icn3d 3.26.0 → 3.26.2

package/icn3d.js

@@ -12858,7 +12858,7 @@ class Events {
 
             if(esmfold_fasta.indexOf('>') != -1) { //FASTA with header
                 let pos = esmfold_fasta.indexOf('\n');
-                ic.esmTitle = esmfold_fasta.substr(1, pos - 1);
+                ic.esmTitle = esmfold_fasta.substr(1, pos - 1).trim();
                 pdbid = ic.esmTitle.substr(0, ic.esmTitle.indexOf(' '));
                 if(pdbid.length < 6) pdbid = pdbid.padEnd(6, '-');
 
@@ -34758,7 +34758,6 @@ class SetColor {
                                 let refnumStr = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
                                 let currStrand = refnumLabel.replace(new RegExp(refnumStr,'g'), '');
                                 color = ic.showSeqCls.getRefnumColor(currStrand);
-
                                 if(ic.residIgLoop.hasOwnProperty(resid)) {                            
                                     color = me.parasCls.thr(me.htmlCls.GREYB);
                                 }
@@ -41028,16 +41027,6 @@ class ShowAnno {
              } // align seq to structure
         }
         //ic.bAnnoShown = true;
-
-        if(ic.bShowRefnum) {
-            ic.opts.color = 'ig strand';
-            //ic.setColorCls.setColorByOptions(ic.opts, ic.atoms);
-            ic.setColorCls.setColorByOptions(ic.opts, ic.dAtoms);
-
-            ic.selectionCls.selectAll_base();
-            ic.hlUpdateCls.updateHlAll();
-            //ic.drawCls.draw();
-        }
     }
 
     async showAnnoSeqData(nucleotide_chainid, chemical_chainid, chemical_set) { let ic = this.icn3d, me = ic.icn3dui;
@@ -42050,18 +42039,25 @@ class ShowSeq {
         html += result.html;
         html3 += result.html3;
 
+        if(ic.bShowRefnum) {
+            ic.opts.color = 'ig strand';
+            //ic.setColorCls.setColorByOptions(ic.opts, ic.atoms);
+            ic.setColorCls.setColorByOptions(ic.opts, ic.dAtoms);
+
+            ic.selectionCls.selectAll_base();
+            ic.hlUpdateCls.updateHlAll();
+            //ic.drawCls.draw();
+        }
+
         return {'html': html, 'html3': html3};
     }
 
     showRefNum(giSeq, chnid, kabat_or_imgt, bCustom) {  let ic = this.icn3d, me = ic.icn3dui;
         let html = '', html3 = '';
 
-        let chainList = '';
         if(!ic.chainid2refpdbname[chnid]) return {html: html, html3: html3};
 
-        for(let i = 0, il = ic.chainid2refpdbname[chnid].length; i < il; ++i) {
-            chainList += ic.chainid2refpdbname[chnid][i] + " ";
-        }
+        let chainList = ic.refnumCls.getTemplateList(chnid);
 
         let refStruTitle = (chainList) ? "based on " + chainList : "";
 
@@ -42100,7 +42096,7 @@ class ShowSeq {
             return {html: '', html3: ''};
         }
 
-        //check if Kabat refnum available
+        //check if IMGT refnum available
         let bImgtFound = false;
         for(let i = 0, il = giSeq.length; i < il; ++i) {
             let currResi = ic.ParserUtilsCls.getResi(chnid, i);
@@ -42507,7 +42503,7 @@ class ShowSeq {
                             }
                         }
                     }
-                    else {
+                    else {                       
                         if(currStrand != ' ') {
                             bLoop = ic.residIgLoop[residueid];
                             html += this.getRefnumHtml(residueid, refnumStr, refnumStr_ori, refnumLabel, currStrand, bLoop, bHidelabel);
@@ -42785,6 +42781,8 @@ class HlSeq {
            //});
 
             // remove possible text selection
+            // the following code caused the scroll of seqeunce window to the top, remove it for now
+            /*
             if(window.getSelection) {
               if(window.getSelection().empty) {  // Chrome
                 window.getSelection().empty();
@@ -42794,6 +42792,7 @@ class HlSeq {
             } else if(document.selection) {  // IE?
               document.selection.empty();
             }
+            */
       });
     }
 
@@ -44301,61 +44300,6 @@ class LineGraph {
     async showIgRefNum() { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
-        // if(ic.pdbDataArray) {
-        //     await thisClass.parseRefPdbData(ic.pdbDataArray);
-        // }
-        // 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'];
 
@@ -44423,11 +44367,6 @@ class LineGraph {
         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 pdbAjaxArray = [];
         for(let k = 0, kl = ic.refpdbArray.length; k < kl; ++k) {
             //let urlpdb = me.htmlCls.baseUrl + "icn3d/refpdb/" + ic.refpdbArray[k] + ".pdb";
@@ -44533,7 +44472,11 @@ class LineGraph {
                 for(let k = 0, kl = domainAtomsArray.length; k < kl; ++k) {
                     let pdb_target = ic.saveFileCls.getAtomPDB(domainAtomsArray[k], undefined, undefined, undefined, undefined, struct);
                     // ig strand for any subset will have the same k, use the number of residue to separate them
-                    let domainid = chainid + '-' + k + '_' + Object.keys(domainAtomsArray[k]).length; 
+                    let atomFirst = ic.firstAtomObjCls.getFirstAtomObj(domainAtomsArray[k]);
+                    let atomLast = ic.firstAtomObjCls.getLastAtomObj(domainAtomsArray[k]);
+                    let resiSum = parseInt(atomFirst.resi) + parseInt(atomLast.resi);
+                    //let domainid = chainid + '-' + k + '_' + Object.keys(domainAtomsArray[k]).length; 
+                    let domainid = chainid + '-' + k + '_' + resiSum; 
                     ic.domainid2pdb[domainid] = pdb_target;
 
                     for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
@@ -44556,6 +44499,8 @@ class LineGraph {
         try {
             let dataArray2 = [];
             let allPromise = Promise.allSettled(ajaxArray);
+            // // reject if any ajax call is failed so that we don't miss the best alignment
+            // let allPromise = Promise.all(ajaxArray);
             dataArray2 = await allPromise;
         
             let bRound1 = true;
@@ -44564,12 +44509,42 @@ class LineGraph {
             /// if(ic.deferredRefnum !== undefined) ic.deferredRefnum.resolve();
         }
         catch(err) {
-            if(!me.bNode) console.log("Error in aligning with TM-align...");
+            let mess = "Some of " + ajaxArray.length + " TM-align alignments failed. Please select a chain or a subset to assing reference numbers to avoid overloading the server...";
+            if(!me.bNode) {
+                var aaa = 1; //alert(mess);
+            }
+            else {
+                console.log(mess);
+            }
             //console.log("Error in aligning with TM-align...");
             return;
         }                       
     }
 
+    getTemplateList(chainid) { let ic = this.icn3d; ic.icn3dui;
+        let domainid2refpdbname = {};
+
+        for(let i = 0, il = ic.chainid2refpdbname[chainid].length; i < il; ++i) {
+            let refpdbname_domainid = ic.chainid2refpdbname[chainid][i].split('|');
+            domainid2refpdbname[refpdbname_domainid[1]] = refpdbname_domainid[0];
+        }
+
+        let domainidArray = Object.keys(domainid2refpdbname);
+        domainidArray.sort(function(id1, id2) {
+            let resi1 = parseInt(id1.substr(id1.lastIndexOf('_') + 1));
+            let resi2 = parseInt(id2.substr(id2.lastIndexOf('_') + 1));
+            return resi1 - resi2;
+        });
+
+        let chainList = '';
+        for(let i = 0, il = domainidArray.length; i < il; ++i) {
+            chainList += domainid2refpdbname[domainidArray[i]];
+            if(i < il - 1) chainList += ", ";
+        }
+
+        return chainList;
+    }
+
     async parseAlignData(dataArray, domainidpairArray, bRound1) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
@@ -44635,7 +44610,10 @@ class LineGraph {
             }
 
             //if(!(bBstrand && bCstrand && bEstrand && bFstrand && bGstrand)) continue;
-            if(!(bBstrand && bCstrand && bEstrand && bFstrand)) continue;
+            if(!(bBstrand && bCstrand && bEstrand && bFstrand)) {
+                if(!me.bNode) console.log("some of the Ig strands B, C, E, F are missing...");
+                continue;
+            }
 
             if(!domainid2score.hasOwnProperty(domainid) || queryData[0].score > domainid2score[domainid]) {
                 domainid2score[domainid] = queryData[0].score;    
@@ -44709,10 +44687,15 @@ class LineGraph {
         }
 
         // combine domainid into chainid
+        let processedChainid = {};
         for(let domainid in ic.domainid2refpdbname) {
             let chainid = domainid.split('-')[0];
+
+            if(!processedChainid.hasOwnProperty(chainid)) ic.chainid2refpdbname[chainid] = [];
+            processedChainid[chainid] = 1;
+
             if(!ic.chainid2refpdbname.hasOwnProperty(chainid)) ic.chainid2refpdbname[chainid] = [];
-            ic.chainid2refpdbname[chainid].push(ic.domainid2refpdbname[domainid]);
+            ic.chainid2refpdbname[chainid].push(ic.domainid2refpdbname[domainid] + '|' + domainid);
         }
         
         // combine domainid into chainid
@@ -44729,15 +44712,15 @@ class LineGraph {
         for(let chainid in chainid2segs) {
             let segArray = chainid2segs[chainid];
 
-            let chainList = '';
-            for(let i = 0, il = ic.chainid2refpdbname[chainid].length; i < il; ++i) {
-                chainList += ic.chainid2refpdbname[chainid][i] + " ";
-            }
+            let refpdbnameArray = ic.chainid2refpdbname[chainid];
+
+            let chainList = this.getTemplateList(chainid);
+
             //if(!me.bNode) console.log("The reference PDB(s) for chain " + chainid + " are " + chainList);
             console.log("The reference PDB(s) for chain " + chainid + " are " + chainList);
 
             let prevStrand;
-            let bCd19 = ic.chainid2refpdbname[chainid].length == 1 && ic.chainid2refpdbname[chainid][0] == 'CD19_6al5A_human_C2orV-n1';
+            let bCd19 = refpdbnameArray.length == 1 && refpdbnameArray[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;
@@ -68246,7 +68229,7 @@ class ShareLink {
            outputCmd = tmpUrl;
 
            statefile = statefile.replace(/!/g, Object.keys(ic.structures)[0] + '_');
-           if(ic.bEmsfold || (ic.bInputfile && !ic.bInputUrlfile) || (ic.bInputUrlfile && ic.bAppend) || url.length > 4000) url = statefile;
+           if(ic.bEsmfold || (ic.bInputfile && !ic.bInputUrlfile) || (ic.bInputUrlfile && ic.bAppend) || url.length > 4000) url = statefile;
            let id;
            if(ic.structures !== undefined && Object.keys(ic.structures).length == 1 && ic.inputid !== undefined) {
                id = Object.keys(ic.structures)[0];