icn3d 3.34.1 → 3.34.3

package/icn3d.module.js

@@ -15030,10 +15030,10 @@ class SetDialog {
 
         html += me.htmlCls.divStr + "dl_blast_rep_id' style='max-width:600px;' class='" + dialogClass + "'>";
         html += this.addNotebookTitle('dl_blast_rep_id', 'Align sequence to structure');
-        html += "Enter a Sequence ID (or FASTA sequence) and the aligned protein accession, which can be found using the <a href='https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch' target='_blank'>BLAST</a> search with the Sequence ID or FASTA sequence as input. If the protein accession is not a PDB chain, the corresponding AlphaFold UniProt structure is used.<br><br> ";
-        html += "<b>Sequence ID</b>(NCBI protein accession of a sequence): " + me.htmlCls.inputTextStr + "id='" + me.pre + "query_id' value='NP_001108451.1' size=8><br> ";
+        html += "Enter a protein sequence ID (or FASTA sequence) and the aligned protein accession, which can be found using the <a href='https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch' target='_blank'>BLAST</a> search with the protein sequence ID or FASTA sequence as input. If the protein accession is not a PDB chain, the corresponding AlphaFold UniProt structure is used.<br><br> ";
+        html += "<b>Protein Sequence ID</b>(NCBI protein accession of a sequence): " + me.htmlCls.inputTextStr + "id='" + me.pre + "query_id' value='NP_001108451.1' size=8><br> ";
         html += "or FASTA sequence: <br><textarea id='" + me.pre + "query_fasta' rows='5' style='width: 100%; height: " +(me.htmlCls.LOG_HEIGHT) + "px; padding: 0px; border: 0px;'></textarea><br><br>";
-        html += "<b>NCBI protein accession</b> (or a chain of a PDB): " + me.htmlCls.inputTextStr + "id='" + me.pre + "blast_rep_id' value='1TSR_A' size=8><br> ";
+        html += "<b>Aligned Protein Accession</b> (or a chain of a PDB): " + me.htmlCls.inputTextStr + "id='" + me.pre + "blast_rep_id' value='1TSR_A' size=8><br> ";
         //html += me.htmlCls.buttonStr + "reload_blast_rep_id'>Load</button>";
         html += me.htmlCls.buttonStr + "reload_blast_rep_id'>Align with BLAST</button> " + me.htmlCls.wifiStr
             + me.htmlCls.buttonStr + "reload_alignsw' style='margin-left:30px'>Align with Global Smith-Waterman</button>"
@@ -15444,7 +15444,7 @@ class SetDialog {
         html += me.htmlCls.divStr + "dl_ligplot' sty2D Interaction for One Ligand/Residule='background-color:white' class='" + dialogClass + "'>";
         html += this.addNotebookTitle('dl_ligplot', 'e with Atom Details');
 
-        html += me.htmlCls.divNowrapStr + "<b>Note</b>: Nodes can be dragged or clicked. Hold Ctrl key to select multiple nodes. " + me.htmlCls.space3;
+        html += me.htmlCls.divNowrapStr + "<b>Note</b>: Nodes/Residues can be dragged. Both nodes and dashed lines/interactions can be clicked to select residues. " + me.htmlCls.space3;
 
         html += '<div style="width:20px; margin-top:6px; display:inline-block;"><span id="'
           + me.pre + 'dl_ligplotcolor_expand" class="ui-icon ui-icon-plus icn3d-expand icn3d-link" style="display:none; width:15px;" title="Expand"></span><span id="'
@@ -15453,7 +15453,8 @@ class SetDialog {
         html += me.htmlCls.divStr + "dl_ligplotcolor' style='inline-block;'>";
 
         // html += "The real interaction distances are not in scale, and are about twice the distances of dashed line segments.<br>Some \"Contact\" lines are only shown partially to simplify the view.<br>";
-        html += "Color legend for interactions (dashed lines): <br>";
+        // html += "Mouseover the dashed lines to see interaction types and distances.<br>";
+        html += "<b>Color legend</b> for interactions (dashed lines): <br>";
 
         html += me.htmlCls.setHtmlCls.setColorHints();
 
@@ -16515,8 +16516,8 @@ class Events {
         hostUrl = (pos == -1) ? hostUrl : hostUrl.substr(0, pos);
 
         // some URLs from VAST search are like https://www.ncbi.nlm.nih.gov/Structure/vast/icn3d/
-        if(hostUrl == 'https://www.ncbi.nlm.nih.gov/Structure/vast/icn3d/') {
-            hostUrl = 'https://www.ncbi.nlm.nih.gov/Structure/icn3d/';
+        if(hostUrl.indexOf('/vast/icn3d/')) {
+            hostUrl = hostUrl.replace(/\/vast\/icn3d\//g, '/icn3d/');
         }
 
         ic.definedSetsCls.clickCustomAtoms();
@@ -17337,7 +17338,11 @@ class Events {
         me.myEventCls.onIds("#" + me.pre + "reload_blast_rep_id", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
-           let query_id = $("#" + me.pre + "query_id").val();
+           let query_id = $("#" + me.pre + "query_id").val().trim();
+           if(query_id.substr(1, 2) == 'M_') { // e.g., NM_..., XM_...
+                alert("You are inputting a nucleotide accession " + query_id + ". Please use a protein accession instead.");
+                return;
+           }
            let query_fasta = encodeURIComponent($("#" + me.pre + "query_fasta").val());
            let blast_rep_id = $("#" + me.pre + "blast_rep_id").val();
            thisClass.setLogCmd("load seq_struct_ids " + query_id + "," + blast_rep_id, false);
@@ -17404,7 +17409,11 @@ class Events {
         me.myEventCls.onIds("#" + me.pre + "reload_alignsw", "click", function(e) { let ic = me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
-            let query_id = $("#" + me.pre + "query_id").val();
+            let query_id = $("#" + me.pre + "query_id").val().trim();
+            if(query_id.substr(1, 2) == 'M_') { // e.g., NM_..., XM_...
+                alert("You are inputting a nucleotide accession " + query_id + ". Please use a protein accession instead.");
+                return;
+            }
             let query_fasta = encodeURIComponent($("#" + me.pre + "query_fasta").val());
             let blast_rep_id = $("#" + me.pre + "blast_rep_id").val();
             thisClass.setLogCmd("load seq_struct_ids_smithwm " + query_id + "," + blast_rep_id, false);
@@ -17420,7 +17429,11 @@ class Events {
          me.myEventCls.onIds("#" + me.pre + "reload_alignswlocal", "click", function(e) { let ic = me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
-            let query_id = $("#" + me.pre + "query_id").val();
+            let query_id = $("#" + me.pre + "query_id").val().trim();
+            if(query_id.substr(1, 2) == 'M_') { // e.g., NM_..., XM_...
+                alert("You are inputting a nucleotide accession " + query_id + ". Please use a protein accession instead.");
+                return;
+            }
             let query_fasta = encodeURIComponent($("#" + me.pre + "query_fasta").val());
             let blast_rep_id = $("#" + me.pre + "blast_rep_id").val();
             thisClass.setLogCmd("load seq_struct_ids_local_smithwm " + query_id + "," + blast_rep_id, false);
@@ -18291,6 +18304,7 @@ class Events {
             
             let scale = $("#" + me.ligplotid + "_scale").val();
             $("#" + me.ligplotid).attr("width",(ic.ligplotWidth * parseFloat(scale)).toString() + "px");
+            ic.ligplotScale = parseFloat(scale);
             thisClass.setLogCmd("ligplot scale " + scale, true);
          });
 
@@ -19541,7 +19555,7 @@ class SetHtml {
 
         html += me.htmlCls.divNowrapStr + '<span style="margin-left:33px; color:#00FF00; font-weight:bold">Green</span>: H-Bonds; ';
         html += '<span style="color:#00FFFF; font-weight:bold">Cyan</span>: Salt Bridge/Ionic; ';
-        html += '<span style="font-weight:bold">Grey</span>: contacts</div>';
+        html += '<span style="font-weight:bold">Grey</span>: Contacts</div>';
         html += me.htmlCls.divNowrapStr + '<span style="margin-left:33px; color:#FF00FF; font-weight:bold">Magenta</span>: Halogen Bonds; ';
         html += '<span style="color:#FF0000; font-weight:bold">Red</span>: &pi;-Cation; ';
         html += '<span style="color:#0000FF; font-weight:bold">Blue</span>: &pi;-Stacking</div>';
@@ -34812,7 +34826,7 @@ class ApplyDisplay {
             atomsObj = {};
         } // end if(bHighlight === 1)
 
-        if(ic.bInitial) {
+        if(ic.bInitial && ic.bMembrane === undefined) {
             if(me.htmlCls.setHtmlCls.getCookie('membrane') != '') {
                 let bMembrane = parseInt(me.htmlCls.setHtmlCls.getCookie('membrane'));
 
@@ -35106,7 +35120,7 @@ class ApplyOther {
             }
         }
 
-        if(ic.bInitial) {
+        if(ic.bInitial && ic.bGlycansCartoon === undefined) {
             if(me.htmlCls.setHtmlCls.getCookie('glycan') != '') {
                 let bGlycansCartoon = parseInt(me.htmlCls.setHtmlCls.getCookie('glycan'));
 
@@ -39495,15 +39509,16 @@ class SetColor {
         atoms = me.hashUtilsCls.intHash(atoms, ic.hAtoms);
 
         for (let i in atoms) {
-            let atom = ic.atoms[i];
-            if(!atom.het) ++cnt;
+            ic.atoms[i];
+            // if(!atom.het) ++cnt;
+            ++cnt;
         }
 
         let lastTerSerialInv = (cnt > 1) ? 1 / (cnt - 1) : 1;
         for (let i in atoms) {
             let atom = ic.atoms[i];
-            //atom.color = atom.het ? me.parasCls.atomColors[atom.elem] || me.parasCls.defaultAtomColor : me.parasCls.thr().setHSL(2 / 3 * (1 - idx++ * lastTerSerialInv), 1, 0.45);
-            atom.color = atom.het ? me.parasCls.atomColors[atom.elem] || me.parasCls.defaultAtomColor : me.parasCls.thr().setHSL(3 / 4 * (1 - idx++ * lastTerSerialInv), 1, 0.45);
+            // atom.color = atom.het ? me.parasCls.atomColors[atom.elem] || me.parasCls.defaultAtomColor : me.parasCls.thr().setHSL(3 / 4 * (1 - idx++ * lastTerSerialInv), 1, 0.45);
+            atom.color = me.parasCls.thr().setHSL(3 / 4 * (1 - idx++ * lastTerSerialInv), 1, 0.45);
 
             ic.atomPrevColors[i] = atom.color;
         }
@@ -39517,14 +39532,16 @@ class SetColor {
         atoms = me.hashUtilsCls.intHash(atoms, ic.hAtoms);
 
         for (let i in atoms) {
-            let atom = ic.atoms[i];
-            if(!atom.het) ++cnt;
+            ic.atoms[i];
+            // if(!atom.het) ++cnt;
+            ++cnt;
         }
 
         let lastTerSerialInv = (cnt > 1) ? 1 / (cnt - 1) : 1;
         for (let i in atoms) {
             let atom = ic.atoms[i];
-            atom.color = atom.het ? me.parasCls.atomColors[atom.elem] || me.parasCls.defaultAtomColor : me.parasCls.thr().setHSL(3 / 4 *  idx++ * lastTerSerialInv, 1, 0.45);
+            // atom.color = atom.het ? me.parasCls.atomColors[atom.elem] || me.parasCls.defaultAtomColor : me.parasCls.thr().setHSL(3 / 4 *  idx++ * lastTerSerialInv, 1, 0.45);
+            atom.color = me.parasCls.thr().setHSL(3 / 4 *  idx++ * lastTerSerialInv, 1, 0.45);
 
             ic.atomPrevColors[i] = atom.color;
         }
@@ -40974,6 +40991,7 @@ class AnnoCddSite {
         if(me.bNode) {
             if(!ic.resid2cdd) ic.resid2cdd = {};
             if(!ic.resid2site) ic.resid2site = {};
+            if(!ic.chainid2cdd) ic.chainid2cdd = {};
         }
 
         for(let i = 0, il = dataArray.length; i < il; ++i) {
@@ -40996,6 +41014,8 @@ class AnnoCddSite {
                 let html3 = html;
                 let domainArray = cddData.doms;
                 if(me.bNode && !ic.resid2cdd[chnid]) ic.resid2cdd[chnid] = [];
+                if(me.bNode && !ic.chainid2cdd[chnid]) ic.chainid2cdd[chnid] = [];
+
                 let result = thisClass.setDomainFeature(domainArray, chnid, 'domain', html, html2, html3);
 
                 ic.chainid2pssmid[chnid] = {pssmid2name: result.pssmid2name, pssmid2fromArray: result.pssmid2fromArray, pssmid2toArray: result.pssmid2toArray};
@@ -41287,6 +41307,10 @@ class AnnoCddSite {
 
                 if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGap(ic.seqStartLen[chnid], '-');
 
+                if(me.bNode && type == 'domain') {
+                    ic.chainid2cdd[chnid].push(fulltitle + "_from_" + fromArray + "_to_" + toArray);
+                }
+
                 for(let i = 0, il = ic.giSeq[chnid].length; i < il; ++i) {
                   html += ic.showSeqCls.insertGap(chnid, i, '-');
 
@@ -43323,7 +43347,7 @@ class AnnoSnpClinVar {
                                     }
 
                                     //snpTitle += "<br>Links: <span class='" + ic.pre + "snpin3d icn3d-snplink' snp='" + chnid + "_" + pos + "_" + resi2snp[i][j] + "'>SNP in 3D with scap</span>, <span class='" + ic.pre + "snpinter icn3d-snplink' snp='" + chnid + "_" + pos + "_" + resi2snp[i][j] + "'>SNP Interactions in 3D</span>, <span class='" + ic.pre + "snppdb icn3d-snplink' snp='" + chnid + "_" + pos + "_" + resi2snp[i][j] + "'>SNP PDB</span>, <a href='https://www.ncbi.nlm.nih.gov/clinvar/?term=" + resi2clinAllele[i][j] + "[AlleleID]' target='_blank'>ClinVar</a>, <a href='https://www.ncbi.nlm.nih.gov/snp/?term=" + resi2rsnum[i][j] + "' target='_blank'>dbSNP(rs" + resi2rsnum[i][j] + ")</a>";
-                                    snpTitle += "<br>Links: <a href='https://www.ncbi.nlm.nih.gov/clinvar/?term=" + resi2clinAllele[i][j] + "[AlleleID]' target='_blank'>ClinVar</a>, <a href='https://www.ncbi.nlm.nih.gov/snp/?term=" + resi2rsnum[i][j] + "' target='_blank'>dbSNP(rs" + resi2rsnum[i][j] + ")</a>";
+                                    snpTitle += "<br>Links: <a href='https://www.ncbi.nlm.nih.gov/clinvar/?term=" + resi2clinAllele[i][j] + "[AlleleID]' style='color:blue' target='_blank'>ClinVar</a>, <a href='https://www.ncbi.nlm.nih.gov/snp/?term=" + resi2rsnum[i][j] + "' style='color:blue' target='_blank'>dbSNP(rs" + resi2rsnum[i][j] + ")</a>";
                                 }
                                 else {
                                     if(bCoord && !me.cfg.hidelicense) {
@@ -43405,7 +43429,7 @@ class AnnoSnpClinVar {
                                 }
 
                                 //snpTitle += "<br>Links: <span class='" + ic.pre + "snpin3d icn3d-snplink' snp='" + chnid + "_" + pos + "_" + resi2snp[i][j] + "'>SNP in 3D with scap</span>, <span class='" + ic.pre + "snpinter icn3d-snplink' snp='" + chnid + "_" + pos + "_" + resi2snp[i][j] + "'>SNP Interactions in 3D</span>, <span class='" + ic.pre + "snppdb icn3d-snplink' snp='" + chnid + "_" + pos + "_" + resi2snp[i][j] + "'>SNP PDB</span>, <a href='https://www.ncbi.nlm.nih.gov/clinvar/?term=" + resi2clinAllele[i][j] + "[AlleleID]' target='_blank'>ClinVar</a>, <a href='https://www.ncbi.nlm.nih.gov/snp/?term=" + resi2rsnum[i][j] + "' target='_blank'>dbSNP(rs" + resi2rsnum[i][j] + ")</a>";
-                                snpTitle += "<br>Links: <a href='https://www.ncbi.nlm.nih.gov/clinvar/?term=" + resi2clinAllele[i][j] + "[AlleleID]' target='_blank'>ClinVar</a>, <a href='https://www.ncbi.nlm.nih.gov/snp/?term=" + resi2rsnum[i][j] + "' target='_blank'>dbSNP(rs" + resi2rsnum[i][j] + ")</a>";
+                                snpTitle += "<br>Links: <a href='https://www.ncbi.nlm.nih.gov/clinvar/?term=" + resi2clinAllele[i][j] + "[AlleleID]' style='color:blue' target='_blank'>ClinVar</a>, <a href='https://www.ncbi.nlm.nih.gov/snp/?term=" + resi2rsnum[i][j] + "' style='color:blue' target='_blank'>dbSNP(rs" + resi2rsnum[i][j] + ")</a>";
                                 if(j < jl - 1) {
                                     snpTitle += '<br><br>';
                                 }
@@ -45597,7 +45621,8 @@ class AddTrack {
         $("#" + ic.pre + "tt_custom_" + chnid).append("<div id='" + ic.pre + "tt_custom_" + chnid + "_" + simpTitle + "'></div>");
         $("#" + ic.pre + "tt_custom_" + chnid + "_" + simpTitle).width(divLength);
 
-        let html = '<div id="' + ic.pre + 'giseq_sequence" class="icn3d-dl_sequence">';
+        // let html = '<div id="' + ic.pre + 'giseq_sequence" class="icn3d-dl_sequence">';
+        let html = '<div class="icn3d-dl_sequence">';
         let htmlExon = html;
         let html2 = html;
         let html3 = html;
@@ -46892,6 +46917,7 @@ class AddTrack {
             let title =(trackTitleArray[j].length < 20) ? trackTitleArray[j] : trackTitleArray[j].substr(0, 20) + '...';
             let bMsa = true;
             let exonArray = (acc2exons) ? acc2exons[trackTitleArray[j]] : undefined;
+
             this.showNewTrack(chainid, title, text, undefined, undefined, type, undefined, bMsa, fromArray, toArray, seqStartLen, exonArray, offsetArray);
         }
 
@@ -47103,6 +47129,7 @@ class AddTrack {
         await thisClass.showMsaTracks(chainid, seqFirst, trackTitleArray, trackSeqArray, startpos, type, acc2exons);
 
         me.htmlCls.clickMenuCls.setLogCmd("add exon track | chainid " + chainid + " | geneid " + geneid + " | startpos " + startpos + " | type " + type, true);
+        me.htmlCls.clickMenuCls.setLogCmd("set annotation custom", true);
     }
 
     async addMsaTracks(chainid, startpos, type, fastaList) { let ic = this.icn3d, me = ic.icn3dui;
@@ -48243,7 +48270,8 @@ class ShowAnno {
         $("#" + ic.pre + "anno_" + name).append("<div id='" + ic.pre + "giseq_" + name + "'><div id='" + ic.pre + "dt_giseq_" + name + "' style='display:none'></div><div id='" + ic.pre + "ov_giseq_" + name + "'></div></div>");
         $("#" + ic.pre + "anno_" + name).append("<br><hr><br>");
         // sequence, detailed view
-        let htmlTmp = '<div id="' + ic.pre + 'giseq_sequence" class="icn3d-dl_sequence">';
+        // let htmlTmp = '<div id="' + ic.pre + 'giseq_sequence" class="icn3d-dl_sequence">';
+        let htmlTmp = '<div class="icn3d-dl_sequence">';
         let chainType = 'Chem.', chainTypeFull = 'Chemical';
         //htmlTmp += '<div class="icn3d-seqTitle2" anno="sequence"><span style="white-space:nowrap;" title="' + chainTypeFull + ' ' + name + '">' + chainType + ' ' + name + '</span></div>';
         htmlTmp += '<div class="icn3d-seqTitle icn3d-link icn3d-blue" anno="sequence" gi="' + name + '" resn="' + name + '"><span style="white-space:nowrap;" title="' + chainTypeFull + ' ' + name + '">' + chainType + ' ' + name + '</span></div>';
@@ -48280,6 +48308,8 @@ class ShowAnno {
     }
 
     async processSeqData(chainid_seq) { let ic = this.icn3d, me = ic.icn3dui;
+        ic.bAnnoShown = true;
+
         for(let chnid in ic.protein_chainid) {
             let chnidBase = ic.protein_chainid[chnid];
             //if(chainid_seq.hasOwnProperty(chnid)) {
@@ -48797,11 +48827,17 @@ class ShowSeq {
         html += '</div>';
         html += '</div>'; // corresponds to above: html += '<div class="icn3d-dl_sequence">';
         html3 += '</div></div>';
+        // if(me.cfg.blast_rep_id === chnid) {
+        //     htmlTmp = '<div id="' + ic.pre + 'giseq_sequence" class="icn3d-dl_sequence" style="border: solid 1px #000">';
+        // }
+        // else {
+        //     htmlTmp = '<div id="' + ic.pre + 'giseq_sequence" class="icn3d-dl_sequence">';
+        // }
         if(me.cfg.blast_rep_id === chnid) {
-            htmlTmp = '<div id="' + ic.pre + 'giseq_sequence" class="icn3d-dl_sequence" style="border: solid 1px #000">';
+            htmlTmp = '<div class="icn3d-dl_sequence" style="border: solid 1px #000">';
         }
         else {
-            htmlTmp = '<div id="' + ic.pre + 'giseq_sequence" class="icn3d-dl_sequence">';
+            htmlTmp = '<div class="icn3d-dl_sequence">';
         }
         let chainType = 'Protein', chainTypeFull = 'Protein';
         if(type !== undefined) {
@@ -52368,7 +52404,7 @@ class ViewInterPairs {
                 if(index2xy) {
                     let serialArray1 = resid1Ori.substr(pos1 + 1).split(',');
 
-                    let result = ic.ligplotCls.getSvgPerPair(serialArray1, resid1, resid2, interactionType, index2xy, xlen, ylen, xcenter, ycenter);
+                    let result = ic.ligplotCls.getSvgPerPair(serialArray1, resid1, resid2, interactionType, index2xy, xlen, ylen, xcenter, ycenter, dist);
                     svgHtmlNode += result.node;
                     svgHtmlLine += result.line;
                 }
@@ -52470,9 +52506,12 @@ class ViewInterPairs {
                         let resids = resid1 + '|' + resid2;
             
                         let serialArray1 = resids2distCnt[resids].serialArray1;
-
+                        let dist1_dist2_atom1_atom2 = resids2distCnt[resids].dist1_dist2_atom1_atom2;
+                        let dist1 = dist1_dist2_atom1_atom2[0]; // min dist
+                        dist1_dist2_atom1_atom2[1]; // c-alpha dist
+                        // let dist = (dist1 < dist2) ? dist1 : dist2;
                         let bNotDrawNode = (i == 0) ? false : true;
-                        let result = ic.ligplotCls.getSvgPerPair(serialArray1, resid1, resid2, interactionType, index2xy, xlen, ylen, xcenter, ycenter, bNotDrawNode, prevX2, prevY2);
+                        let result = ic.ligplotCls.getSvgPerPair(serialArray1, resid1, resid2, interactionType, index2xy, xlen, ylen, xcenter, ycenter, dist1, bNotDrawNode, prevX2, prevY2);
                         svgHtmlNode += result.node;
                         svgHtmlLine += result.line;
                         prevX2 = result.x2;
@@ -53859,16 +53898,17 @@ class ChainalignParser {
             // calculate secondary structures with applyCommandDssp
             //$.when(ic.pdbParserCls.applyCommandDssp(true)).then(function() {
                 await ic.pdbParserCls.applyCommandDssp(true);
-
+//!!!
+/*
                 // original version =============
                 // align PDB chains
                 for(let index in ic.pdbChainIndexHash) {
                     //ic.pdbChainIndexHash[index] = mmdbid_q_tmp + "_" + ic.chain_q + "_" + ic.mmdbid_t + "_" + ic.chain_t;
                     let idArray = ic.pdbChainIndexHash[index].split('_');
                     mmdbid_q = idArray[0];
-                    idArray[1];
+                    let chain_q = idArray[1];
                     mmdbid_t = idArray[2];
-                    idArray[3];
+                    let chain_t = idArray[3];
 
                     thisClass.transformStructure(mmdbid_q, index-1, 'query');                
                 }
@@ -53878,7 +53918,7 @@ class ChainalignParser {
                 let urlalign = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi";
                 let urltmalign = me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
 
-                let resRangeArray = (me.cfg.resrange) ? me.cfg.resrange.split(' | ') : [];
+                let resRangeArray = (me.cfg.resrange) ? me.cfg.resrange.split(',') : [];
 
                 for(let index in ic.afChainIndexHash) {
                     let idArray = ic.afChainIndexHash[index].split('_');
@@ -53890,25 +53930,26 @@ class ChainalignParser {
                     let chain_t = idArray[3];
                     let chainid_t = mmdbid_t + '_' + chain_t;
 
-                    let atomSet_t = (resRangeArray[0]) ? ic.realignParserCls.getSeqCoorResid(resRangeArray[0].split(','), chainid_t).hAtoms : ic.chains[chainid_t];
-                    let atomSet_q = (resRangeArray[index]) ? ic.realignParserCls.getSeqCoorResid(resRangeArray[index].split(','), chainid_q).hAtoms : ic.chains[chainid_q];
+                    // let atomSet_t = (resRangeArray[0]) ? ic.realignParserCls.getSeqCoorResid(resRangeArray[0].split(','), chainid_t, true).hAtoms : ic.chains[chainid_t];
+                    // let atomSet_q = (resRangeArray[index]) ? ic.realignParserCls.getSeqCoorResid(resRangeArray[index].split(','), chainid_q, true).hAtoms : ic.chains[chainid_q];
+                    let atomSet_t = (resRangeArray[0]) ? ic.realignParserCls.getSeqCoorResid([resRangeArray[0]], chainid_t, true).hAtoms : ic.chains[chainid_t];
+                    let atomSet_q = (resRangeArray[index]) ? ic.realignParserCls.getSeqCoorResid([resRangeArray[index]], chainid_q, true).hAtoms : ic.chains[chainid_q];
                 // end of original version =============
-                
-/*
+*/                
+
                 // new version to be done for VASTsrv ==============
                 // dynamically align pairs in all chainids
                 let ajaxArray = [], indexArray = [], struArray = [];
                 let urlalign = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi";
                 let urltmalign = me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
 
-                let resRangeArray = (me.cfg.resrange) ? me.cfg.resrange.split(' | ') : [];
+                let resRangeArray = (me.cfg.resrange) ? me.cfg.resrange.split(',') : [];
 
                 // dynamically align pairs in all chainids
-                let atomSet_t = (me.cfg.resrange) ? ic.realignParserCls.getSeqCoorResid(resRangeArray[0].split(','), chainidArray[0]).hAtoms : ic.chains[chainidArray[0]];
+                let atomSet_t = (me.cfg.resrange) ? ic.realignParserCls.getSeqCoorResid([resRangeArray[0]], chainidArray[0], true).hAtoms : ic.chains[chainidArray[0]];
                 for(let index = 1, indexl = chainidArray.length; index < indexl; ++index) {
-                    let atomSet_q = (me.cfg.resrange) ? ic.realignParserCls.getSeqCoorResid(resRangeArray[index].split(','), chainidArray[index]).hAtoms : ic.chains[chainidArray[index]];
+                    let atomSet_q = (me.cfg.resrange) ? ic.realignParserCls.getSeqCoorResid([resRangeArray[index]], chainidArray[index], true).hAtoms : ic.chains[chainidArray[index]];
                 // end of new version to be done for VASTsrv ==============
-*/
 
                     let alignAjax;
                     if(me.cfg.aligntool != 'tmalign') {
@@ -54136,10 +54177,11 @@ class ChainalignParser {
 
             // chainid1 is target
             aligType = 'target';
-            this.transformStructure(target, index, aligType);
+            let bForce = true;
+            this.transformStructure(target, index, aligType, bForce);
 
             aligType = 'query';
-            this.transformStructure(query, index, aligType);
+            this.transformStructure(query, index, aligType, bForce);
 
             allChainidHash[chainidArray[0]] = 1;
             allChainidHash[chainidArray[1]] = 1;
@@ -54817,8 +54859,12 @@ class ChainalignParser {
 
         if(bQuery && me.cfg.matchedchains) {          
            // $.when(ic.pdbParserCls.applyCommandDssp(true)).then(function() {
-                let bRealign = true, bPredefined = true;
-                await ic.realignParserCls.realignChainOnSeqAlign(undefined, ic.chainidArray, bRealign, bPredefined);
+                // let bRealign = true, bPredefined = true;
+                // await ic.realignParserCls.realignChainOnSeqAlign(undefined, ic.chainidArray, bRealign, bPredefined);
+
+                ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(ic.chainidArray);
+                await ic.realignParserCls.realignOnStructAlign();
+
                 // reset annotations
                 $("#" + ic.pre + "dl_annotations").html("");
                 ic.bAnnoShown = false;
@@ -59389,7 +59435,7 @@ class RealignParser {
         }
     }
 
-    getSeqCoorResid(resiArray, chainid) { let ic = this.icn3d, me = ic.icn3dui;
+    getSeqCoorResid(resiArray, chainid, bNCBI) { let ic = this.icn3d, me = ic.icn3dui;
         let seq = '', coorArray = [], residArray = [];
         let hAtoms = {};
 
@@ -59397,15 +59443,7 @@ class RealignParser {
             if(resiArray[j].indexOf('-') != -1) {
                 let startEnd = resiArray[j].split('-');
                 for(let k = parseInt(startEnd[0]); k <= parseInt(startEnd[1]); ++k) {
-                    // from VAST neighbor page, use NCBI residue number
-                    //if(me.cfg.usepdbnum === false) k += base - 1;
-
-                    //let seqIndex = k - base;
-                    let seqIndex = ic.setSeqAlignCls.getPosFromResi(chainid, k);
-                    // if(ic.bNCBI) {
-                    //     let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[chainid + '_' + k]);
-                    //     if(atom && atom.resiNCBI) seqIndex = atom.resiNCBI - 1;
-                    // }
+                    let seqIndex = (bNCBI) ? k : ic.setSeqAlignCls.getPosFromResi(chainid, k);
 
                     // don't align solvent or chemicals
                     if(!ic.chainsSeq[chainid] || !ic.chainsSeq[chainid][seqIndex] || me.parasCls.b62ResArray.indexOf(ic.chainsSeq[chainid][seqIndex].name.toUpperCase()) == -1) continue;
@@ -59417,20 +59455,14 @@ class RealignParser {
                     residArray.push(chainid + '_' + k);
                 }            
             }
+            else if(resiArray[j] == 0) { // 0 means the whole chain
+                let residueHash = ic.firstAtomObjCls.getResiduesFromAtoms(ic.chains[chainid]);
+                residArray = Object.keys(residueHash);
+            }
             else { // one residue
-                
-                //let k = parseInt(resiArray[j]);
                 let k = resiArray[j];
-                // from VAST neighbor page, use NCBI residue number
-                //if(me.cfg.usepdbnum === false) k += base - 1;
-
-                //let seqIndex = k - base;
-                let seqIndex = ic.setSeqAlignCls.getPosFromResi(chainid, k);
 
-                // if(ic.bNCBI) {
-                //     let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[chainid + '_' + k]);
-                //     if(atom && atom.resiNCBI) seqIndex = atom.resiNCBI - 1;
-                // }
+                let seqIndex = (bNCBI) ? k : ic.setSeqAlignCls.getPosFromResi(chainid, k);
 
                 if(!ic.chainsSeq[chainid][seqIndex]) continue;
 
@@ -61135,10 +61167,7 @@ class ParserUtils {
       // display the structure right away. load the mns and sequences later
       setTimeout(async function(){
             if(ic.bInitial) {
-        //   if(!ic.bAnnoShown || ic.bResetAnno) {
-            //   if(me.cfg.showsets) {
-            //        ic.definedSetsCls.showSets();
-            //   }
+            // if(ic.bInitial && (!ic.bAnnoShown || ic.bResetAnno)) {
               if(me.cfg.align !== undefined || me.cfg.chainalign !== undefined) {
                   // expand the toolbar
                   let id = ic.pre + 'selection';
@@ -67277,6 +67306,7 @@ class ApplyCommand {
         let scale = command.substr(pos + 1);
 
         $("#" + me.ligplotid + "_scale").val(scale);
+        ic.ligplotScale = parseFloat(scale);
 
         $("#" + me.ligplotid).attr("width",(ic.ligplotWidth * parseFloat(scale)).toString() + "px");
       }
@@ -67505,6 +67535,7 @@ class ApplyCommand {
       }
       else if(command.indexOf('glycans cartoon') == 0) {
         let value = command.substr(command.lastIndexOf(' ') + 1);
+
         if(value == 'yes') {
             ic.bGlycansCartoon = true;
         }
@@ -67967,21 +67998,21 @@ class DefinedSets {
 
     setProtNuclLigInMenu() { let ic = this.icn3d; ic.icn3dui;
         // Initially, add proteins, nucleotides, chemicals, ions, water into the menu "custom selections"
-        if(Object.keys(ic.proteins).length > 0) {
+        if(ic.proteins && Object.keys(ic.proteins).length > 0) {
           //ic.defNames2Atoms['proteins'] = Object.keys(ic.proteins);
           ic.defNames2Residues['proteins'] = Object.keys(ic.firstAtomObjCls.getResiduesFromAtoms(ic.proteins));
           ic.defNames2Descr['proteins'] = 'proteins';
           ic.defNames2Command['proteins'] = 'select :proteins';
         }
 
-        if(Object.keys(ic.nucleotides).length > 0) {
+        if(ic.nucleotides && Object.keys(ic.nucleotides).length > 0) {
           //ic.defNames2Atoms['nucleotides'] = Object.keys(ic.nucleotides);
           ic.defNames2Residues['nucleotides'] = Object.keys(ic.firstAtomObjCls.getResiduesFromAtoms(ic.nucleotides));
           ic.defNames2Descr['nucleotides'] = 'nucleotides';
           ic.defNames2Command['nucleotides'] = 'select :nucleotides';
         }
 
-        if(Object.keys(ic.chemicals).length > 0) {
+        if(ic.chemicals && Object.keys(ic.chemicals).length > 0) {
           //ic.defNames2Atoms['chemicals'] = Object.keys(ic.chemicals);
           if(ic.bOpm) {
               let chemicalResHash = {}, memResHash = {};
@@ -68015,14 +68046,14 @@ class DefinedSets {
           }
         }
 
-        if(Object.keys(ic.ions).length > 0) {
+        if(ic.ions && Object.keys(ic.ions).length > 0) {
           //ic.defNames2Atoms['ions'] = Object.keys(ic.ions);
           ic.defNames2Residues['ions'] = Object.keys(ic.firstAtomObjCls.getResiduesFromAtoms(ic.ions));
           ic.defNames2Descr['ions'] = 'ions';
           ic.defNames2Command['ions'] = 'select :ions';
         }
 
-        if(Object.keys(ic.water).length > 0) {
+        if(ic.water && Object.keys(ic.water).length > 0) {
           //ic.defNames2Atoms['water'] = Object.keys(ic.water);
           ic.defNames2Residues['water'] = Object.keys(ic.firstAtomObjCls.getResiduesFromAtoms(ic.water));
           ic.defNames2Descr['water'] = 'water';
@@ -68153,7 +68184,7 @@ class DefinedSets {
         }
 
         // select whole structure
-        if(Object.keys(ic.structures) == 1) {
+        if(ic.structures && Object.keys(ic.structures) == 1) {
           let structure = Object.keys(ic.structures)[0];
 
           ic.defNames2Residues[structure] = Object.keys(ic.residues);
@@ -68161,7 +68192,7 @@ class DefinedSets {
 
           ic.defNames2Command[structure] = 'select $' + structure;
         }
-        else {
+        else if(ic.residues) {
             let resArray = Object.keys(ic.residues);
             let structResHash = {};
             for(let i = 0, il = resArray.length; i < il; ++i) {
@@ -69240,7 +69271,7 @@ class LoadScript {
 
             let chainid = paraArray[1].substr(8);
             let geneid = paraArray[2].substr(7);
-            let startpos = paraArray[3].substr(9);
+            let startpos = parseInt(paraArray[3].substr(9));
             let type = paraArray[4].substr(5);
 
             if($("#" + ic.pre + "anno_custom")[0]) {
@@ -69431,9 +69462,10 @@ class LoadScript {
 
       if(command.indexOf('load') !== -1) { // 'load pdb [pdbid]'
         let load_parameters = command.split(' | ');
-
         let loadStr = load_parameters[0];
-        if(load_parameters.length > 1) {
+
+        // do not reset me.cfg.inpara from "command=..." part if it was not empty
+        if(load_parameters.length > 1 && !me.cfg.inpara) {
             let firstSpacePos = load_parameters[load_parameters.length - 1].indexOf(' ');
             me.cfg.inpara = load_parameters[load_parameters.length - 1].substr(firstSpacePos + 1);
             if(me.cfg.inpara === 'undefined') {
@@ -76558,6 +76590,12 @@ class Diagram2d {
             thisClass.clickInteraction(this);
         });
 
+        $(document).on("click", "#" + ic.pre + "dl_ligplot .icn3d-interaction", function(e) { thisClass.icn3d;
+            e.stopImmediatePropagation();
+
+            thisClass.clickInteraction(this);
+        });
+
         $(document).on("click", "#" + ic.pre + "dl_alignerrormap .icn3d-node", function(e) { thisClass.icn3d;
             e.stopImmediatePropagation();
 
@@ -77806,7 +77844,7 @@ class Ligplot {
     }
 
     
-    getSvgPerPair(serialArray1, resid1, resid2, interactionType, index2xy, xlen, ylen, xcenter, ycenter, bNotDrawNode, prevX2, prevY2) { let ic = this.icn3d, me = ic.icn3dui;
+    getSvgPerPair(serialArray1, resid1, resid2, interactionType, index2xy, xlen, ylen, xcenter, ycenter, dist, bNotDrawNode, prevX2, prevY2) { let ic = this.icn3d, me = ic.icn3dui;
         let xOffset = 1, yOffset = -1;
         let bondLen = (interactionType == 'hbond' || interactionType == 'contact' || interactionType == 'halogen') ? ic.len4ang : ic.len4ang * 1.5; // real distance should be bout 120, not 80
         let shortBondLen = ic.len4ang / 2;
@@ -77918,6 +77956,26 @@ class Ligplot {
         // sometimes the same ligand atom is used in both Hbond and contact. THus we add "interactionType"
         let idpair = resid2Real + '--' + serialArray1.join('-') + interactionType; 
 
+        let interactionTypeStr;
+        if(interactionType == 'hbond') {
+            interactionTypeStr = 'H-Bonds';
+        }
+        else if(interactionType == 'ionic') {
+            interactionTypeStr = 'Salt Bridge/Ionic';
+        }
+        else if(interactionType == 'halogen') {
+            interactionTypeStr = 'Halogen Bonds';
+        }
+        else if(interactionType == 'pi-cation') {
+            interactionTypeStr = '&pi;-Cation';
+        }
+        else if(interactionType == 'pi-stacking') {
+            interactionTypeStr = '&pi;-Stacking';
+        }
+        else if(interactionType == 'contact') {
+            interactionTypeStr = 'Contacts';
+        }
+
         let id = resid2Real;
         if(bNotDrawNode || ic.resid2ToXy.hasOwnProperty(id)) {
             x2 = (ic.resid2ToXy.hasOwnProperty(id)) ? ic.resid2ToXy[id].x2 : prevX2;
@@ -77934,11 +77992,12 @@ class Ligplot {
                 }
             }
 
-            line += '<line id="' + idpair + '" x1="' + x1b.toFixed(2)  + '" y1="' + y1b.toFixed(2)  + '" x2="' + x2.toFixed(2)  + '" y2="' + y2.toFixed(2)  + '" x0="' + x1.toFixed(2)  + '" y0="' + y1.toFixed(2)  + '" short="' + bShort + '" opacity="1.0" stroke="' + lineColor + '"  stroke-width="' + strokeWidth + '" stroke-dasharray="5,5"/>\n';
+            line +='<g><title>Interaction type: ' + interactionTypeStr + '; Distance: ' + parseFloat(dist).toFixed(1) + ' &#197;</title>';
+            line += '<line class="icn3d-interaction" id="' + idpair + '" resid1="' + resid1Real + '" resid2="' + resid2Real + '" x1="' + x1b.toFixed(2)  + '" y1="' + y1b.toFixed(2)  + '" x2="' + x2.toFixed(2)  + '" y2="' + y2.toFixed(2)  + '" x0="' + x1.toFixed(2)  + '" y0="' + y1.toFixed(2)  + '" short="' + bShort + '" opacity="1.0" stroke="' + lineColor + '"  stroke-width="' + strokeWidth + '" stroke-dasharray="5,5"/>\n';
+            line += '</g>\n';
         }
         else {
-            node +='<g>';
-            node += '<title>' + resName2 + '</title>';
+            node +='<g><title>' + resName2 + '</title>';
             // node += '<circle class='icn3d-ctnode' cx="' + x2.toFixed(2) + '" cy="' + y2.toFixed(2)  + '" r="10" fill="#' + textColor2 + '" stroke-width="1" stroke="' + textColor2 + '" resid="' + resid2Real + '"/>';
             let boxWidth = 28, boxHeight = 14;
             node += '<rect id="' + id + '_node" x="' + (x2 - boxWidth*0.5).toFixed(2) + '" y="' + (y2 - boxHeight*0.5).toFixed(2)  + '" width="' + boxWidth + '" height="' + boxHeight + '" rx="2" ry="2" fill="#' + textColor2 + '" stroke-width="1" stroke="' + textColor2 + '" resid="' + resid2Real + '"/>';
@@ -77946,7 +78005,9 @@ class Ligplot {
             node += '<text class="icn3d-ctnode" resid="' + id + '" id="' + id + '" x="' + x2.toFixed(2)  + '" y="' + y2.toFixed(2)  + '" fill="#000" stroke="none" text-anchor="middle" alignment-baseline="central" style="font-size:10px">' + resName2 + '</text>';
             node += '</g>\n';
 
-            line += '<line id="' + idpair + '" x1="' + x1.toFixed(2)  + '" y1="' + y1.toFixed(2)  + '" x2="' + x2.toFixed(2)  + '" y2="' + y2.toFixed(2)  + '" opacity="1.0" stroke="' + lineColor + '"  stroke-width="' + strokeWidth + '" stroke-dasharray="5,5"/>\n';
+            line +='<g><title>Interaction type: ' + interactionTypeStr + '; Distance: ' + parseFloat(dist).toFixed(1) + ' &#197;</title>';
+            line += '<line class="icn3d-interaction" id="' + idpair + '" resid1="' + resid1Real + '" resid2="' + resid2Real + '" x1="' + x1.toFixed(2)  + '" y1="' + y1.toFixed(2)  + '" x2="' + x2.toFixed(2)  + '" y2="' + y2.toFixed(2)  + '" opacity="1.0" stroke="' + lineColor + '"  stroke-width="' + strokeWidth + '" stroke-dasharray="5,5"/>';
+            line += '</g>\n';
 
             if(interactionType != 'contact') {
                 if(!ic.resid2ToXy.hasOwnProperty(resid2Real)) ic.resid2ToXy[resid2Real] = {x2: x2, y2: y2};
@@ -77966,26 +78027,29 @@ class Ligplot {
             start: function( e, ui ) {
                 let oriX= parseFloat(e.target.getAttribute('x'));
                 let oriY = parseFloat(e.target.getAttribute('y'));
-
                 e.target.setAttribute('x', oriX);
                 e.target.setAttribute('y', oriY);
             },
             drag: function( e, ui ) {
-                let offsetX = $("#" + me.ligplotid).offset().left + ic.len4ang; // ic.len4ang was defined in svg viewbox
-                let offsetY = $("#" + me.ligplotid).offset().top + ic.len4ang;
+                let ligplotScale = (ic.ligplotScale) ? ic.ligplotScale : 1;
+
+                let offsetX = $("#" + me.ligplotid).offset().left + ic.len4ang * ligplotScale; // ic.len4ang was defined in svg viewbox
+                let offsetY = $("#" + me.ligplotid).offset().top + ic.len4ang * ligplotScale;
 
                 let id = e.target.getAttribute('resid');
-                let x = (e.clientX - offsetX);
-                let y = (e.clientY - offsetY);
+                let x = (e.clientX - offsetX) / ligplotScale;
+                let y = (e.clientY - offsetY) / ligplotScale;
 
                 let oriX = parseFloat(e.target.getAttribute('x'));
                 let oriY = parseFloat(e.target.getAttribute('y'));
 
                 // change for each step
-                let dx = (x - oriX) / ic.resizeRatioX;
-                let dy = (y - oriY) / ic.resizeRatioY;
+                // let dx = (x - oriX) / ic.resizeRatioX;
+                // let dy = (y - oriY) / ic.resizeRatioY;
+                let dx = (x - oriX);
+                let dy = (y - oriY);
 
-                // move the text label
+                // move the node
                 oriX = parseFloat($("#" + id + "_node").attr('x'));
                 oriY = parseFloat($("#" + id + "_node").attr('y'));
 
@@ -82811,7 +82875,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.34.0';
+    this.REVISION = '3.34.1';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -83001,7 +83065,8 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
                 await ic.realignParserCls.realignChainOnSeqAlign(undefined, chainidArray, bRealign, bPredefined);
             }
         }
-        else if(me.cfg.resdef !== undefined && me.cfg.matchedchains !== undefined) {
+        // else if(me.cfg.resdef !== undefined && me.cfg.matchedchains !== undefined) {
+        else if(me.cfg.matchedchains !== undefined) {
             let stru_t = Object.keys(ic.structures)[0];
 
             let chain_t = stru_t + '_' + me.cfg.masterchain;
@@ -83029,7 +83094,7 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
             ic.chainidArray = [chain_t].concat(chainidArray);
             ic.chainidArray = ic.chainalignParserCls.addPostfixForChainids(ic.chainidArray);
 
-            me.htmlCls.clickMenuCls.setLogCmd('resdef ' + me.cfg.resdef, true);
+            // me.htmlCls.clickMenuCls.setLogCmd('resdef ' + me.cfg.resdef, true);
 
             ic.loadCmd = 'vast_search_chainid ' + ic.chainidArray;
             me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
@@ -83255,7 +83320,8 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
         ic.bChainAlign = true;
         ic.inputid = me.cfg.chainalign;
         let resrangeStr = (me.cfg.resrange) ? ' | resrange ' + me.cfg.resrange : '';
-        ic.loadCmd = 'load chainalignment ' + me.cfg.chainalign + ' | resnum ' + me.cfg.resnum + ' | resdef ' + me.cfg.resdef + ' | aligntool ' + me.cfg.aligntool + ' | parameters ' + me.cfg.inpara + resrangeStr;
+        let resdef = (me.cfg.resdef) ? me.cfg.resdef : '';
+        ic.loadCmd = 'load chainalignment ' + me.cfg.chainalign + ' | resnum ' + me.cfg.resnum + ' | resdef ' + resdef + ' | aligntool ' + me.cfg.aligntool + ' | parameters ' + me.cfg.inpara + resrangeStr;
         me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
         await ic.chainalignParserCls.downloadChainalignment(me.cfg.chainalign);
     }