icn3d 3.13.0 → 3.13.2

package/icn3d.module.js

@@ -5127,7 +5127,11 @@ class UtilsCls {
         let dz = atom0.coord.z - atom1.coord.z;
         let distSq = dx*dx + dy*dy + dz*dz;
 
-        return distSq < 1.3 * r * r;
+        // r(N) = 0.71, r(H) = 0.31, N-H in residues are about 1.5
+        // factor = (1.5 / 1.02) * (1.5 / 1.02) = 2.16
+        let factor = ((atom0.elem == 'N' && atom1.elem.substr(0,1) == 'H') || (atom1.elem == 'N' && atom0.elem.substr(0,1) == 'H')) ? 2.2 : 1.3;
+
+        return distSq < factor * r * r;
     }
 
     //Convert a three-letter residue name to a one-letter residue abbreviation, e.g., 'LYS' to 'K', or ' A' to 'A' for nucleotides.
@@ -18350,7 +18354,7 @@ class ShowInter {
                         for(let j = 0, jl = ic.atoms[atom.serial].bonds.length; j < jl; ++j) {
                             let serial = ic.atoms[atom.serial].bonds[j];
                             //if(ic.atoms[serial].name === 'H') {
-                            if(atom.elem.substr(0, 1) === 'H') {
+                            if(ic.atoms[serial].elem.substr(0, 1) === 'H') {
                                 ic.dAtoms[serial] = 1;
                                 ic.hAtoms[serial] = 1;
                             }
@@ -18359,11 +18363,29 @@ class ShowInter {
             }
         }
         else {
+            // for(let serial in ic.atoms) {
+            //     ic.dAtoms[serial] = 1;
+            //     ic.hAtoms[serial] = 1;
+            // }  
+
+            // add bonds in heavy atoms
+            //for(let serial in ic.hAtoms) {
             for(let serial in ic.atoms) {
-                ic.dAtoms[serial] = 1;
-                ic.hAtoms[serial] = 1;
-            }            
+                let atom = ic.atoms[serial];
+                //if(atom.name === 'H') {
+                if(atom.elem.substr(0, 1) === 'H') {                   
+                    if(ic.atoms[serial].bonds.length > 0) {
+                        let otherSerial = ic.atoms[serial].bonds[0];
+                        ic.atoms[otherSerial].bonds.push(atom.serial);
+                        if(ic.atoms[otherSerial].bondOrder) ic.atoms[otherSerial].bondOrder.push(1);
+                    }        
+                    
+                    ic.dAtoms[serial] = 1;
+                }
+            }
         }
+
+        ic.bShowHighlight = false;
     }
 
     hideHydrogens() { let ic = this.icn3d; ic.icn3dui;
@@ -19844,7 +19866,7 @@ class Delphi {
 
        ic.loadPhiFrom = 'delphi';
 
-       let url = "https://www.ncbi.nlm.nih.gov/Structure/delphi/delphi.cgi";
+       let url = me.htmlCls.baseUrl + "delphi/delphi.cgi";
        let pdbid =(me.cfg.cid) ? me.cfg.cid : Object.keys(ic.structures).toString();
        let dataObj = {};
 
@@ -20656,7 +20678,7 @@ class Symd {
        let thisClass = this;
 
        //var url = "https://data.rcsb.org/rest/v1/core/assembly/" + pdbid + "/1";
-       let url = "https://www.ncbi.nlm.nih.gov/Structure/symd/symd.cgi";
+       let url = me.htmlCls.baseUrl + "symd/symd.cgi";
 
        let atomHash = me.hashUtilsCls.intHash(ic.dAtoms, ic.hAtoms);
 
@@ -21803,7 +21825,7 @@ class LoadPDB {
             }
 
             if(!(curChain === atom.chain && curResi === atom.resi)) {
-                // a new residue, add the residue-residue bond beides the regular bonds               
+                // a new residue, add the residue-residue bond besides the regular bonds               
                 this.refreshBonds(curResAtoms, prevCarbonArray[0]);
 
                 prevCarbonArray.splice(0, 1); // remove the first carbon
@@ -24818,13 +24840,13 @@ class OpmParser {
        });
     }
 
-    loadOpmData(data, pdbid, bFull, type, pdbid2) { let ic = this.icn3d; ic.icn3dui;
+    loadOpmData(data, pdbid, bFull, type, pdbid2) { let  ic = this.icn3d, me = ic.icn3dui;
         let  thisClass = this;
         let  url, dataType;
 
         if(!pdbid) pdbid = 'stru';
 
-        url = "https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdb_strview.cgi?v=2&program=icn3d&opm&uid=" + pdbid.toLowerCase();
+        url = me.htmlCls.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&opm&uid=" + pdbid.toLowerCase();
         dataType = "jsonp";
 
         $.ajax({
@@ -26101,6 +26123,7 @@ class ChainalignParser {
                 let  ajaxArray = [], indexArray = [], struArray = [];
                 let urlalign = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi";
                 let urltmalign = me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
+                //let urltmalign = "https://test.ncbi.nlm.nih.gov/Structure/tmalign/tmalign.cgi";
 
                 for(let index in ic.afChainIndexHash) {
                     let idArray = ic.afChainIndexHash[index].split('_');
@@ -29640,7 +29663,7 @@ class ResizeCanvas {
         //let  itemArray = ['dl_selectannotations', 'dl_alignment', 'dl_2ddgm', 'dl_definedsets', 'dl_graph',
         //    'dl_linegraph', 'dl_scatterplot', 'dl_contactmap', 'dl_allinteraction', 'dl_copyurl',
         //    'dl_symmetry', 'dl_symd', 'dl_rmsd', 'dl_legend', 'dl_disttable'];
-        let itemArray = ['dl_2ddgm', 'dl_2dctn', 'dl_alignment', 'dl_sequence2', 'dl_definedsets', 'dl_setsmenu', 'dl_command', 'dl_setoperations', 'dl_vast', 'dl_foldseek', 'dl_mmtfid', 'dl_pdbid', 'dl_afid', 'dl_opmid', 'dl_pdbfile', 'dl_pdbfile_app', 'dl_rescolorfile', 'dl_customcolor', 'dl_align', 'dl_alignaf', 'dl_chainalign', 'dl_mutation', 'dl_mol2file', 'dl_sdffile', 'dl_xyzfile', 'dl_afmapfile', 'dl_urlfile', 'dl_mmciffile', 'dl_mmcifid', 'dl_mmdbid', 'dl_mmdbafid', 'dl_blast_rep_id', 'dl_yournote', 'dl_gi', 'dl_uniprotid', 'dl_cid', 'dl_pngimage', 'dl_state', 'dl_fixedversion', 'dl_selection', 'dl_dsn6', 'dl_dsn6url', 'dl_clr', 'dl_symmetry', 'dl_symd', 'dl_contact', 'dl_hbonds', 'dl_realign', 'dl_realignbystruct', 'dl_allinteraction', 'dl_interactionsorted', 'dl_linegraph', 'dl_linegraphcolor', 'dl_scatterplot', 'dl_scatterplotcolor', 'dl_contactmap', 'dl_alignerrormap', 'dl_elecmap2fofc', 'dl_elecmapfofc', 'dl_emmap', 'dl_aroundsphere', 'dl_adjustmem', 'dl_selectplane', 'dl_addlabel', 'dl_addlabelselection', 'dl_labelColor', 'dl_distance', 'dl_stabilizer', 'dl_disttwosets', 'dl_distmanysets', 'dl_stabilizer_rm', 'dl_thickness', 'dl_thickness2', 'dl_addtrack', 'dl_addtrack_tabs', 'dl_saveselection', 'dl_copyurl', 'dl_selectannotations', 'dl_annotations_tabs', 'dl_anno_view_tabs', 'dl_annotations', 'dl_graph', 'dl_svgcolor', 'dl_area', 'dl_colorbyarea', 'dl_rmsd', 'dl_buriedarea', 'dl_propbypercentout', 'dl_propbybfactor', 'dl_legend', 'dl_disttable'];
+        let itemArray = ['dl_2ddgm', 'dl_2dctn', 'dl_alignment', 'dl_sequence2', 'dl_definedsets', 'dl_setsmenu', 'dl_command', 'dl_setoperations', 'dl_vast', 'dl_foldseek', 'dl_mmtfid', 'dl_pdbid', 'dl_afid', 'dl_opmid', 'dl_pdbfile', 'dl_pdbfile_app', 'dl_rescolorfile', 'dl_customcolor', 'dl_align', 'dl_alignaf', 'dl_chainalign', 'dl_chainalign2', 'dl_chainalign3', 'dl_mutation', 'dl_mol2file', 'dl_sdffile', 'dl_xyzfile', 'dl_afmapfile', 'dl_urlfile', 'dl_mmciffile', 'dl_mmcifid', 'dl_mmdbid', 'dl_mmdbafid', 'dl_blast_rep_id', 'dl_yournote', 'dl_gi', 'dl_uniprotid', 'dl_cid', 'dl_pngimage', 'dl_state', 'dl_fixedversion', 'dl_selection', 'dl_dsn6', 'dl_dsn6url', 'dl_clr', 'dl_symmetry', 'dl_symd', 'dl_contact', 'dl_hbonds', 'dl_realign', 'dl_realignbystruct', 'dl_allinteraction', 'dl_interactionsorted', 'dl_linegraph', 'dl_linegraphcolor', 'dl_scatterplot', 'dl_scatterplotcolor', 'dl_contactmap', 'dl_alignerrormap', 'dl_elecmap2fofc', 'dl_elecmapfofc', 'dl_emmap', 'dl_aroundsphere', 'dl_adjustmem', 'dl_selectplane', 'dl_addlabel', 'dl_addlabelselection', 'dl_labelColor', 'dl_distance', 'dl_stabilizer', 'dl_disttwosets', 'dl_distmanysets', 'dl_stabilizer_rm', 'dl_thickness', 'dl_thickness2', 'dl_addtrack', 'dl_addtrack_tabs', 'dl_saveselection', 'dl_copyurl', 'dl_selectannotations', 'dl_annotations_tabs', 'dl_anno_view_tabs', 'dl_annotations', 'dl_graph', 'dl_svgcolor', 'dl_area', 'dl_colorbyarea', 'dl_rmsd', 'dl_buriedarea', 'dl_propbypercentout', 'dl_propbybfactor', 'dl_legend', 'dl_disttable'];
 
         for(let i in itemArray) {
             let  item = itemArray[i];
@@ -32677,7 +32700,7 @@ class AnnoCddSite {
         let chnidArray = Object.keys(ic.protein_chainid);
         // show conserved domains and binding sites
         // live search
-        let url = me.htmlCls.baseUrl + "cdannots/cdannots.fcgi?fmt&frclive&live=lcl&queries=" + chnidBaseArray;
+        let url = me.htmlCls.baseUrl + "cdannots/cdannots.fcgi?fmt&frclive&live=lcl&queries=" + chnidBaseArray;     
         // precalculated
         //let url = me.htmlCls.baseUrl + "cdannots/cdannots.fcgi?fmt&live=lcl&queries=" + chnidBaseArray;
         // live search for AlphaFold structures
@@ -32723,7 +32746,7 @@ class AnnoCddSite {
 
                //url = me.htmlCls.baseUrl + "cdannots/cdannots.fcgi?fmt&live=lcl&queries=" + ic.giSeq[chnidArray[0]].join('');
                // live searchE
-               url = me.htmlCls.baseUrl + "cdannots/cdannots.fcgi?fmt&frclive&live=lcl&queries=" + seq;
+               url = me.htmlCls.baseUrl + "cdannots/cdannots.fcgi?fmt&frclive&live=lcl&queries=" + seq;             
                // precalculated
                //url = me.htmlCls.baseUrl + "cdannots/cdannots.fcgi?fmt&live=lcl&queries=" + seq;
 
@@ -36505,11 +36528,15 @@ class SetSeqAlign {
         // start and end of MSA
         let start_t = 9999, end_t = -1;
 
+        let baseResi = ic.chainsSeq[chainid1][0].resi - 1;
+
         for(let index = 1, indexl = chainidArray.length; index < indexl; ++index) { 
             let chainIndex = index - 1;
+            if(!ic.qt_start_end[chainIndex]) continue;
+
             for(let i = 0, il = ic.qt_start_end[chainIndex].length; i < il; ++i) {
                 let  start1, end1;
-                if(bRealign) { // realresidue numbers are stored
+                if(bRealign) { // real residue numbers are stored
                     start1 = ic.qt_start_end[chainIndex][i].t_start;
                     end1 = ic.qt_start_end[chainIndex][i].t_end;
                 }
@@ -36517,9 +36544,9 @@ class SetSeqAlign {
                     start1 = ic.qt_start_end[chainIndex][i].t_start - 1;
                     end1 = ic.qt_start_end[chainIndex][i].t_end - 1;
                 }
-
                 for(let j = start1; j <= end1; ++j) {
-                    let resi = this.getResi(chainidArray[0], j, bRealign);
+                    let resiPos = j - baseResi;
+                    let resi = this.getResi(chainidArray[0], resiPos, bRealign);
                     resi2range_t[resi] = 1;
                     if(j < start_t) start_t = j;
                     if(j > end_t) end_t = j;
@@ -36527,6 +36554,9 @@ class SetSeqAlign {
             }
         }
 
+        // TM-align should use "start1 = ic.qt_start_end[chainIndex][i].t_start - 1", but the rest are the same as ""bRealign"
+        if(me.cfg.aligntool == 'tmalign') bRealign = true; // real residue numbers are stored
+
         let resi2rangeArray = Object.keys(resi2range_t);
         resi2rangeArray.sort(function(a, b) {
             return parseInt(a) - parseInt(b);
@@ -36573,7 +36603,7 @@ class SetSeqAlign {
         for(let j = 0, jl = ic.chainsSeq[chainid1].length; j < jl; ++j) { 
             let resi = ic.chainsSeq[chainid1][j].resi;
 
-            if((j < start_t || j > end_t) ) {
+            if((j + baseResi < start_t || j + baseResi > end_t) ) {
                 continue;
             }
 
@@ -37811,7 +37841,7 @@ class ParserUtils {
               if(me.cfg.showanno) {
                    let  cmd = "view annotations";
                    me.htmlCls.clickMenuCls.setLogCmd(cmd, true);
-                   ic.showAnnoCls.showAnnotations();
+                   ic.showAnnoCls.showAnnotations(); 
               }
               if(me.cfg.closepopup) {
                   ic.resizeCanvasCls.closeDialogs();
@@ -38817,9 +38847,11 @@ class ShowAnno {
         }
 
         let nucleotide_chainid = {}, chemical_chainid = {}, chemical_set = {};
-        ic.protein_chainid = {};
+        //ic.protein_chainid = {};
 
         if(ic.bAnnoShown === undefined || !ic.bAnnoShown || ic.bResetAnno) { // ic.bResetAnno when loading another structure
+            ic.protein_chainid = {};
+
             let chainArray = Object.keys(ic.chains);
 
             if(ic.giSeq === undefined) ic.giSeq = {};
@@ -38860,6 +38892,7 @@ class ShowAnno {
                     chainidBase = chainArray[i];
                 }
                 //if(me.cfg.mmdbid !== undefined) { // protein and chemicals/ions are in different chains
+
                 if(ic.proteins.hasOwnProperty(atom.serial) && ic.chainsSeq[chainArray[i]].length > 1) {
                     ic.protein_chainid[chainArray[i]] = chainidBase;
                 }
@@ -40648,11 +40681,11 @@ class AnnoSnpClinVar {
             if(ic.deferredClinvar !== undefined) ic.deferredClinvar.resolve();
         }
     }
-    showClinvarPart2(chnid, chnidBase, gi) { let ic = this.icn3d; ic.icn3dui;
+    showClinvarPart2(chnid, chnidBase, gi) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
         //var url = "https://www.ncbi.nlm.nih.gov/projects/SNP/beVarSearch_mt.cgi?appname=iCn3D&format=bed&report=pdb2bed&acc=" + chnidBase;
         //var url = "https://www.ncbi.nlm.nih.gov/Structure/icn3d/clinvar.txt";
-        let url = "https://www.ncbi.nlm.nih.gov/Structure/vastdyn/vastdyn.cgi?chainid_clinvar=" + chnidBase;
+        let url = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi?chainid_clinvar=" + chnidBase;
         if(ic.chainsGene[chnid] && ic.chainsGene[chnid].geneSymbol) {
             url += "&gene=" + ic.chainsGene[chnid].geneSymbol;
         }
@@ -40687,7 +40720,7 @@ class AnnoSnpClinVar {
         });
     }
 
-    showSnpPart2(chnid, chnidBase, gi) { let ic = this.icn3d; ic.icn3dui;
+    showSnpPart2(chnid, chnidBase, gi) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
         if(gi !== undefined) {
       /*      
@@ -40706,7 +40739,7 @@ class AnnoSnpClinVar {
                 } //if(data3 != "") {
                 else {
        */             
-                    let url4 = "https://www.ncbi.nlm.nih.gov/Structure/vastdyn/vastdyn.cgi?chainid_snp=" + chnidBase;
+                    let url4 = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi?chainid_snp=" + chnidBase;
                     if(ic.chainsGene[chnid] && ic.chainsGene[chnid].geneSymbol) {
                         url4 += "&gene=" + ic.chainsGene[chnid].geneSymbol;
                     }
@@ -45512,7 +45545,8 @@ class VRButton {
             button.style.display = '';
 
             button.style.cursor = 'pointer';
-            button.style.left = 'calc(50% - 50px)';
+            //button.style.left = 'calc(50% - 50px)';
+            button.style.left = 'calc(33% - 50px)';
             button.style.width = '100px';
 
             button.textContent = 'ENTER VR';
@@ -45566,7 +45600,7 @@ class VRButton {
             button.style.display = '';
 
             button.style.cursor = 'auto';
-            button.style.left = 'calc(50% - 75px)';
+            button.style.left = 'calc(33% - 75px)'; //'calc(50% - 75px)';
             button.style.width = '150px';
 
             button.onmouseenter = null;
@@ -45759,7 +45793,8 @@ class ARButton {
 			button.style.display = '';
 
 			button.style.cursor = 'pointer';
-			button.style.left = 'calc(50% - 50px)';
+			//button.style.left = 'calc(50% - 50px)';
+			button.style.left = 'calc(66% - 50px)';
 			button.style.width = '100px';
 
 			button.textContent = 'START AR';
@@ -45807,7 +45842,7 @@ class ARButton {
 			button.style.display = '';
 
 			button.style.cursor = 'auto';
-			button.style.left = 'calc(50% - 75px)';
+			button.style.left = 'calc(66% - 50px)'; //'calc(50% - 75px)';
 			button.style.width = '150px';
 
 			button.onmouseenter = null;
@@ -45904,7 +45939,7 @@ class ARButton {
 
 			}
 
-			message.style.left = 'calc(50% - 90px)';
+			message.style.left = 'calc(66% - 90px)'; //'calc(50% - 90px)';
 			message.style.width = '180px';
 			message.style.textDecoration = 'none';
 
@@ -54286,9 +54321,17 @@ class ClickMenu {
     //    },
     //    clkMn1_chainalign: function() {
         me.myEventCls.onIds("#" + me.pre + "mn1_chainalign", "click", function(e) { me.icn3d;
-           me.htmlCls.dialogCls.openDlg('dl_chainalign', 'Align multiple chains of 3D structures');
+           me.htmlCls.dialogCls.openDlg('dl_chainalign', 'Align multiple chains by structure alignment');
         });
 
+        me.myEventCls.onIds("#" + me.pre + "mn1_chainalign2", "click", function(e) { me.icn3d;
+            me.htmlCls.dialogCls.openDlg('dl_chainalign2', 'Align multiple chains by sequence alignment');
+         });
+
+        me.myEventCls.onIds("#" + me.pre + "mn1_chainalign3", "click", function(e) { me.icn3d;
+            me.htmlCls.dialogCls.openDlg('dl_chainalign3', 'Align multiple chains residue by residue');
+         });
+
         me.myEventCls.onIds("#" + me.pre + "mn1_mutation", "click", function(e) { me.icn3d;
            me.htmlCls.dialogCls.openDlg('dl_mutation', 'Show the mutations in 3D');
         });
@@ -54467,6 +54510,12 @@ class ClickMenu {
            thisClass.setLogCmd("export pqr", true);
         });
 
+        me.myEventCls.onIds(["#" + me.pre + "delphipdbh", "#" + me.pre + "phipqr", "#" + me.pre + "phiurlpqr"], "click", function(e) { me.icn3d;
+            let bPdb = true;
+            me.htmlCls.setHtmlCls.exportPqr(bPdb);
+            thisClass.setLogCmd("export pdbh", false);
+         });
+
     //    clkMn1_exportStl: function() {
         me.myEventCls.onIds("#" + me.pre + "mn1_exportStl", "click", function(e) { let ic = me.icn3d;
            thisClass.setLogCmd("export stl file", false);
@@ -56881,15 +56930,22 @@ class SetMenu {
         html += "</li>";
         html += "<li><span>Align</span>";
         html += "<ul>";
-        html += me.htmlCls.setHtmlCls.getLink('mn1_blast_rep_id', 'Sequence to Structure');
-        //html += me.htmlCls.setHtmlCls.getLink('mn1_align', 'Structure to Structure ' + me.htmlCls.wifiStr);
+        
+        html += "<li><span>Multiple Chains</span>";
+        html += "<ul>";
+        html += me.htmlCls.setHtmlCls.getRadio('mn1_chainalignRad', 'mn1_chainalign', 'by Structure Alignment ' + me.htmlCls.wifiStr);
+        html += me.htmlCls.setHtmlCls.getRadio('mn1_chainalignRad', 'mn1_chainalign2', 'by Sequence Alignment ' + me.htmlCls.wifiStr);
+        html += me.htmlCls.setHtmlCls.getRadio('mn1_chainalignRad', 'mn1_chainalign3', 'Residue by Residue');
+        html += "</ul>";
+        html += "</li>";
+
         html += "<li><span>Structure to Structure</span>";
         html += "<ul>";
         html += me.htmlCls.setHtmlCls.getLink('mn1_align', 'Two PDB Structures ' + me.htmlCls.wifiStr);
         html += me.htmlCls.setHtmlCls.getLink('mn1_alignaf', 'Two AlphaFold Structures ' + me.htmlCls.wifiStr);
         html += "</ul>";
 
-        html += me.htmlCls.setHtmlCls.getLink('mn1_chainalign', 'Multiple Chains ' + me.htmlCls.wifiStr);
+        html += me.htmlCls.setHtmlCls.getLink('mn1_blast_rep_id', 'Sequence to Structure');
 
         html += "</ul>";
         html += "</li>";
@@ -56965,6 +57021,7 @@ class SetMenu {
     */
 
         html += me.htmlCls.setHtmlCls.getLink('mn1_exportPdbRes', 'PDB');
+        html += me.htmlCls.setHtmlCls.getLink('delphipdbh', 'PDB with Hydrogens');
 
         if(me.cfg.cid === undefined) {
             html += me.htmlCls.setHtmlCls.getLink('mn1_exportSecondary', 'Secondary Structure');
@@ -59002,18 +59059,36 @@ class SetDialog {
         html += "<div style='width:550px'>";
         html += "All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).<br/><br/>";
         html += "<b>Chain IDs</b>: " + me.htmlCls.inputTextStr + "id='" + me.pre + "chainalignids' value='P69905,P01942,1HHO_A' size=50><br/><br/>";
-        html += "<b>Optional 1</b>, full chains are used for structure alignment<br/><br/>";
-        html += "<b>Optional 2</b>, sequence alignment (followed by structure alignemnt) based on residue numbers in the First/Master chain: <br>" + me.htmlCls.inputTextStr + "id='" + me.pre + "resalignids' placeholder='1,5,10-50' size=50><br/><br/>";
-        html += "<b>Optional 3</b>, predefined alignment with the first chain as the master. The rest chains are aligned to the master chain. Each alignment is defined as \" | \"-separated residue lists in one line. \"10-50\" means a range of residues from 10 to 50.<br><textarea id='" + me.pre + "predefinedres' rows='5' style='width: 100%; height: " +(me.htmlCls.LOG_HEIGHT) + "px; padding: 0px; border: 0px;' placeholder='1,5,10-50 | 1,5,10-50     \n2,6,11-51 | 1,5,10-50'></textarea><br/><br/>";
-        //html += me.htmlCls.buttonStr + "reload_chainalign_asym'>Align Asymmetric Unit</button>" + me.htmlCls.buttonStr + "reload_chainalign' style='margin-left:30px'>Align Biological Unit</button><br/><br/>";
-        html += me.htmlCls.buttonStr + "reload_chainalign_tmalign'>Align with TM-align</button>" + me.htmlCls.buttonStr + "reload_chainalign_asym' style='margin-left:30px'>Align with VAST</button><br/><br/>";
+        html += me.htmlCls.buttonStr + "reload_chainalign_tmalign'><b>Align with TM-align</b></button>" + me.htmlCls.buttonStr + "reload_chainalign_asym' style='margin-left:30px'><b>Align with VAST</b></button><br/><br/>";
+
+        html += "(Note: To align chains in custom PDB files, you could load them in \"File > Open File > PDB Files (appendable)\" and click \"Analysis > Defined Sets\". Finally select multiple chains in Defined Sets and click \"File > Realign Selection\".)<br><br>";
+        html += "</div></div>";
+
+        html += me.htmlCls.divStr + "dl_chainalign2' class='" + dialogClass + "'>";
+        html += "<div style='width:550px'>";
+        html += "All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).<br/><br/>";
+        html += "<b>Chain IDs</b>: " + me.htmlCls.inputTextStr + "id='" + me.pre + "chainalignids2' value='P69905,P01942,1HHO_A' size=50><br/><br/>";
+
+        html += "The sequence alignment (followed by structure alignemnt) is based on residue numbers in the First/Master chain: <br>" + me.htmlCls.inputTextStr + "id='" + me.pre + "resalignids' value='1,5,10-50' size=50><br/>";
+        html += me.htmlCls.buttonStr + "reload_chainalign_asym2' style='margin-top:3px;'><b>Align by Sequence Alignment</b></button><br/><br/>";
+
+        html += "(Note: To align chains in custom PDB files, you could load them in \"File > Open File > PDB Files (appendable)\" and click \"Analysis > Defined Sets\". Finally select multiple chains in Defined Sets and click \"File > Realign Selection\".)<br><br>";
+        html += "</div></div>";
+
+        html += me.htmlCls.divStr + "dl_chainalign3' class='" + dialogClass + "'>";
+        html += "<div style='width:550px'>";
+        html += "All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).<br/><br/>";
+        html += "<b>Chain IDs</b>: " + me.htmlCls.inputTextStr + "id='" + me.pre + "chainalignids3' value='P69905,P01942,1HHO_A' size=50><br/><br/>";
+        
+        html += "Each alignment is defined as \" | \"-separated residue lists in one line. \"10-50\" means a range of residues from 10 to 50.<br><textarea id='" + me.pre + "predefinedres' rows='5' style='width: 100%; height: " +(me.htmlCls.LOG_HEIGHT) + "px; padding: 0px; border: 0px;'>1,5,10-50 | 1,5,10-50     \n2,6,11-51 | 1,5,10-50</textarea><br/>";
+        html += me.htmlCls.buttonStr + "reload_chainalign_asym3'><b>Align Residue by Residue</b></button><br/><br/>";
 
         html += "(Note: To align chains in custom PDB files, you could load them in \"File > Open File > PDB Files (appendable)\" and click \"Analysis > Defined Sets\". Finally select multiple chains in Defined Sets and click \"File > Realign Selection\".)<br><br>";
         html += "</div></div>";
 
         html += me.htmlCls.divStr + "dl_mutation' class='" + dialogClass + "'>";
         html += "<div style='width:500px'>";
-        html += 'Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[PDB ID]_[Chain ID]_[Residue Number]_[One Letter Mutatnt Residue]". E.g., the mutation of N501Y in the E chain of PDB 6M0J can be specified as "6M0J_E_501_Y". <br/><br/>';
+        html += 'Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[PDB ID or AlphaFold UniProt ID]_[Chain ID]_[Residue Number]_[One Letter Mutatnt Residue]". E.g., the mutation of N501Y in the E chain of PDB 6M0J can be specified as "6M0J_E_501_Y". For AlphaFold structures, the "Chain ID" is "A".<br/><br/>';
         html += "<div style='display:inline-block; width:110px'>Mutations: </div>" + me.htmlCls.inputTextStr + "id='" + me.pre + "mutationids' value='6M0J_E_484_K,6M0J_E_501_Y,6M0J_E_417_N' size=50><br/><br/>";
 
         html += "<b>Data Source</b>: <select id='" + me.pre + "idsource'>";
@@ -59997,7 +60072,7 @@ class Events {
 
     saveHtml(id) { let me = this.icn3dui, ic = me.icn3d;
         let html = '';
-        html += '<link rel="stylesheet" href="https:///structure.ncbi.nlm.nih.gov/icn3d/lib/jquery-ui-1.12.1.min.css">\n';
+        html += '<link rel="stylesheet" href="https:///structure.ncbi.nlm.nih.gov/icn3d/lib/jquery-ui-1.13.2.min.css">\n';
         html += '<link rel="stylesheet" href="https:///structure.ncbi.nlm.nih.gov/icn3d/icn3d_full_ui.css">\n';
         html += $("#" + id).html();
         let idArray = id.split('_');
@@ -60007,24 +60082,6 @@ class Events {
         ic.saveFileCls.saveFile(structureStr + '-' + idStr + '.html', 'html', encodeURIComponent(html));
     }
 
-    getAlignParas() { let me = this.icn3dui; me.icn3d;
-        let alignment = $("#" + me.pre + "chainalignids").val();
-        let idArray = alignment.split(',');
-        let alignment_final = '';
-        for(let i = 0, il = idArray.length; i < il; ++i) {
-            alignment_final += (idArray[i].indexOf('_') != -1) ? idArray[i] : idArray[i] + '_A'; // AlphaFold ID
-            if(i < il - 1) alignment_final += ',';
-        }
-        let resalign = $("#" + me.pre + "resalignids").val();
-        let predefinedres = $("#" + me.pre + "predefinedres").val().trim().replace(/\n/g, '; ');
-        if(predefinedres && alignment_final.split(',').length - 1 != predefinedres.split('; ').length) {
-            alert("Please make sure the number of chains and the lines of predefined residues are the same...");
-            return;
-        }
-
-        return {"alignment": alignment_final, "resalign": resalign, "predefinedres": predefinedres};
-    }
-
     //Hold all functions related to click events.
     allEventFunctions() { let me = this.icn3dui, ic = me.icn3d;
         let thisClass = this;
@@ -60181,6 +60238,8 @@ class Events {
     //    },
     //    clickRealignonseqalign: function() {
         me.myEventCls.onIds("#" + me.pre + "mn2_realignonseqalign", "click", function(e) { let ic = me.icn3d;
+            if(ic.bRender) me.htmlCls.dialogCls.openDlg('dl_realign', 'Please select two sets to realign');
+
             if(Object.keys(ic.structures).length < 2) {
                 alert("At least two structuresare required for alignment...");
                 return;
@@ -60196,15 +60255,14 @@ class Events {
             if($("#" + me.pre + "atomsCustomRealign").length) {
                 $("#" + me.pre + "atomsCustomRealign").html(definedAtomsHtml);
             }
-            //if($("#" + me.pre + "atomsCustomRealign2").length) {
-            //    $("#" + me.pre + "atomsCustomRealign2").html(definedAtomsHtml);
-            //}
-            if(ic.bRender) me.htmlCls.dialogCls.openDlg('dl_realign', 'Please select two sets to realign');
+            
             $("#" + me.pre + "atomsCustomRealign").resizable();
             //$("#" + me.pre + "atomsCustomRealign2").resizable();
         });
 
         me.myEventCls.onIds("#" + me.pre + "mn2_realignonstruct", "click", function(e) { let ic = me.icn3d;
+            if(ic.bRender) me.htmlCls.dialogCls.openDlg('dl_realignbystruct', 'Please select two sets to realign');
+
             if(Object.keys(ic.structures).length < 2) {
                 alert("At least two structuresare required for alignment...");
                 return;
@@ -60219,10 +60277,7 @@ class Events {
             if($("#" + me.pre + "atomsCustomRealignByStruct").length) {
                 $("#" + me.pre + "atomsCustomRealignByStruct").html(definedAtomsHtml);
             }
-            //if($("#" + me.pre + "atomsCustomRealign2").length) {
-            //    $("#" + me.pre + "atomsCustomRealign2").html(definedAtomsHtml);
-            //}
-            if(ic.bRender) me.htmlCls.dialogCls.openDlg('dl_realignbystruct', 'Please select two sets to realign');
+            
             $("#" + me.pre + "atomsCustomRealignByStruct").resizable();
             //$("#" + me.pre + "atomsCustomRealign2").resizable();
         });
@@ -60531,34 +60586,99 @@ class Events {
           });
     //    },
     //    clickReload_chainalign: function() {
-        me.myEventCls.onIds("#" + me.pre + "reload_chainalign", "click", function(e) { me.icn3d;
+/*        
+        me.myEventCls.onIds("#" + me.pre + "reload_chainalign", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
 
-           let result = thisClass.getAlignParas();
+           let alignment = $("#" + me.pre + "chainalignids").val();
+           let idArray = alignment.split(',');
+           let alignment_final = '';
+           for(let i = 0, il = idArray.length; i < il; ++i) {
+               alignment_final += (idArray[i].indexOf('_') != -1) ? idArray[i] : idArray[i] + '_A'; // AlphaFold ID
+               if(i < il - 1) alignment_final += ',';
+           }
+           let resalign = $("#" + me.pre + "resalignids").val();
+           let predefinedres = $("#" + me.pre + "predefinedres").val().trim().replace(/\n/g, '; ');
+           if(predefinedres && alignment_final.split(',').length - 1 != predefinedres.split('; ').length) {
+               alert("Please make sure the number of chains and the lines of predefined residues are the same...");
+               return;
+           }
 
-           me.htmlCls.clickMenuCls.setLogCmd("load chains " + result.alignment + " | residues " + result.resalign + " | resdef " + result.predefinedres, false);
-           window.open(hostUrl + '?chainalign=' + result.alignment + '&resnum=' + result.resalign + '&resdef=' + result.predefinedres + '&showalignseq=1', '_blank');
+           me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " | residues " + resalign + " | resdef " + predefinedres, false);
+           window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=' + resalign + '&resdef=' + predefinedres + '&showalignseq=1', '_blank');
         });
+*/
 
         me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym", "click", function(e) { me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
 
-           let result = thisClass.getAlignParas();
+           let alignment = $("#" + me.pre + "chainalignids").val();
+           let idArray = alignment.split(',');
+           let alignment_final = '';
+           for(let i = 0, il = idArray.length; i < il; ++i) {
+               alignment_final += (idArray[i].indexOf('_') != -1) ? idArray[i] : idArray[i] + '_A'; // AlphaFold ID
+               if(i < il - 1) alignment_final += ',';
+           }
 
-           me.htmlCls.clickMenuCls.setLogCmd("load chains " + result.alignment + " on asymmetric unit | residues " + result.resalign + " | resdef " + result.predefinedres, false);
-           window.open(hostUrl + '?chainalign=' + result.alignment + '&resnum=' + result.resalign + '&resdef=' + result.predefinedres + '&showalignseq=1&bu=0', '_blank');
+           me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues | resdef ", false);
+           window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=&resdef=&showalignseq=1&bu=0', '_blank');
         });
 
+        me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym2", "click", function(e) { me.icn3d;
+            e.preventDefault();
+            if(!me.cfg.notebook) dialog.dialog( "close" );
+ 
+            let alignment = $("#" + me.pre + "chainalignids2").val();
+            let idArray = alignment.split(',');
+            let alignment_final = '';
+            for(let i = 0, il = idArray.length; i < il; ++i) {
+                alignment_final += (idArray[i].indexOf('_') != -1) ? idArray[i] : idArray[i] + '_A'; // AlphaFold ID
+                if(i < il - 1) alignment_final += ',';
+            }
+            let resalign = $("#" + me.pre + "resalignids").val();
+ 
+            me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues " + resalign + " | resdef ", false);
+            window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=' + resalign + '&resdef=&showalignseq=1&bu=0', '_blank');
+         });
+
+         me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym3", "click", function(e) { me.icn3d;
+            e.preventDefault();
+            if(!me.cfg.notebook) dialog.dialog( "close" );
+ 
+            let alignment = $("#" + me.pre + "chainalignids3").val();
+            let idArray = alignment.split(',');
+            let alignment_final = '';
+            for(let i = 0, il = idArray.length; i < il; ++i) {
+                alignment_final += (idArray[i].indexOf('_') != -1) ? idArray[i] : idArray[i] + '_A'; // AlphaFold ID
+                if(i < il - 1) alignment_final += ',';
+            }
+
+            let predefinedres = $("#" + me.pre + "predefinedres").val().trim().replace(/\n/g, '; ');
+            if(predefinedres && alignment_final.split(',').length - 1 != predefinedres.split('; ').length) {
+                alert("Please make sure the number of chains and the lines of predefined residues are the same...");
+                return;
+            }
+ 
+            me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues | resdef " + predefinedres, false);
+            window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=&resdef=' + predefinedres + '&showalignseq=1&bu=0', '_blank');
+         });
+
         me.myEventCls.onIds("#" + me.pre + "reload_chainalign_tmalign", "click", function(e) { me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
 
-            let result = thisClass.getAlignParas();
+            let alignment = $("#" + me.pre + "chainalignids").val();
+            let idArray = alignment.split(',');
+            let alignment_final = '';
+            for(let i = 0, il = idArray.length; i < il; ++i) {
+                alignment_final += (idArray[i].indexOf('_') != -1) ? idArray[i] : idArray[i] + '_A'; // AlphaFold ID
+                if(i < il - 1) alignment_final += ',';
+            }
  
-            me.htmlCls.clickMenuCls.setLogCmd("load chains " + result.alignment + " on asymmetric unit | residues " + result.resalign + " | resdef " + result.predefinedres + " | align tmalign", false);
-            window.open(hostUrl + '?chainalign=' + result.alignment + '&aligntool=tmalign&resnum=' + result.resalign + '&resdef=' + result.predefinedres + '&showalignseq=1&bu=0', '_blank');
+            me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues | resdef | align tmalign", false);
+            window.open(hostUrl + '?chainalign=' + alignment_final + '&aligntool=tmalign&resnum=&resdef=&showalignseq=1&bu=0', '_blank');
          });
 
         me.myEventCls.onIds("#" + me.pre + "reload_mutation_3d", "click", function(e) { me.icn3d;
@@ -61665,6 +61785,27 @@ class Events {
             let color = $("#" + me.pre + "colorcustom").val();
             picker.set('#' + color).enter();
         });
+
+        let picker2 = new CP(document.querySelector("#" + me.pre + "labelcolorall"));
+        picker2.on("change", function(color) {
+            this.target.value = color;
+        });
+        me.myEventCls.onIds("#" + me.pre + "labelcolorall", "input", function() {
+            let color = $("#" + me.pre + "labelcolorall").val();
+            picker2.set('#' + color).enter();
+        });
+        me.myEventCls.onIds("#" + me.pre + "labelcolorall", "keyup", function() {
+            let color = $("#" + me.pre + "labelcolorall").val();
+            picker2.set('#' + color).enter();
+        });
+        me.myEventCls.onIds("#" + me.pre + "labelcolorall", "paste", function() {
+            let color = $("#" + me.pre + "labelcolorall").val();
+            picker2.set('#' + color).enter();
+        });
+        me.myEventCls.onIds("#" + me.pre + "labelcolorall", "cut", function() {
+            let color = $("#" + me.pre + "labelcolorall").val();
+            picker2.set('#' + color).enter();
+        });    
     //    },
     //    clickApplypick_stabilizer_rm: function() {
         me.myEventCls.onIds("#" + me.pre + "applypick_stabilizer_rm", "click", function(e) { let ic = me.icn3d;
@@ -62939,7 +63080,7 @@ class SetHtml {
         return html;
     }
 
-    exportPqr() { let me = this.icn3dui, ic = me.icn3d;
+    exportPqr(bPdb) { let me = this.icn3dui, ic = me.icn3d;
        let ionHash = {};
        let atomHash = {};
     /*
@@ -62971,13 +63112,15 @@ class SetHtml {
            }
        }
 
+       let fileExt = (bPdb) ? 'pdb' : 'pqr';
        if(me.cfg.cid) {
           let pqrStr = '';
 ///          pqrStr += ic.saveFileCls.getPDBHeader();
-          pqrStr += ic.saveFileCls.getAtomPDB(atomHash, true) + ic.saveFileCls.getAtomPDB(ionHash, true);
+          let bPqr = (bPdb) ? false : true;
+          pqrStr += ic.saveFileCls.getAtomPDB(atomHash, bPqr) + ic.saveFileCls.getAtomPDB(ionHash, bPqr);
 
           let file_pref =(ic.inputid) ? ic.inputid : "custom";
-          ic.saveFileCls.saveFile(file_pref + '_icn3d.pqr', 'text', [pqrStr]);
+          ic.saveFileCls.saveFile(file_pref + '_icn3d.' + fileExt, 'text', [pqrStr]);
        }
        else {
            let bCalphaOnly = me.utilsCls.isCalphaPhosOnly(me.hashUtilsCls.hash2Atoms(atomHash, ic.atoms));
@@ -63013,8 +63156,40 @@ class SetHtml {
               success: function(data) {
                   let pqrStr = data;
 
+                  if(bPdb) {
+                    let lineArray = pqrStr.split('\n');
+
+                    let pdbStr = '';
+                    for(let i = 0, il = lineArray.length; i < il; ++i) {
+                        let line = lineArray[i];
+                        if(line.substr(0, 6) == 'ATOM  ' || line.substr(0, 6) == 'HETATM') {
+                            let atomName = line.substr(12, 4).trim();
+                            let elem;
+                            if(line.substr(0, 6) == 'ATOM  ') {
+                                elem = atomName.substr(0, 1);
+                            }
+                            else {
+                                let twochar = atomName.substr(0, 2);
+                                if(me.parasCls.vdwRadii.hasOwnProperty(twochar)) {
+                                    elem = twochar;
+                                }
+                                else {
+                                    elem = atomName.substr(0, 1);
+                                }
+                            }
+
+                            pdbStr += line.substr(0, 54) + '                      ' + elem.padStart(2, ' ') + '\n';
+                        }
+                        else {
+                            pdbStr += line + '\n';
+                        }
+                    }
+
+                    pqrStr = pdbStr;
+                  }
+
                   let file_pref =(ic.inputid) ? ic.inputid : "custom";
-                  ic.saveFileCls.saveFile(file_pref + '_icn3d_residues.pqr', 'text', [pqrStr]);
+                  ic.saveFileCls.saveFile(file_pref + '_icn3d_residues.' + fileExt, 'text', [pqrStr]);
               },
               error : function(xhr, textStatus, errorThrown ) {
                 this.tryCount++;
@@ -63379,7 +63554,8 @@ class Html {
     this.simulation = undefined;
 
     //this.baseUrl = "https://structure.ncbi.nlm.nih.gov/";
-    this.baseUrl = "https://www.ncbi.nlm.nih.gov/Structure/";
+    this.baseUrl = (window && window.location && window.location.hostname == 'structure.ncbi.nlm.nih.gov') 
+        ? "https://structure.ncbi.nlm.nih.gov/Structure/" : "https://www.ncbi.nlm.nih.gov/Structure/";
     this.divStr = "<div id='" + this.icn3dui.pre;
     this.divNowrapStr = "<div style='white-space:nowrap'>";
     this.spanNowrapStr = "<span style='white-space:nowrap'>";
@@ -66867,7 +67043,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.13.0';
+    this.REVISION = '3.13.2';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;