                     currStrand = strandArray[strandCnt].strand;
 
                     if(refnumLabel) {
-                        refnumStr = refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').replace(/\+/g, '').replace(/\-/g, '').substr(1); // C', C''
+                        refnumStr = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
                         currRefnum = parseInt(refnumStr);
                         refnumLabelNoPostfix = currStrand + currRefnum;
                         
@@ -43041,7 +43172,7 @@ class ShowSeq {
                         }
                         else if(parseInt(currResi) >= parseInt(strandArray[strandCnt].startResi) && parseInt(currResi) <= parseInt(strandArray[strandCnt].endResi)) {
                             // not in loop any more if you assign ref numbers multiple times
-                            delete ic.residIgLoop[residueid];
+                            //delete ic.residIgLoop[residueid];
 
                             bBeforeAstrand = false;
 
@@ -43131,7 +43262,7 @@ class ShowSeq {
                 let bHidelabel = false;
 
                 if(refnumLabel) {                        
-                    refnumStr_ori = refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').replace(/\+/g, '').replace(/\-/g, '').substr(1); // C', C''
+                    refnumStr_ori = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
                     currStrand = refnumLabel.replace(new RegExp(refnumStr_ori,'g'), '');
                     currStrand_ori = currStrand;
 
@@ -45087,6 +45218,11 @@ class GetGraph {
             if(!bVertical) adjusty += 4 * r;
         }
 
+        // show reference numbers
+        if(ic.bShownRefnum && ic.resid2refnum[resid]) {
+            nodeName = ic.resid2refnum[resid];
+        }
+
         let strokecolor = '#000';
         let strokewidth = '1';
         let textcolor = '#000';
@@ -54729,7 +54865,9 @@ class SetSeqAlign {
           if(!ic.chainsMapping[chainid2]) ic.chainsMapping[chainid2] = {};
 
           let posChain1 = {}, posChain2 = {};
-         
+console.log("###bRealign: " + bRealign);
+ console.log(ic.qt_start_end[chainIndex]);
+
           for(let i = 0, il = ic.qt_start_end[chainIndex].length; i < il; ++i) {
             let start1, start2, end1, end2;
             if(bRealign) { // real residue numbers are stored, could be "100a"
@@ -54844,10 +54982,14 @@ class SetSeqAlign {
 
                   let resi1, resi2, resn1, resn2;
                   if(bRealign) { // tmalign: just one residue in this for loop
-                    // resi1 = j + start1;
-                    // resi2 = j + start2;
-                    resi1 = ic.qt_start_end[chainIndex][i].t_start;
-                    resi2 = ic.qt_start_end[chainIndex][i].q_start;
+                    if(me.cfg.aligntool == 'tmalign') {
+                        resi1 = ic.qt_start_end[chainIndex][i].t_start;
+                        resi2 = ic.qt_start_end[chainIndex][i].q_start;
+                    }
+                    else {
+                        resi1 = j + start1;
+                        resi2 = j + start2;
+                    }
 
                     resn1 = this.getResnFromResi(chainid1, resi1).toUpperCase();
                     resn2 = this.getResnFromResi(chainid2, resi2).toUpperCase();
@@ -55124,7 +55266,12 @@ class SetSeqAlign {
         resObject.mmdbid = chainid.substr(0, pos);
         resObject.chain = chainid.substr(pos+1);
         resObject.resi = (bGap) ? '' : resi; // resi will be empty if there is no coordinates
-        resObject.resn = (bGap) ? '-' : ((bAligned) ? resn.toUpperCase() : resn.toLowerCase());
+        if(!resn) {
+            resObject.resn = '-';
+        }
+        else {
+            resObject.resn = (bGap) ? '-' : ((bAligned) ? resn.toUpperCase() : resn.toLowerCase());
+        }
         resObject.aligned = (bGap) ? false : bAligned;
         resObject.color = (bGap || !bAligned) ? me.htmlCls.GREYC : ((resn == resn_t) ? "#FF0000" : "#0000FF"); // color by identity
         resObject.color2 = (bGap || !bAligned) ? me.htmlCls.GREYC : '#' + ic.showAnnoCls.getColorhexFromBlosum62(resn, resn_t); // color by conservation
@@ -57827,6 +57974,18 @@ class ApplyCommand {
 
          ic.addTrackCls.defineSecondary(chainid, 'coil');
       }
+      else if(commandOri.indexOf('define igstrand sets') == 0) {
+        let chainStr = commandOri.split(' | ')[1];
+        let chainid = chainStr.split(' ')[1];
+
+        ic.addTrackCls.defineIgstrand(chainid, 'igstrand');
+      }
+      else if(commandOri.indexOf('define igloop sets') == 0) {
+        let chainStr = commandOri.split(' | ')[1];
+        let chainid = chainStr.split(' ')[1];
+
+        ic.addTrackCls.defineIgstrand(chainid, 'igloop');
+      }
       else if(commandOri.indexOf('select interaction') == 0) {
         let idArray = commandOri.substr(commandOri.lastIndexOf(' ') + 1).split(',');
         if(idArray !== null) {
@@ -58593,6 +58752,12 @@ class ApplyCommand {
         let dataStr = paraArray[1].replace(/\\n/g, '\n');
         await ic.refnumCls.parseCustomRefFile(dataStr);
       }
+      else if(command.indexOf('show ref number') == 0) {
+        ic.bShownRefnum = true;
+      }
+      else if(command.indexOf('hide ref number') == 0) {
+        ic.bShownRefnum = false;
+      }
 
     // special, select ==========
 
@@ -60627,6 +60792,7 @@ class SelectByCommand {
            // $1,2,3: Structure
            // .A,B,C: chain
            // :5-10,K,chemicals: residues, could be 'proteins', 'nucleotides', 'chemicals', 'ions', and 'water'
+           // :ref_1250,anchors,strands,loops: reference numbers 1250, anchor residues (e.g., 2250), residues in strands, residues in loops
            // @CA,C,C*: atoms
            // wild card * can be used to select all
            //var currHighlightAtoms = {}
@@ -60634,7 +60800,7 @@ class SelectByCommand {
            let dollarPos = commandArray[i].indexOf('$');
            let periodPos = commandArray[i].indexOf('.');
            let colonPos = commandArray[i].indexOf(':');
-           let colonPos2 = commandArray[i].indexOf('%'); // for reference numbers
+           let colonPos2 = commandArray[i].indexOf(':ref_'); // for reference numbers
            let atPos = commandArray[i].indexOf('@');
 
            let moleculeStr, chainStr, residueStr, refResStr, atomStrArray;
@@ -60651,14 +60817,14 @@ class SelectByCommand {
            if(colonPos === -1 && colonPos2 === -1 ) {
              residueStr = "*";
            }
+           else if(colonPos2 != -1) {
+            refResStr = testStr.substr(colonPos2 + 5);
+            testStr = testStr.substr(0, colonPos2);
+           }
            else if(colonPos != -1) {
              residueStr = testStr.substr(colonPos + 1);
              testStr = testStr.substr(0, colonPos);
            }
-           else if(colonPos2 != -1) {
-            refResStr = testStr.substr(colonPos2 + 1);
-            testStr = testStr.substr(0, colonPos2);
-          }
 
            if(periodPos === -1) {
              chainStr = "*";
@@ -60752,7 +60918,9 @@ class SelectByCommand {
                  else if(residueStrArray[j] === '*') { // all resiues
                    bAllResidues = true;
                  }
-                 else if(residueStrArray[j] !== 'proteins' && residueStrArray[j] !== 'nucleotides' && residueStrArray[j] !== 'chemicals' && residueStrArray[j] !== 'ions' && residueStrArray[j] !== 'water') { // residue name
+                 else if(residueStrArray[j] !== 'proteins' && residueStrArray[j] !== 'nucleotides' 
+                   && residueStrArray[j] !== 'chemicals' && residueStrArray[j] !== 'ions' && residueStrArray[j] !== 'water'
+                   && residueStrArray[j] !== 'anchors' && residueStrArray[j] !== 'strands' && residueStrArray[j] !== 'loops') { // residue name
                    let tmpStr = residueStrArray[j].toUpperCase();
                    //oneLetterResidue =(residueStrArray[j].length === 1) ? tmpStr : me.utilsCls.residueName2Abbr(tmpStr);
                    oneLetterResidueStr = tmpStr;
@@ -60821,6 +60989,16 @@ class SelectByCommand {
                      for(let m in chainAtomHash) {
                        // residue could also be 'proteins', 'nucleotides', 'chemicals', 'ions', and 'water'
                        ic.atoms[m].resn.substr(0,3).toUpperCase();
+                       let resid = molecule_chain + '_' + ic.atoms[m].resi; 
+                       let refnumLabel, refnumStr, refnum;
+                       if(bRefnum) {
+                         refnumLabel = ic.resid2refnum[resid];
+                         if(refnumLabel) {
+                          refnumStr = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
+                          refnum = parseInt(refnumStr);
+                         }
+                       }
+
                        if(bAllResidues
                            //|| me.utilsCls.residueName2Abbr(tmpStr) === oneLetterResidue
                            ||(residueStrArray[j] === 'proteins' && m in ic.proteins)
@@ -60828,32 +61006,23 @@ class SelectByCommand {
                            ||(residueStrArray[j] === 'chemicals' && m in ic.chemicals)
                            ||(residueStrArray[j] === 'ions' && m in ic.ions)
                            ||(residueStrArray[j] === 'water' && m in ic.water)
+                           ||(bRefnum && refnumLabel && residueStrArray[j] === 'anchors' && refnum % 100 == 50)
+                           ||(bRefnum && refnumLabel && residueStrArray[j] === 'strands' && !ic.residIgLoop.hasOwnProperty(resid))
+                           ||(bRefnum && refnumLabel && residueStrArray[j] === 'loops' && ic.residIgLoop.hasOwnProperty(resid))
                            ) {
                          // many duplicates
                          if(i === 0) {
-                             residueHash[molecule_chain + '_' + ic.atoms[m].resi] = 1;
+                             residueHash[resid] = 1;
                          }
                          else {
-                             let residTmp = molecule_chain + '_' + ic.atoms[m].resi;
-                             //if(!residueHash.hasOwnProperty(residTmp)) residueHash[residTmp] = undefined;
-                             if(!residueHash.hasOwnProperty(residTmp)) delete residueHash[residTmp];
+                             if(!residueHash.hasOwnProperty(resid)) delete residueHash[resid];
                          }
 
                          for(let n = 0, nl = atomStrArray.length; n < nl; ++n) {
                              let atomStr = atomStrArray[n];
 
                              atomHash = this.processAtomStr(atomStr, atomHash, i, m);
-
-                            //  if(atomStr === '*' || atomStr === ic.atoms[m].name) {
-                            //      if(i === 0) {
-                            //          atomHash[m] = 1;
-                            //      }
-                            //      else {
-                            //          if(!atomHash.hasOwnProperty(m)) delete atomHash[m];
-                            //      }
-                            //  }
                          }
-
                        }
                      } // end for(let m in atomHash) {
 
@@ -62970,72 +63139,155 @@ class Dssp {
     async showIgRefNum() { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
-        // if(ic.resid2refnum  && Object.keys(ic.resid2refnum).length > 0) {
-        //     ic.bShowRefnum = true;
-
-        //     // open sequence view
-        //     ic.hAtomsRefnum = {};
-        //     ic.bResetAnno = true;
-        //     await ic.showAnnoCls.showAnnotations();
-        //     ic.annotationCls.setAnnoViewAndDisplay('detailed view');
+        // if(ic.pdbDataArray) {
+        //     await thisClass.parseRefPdbData(ic.pdbDataArray);
         // }
-        if(ic.pdbDataArray) {
-            await thisClass.parseRefPdbData(ic.pdbDataArray);
-        }
-        else {
-            //ic.refpdbArray = ['1bqu_fn3', '1cd8_igv', '1cdh_cd4', '1dr9_cd80', '1hnf_cd2', '1hxm_d', '1hxm_g', '1ifr_lamin', '1ncn_cd86', '1t6v_vnar', '1yjd_cd28', '2atp_a', '2atp_b', '2dm3_iset', '3kys_tead1', '3pv7_ncr', '4f9l_cd277', '4gos_vtc', '4i0k_cd276', '4jqi_b', '4z18_cd274', '4zqk_pd1', '4zt1_e', '5esv_vh', '5esv_vl', '6al5_cd19', '6jxr_a', '6jxr_b', '6jxr_d', '6jxr_e', '6jxr_g', '6oil_vista', '6rp8_at', '6rp8_t', '6umt_cd273', '6x4g_cd275', '6x4g_icos', '7xq8_a', '7xq8_b', 'q71h61_ild', 'q9um44_hhl', 'p42081_cd86', 'q7z7d3_vtc', '1bqu_x', '1cdh_x', '1hnf_x', '1hxm_dx', '1hxm_gx', '4jqi_x', '4zt1_x', '5esv_vhx', '5esv_vlx', '6jxr_ax', '6jxr_bx', '1dr9_x', '3pv7_x', '4f9l_x', '4iok_x', '4z18_x', '6x4g_cd275x', 'q9um44_x'];
-            
-            //ic.refpdbArray = ['1bqu_fn3', '1cd8_igv', '1cdh_cd4', '1dr9_cd80', '1hnf_cd2', '1hxm_d', '1hxm_g', '1ifr_lamin', '1ncn_cd86', '1t6v_vnar', '1yjd_cd28', '2atp_a', '2atp_b', '2dm3_iset', '3kys_tead1', '3pv7_ncr', '4f9l_cd277', '4gos_vtc', '4i0k_cd276', '4jqi_b', '4z18_cd274', '4zqk_pd1', '4zt1_e', '5esv_vh', '5esv_vl', '6al5_cd19', '6jxr_a', '6jxr_b', '6jxr_d', '6jxr_e', '6jxr_g', '6oil_vista', '6rp8_at', '6rp8_t', '6umt_cd273', '6x4g_cd275', '6x4g_icos', '7xq8_a', '7xq8_b', 'q71h61_ild', 'q9um44_hhl'];
-
-            //ic.refpdbArray = ['ASF1A_2iijA_human', 'BArrestin1_4jqiA_rat_n1', 'BTLA_2aw2A_human_Iset', 'C3_2qkiD_human_n1', 'CD19_6al5A_human_C2orV-n1', 'CD2_1hnfA_human_C2-n2', 'CD2_1hnfA_human_V-n1', 'CD8a_1cd8A_human_V', 'CoAtomerGamma1_1r4xA_human', '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', 'InsulinR_8guyE_human_FN3-n2', 'IsdA_2iteA_bacteria', 'LAG3_7tzgD_human_C2-n2', 'LAG3_7tzgD_human_V-n1', 'LaminAC_1ifrA_human', 'MHCIa_7phrH_human_C1', 'MPT63_1lmiA_bacteria', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'PD1_4zqkB_human_V', 'PDL1_4z18B_human_V-n1', 'Palladin_2dm3A_human_Iset-n1', 'RBPJ_6py8C_human_Unk-n1', 'RBPJ_6py8C_human_Unk-n2', 'TCRa_6jxrm_human_C1-n2', 'TCRa_6jxrm_human_V-n1', 'TEAD1_3kysC_human', 'TP34_2o6cA_bacteria', 'Titin_4uowM_human_Unk-n152', 'VISTA_6oilA_human_V', 'VNAR_1t6vN_shark_V', 'VTCN1_Q7Z7D3_human_V-n2'];
-
-            //ic.refpdbArray2 = ['B2Microglobulin_7phrL_human_C1.pdb', 'Contactin1_2ee2A_human_FN3-n9.pdb', 'IL6Rb_1bquB_human_FN3-n3.pdb', 'InsulinR_8guyE_human_FN3-n1.pdb', 'JAM1_1nbqA_human_VorIset-n2.pdb', 'NaCaExchanger_2fwuA_dog_n2.pdb', 'ORF7a_1xakA_virus.pdb', 'Sidekick2_1wf5A_human_FN3-n7.pdb', 'Siglec3_5j0bB_human_C2-n2.pdb', 'TP47_1o75A_bacteria.pdb'];
-
-            ic.refpdbArray = ['ASF1A_2iijA_human', 'BArrestin1_4jqiA_rat_n1', 'BTLA_2aw2A_human_Iset', 'C3_2qkiD_human_n1', 'CD19_6al5A_human_C2orV-n1', 'CD2_1hnfA_human_C2-n2', 'CD2_1hnfA_human_V-n1', 'CD8a_1cd8A_human_V', 'CoAtomerGamma1_1r4xA_human', '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', 'InsulinR_8guyE_human_FN3-n2', 'IsdA_2iteA_bacteria', 'LAG3_7tzgD_human_C2-n2', 'LAG3_7tzgD_human_V-n1', 'LaminAC_1ifrA_human', 'MHCIa_7phrH_human_C1', 'MPT63_1lmiA_bacteria', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'PD1_4zqkB_human_V', 'PDL1_4z18B_human_V-n1', 'Palladin_2dm3A_human_Iset-n1', 'RBPJ_6py8C_human_Unk-n1', 'RBPJ_6py8C_human_Unk-n2', 'TCRa_6jxrm_human_C1-n2', 'TCRa_6jxrm_human_V-n1', 'TEAD1_3kysC_human', 'TP34_2o6cA_bacteria', 'Titin_4uowM_human_Unk-n152', 'VISTA_6oilA_human_V', 'VNAR_1t6vN_shark_V', 'VTCN1_Q7Z7D3_human_V-n2', 'B2Microglobulin_7phrL_human_C1.pdb', 'Contactin1_2ee2A_human_FN3-n9.pdb', 'IL6Rb_1bquB_human_FN3-n3.pdb', 'InsulinR_8guyE_human_FN3-n1.pdb', 'JAM1_1nbqA_human_VorIset-n2.pdb', 'NaCaExchanger_2fwuA_dog_n2.pdb', 'ORF7a_1xakA_virus.pdb', 'Sidekick2_1wf5A_human_FN3-n7.pdb', 'Siglec3_5j0bB_human_C2-n2.pdb', 'TP47_1o75A_bacteria.pdb'];
-
-            if(ic.pdbDataArray) {
-                await thisClass.parseRefPdbData(ic.pdbDataArray);
-            }
-            else {
-
-                let pdbAjaxArray = [];
-                for(let k = 0, kl = ic.refpdbArray.length; k < kl; ++k) {
-                    //let urlpdb = me.htmlCls.baseUrl + "icn3d/refpdb/" + ic.refpdbArray[k] + ".pdb";
-                    let urlpdb = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi?refpdbid=" + ic.refpdbArray[k];
+        // else {
+        //ic.refpdbArray = ['ASF1A_2iijA_human', 'B2Microglobulin_7phrL_human_C1', 'BArrestin1_4jqiA_rat_n1', 'BTLA_2aw2A_human_Iset', 'C3_2qkiD_human_n1', 'CD19_6al5A_human_C2orV-n1', 'CD2_1hnfA_human_C2-n2', 'CD2_1hnfA_human_V-n1', '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'];
+        
+        //ic.refpdbArray = ['1ASF1A_2iijA_human', '1B2Microglobulin_7phrL_human_C1', '1BArrestin1_4jqiA_rat_n1', '1BTLA_2aw2A_human_Iset', '1C3_2qkiD_human_n1', '1CD19_6al5A_human_C2orV-n1', '1CD2_1hnfA_human_C2-n2', '1CD2_1hnfA_human_V-n1', '1CD8a_1cd8A_human_V', '1CoAtomerGamma1_1r4xA_human', '1Contactin1_2ee2A_human_FN3-n9', '1Contactin1_3s97C_human_C2-n2', '1CuZnSuperoxideDismutase_1hl5C_human', '1ECadherin_4zt1A_human_n2', '1Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', '1FAB-HEAVY_5esv_C1-n2', '1FAB-HEAVY_5esv_V-n1', '1FAB-LIGHT_5esv_C1-n2', '1FAB-LIGHT_5esv_V-n1', '1GHR_1axiB_human_FN3-n1', '1ICOS_6x4gA_human_V', '1IL6Rb_1bquB_human_FN3-n2', '1IL6Rb_1bquB_human_FN3-n3', '1InsulinR_8guyE_human_FN3-n1', '1InsulinR_8guyE_human_FN3-n2', '1IsdA_2iteA_bacteria', '1JAM1_1nbqA_human_VorIset-n2', '1LAG3_7tzgD_human_C2-n2', '1LAG3_7tzgD_human_V-n1', '1LaminAC_1ifrA_human', '1MHCIa_7phrH_human_C1', '1MPT63_1lmiA_bacteria', '1NaCaExchanger_2fwuA_dog_n2', '1NaKATPaseTransporterBeta_2zxeB_spurdogshark', '1ORF7a_1xakA_virus', '1PD1_4zqkB_human_V', '1PDL1_4z18B_human_V-n1', '1Palladin_2dm3A_human_Iset-n1', '1RBPJ_6py8C_human_Unk-n1', '1RBPJ_6py8C_human_Unk-n2', '1Sidekick2_1wf5A_human_FN3-n7', '1Siglec3_5j0bB_human_C2-n2', '1TCRa_6jxrm_human_C1-n2', '1TCRa_6jxrm_human_V-n1', '1TEAD1_3kysC_human', '1TP34_2o6cA_bacteria', '1TP47_1o75A_bacteria', '1Titin_4uowM_human_Unk-n152', '1VISTA_6oilA_human_V', '1VNAR_1t6vN_shark_V', '1VTCN1_Q7Z7D3_human_V-n2'];
+     
+/*
+        // round 1
+        ic.refpdbArray = ['NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'GHR_1axiB_human_FN3-n1', 'FAB-HEAVY_5esv_C1-n2', 'IL6Rb_1bquB_human_FN3-n2', 'LAG3_7tzgD_human_C2-n2', 'VNAR_1t6vN_shark_V', 'VISTA_6oilA_human_V', 'CD19_6al5A_human_C2orV-n1', 'TP47_1o75A_bacteria', 'TP34_2o6cA_bacteria'];
+        // round 2
+        ic.refpdbHash = {};
+
+        ic.refpdbHash['NaKATPaseTransporterBeta_2zxeB_spurdogshark'] = ['NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'ORF7a_1xakA_virus', 'NaCaExchanger_2fwuA_dog_n2', 'BArrestin1_4jqiA_rat_n1', 'ECadherin_4zt1A_human_n2', 'C3_2qkiD_human_n1', 'RBPJ_6py8C_human_Unk-n1'];
+        ic.refpdbHash['GHR_1axiB_human_FN3-n1'] = ['GHR_1axiB_human_FN3-n1', 'Siglec3_5j0bB_human_C2-n2', 'ICOS_6x4gA_human_V', 'CD2_1hnfA_human_C2-n2', 'Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'];
+        ic.refpdbHash['FAB-HEAVY_5esv_C1-n2'] = ['FAB-HEAVY_5esv_C1-n2', 'B2Microglobulin_7phrL_human_C1', 'VTCN1_Q7Z7D3_human_V-n2', 'FAB-LIGHT_5esv_C1-n2', 'MHCIa_7phrH_human_C1'];
+        ic.refpdbHash['IL6Rb_1bquB_human_FN3-n2'] = ['IL6Rb_1bquB_human_FN3-n2', 'Contactin1_2ee2A_human_FN3-n9', 'IL6Rb_1bquB_human_FN3-n3', 'InsulinR_8guyE_human_FN3-n1', 'Sidekick2_1wf5A_human_FN3-n7', 'InsulinR_8guyE_human_FN3-n2'];
+        ic.refpdbHash['LAG3_7tzgD_human_C2-n2'] = ['LAG3_7tzgD_human_C2-n2', 'JAM1_1nbqA_human_VorIset-n2', 'Contactin1_3s97C_human_C2-n2', 'Palladin_2dm3A_human_Iset-n1', 'BTLA_2aw2A_human_Iset', 'Titin_4uowM_human_Unk-n152'];
+        ic.refpdbHash['VNAR_1t6vN_shark_V'] = ['VNAR_1t6vN_shark_V', 'PD1_4zqkB_human_V', 'CD8a_1cd8A_human_V', 'TCRa_6jxrm_human_V-n1', 'FAB-HEAVY_5esv_V-n1', 'FAB-LIGHT_5esv_V-n1'];
+        ic.refpdbHash['VISTA_6oilA_human_V'] = ['VISTA_6oilA_human_V', 'LAG3_7tzgD_human_V-n1', 'PDL1_4z18B_human_V-n1', 'CD2_1hnfA_human_V-n1'];
+        ic.refpdbHash['CD19_6al5A_human_C2orV-n1'] = ['CD19_6al5A_human_C2orV-n1'];
+        ic.refpdbHash['TP47_1o75A_bacteria'] = ['TP47_1o75A_bacteria', 'TEAD1_3kysC_human', 'RBPJ_6py8C_human_Unk-n2', 'CuZnSuperoxideDismutase_1hl5C_human', 'ASF1A_2iijA_human'];
+        ic.refpdbHash['TP34_2o6cA_bacteria'] = ['TP34_2o6cA_bacteria', 'TCRa_6jxrm_human_C1-n2', 'IsdA_2iteA_bacteria', 'LaminAC_1ifrA_human', 'CoAtomerGamma1_1r4xA_human', 'MPT63_1lmiA_bacteria'];
+*/
+/*
+        // round 1
+        ic.refpdbArray = ['NaCaExchanger_2fwuA_dog_n2', 'C3_2qkiD_human_n1', 'Siglec3_5j0bB_human_C2-n2', 'ICOS_6x4gA_human_V', 'B2Microglobulin_7phrL_human_C1', 'VTCN1_Q7Z7D3_human_V-n2', 'Contactin1_2ee2A_human_FN3-n9', 'InsulinR_8guyE_human_FN3-n1', 'JAM1_1nbqA_human_VorIset-n2', 'LAG3_7tzgD_human_C2-n2', 'Palladin_2dm3A_human_Iset-n1', 'PD1_4zqkB_human_V', 'CD8a_1cd8A_human_V', 'VISTA_6oilA_human_V', 'LAG3_7tzgD_human_V-n1', 'TP47_1o75A_bacteria', 'TP34_2o6cA_bacteria', 'TEAD1_3kysC_human', 'RBPJ_6py8C_human_Unk-n2', 'TCRa_6jxrm_human_C1-n2', 'IsdA_2iteA_bacteria', 'LaminAC_1ifrA_human', 'CD19_6al5A_human_C2orV-n1'];
+
+        // round 2
+        ic.refpdbHash = {};
+        ic.refpdbHash['NaCaExchanger_2fwuA_dog_n2'] = ['NaCaExchanger_2fwuA_dog_n2', 'ORF7a_1xakA_virus', 'ECadherin_4zt1A_human_n2', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark'];
+        ic.refpdbHash['C3_2qkiD_human_n1'] = ['C3_2qkiD_human_n1', 'RBPJ_6py8C_human_Unk-n1', 'BArrestin1_4jqiA_rat_n1'];
+        ic.refpdbHash['Siglec3_5j0bB_human_C2-n2'] = ['Siglec3_5j0bB_human_C2-n2', 'CD2_1hnfA_human_C2-n2', 'GHR_1axiB_human_FN3-n1'];
+        ic.refpdbHash['ICOS_6x4gA_human_V'] = ['ICOS_6x4gA_human_V', 'Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'];
+        ic.refpdbHash['B2Microglobulin_7phrL_human_C1'] = ['B2Microglobulin_7phrL_human_C1', 'FAB-HEAVY_5esv_C1-n2', 'MHCIa_7phrH_human_C1'];
+        ic.refpdbHash['VTCN1_Q7Z7D3_human_V-n2'] = ['VTCN1_Q7Z7D3_human_V-n2', 'FAB-LIGHT_5esv_C1-n2'];
+        ic.refpdbHash['Contactin1_2ee2A_human_FN3-n9'] = ['Contactin1_2ee2A_human_FN3-n9', 'IL6Rb_1bquB_human_FN3-n3', 'Sidekick2_1wf5A_human_FN3-n7'];
+        ic.refpdbHash['InsulinR_8guyE_human_FN3-n1'] = ['InsulinR_8guyE_human_FN3-n1', 'InsulinR_8guyE_human_FN3-n2', 'IL6Rb_1bquB_human_FN3-n2'];
+        ic.refpdbHash['JAM1_1nbqA_human_VorIset-n2'] = ['JAM1_1nbqA_human_VorIset-n2', 'Contactin1_3s97C_human_C2-n2'];
+        ic.refpdbHash['LAG3_7tzgD_human_C2-n2'] = ['LAG3_7tzgD_human_C2-n2', 'BTLA_2aw2A_human_Iset'];
+        ic.refpdbHash['Palladin_2dm3A_human_Iset-n1'] = ['Palladin_2dm3A_human_Iset-n1', 'Titin_4uowM_human_Unk-n152'];
+        ic.refpdbHash['PD1_4zqkB_human_V'] = ['PD1_4zqkB_human_V', 'TCRa_6jxrm_human_V-n1', 'FAB-LIGHT_5esv_V-n1'];
+        ic.refpdbHash['CD8a_1cd8A_human_V'] = ['CD8a_1cd8A_human_V', 'FAB-HEAVY_5esv_V-n1', 'VNAR_1t6vN_shark_V'];
+        ic.refpdbHash['VISTA_6oilA_human_V'] = ['VISTA_6oilA_human_V', 'PDL1_4z18B_human_V-n1', 'CD2_1hnfA_human_V-n1'];
+        ic.refpdbHash['LAG3_7tzgD_human_V-n1'] = ['LAG3_7tzgD_human_V-n1'];
+        ic.refpdbHash['TP47_1o75A_bacteria'] = ['TP47_1o75A_bacteria'];
+        ic.refpdbHash['TP34_2o6cA_bacteria'] = ['TP34_2o6cA_bacteria'];
+        ic.refpdbHash['TEAD1_3kysC_human'] = ['TEAD1_3kysC_human', 'CuZnSuperoxideDismutase_1hl5C_human'];
+        ic.refpdbHash['RBPJ_6py8C_human_Unk-n2'] = ['RBPJ_6py8C_human_Unk-n2', 'ASF1A_2iijA_human'];
+        ic.refpdbHash['TCRa_6jxrm_human_C1-n2'] = ['TCRa_6jxrm_human_C1-n2'];
+        ic.refpdbHash['IsdA_2iteA_bacteria'] = ['IsdA_2iteA_bacteria', 'CoAtomerGamma1_1r4xA_human'];
+        ic.refpdbHash['LaminAC_1ifrA_human'] = ['LaminAC_1ifrA_human', 'MPT63_1lmiA_bacteria'];
+        ic.refpdbHash['CD19_6al5A_human_C2orV-n1'] = ['CD19_6al5A_human_C2orV-n1'];
+*/
+        // round 1, 16 templates
+        ic.refpdbArray = ['1InsulinR_8guyE_human_FN3-n1', '1Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', '1CoAtomerGamma1_1r4xA_human', '1C3_2qkiD_human_n1', '1CuZnSuperoxideDismutase_1hl5C_human', '1ASF1A_2iijA_human', '1FAB-LIGHT_5esv_C1-n2', '1CD2_1hnfA_human_C2-n2', '1NaCaExchanger_2fwuA_dog_n2', '1FAB-HEAVY_5esv_V-n1', '1PDL1_4z18B_human_V-n1', '1BTLA_2aw2A_human_Iset', '1LaminAC_1ifrA_human', '1IsdA_2iteA_bacteria', '1TCRa_6jxrm_human_C1-n2', '1CD19_6al5A_human_C2orV-n1'];
+
+        // round 2
+        ic.refpdbHash = {};
+        ic.refpdbHash['1InsulinR_8guyE_human_FN3-n1'] = ['InsulinR_8guyE_human_FN3-n1', 'IL6Rb_1bquB_human_FN3-n3', 'Sidekick2_1wf5A_human_FN3-n7', 'InsulinR_8guyE_human_FN3-n2', 'Contactin1_2ee2A_human_FN3-n9', 'IL6Rb_1bquB_human_FN3-n2'];
+        ic.refpdbHash['1Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'] = ['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', 'ICOS_6x4gA_human_V'];
+        ic.refpdbHash['1CoAtomerGamma1_1r4xA_human'] = ['CoAtomerGamma1_1r4xA_human', 'TP34_2o6cA_bacteria', 'RBPJ_6py8C_human_Unk-n2', 'TP47_1o75A_bacteria'];
+        ic.refpdbHash['1C3_2qkiD_human_n1'] = ['C3_2qkiD_human_n1', 'BArrestin1_4jqiA_rat_n1', 'RBPJ_6py8C_human_Unk-n1'];
+        ic.refpdbHash['1CuZnSuperoxideDismutase_1hl5C_human'] = ['CuZnSuperoxideDismutase_1hl5C_human', 'TEAD1_3kysC_human'];
+        ic.refpdbHash['1ASF1A_2iijA_human'] = ['ASF1A_2iijA_human', 'MPT63_1lmiA_bacteria'];
+        ic.refpdbHash['1FAB-LIGHT_5esv_C1-n2'] = ['FAB-LIGHT_5esv_C1-n2', 'GHR_1axiB_human_FN3-n1', 'VTCN1_Q7Z7D3_human_V-n2', 'B2Microglobulin_7phrL_human_C1', 'FAB-HEAVY_5esv_C1-n2', 'MHCIa_7phrH_human_C1'];
+        ic.refpdbHash['1CD2_1hnfA_human_C2-n2'] = ['CD2_1hnfA_human_C2-n2', 'Siglec3_5j0bB_human_C2-n2'];
+        ic.refpdbHash['1NaCaExchanger_2fwuA_dog_n2'] = ['NaCaExchanger_2fwuA_dog_n2', 'ORF7a_1xakA_virus', 'ECadherin_4zt1A_human_n2', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark'];
+        ic.refpdbHash['1FAB-HEAVY_5esv_V-n1'] = ['FAB-HEAVY_5esv_V-n1', 'FAB-LIGHT_5esv_V-n1', 'VNAR_1t6vN_shark_V', 'TCRa_6jxrm_human_V-n1', 'VISTA_6oilA_human_V', 'CD8a_1cd8A_human_V', 'PD1_4zqkB_human_V'];
+        ic.refpdbHash['1PDL1_4z18B_human_V-n1'] = ['PDL1_4z18B_human_V-n1', 'CD2_1hnfA_human_V-n1', 'LAG3_7tzgD_human_V-n1'];
+        ic.refpdbHash['1BTLA_2aw2A_human_Iset'] = ['BTLA_2aw2A_human_Iset', 'Palladin_2dm3A_human_Iset-n1', 'Titin_4uowM_human_Unk-n152', 'LAG3_7tzgD_human_C2-n2', 'JAM1_1nbqA_human_VorIset-n2', 'Contactin1_3s97C_human_C2-n2'];
+        ic.refpdbHash['1LaminAC_1ifrA_human'] = ['LaminAC_1ifrA_human'];
+        ic.refpdbHash['1IsdA_2iteA_bacteria'] = ['IsdA_2iteA_bacteria'];
+        ic.refpdbHash['1TCRa_6jxrm_human_C1-n2'] = ['TCRa_6jxrm_human_C1-n2'];
+        ic.refpdbHash['1CD19_6al5A_human_C2orV-n1'] = ['CD19_6al5A_human_C2orV-n1'];         
+
+        // use known ref structure
+        ic.refpdbHash['5ESV'] = ['FAB-HEAVY_5esv_V-n1', 'FAB-LIGHT_5esv_V-n1', 'FAB-HEAVY_5esv_C1-n2', 'FAB-LIGHT_5esv_C1-n2'];
+        ic.refpdbHash['8GUY'] = ['InsulinR_8guyE_human_FN3-n1', 'InsulinR_8guyE_human_FN3-n2'];
+        ic.refpdbHash['6JXR'] = ['TCRa_6jxrm_human_V-n1', 'TCRa_6jxrm_human_C1-n2'];
+        ic.refpdbHash['1HNF'] = ['CD2_1hnfA_human_V-n1', 'CD2_1hnfA_human_C2-n2'];
+        ic.refpdbHash['7TZG'] = ['LAG3_7tzgD_human_V-n1', 'LAG3_7tzgD_human_C2-n2'];
+        ic.refpdbHash['6PY8'] = ['RBPJ_6py8C_human_Unk-n1', 'RBPJ_6py8C_human_Unk-n2'];
+        ic.refpdbHash['1BQU'] = ['IL6Rb_1bquB_human_FN3-n2', 'IL6Rb_1bquB_human_FN3-n3'];
+
+        ic.refpdbHash['1R4X'] = ['CoAtomerGamma1_1r4xA_human'];
+        ic.refpdbHash['6OIL'] = ['VISTA_6oilA_human_V'];
+        ic.refpdbHash['2ZXE'] = ['NaKATPaseTransporterBeta_2zxeB_spurdogshark'];
+        ic.refpdbHash['1I8A'] = ['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'];
+        ic.refpdbHash['2FWU'] = ['NaCaExchanger_2fwuA_dog_n2'];
+        ic.refpdbHash['4JQI'] = ['BArrestin1_4jqiA_rat_n1'];
+        ic.refpdbHash['1NBQ'] = ['JAM1_1nbqA_human_VorIset-n2'];
+        ic.refpdbHash['1O75'] = ['TP47_1o75A_bacteria'];
+        ic.refpdbHash['7PHR'] = ['MHCIa_7phrH_human_C1'];
+        ic.refpdbHash['2IIJ'] = ['ASF1A_2iijA_human'];
+        ic.refpdbHash['4Z18'] = ['PDL1_4z18B_human_V-n1'];
+        ic.refpdbHash['1T6V'] = ['VNAR_1t6vN_shark_V'];
+        ic.refpdbHash['2O6C'] = ['TP34_2o6cA_bacteria'];
+        ic.refpdbHash['3KYS'] = ['TEAD1_3kysC_human'];
+        ic.refpdbHash['7PHR'] = ['B2Microglobulin_7phrL_human_C1'];
+        ic.refpdbHash['2AW2'] = ['BTLA_2aw2A_human_Iset'];
+        ic.refpdbHash['1HL5'] = ['CuZnSuperoxideDismutase_1hl5C_human'];
+        ic.refpdbHash['1WF5'] = ['Sidekick2_1wf5A_human_FN3-n7'];
+        ic.refpdbHash['5J0B'] = ['Siglec3_5j0bB_human_C2-n2'];
+        ic.refpdbHash['1IFR'] = ['LaminAC_1ifrA_human'];
+        ic.refpdbHash['Q7Z7D3'] = ['VTCN1_Q7Z7D3_human_V-n2'];
+        ic.refpdbHash['4ZQK'] = ['PD1_4zqkB_human_V'];
+        ic.refpdbHash['2DM3'] = ['Palladin_2dm3A_human_Iset-n1'];
+        ic.refpdbHash['2ITE'] = ['IsdA_2iteA_bacteria'];
+        ic.refpdbHash['1XAK'] = ['ORF7a_1xakA_virus'];
+        ic.refpdbHash['4ZT1'] = ['ECadherin_4zt1A_human_n2'];
+        ic.refpdbHash['1LMI'] = ['MPT63_1lmiA_bacteria'];
+        ic.refpdbHash['1CD8'] = ['CD8a_1cd8A_human_V'];
+        ic.refpdbHash['3S97'] = ['Contactin1_3s97C_human_C2-n2'];
+        ic.refpdbHash['1AXI'] = ['GHR_1axiB_human_FN3-n1'];
+        ic.refpdbHash['6X4G'] = ['ICOS_6x4gA_human_V'];
+        ic.refpdbHash['2EE2'] = ['Contactin1_2ee2A_human_FN3-n9'];
+        ic.refpdbHash['4UOW'] = ['Titin_4uowM_human_Unk-n152'];
+        ic.refpdbHash['6A15'] = ['CD19_6al5A_human_C2orV-n1'];
+        ic.refpdbHash['2QKI'] = ['C3_2qkiD_human_n1'];
+
+        // if(ic.pdbDataArray) {
+        //     await thisClass.parseRefPdbData(ic.pdbDataArray);
+        // }
+        // else {
 
-                    let pdbAjax = me.getAjaxPromise(urlpdb, 'text');
+        let pdbAjaxArray = [];
+        for(let k = 0, kl = ic.refpdbArray.length; k < kl; ++k) {
+            //let urlpdb = me.htmlCls.baseUrl + "icn3d/refpdb/" + ic.refpdbArray[k] + ".pdb";
+            let urlpdb = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi?refpdbid=" + ic.refpdbArray[k];
 
-                    pdbAjaxArray.push(pdbAjax);
-                }
+            let pdbAjax = me.getAjaxPromise(urlpdb, 'text');
 
-                // try {
-                    // if(!me.bNode) {
-                        let allPromise = Promise.allSettled(pdbAjaxArray);
-                        ic.pdbDataArray = await allPromise;
-                        await thisClass.parseRefPdbData(ic.pdbDataArray);
-                    // }
-                    // else { 
-                    //     ic.pdbDataArray = [];
-                    //     for(let i = 0, il = pdbAjaxArray.length; i < il; ++i) {
-                    //         try {
-                    //             let dataTmp = await pdbAjaxArray[i];
-                    //             ic.pdbDataArray.push({'value': dataTmp});
-                    //         }
-                    //         catch(err) {
-                    //             ic.pdbDataArray.push({'value': ''});
-                    //         }
-                    //     }
-
-                    //     await thisClass.parseRefPdbData(ic.pdbDataArray);
-                    // }
-                // }
-                // catch(err) {
-                //     if(!me.bNode) alert("Error in retrieveing reference PDB data...");
-                //     //alert("Error in retrieveing reference PDB data...");
-                //     return;
-                // }             
-            }
+            pdbAjaxArray.push(pdbAjax);
         }
+
+        // try {
+            let allPromise = Promise.allSettled(pdbAjaxArray);
+            ic.pdbDataArray = await allPromise;
+            await thisClass.parseRefPdbData(ic.pdbDataArray);
+        // }
+        // catch(err) {
+        //     if(!me.bNode) alert("Error in retrieveing reference PDB data...");
+        //     //alert("Error in retrieveing reference PDB data...");
+        //     return;
+        // }             
+        // }
+        // }
     }
 
     async parseRefPdbData(dataArray) { let ic = this.icn3d, me = ic.icn3dui;
@@ -63050,6 +63302,9 @@ class Dssp {
 
         // if(!ic.resid2domainid) ic.resid2domainid = {};
         ic.resid2domainid = {};
+        ic.domainid2pdb = {};
+
+        let minResidues = 20;
 
         for(let i = 0, il = struArray.length; i < il; ++i) {
             let struct = struArray[i];
@@ -63060,7 +63315,7 @@ class Dssp {
 
                 if(!ic.proteins.hasOwnProperty(ic.firstAtomObjCls.getFirstAtomObj(ic.chains[chainid]).serial)
                 && !ic.proteins.hasOwnProperty(ic.firstAtomObjCls.getMiddleAtomObj(ic.chains[chainid]).serial)) continue;
-                if(ic.chainsSeq[chainid].length < 50) continue; // peptide
+                if(ic.chainsSeq[chainid].length < minResidues) continue; // peptide
 
                 let currAtoms = me.hashUtilsCls.intHash(ic.chains[chainid], ic.hAtoms);
                 if(Object.keys(currAtoms).length == 0) continue;
@@ -63077,11 +63332,6 @@ class Dssp {
                     //domainAtomsArray.push(ic.chains[chainid]);
                     domainAtomsArray.push(currAtoms);
 
-                    // for(let n = 0, nl = ic.chainsSeq[chainid].length; n < nl; ++n) {
-                    //     let resid = chainid + '_' + ic.chainsSeq[chainid][n].resi;
-                    //     ic.resid2domainid[resid] = chainid + '-0';
-                    // }    
-                    
                     let residueArray = ic.resid2specCls.atoms2residues(Object.keys(currAtoms));
                     for(let n = 0, nl = residueArray.length; n < nl; ++n) {
                         let resid = residueArray[n];
@@ -63108,10 +63358,11 @@ class Dssp {
                         domainAtomsArray.push(domainAtoms);
                     }
                 }
-       
+console.log("###subdomains.length: " + subdomains.length + " domainAtomsArray.length: " + domainAtomsArray.length);       
                 for(let k = 0, kl = domainAtomsArray.length; k < kl; ++k) {
                     let pdb_target = ic.saveFileCls.getAtomPDB(domainAtomsArray[k], undefined, undefined, undefined, undefined, struct);
                     let domainid = chainid + '-' + k;
+                    ic.domainid2pdb[domainid] = pdb_target;
 
                     for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
                         let struct2 = ic.defaultPdbId + index;
@@ -63123,31 +63374,19 @@ class Dssp {
                         let alignAjax = me.getAjaxPostPromise(urltmalign, dataObj);
                         ajaxArray.push(alignAjax);
                         
-                        domainidpairArray.push(domainid + "," + index);
+                        domainidpairArray.push(domainid + "|" + ic.refpdbArray[index]);
                     }
                 }
             }
-       }
+        }
 
         // try {
             let dataArray2 = [];
-            // if(!me.bNode) {
-                let allPromise = Promise.allSettled(ajaxArray);
-                dataArray2 = await allPromise;
-            // }
-            // else {
-            //     for(let i = 0, il = ajaxArray.length; i < il; ++i) {
-            //         try {
-            //             let dataTmp = await ajaxArray[i];
-            //             dataArray2.push({'value': dataTmp});
-            //         }
-            //         catch(err) {
-            //             dataArray2.push({'value': []});
-            //         }
-            //     }
-            // }
-            
-            await thisClass.parseAlignData(dataArray2, domainidpairArray);
+            let allPromise = Promise.allSettled(ajaxArray);
+            dataArray2 = await allPromise;
+        
+            let bRound1 = true;
+            await thisClass.parseAlignData(dataArray2, domainidpairArray, bRound1);
 
             /// if(ic.deferredRefnum !== undefined) ic.deferredRefnum.resolve();
         // }
@@ -63158,23 +63397,25 @@ class Dssp {
         // }                       
     }
 
-    async parseAlignData(dataArray, domainidpairArray) { let ic = this.icn3d, me = ic.icn3dui;
+    async parseAlignData(dataArray, domainidpairArray, bRound1) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
-        let tmscoreThreshold = 0.4; //0.5;
+        let tmscoreThreshold = 0.4; // 0.4; //0.5;
 
         // find the best alignment for each chain
         let domainid2score = {}, domainid2segs = {}, chainid2segs = {};
 
-        if(!ic.chainid2index) ic.chainid2index = {};
-        if(!ic.domainid2index) ic.domainid2index = {};
-        if(!ic.domainid2ig2kabat) ic.domainid2ig2kabat = {};
-        if(!ic.domainid2ig2imgt) ic.domainid2ig2imgt = {};
+        // if(!ic.chainid2refpdbname) ic.chainid2refpdbname = {};
+        // if(!ic.domainid2refpdbname) ic.domainid2refpdbname = {};
+        // if(!ic.domainid2ig2kabat) ic.domainid2ig2kabat = {};
+        // if(!ic.domainid2ig2imgt) ic.domainid2ig2imgt = {};
 
-        // ic.chainid2index = {};
-        // ic.domainid2index = {};
-        // ic.domainid2ig2kabat = {};
-        // ic.domainid2ig2imgt = {};
+        ic.chainid2refpdbname = {};
+        ic.domainid2refpdbname = {};
+        ic.domainid2ig2kabat = {};
+        ic.domainid2ig2imgt = {};
+
+        let minResidues = 20;
 
         for(let i = 0, il = domainidpairArray.length; i < il; ++i) {
             let queryData = dataArray[i].value; //[0];
@@ -63185,12 +63426,16 @@ class Dssp {
             }
 
             if(queryData.length == 0) continue;
+            
+            if(queryData[0].score < tmscoreThreshold || queryData[0].num_res < minResidues) {
+                continue;
+            }
 
-            if(queryData[0].score < tmscoreThreshold || queryData[0].num_res < 50) continue;
-
-            let domainid_index = domainidpairArray[i].split(',');
-            let domainid = domainid_index[0];
-            domainid.split('-')[0];
+            //let domainid_index = domainidpairArray[i].split(',');
+            //let domainid = domainid_index[0];
+            let domainid = domainidpairArray[i].substr(0, domainidpairArray[i].indexOf('|'));
+            let refpdbname = domainidpairArray[i].substr(domainidpairArray[i].indexOf('|') + 1);
+            //let chainid = domainid.split('-')[0];
 
             // Ig-like domains: B (2150, 2150a, 2150b), C (3150, 3250), E (7150, 7250), F (8150, 8250) strands
             // Ig domain may require G (7050). But we'll leave that out for now.
@@ -63219,22 +63464,81 @@ class Dssp {
             if(!(bBstrand && bCstrand && bEstrand && bFstrand)) continue;
 
             if(!domainid2score.hasOwnProperty(domainid) || queryData[0].score > domainid2score[domainid]) {
-                domainid2score[domainid] = queryData[0].score;
-if(!me.bNode) console.log(domainid + ' TM-score: ' + domainid2score[domainid] + ' matched ' + ic.refpdbArray[domainid_index[1]]);     
+                domainid2score[domainid] = queryData[0].score;    
 
-                //ic.chainid2index[chainid] = domainid_index[1]; // could be several, just take the recent one for simplicity
-                ic.domainid2index[domainid] = domainid_index[1];
+                ic.domainid2refpdbname[domainid] = refpdbname;
                 domainid2segs[domainid] = queryData[0].segs;
                 ic.domainid2ig2kabat[domainid] = queryData[0].ig2kabat;
                 ic.domainid2ig2imgt[domainid] = queryData[0].ig2imgt;
             }
         }
 
+        if(bRound1) {
+            if(!me.bNode) console.log("Start round 2 alignment with the reference culsters " + JSON.stringify(ic.domainid2refpdbname));   
+
+            // start round2
+            let ajaxArray = [];
+            let domainidpairArray3 = [];
+            let urltmalign = me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
+            for(let domainid in ic.domainid2refpdbname) {
+                let pdbAjaxArray = [];
+                let refpdbname = ic.domainid2refpdbname[domainid];
+                let pdbid = domainid.substr(0, domainid.indexOf('_'));
+
+                if(ic.refpdbHash.hasOwnProperty(pdbid)) {
+                    // use itself as the ref structure
+                    refpdbname = pdbid;
+
+                    if(!me.bNode) console.log("Adjusted refpdbname for domainid " + domainid + ": " + refpdbname);   
+                }
+
+                if(!ic.refpdbHash[refpdbname]) {
+                    console.log("### refpdbname: " + refpdbname);
+                    continue;
+                }
+
+                for(let k = 0, kl = ic.refpdbHash[refpdbname].length; k < kl; ++k) {
+                    let urlpdb = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi?refpdbid=" + ic.refpdbHash[refpdbname][k];
+
+                    let pdbAjax = me.getAjaxPromise(urlpdb, 'text');
+
+                    pdbAjaxArray.push(pdbAjax);
+                }
+
+                let allPromise2 = Promise.allSettled(pdbAjaxArray);
+                ic.pdbDataArray = await allPromise2;
+
+                let pdb_target = ic.domainid2pdb[domainid];
+                for(let index = 0, indexl = ic.pdbDataArray.length; index < indexl; ++index) {
+                    let struct2 = ic.defaultPdbId + index;
+                    let pdb_query = ic.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]);
+                }
+            }
+
+            let dataArray3 = [];
+            let allPromise = Promise.allSettled(ajaxArray);
+            dataArray3 = await allPromise;
+        
+            await thisClass.parseAlignData(dataArray3, domainidpairArray3);
+
+            // end of round 2
+            return;
+        }
+
         // combine domainid into chainid
-        for(let domainid in ic.domainid2index) {
+        for(let domainid in ic.domainid2refpdbname) {
             let chainid = domainid.split('-')[0];
-            if(!ic.chainid2index.hasOwnProperty(chainid)) ic.chainid2index[chainid] = [];
-            ic.chainid2index[chainid].push(ic.domainid2index[domainid]);
+            if(!ic.chainid2refpdbname.hasOwnProperty(chainid)) ic.chainid2refpdbname[chainid] = [];
+            ic.chainid2refpdbname[chainid].push(ic.domainid2refpdbname[domainid]);
         }
         
         // combine domainid into chainid
@@ -63250,16 +63554,15 @@ if(!me.bNode) console.log(domainid + ' TM-score: ' + domainid2score[domainid] +
         if(!ic.chainsMapping) ic.chainsMapping = {};
         for(let chainid in chainid2segs) {
             let segArray = chainid2segs[chainid];
-if(!me.bNode) {
-    let chainList = '';
-    for(let i = 0, il = ic.chainid2index[chainid].length; i < il; ++i) {
-        chainList += ic.refpdbArray[ic.chainid2index[chainid][i]] + " ";
-    }
-    console.log("The reference PDB(s) for chain " + chainid + " are " + chainList);
-}
+
+            let chainList = '';
+            for(let i = 0, il = ic.chainid2refpdbname[chainid].length; i < il; ++i) {
+                chainList += ic.chainid2refpdbname[chainid][i] + " ";
+            }
+            if(!me.bNode) console.log("The reference PDB(s) for chain " + chainid + " are " + chainList);
 
             let prevStrand;
-            let bCd19 = ic.chainid2index[chainid].length == 1 && ic.refpdbArray[ic.chainid2index[chainid][0]] == '6al5_cd19';
+            let bCd19 = ic.chainid2refpdbname[chainid].length == 1 && ic.chainid2refpdbname[chainid][0] == 'CD19_6al5A_human_C2orV-n1';
             for(let i = 0, il = segArray.length; i < il; ++i) {
                 let seg = segArray[i];
                 let qStart = seg.q_start;
@@ -63429,6 +63732,10 @@ if(!me.bNode) {
         await ic.showAnnoCls.showAnnotations();
         ic.annotationCls.setAnnoViewAndDisplay('detailed view');
     }
+
+    rmStrandFromRefnumlabel(refnumLabel) {
+        return refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').replace(/\+/g, '').replace(/\-/g, '').substr(1); // C', C''
+    }
  }
 
 /**
@@ -71411,7 +71718,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.25.1';
+    this.REVISION = '3.25.2';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;