icn3d 3.25.12 → 3.25.13

package/icn3d.js

@@ -6235,19 +6235,19 @@ 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);
@@ -6271,8 +6271,8 @@ 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';
@@ -6280,7 +6280,6 @@ 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);
@@ -6294,7 +6293,6 @@ 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);
@@ -11008,11 +11006,11 @@ 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="';
 
@@ -13425,11 +13423,29 @@ 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
@@ -41093,7 +41109,7 @@ 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);
@@ -41219,7 +41235,7 @@ 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);
             }
                      
@@ -44301,6 +44317,11 @@ 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';
@@ -53943,7 +53964,9 @@ 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"
@@ -54058,10 +54081,14 @@ 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();
@@ -54338,7 +54365,12 @@ 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
@@ -57819,6 +57851,12 @@ 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 ==========
 
@@ -59853,7 +59891,7 @@ class SelectByCommand {
            // $1,2,3: Structure
            // .A,B,C: chain
            // :5-10,K,chemicals: residues, could be 'proteins', 'nucleotides', 'chemicals', 'ions', and 'water'
-           // :refnum_1250,anchors,strands,loops: reference numbers 1250, anchor residues (e.g., 2250), residues in strands, residues in loops
+           // :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 = {}
@@ -62255,40 +62293,27 @@ class Dssp {
         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
-        ic.refpdbArray = ['1FAB-HEAVY_5esv_V-n1', '1CD2_1hnfA_human_V-n1', '1LAG3_7tzgD_human_C2-n2', '1BTLA_2aw2A_human_Iset', '1JAM1_1nbqA_human_VorIset-n2', '1Palladin_2dm3A_human_Iset-n1', '1FAB-HEAVY_5esv_C1-n2', '1FAB-LIGHT_5esv_C1-n2', '1BArrestin1_4jqiA_rat_n1', '1IL6Rb_1bquB_human_FN3-n3', '1Contactin1_2ee2A_human_FN3-n9', '1InsulinR_8guyE_human_FN3-n1', '1NaCaExchanger_2fwuA_dog_n2', '1CuZnSuperoxideDismutase_1hl5C_human', '1CoAtomerGamma1_1r4xA_human', '1RBPJ_6py8C_human_Unk-n2', '1CD2_1hnfA_human_C2-n2', '1GHR_1axiB_human_FN3-n1', '1Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', '1ICOS_6x4gA_human_V', '1TCRa_6jxrm_human_C1-n2', '1LaminAC_1ifrA_human', '1IsdA_2iteA_bacteria', '1MPT63_1lmiA_bacteria', '1CD19_6al5A_human_C2orV-n1', '1ORF7a_1xakA_virus', '1ECadherin_4zt1A_human_n2', '1ASF1A_2iijA_human'];
+        // 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['1FAB-HEAVY_5esv_V-n1'] = ['FAB-HEAVY_5esv_V-n1', 'CD8a_1cd8A_human_V', 'FAB-LIGHT_5esv_V-n1', 'VNAR_1t6vN_shark_V'];
-        ic.refpdbHash['1CD2_1hnfA_human_V-n1'] = ['CD2_1hnfA_human_V-n1', 'Contactin1_3s97C_human_C2-n2', 'LAG3_7tzgD_human_V-n1'];
-        ic.refpdbHash['1LAG3_7tzgD_human_C2-n2'] = ['LAG3_7tzgD_human_C2-n2', 'Siglec3_5j0bB_human_C2-n2'];
-        ic.refpdbHash['1BTLA_2aw2A_human_Iset'] = ['BTLA_2aw2A_human_Iset', 'PD1_4zqkB_human_V', 'TCRa_6jxrm_human_V-n1'];
-        ic.refpdbHash['1JAM1_1nbqA_human_VorIset-n2'] = ['JAM1_1nbqA_human_VorIset-n2', 'PDL1_4z18B_human_V-n1'];
-        ic.refpdbHash['1Palladin_2dm3A_human_Iset-n1'] = ['Palladin_2dm3A_human_Iset-n1', 'Titin_4uowM_human_Unk-n152', 'VISTA_6oilA_human_V'];
-        ic.refpdbHash['1FAB-HEAVY_5esv_C1-n2'] = ['FAB-HEAVY_5esv_C1-n2', 'B2Microglobulin_7phrL_human_C1', 'MHCIa_7phrH_human_C1'];
-        ic.refpdbHash['1FAB-LIGHT_5esv_C1-n2'] = ['FAB-LIGHT_5esv_C1-n2', 'VTCN1_Q7Z7D3_human_V-n2'];
-        ic.refpdbHash['1BArrestin1_4jqiA_rat_n1'] = ['BArrestin1_4jqiA_rat_n1', 'C3_2qkiD_human_n1', 'RBPJ_6py8C_human_Unk-n1'];
-        ic.refpdbHash['1IL6Rb_1bquB_human_FN3-n3'] = ['IL6Rb_1bquB_human_FN3-n3', 'Sidekick2_1wf5A_human_FN3-n7'];
-        ic.refpdbHash['1Contactin1_2ee2A_human_FN3-n9'] = ['Contactin1_2ee2A_human_FN3-n9', 'IL6Rb_1bquB_human_FN3-n2'];
-        ic.refpdbHash['1InsulinR_8guyE_human_FN3-n1'] = ['InsulinR_8guyE_human_FN3-n1', 'InsulinR_8guyE_human_FN3-n2'];
-        ic.refpdbHash['1NaCaExchanger_2fwuA_dog_n2'] = ['NaCaExchanger_2fwuA_dog_n2', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark'];
+        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['1CoAtomerGamma1_1r4xA_human'] = ['CoAtomerGamma1_1r4xA_human', 'TP34_2o6cA_bacteria'];
-        ic.refpdbHash['1RBPJ_6py8C_human_Unk-n2'] = ['RBPJ_6py8C_human_Unk-n2', 'TP47_1o75A_bacteria'];
-
-        ic.refpdbHash['1CD2_1hnfA_human_C2-n2'] = ['CD2_1hnfA_human_C2-n2'];
-        ic.refpdbHash['1GHR_1axiB_human_FN3-n1'] = ['GHR_1axiB_human_FN3-n1'];
-        ic.refpdbHash['1Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'] = ['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'];
-        ic.refpdbHash['1ICOS_6x4gA_human_V'] = ['ICOS_6x4gA_human_V'];
-        ic.refpdbHash['1TCRa_6jxrm_human_C1-n2'] = ['TCRa_6jxrm_human_C1-n2'];
+        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['1MPT63_1lmiA_bacteria'] = ['MPT63_1lmiA_bacteria'];
-        ic.refpdbHash['1CD19_6al5A_human_C2orV-n1'] = ['CD19_6al5A_human_C2orV-n1'];
-        ic.refpdbHash['1ORF7a_1xakA_virus'] = ['ORF7a_1xakA_virus'];
-        ic.refpdbHash['1ECadherin_4zt1A_human_n2'] = ['ECadherin_4zt1A_human_n2'];
-        ic.refpdbHash['1ASF1A_2iijA_human'] = ['ASF1A_2iijA_human'];          
+        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'];
@@ -62432,7 +62457,7 @@ 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;
@@ -62448,7 +62473,7 @@ class Dssp {
                         let alignAjax = me.getAjaxPostPromise(urltmalign, dataObj);
                         ajaxArray.push(alignAjax);
                         
-                        domainidpairArray.push(domainid + "," + ic.refpdbArray[index]);
+                        domainidpairArray.push(domainid + "|" + ic.refpdbArray[index]);
                     }
                 }
             }
@@ -62474,20 +62499,20 @@ class Dssp {
     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.chainid2refpdbname) ic.chainid2refpdbname = {};
-        if(!ic.domainid2refpdbname) ic.domainid2refpdbname = {};
-        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.chainid2refpdbname = {};
-        // ic.domainid2refpdbname = {};
-        // ic.domainid2ig2kabat = {};
-        // ic.domainid2ig2imgt = {};
+        ic.chainid2refpdbname = {};
+        ic.domainid2refpdbname = {};
+        ic.domainid2ig2kabat = {};
+        ic.domainid2ig2imgt = {};
 
         let minResidues = 20;
 
@@ -62501,12 +62526,14 @@ 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 < minResidues) {
+                continue;
+            }
 
             //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 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
@@ -62564,6 +62591,11 @@ class Dssp {
                     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];
 
@@ -62587,7 +62619,7 @@ class Dssp {
                     ajaxArray.push(alignAjax);
                     
                     //domainidpairArray3.push(domainid + "," + refpdbname);
-                    domainidpairArray3.push(domainid + "," + ic.refpdbHash[refpdbname][index]);
+                    domainidpairArray3.push(domainid + "|" + ic.refpdbHash[refpdbname][index]);
                 }
             }
 
@@ -70785,7 +70817,7 @@ 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;