icn3d 3.12.8 → 3.13.2

package/icn3d.js

@@ -4227,7 +4227,11 @@ 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.
@@ -17450,7 +17454,7 @@ 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;
                             }
@@ -17459,11 +17463,29 @@ 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;
@@ -18944,7 +18966,7 @@ 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 = {};
 
@@ -19756,7 +19778,7 @@ 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);
 
@@ -20903,7 +20925,7 @@ 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
@@ -23918,13 +23940,13 @@ 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({
@@ -24787,6 +24809,7 @@ class RealignParser {
 
         let ajaxArray = [], chainidPairArray = [];
         let urlalign = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi";
+        let urltmalign = me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
         let structArray = Object.keys(struct2domain);
         for(let s = 0, sl = structArray.length; s < sl; ++s) {
             let struct1 = structArray[s];
@@ -24802,16 +24825,32 @@ class RealignParser {
                     for(let j = 0, jl = chainidArray2.length; j < jl; ++j) {
                         let chainid2 = chainidArray2[j];
 
-                        let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(struct2domain[struct1][chainid1]);
-                        let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(struct2domain[struct2][chainid2]);
-                      
-                        let alignAjax = $.ajax({
-                            url: urlalign,
-                            type: 'POST',
-                            data: {'domains1': jsonStr_q, 'domains2': jsonStr_t},
-                            dataType: 'jsonp',
-                            cache: true
-                        });
+                        let alignAjax;
+
+                        if(me.cfg.aligntool != 'tmalign') {
+                            let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(struct2domain[struct1][chainid1]);
+                            let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(struct2domain[struct2][chainid2]);
+                        
+                            alignAjax = $.ajax({
+                                url: urlalign,
+                                type: 'POST',
+                                data: {'domains1': jsonStr_q, 'domains2': jsonStr_t},
+                                dataType: 'jsonp',
+                                cache: true
+                            });
+                        }
+                        else {
+                            let pdb_target = ic.saveFileCls.getAtomPDB(struct2domain[struct1][chainid1]);
+                            let pdb_query = ic.saveFileCls.getAtomPDB(struct2domain[struct2][chainid2]);
+                        
+                            alignAjax = $.ajax({
+                                url: urltmalign,
+                                type: 'POST',
+                                data: {'pdb_query': pdb_query, 'pdb_target': pdb_target},
+                                dataType: 'jsonp',
+                                cache: true
+                            });                            
+                        }
 
                         ajaxArray.push(alignAjax);
                         chainidPairArray.push(chainid1 + ',' + chainid2); // chainid2 is target
@@ -25183,6 +25222,8 @@ class ChainalignParser {
                 // dynamicly align pairs in ic.afChainIndexHash
                 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('_');
@@ -25191,17 +25232,31 @@ class ChainalignParser {
                     mmdbid_t = idArray[2];
                     let chain_t = idArray[3];
 
-                    let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(ic.chains[mmdbid_q + '_' + chain_q]);
-
-                    let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(ic.chains[mmdbid_t + '_' + chain_t]);
-                        
-                    let alignAjax = $.ajax({
-                        url: urlalign,
-                        type: 'POST',
-                        data: {'domains1': jsonStr_q, 'domains2': jsonStr_t},
-                        dataType: 'jsonp',
-                        cache: true
-                    });
+                    let alignAjax;
+                    if(me.cfg.aligntool != 'tmalign') {
+                        let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(ic.chains[mmdbid_q + '_' + chain_q]);
+                        let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(ic.chains[mmdbid_t + '_' + chain_t]);
+                            
+                        alignAjax = $.ajax({
+                            url: urlalign,
+                            type: 'POST',
+                            data: {'domains1': jsonStr_q, 'domains2': jsonStr_t},
+                            dataType: 'jsonp',
+                            cache: true
+                        });
+                    }
+                    else {
+                        let pdb_query = ic.saveFileCls.getAtomPDB(ic.chains[mmdbid_q + '_' + chain_q]);
+                        let pdb_target= ic.saveFileCls.getAtomPDB(ic.chains[mmdbid_t + '_' + chain_t]);
+                            
+                        alignAjax = $.ajax({
+                            url: urltmalign,
+                            type: 'POST',
+                            data: {'pdb_query': pdb_query, 'pdb_target': pdb_target},
+                            dataType: 'jsonp',
+                            cache: true
+                        });                        
+                    }
 
                     ajaxArray.push(alignAjax);
                     indexArray.push(index - 1);
@@ -25333,6 +25388,9 @@ class ChainalignParser {
         // set trans and rotation matrix
         ic.t_trans_add = [];
         ic.q_trans_sub = [];
+
+        if(me.cfg.aligntool == 'tmalign') ic.q_trans_add = [];
+
         ic.q_rotation = [];
         ic.qt_start_end = [];
 
@@ -25477,30 +25535,37 @@ class ChainalignParser {
         for(let i = 0, il = chainidArray.length; i < il; ++i) {
             for(let serial in ic.chains[chainidArray[i]]) {
                 let atm = ic.atoms[serial];
-                //atm.coord = new THREE.Vector3(atm.coord[0], atm.coord[1], atm.coord[2]);
-                if(ic.q_rotation !== undefined && ic.t_trans_add.length > 0 && !me.cfg.resnum && !me.cfg.resdef) {
+                //if(ic.q_rotation !== undefined && ic.t_trans_add.length > 0 && !me.cfg.resnum && !me.cfg.resdef) {
+                if(ic.q_rotation !== undefined && !me.cfg.resnum && !me.cfg.resdef) {
                     atm = this.transformAtom(atm, index, alignType);
                 }
             }
         }
-
-
     }
 
-    transformAtom(atm, index, alignType) { let ic = this.icn3d; ic.icn3dui;
+    transformAtom(atm, index, alignType) { let  ic = this.icn3d, me = ic.icn3dui;
         if(alignType === 'target') ;
         else if(alignType === 'query') {
-            atm.coord.x -= ic.q_trans_sub[index].x;
-            atm.coord.y -= ic.q_trans_sub[index].y;
-            atm.coord.z -= ic.q_trans_sub[index].z;
+            if(me.cfg.aligntool != 'tmalign') {
+                atm.coord.x -= ic.q_trans_sub[index].x;
+                atm.coord.y -= ic.q_trans_sub[index].y;
+                atm.coord.z -= ic.q_trans_sub[index].z;
+            }
 
             let  x = atm.coord.x * ic.q_rotation[index].x1 + atm.coord.y * ic.q_rotation[index].y1 + atm.coord.z * ic.q_rotation[index].z1;
             let  y = atm.coord.x * ic.q_rotation[index].x2 + atm.coord.y * ic.q_rotation[index].y2 + atm.coord.z * ic.q_rotation[index].z2;
             let  z = atm.coord.x * ic.q_rotation[index].x3 + atm.coord.y * ic.q_rotation[index].y3 + atm.coord.z * ic.q_rotation[index].z3;
 
-            x -= ic.t_trans_add[index].x;
-            y -= ic.t_trans_add[index].y;
-            z -= ic.t_trans_add[index].z;
+            if(me.cfg.aligntool != 'tmalign') {
+                x -= ic.t_trans_add[index].x;
+                y -= ic.t_trans_add[index].y;
+                z -= ic.t_trans_add[index].z;
+            }
+            else {
+                x += ic.q_trans_add[index].x;
+                y += ic.q_trans_add[index].y;
+                z += ic.q_trans_add[index].z;
+            }
 
             atm.coord.x = x;
             atm.coord.y = y;
@@ -25685,7 +25750,8 @@ class ChainalignParser {
                 let  chainalignFinal = ic.mmdbid_q + "_" + ic.chain_q + "," + ic.mmdbid_t + "_" + ic.chain_t;
                 let domainalign = (domainArray.length > 0) ? domainArray[index] + "," + domainArray[0] : undefined;
 
-                if(ic.mmdbid_t.length == 4 && ic.mmdbid_q.length == 4) {
+                // TM-align (me.cfg.aligntool == 'tmalign') needs to input PDB
+                if(me.cfg.aligntool != 'tmalign' && ic.mmdbid_t.length == 4 && ic.mmdbid_q.length == 4) {
                     let  urlalign;
                     
                     if(domainArray.length > 0) {
@@ -25719,7 +25785,8 @@ class ChainalignParser {
           thisClass.parseChainAlignData(dataArray, alignArray, ic.mmdbid_t, ic.chain_t);
         })
         .fail(function() {
-            var aaa = 1; //alert("These chains can not be aligned by VAST server. You can specify the residue range and try it again...");
+            let serverName = (me.cfg.aligntool == 'tmalign') ? 'TM-align' : 'VAST';
+            var aaa = 1; //alert("These chains can not be aligned by " + serverName + ". You can specify the residue range and try it again...");
 //          thisClass.parseChainAlignData(arguments, alignArray, ic.mmdbid_t, ic.chain_t);
         });
     }
@@ -25737,6 +25804,9 @@ class ChainalignParser {
 
         ic.t_trans_add = [];
         ic.q_trans_sub = [];
+
+        if(me.cfg.aligntool == 'tmalign') ic.q_trans_add = [];
+
         ic.q_rotation = [];
         ic.qt_start_end = [];
 
@@ -25782,6 +25852,9 @@ class ChainalignParser {
                     // need to pass C-alpha coords and get transformation matrix from backend
                     ic.t_trans_add[index-1] = {"x":0, "y":0, "z":0};
                     ic.q_trans_sub[index-1] = {"x":0, "y":0, "z":0};
+
+                    if(me.cfg.aligntool == 'tmalign') ic.q_trans_add[index-1] = {"x":0, "y":0, "z":0};
+
                     ic.q_rotation[index-1] = {"x1":1, "y1":0, "z1":0, "x2":0, "y2":1, "z2":0, "x3":0, "y3":0, "z3":1};
                     ic.qt_start_end[index-1] = undefined;
                 }
@@ -25804,7 +25877,8 @@ class ChainalignParser {
     processAlign(align, index, queryData, bEqualMmdbid, bEqualChain, bNoAlert) { let  ic = this.icn3d, me = ic.icn3dui;
         let bAligned = false;
         if((!align || align.length == 0) && !bNoAlert) {
-            var aaa = 1; //alert("These chains can not be aligned by VAST server.");
+            let serverName = (me.cfg.aligntool == 'tmalign') ? 'TM-align' : 'VAST';
+            var aaa = 1; //alert("These chains can not be aligned by " + serverName + ".");
             return bAligned;
         }
 
@@ -25837,13 +25911,20 @@ class ChainalignParser {
                 */
                 ic.t_trans_add[index] = align[0].t_trans_add;
                 ic.q_trans_sub[index] = align[0].q_trans_sub;
+
+                if(me.cfg.aligntool == 'tmalign') ic.q_trans_add[index] = align[0].q_trans_add;
+
                 ic.q_rotation[index] = align[0].q_rotation;
                 ic.qt_start_end[index] = align[0].segs;
 
                 let  rmsd = align[0].super_rmsd;
 
-                me.htmlCls.clickMenuCls.setLogCmd("RMSD of alignment: " + rmsd.toPrecision(4), false);
-                $("#" + ic.pre + "realignrmsd").val(rmsd.toPrecision(4));
+                let logStr = "alignment RMSD: " + rmsd.toPrecision(4);
+                if(me.cfg.aligntool == 'tmalign') logStr += "; TM-score: " + align[0].score.toPrecision(4);
+                me.htmlCls.clickMenuCls.setLogCmd(logStr, false);
+                let html = "<br><b>Alignment RMSD</b>: " + rmsd.toPrecision(4) + " &#8491;<br>";
+                if(me.cfg.aligntool == 'tmalign') html += "<b>TM-score</b>: " + align[0].score.toPrecision(4) + "<br><br>";
+                $("#" + ic.pre + "dl_rmsd").html(html);
                 if(!me.cfg.bSidebyside) me.htmlCls.dialogCls.openDlg('dl_rmsd', 'RMSD of alignment');
 
                 bAligned = true;
@@ -27729,6 +27810,24 @@ class LoadScript {
 
             return;
           }
+          else if(ic.commands[i].trim().indexOf('realign on tmalign') == 0) {
+            let  strArray = ic.commands[i].split("|||");
+            let  command = strArray[0].trim();
+
+            let  paraArray = command.split(' | ');
+            if(paraArray.length == 2) {
+                let  nameArray = paraArray[1].split(',');
+                ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
+            }
+
+            me.cfg.aligntool = 'tmalign';
+
+            $.when(thisClass.applyCommandRealignByStruct(command)).then(function() {
+               thisClass.execCommandsBase(i + 1, end, steps);
+            });
+
+            return;
+          }
           else if(ic.commands[i].trim().indexOf('graph interaction pairs') == 0) {
             let  strArray = ic.commands[i].split("|||");
             let  command = strArray[0].trim();
@@ -27917,6 +28016,17 @@ class LoadScript {
                         }
                         thisClass.applyCommandRealignByStruct(lastCommand);
                     }
+                    else if(lastCommand.indexOf('realign on tmalign') == 0) {
+                        let  paraArray = lastCommand.split(' | ');
+                        if(paraArray.length == 2) {
+                            let  nameArray = paraArray[1].split(',');
+                            ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
+                        }
+                        
+                        me.cfg.aligntool = 'tmalign';
+
+                        thisClass.applyCommandRealignByStruct(lastCommand);
+                    }
                     else if(lastCommand.indexOf('graph interaction pairs') == 0) {
                         thisClass.applyCommandGraphinteraction(lastCommand);
                     }
@@ -28048,14 +28158,20 @@ class LoadScript {
           ic.alignParserCls.downloadAlignment(id);
         }
         else if(command.indexOf('load chainalignment') !== -1) {
-          //load chainalignment [id] | resnum [resnum] | parameters [inpara]
+          //load chainalignment [id] | resnum [resnum] | resdef [resnum] | aligntool [aligntool] | parameters [inpara]
           let  urlArray = command.split(" | ");
-          if(urlArray[1].indexOf('resnum') != -1) {
-              me.cfg.resnum = urlArray[1].substr(urlArray[1].indexOf('resnum') + 7);
+          if(urlArray.length > 1 && urlArray[1].indexOf('resnum') != -1) {
+                me.cfg.resnum = urlArray[1].substr(urlArray[1].indexOf('resnum') + 7);
+          }
+          if(urlArray.length > 2 && urlArray[2].indexOf('resdef') != -1) {
+                me.cfg.resdef = urlArray[2].substr(urlArray[1].indexOf('resdef') + 7);
+          }
+          if(urlArray.length > 3 && urlArray[3].indexOf('aligntool') != -1) {
+                me.cfg.aligntool = urlArray[3].substr(urlArray[1].indexOf('aligntool') + 10);
           }
 
           me.cfg.chainalign = id;
-          ic.chainalignParserCls.downloadChainalignment(id, me.cfg.resnum);
+          ic.chainalignParserCls.downloadChainalignment(id, me.cfg.resnum, me.cfg.resdef);
         }
         else if(command.indexOf('load url') !== -1) {
             let  typeStr = load_parameters[1]; // type pdb
@@ -28647,7 +28763,7 @@ 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];
@@ -31684,7 +31800,7 @@ 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
@@ -31730,7 +31846,7 @@ 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;
 
@@ -35512,11 +35628,15 @@ 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;
                 }
@@ -35524,9 +35644,9 @@ 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;
@@ -35534,6 +35654,9 @@ 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);
@@ -35580,7 +35703,7 @@ 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;
             }
 
@@ -36199,7 +36322,7 @@ class ParserUtils {
 
               if(rmsd) {
                   me.htmlCls.clickMenuCls.setLogCmd("realignment RMSD: " + rmsd.toPrecision(4), false);
-                  $("#" + ic.pre + "realignrmsd").val(rmsd.toPrecision(4));
+                  $("#" + ic.pre + "dl_rmsd").html("<br><b>Realignment RMSD</b>: " + rmsd.toPrecision(4) + " &#8491;<br><br>");
                   if(!me.cfg.bSidebyside) me.htmlCls.dialogCls.openDlg('dl_rmsd', 'Realignment RMSD');
               }
 
@@ -36569,7 +36692,7 @@ class ParserUtils {
                   let  rmsd = ic.rmsd_supr.rmsd;
 
                   me.htmlCls.clickMenuCls.setLogCmd("RMSD of alignment to OPM: " + rmsd.toPrecision(4), false);
-                  $("#" + ic.pre + "realignrmsd").val(rmsd.toPrecision(4));
+                  $("#" + ic.pre + "dl_rmsd").html("<br><b>RMSD of alignment to OPM</b>: " + rmsd.toPrecision(4) + " &#8491;<br><br>");
                   if(!me.cfg.bSidebyside) me.htmlCls.dialogCls.openDlg('dl_rmsd', 'RMSD of alignment to OPM');
 
                   let  dxymaxsq = 0;
@@ -36818,7 +36941,7 @@ 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();
@@ -37824,9 +37947,11 @@ 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 = {};
@@ -37867,6 +37992,7 @@ 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;
                 }
@@ -38136,7 +38262,7 @@ class ShowAnno {
                     return;
                 }
                 thisClass.enableHlSeq();
-                console.log( "No data were found for the protein " + chnidBaseArray + "..." );
+                if(!me.bNode) console.log( "No 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);
@@ -38262,7 +38388,7 @@ class ShowAnno {
                 }
             }
             else {
-                console.log( "No data were found for the protein " + chnid + "..." );
+                if(!me.bNode) console.log( "No data were found for the protein " + chnid + "..." );
                 ic.showSeqCls.setAlternativeSeq(chnid, chnidBase);
             }
             if(me.cfg.blast_rep_id != chnid) {
@@ -39655,11 +39781,11 @@ 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;
         }
@@ -39694,7 +39820,7 @@ 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) {
       /*      
@@ -39713,7 +39839,7 @@ 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;
                     }
@@ -44519,7 +44645,8 @@ 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';
@@ -44573,7 +44700,7 @@ 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;
@@ -44766,7 +44893,8 @@ 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';
@@ -44814,7 +44942,7 @@ 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;
@@ -44911,7 +45039,7 @@ 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';
 
@@ -53293,9 +53421,17 @@ 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');
         });
@@ -53474,6 +53610,12 @@ 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);
@@ -55639,10 +55781,10 @@ class SetMenu {
         return "<div style='margin:3px 0px 0px 10px;'><button style='-webkit-appearance:" + buttonStyle + "; height:36px;" + bkgdColor + "' id='" + me.pre + id + "'><span style='white-space:nowrap;" + color + "' class='icn3d-commandTitle' title='" + title + "'>" + text + "</span></button></div>";
     }
 
-    setIcon(iconType, id, title, iconStyle, url, bText) { let me = this.icn3dui;
+    setIcon(iconType, id, title, iconStyle, url, bText, bHighlight) { let me = this.icn3dui;
         if(me.bNode) return '';
 
-        let color = 'color:#1c94c4; ';
+        let color = (bHighlight) ? 'color:#f8b84e; ' : 'color:#1c94c4; ';
         let bkgdColor = ' background-color:#EEE; ';
         let cssCursor = (iconType == 'text') ? '' : 'cursor:pointer;';
 
@@ -55689,7 +55831,7 @@ class SetMenu {
         // View menu
         html += tdStrBorder + this.setIcon(iconType, 'show_selected', 'View Selection', 'eye') + "</td>";
         html += tdStr + this.setIcon(iconType, 'tool_selectedcenter', 'Zoom in Selection', 'search-plus') + "</td>";
-        html += tdStr + this.setIcon(iconType, 'alternate', "Alternate the Structures by keying the letter 'a'", 'a', undefined, true) + "</td>";
+        html += tdStr + this.setIcon(iconType, 'alternate', "Alternate the Structures by keying the letter 'a'", 'a', undefined, true, true) + "</td>";
         html += tdStr + this.setIcon(iconType, 'tool_resetOrientation', 'Reset Orientation', 'undo-alt') + "</td>";
 
         // Style menu
@@ -55888,22 +56030,31 @@ 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>";
 
         html += "<li id='" + me.pre + "mn2_realignWrap'><span>Realign Selection</span>";
         html += "<ul>";
-        html += me.htmlCls.setHtmlCls.getRadio('mn2_realign', 'mn2_realignonstruct', 'by Structure Alignment ' + me.htmlCls.wifiStr, true);
+
+        html += me.htmlCls.setHtmlCls.getRadio('mn2_realign', 'mn2_realignonstruct', 'by Structure Alignment ' + me.htmlCls.wifiStr);
+
         html += me.htmlCls.setHtmlCls.getRadio('mn2_realign', 'mn2_realignonseqalign', 'by Sequence Alignment ' + me.htmlCls.wifiStr);
         html += me.htmlCls.setHtmlCls.getRadio('mn2_realign', 'mn2_realignresbyres', 'Residue by Residue');
         html += "</ul>";
@@ -55970,6 +56121,7 @@ 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');
@@ -57687,10 +57839,10 @@ class Dialog {
                     height = 500;
                 }
                 else if(id === me.pre + 'dl_rmsd') {
-                    position ={ my: "right top", at: "right top", of: "#" + me.pre + "canvas", collision: "none" };
+                    position ={ my: "left bottom", at: "left+20 bottom-20", of: "#" + me.pre + "canvas", collision: "none" };
                 }
                 else if(id === me.pre + 'dl_legend') {
-                    position ={ my: "right top", at: "right-20 top+60", of: "#" + me.pre + "canvas", collision: "none" };
+                    position ={ my: "left bottom", at: "left+20 bottom-20", of: "#" + me.pre + "canvas", collision: "none" };
                 }
                 else if(id === me.pre + 'dl_symd') {
                     position ={ my: "left top", at: "right-200 bottom-200", of: "#" + me.pre + "canvas", collision: "none" };
@@ -58000,29 +58152,43 @@ class SetDialog {
 
         html += me.htmlCls.divStr + "dl_alignaf' class='" + dialogClass + "'>";
         html += "Enter two <a href='https://alphafold.ebi.ac.uk/' target='_blank'>AlphaFold Uniprot</a> IDs: <br/><br/>ID1: " + me.htmlCls.inputTextStr + "id='" + me.pre + "alignafid1' value='P41327' size=8>" + me.htmlCls.space3 + me.htmlCls.space3 + "ID2: " + me.htmlCls.inputTextStr + "id='" + me.pre + "alignafid2' value='P41331' size=8><br/><br/>";
-        html += me.htmlCls.buttonStr + "reload_alignaf'>Align</button>";
+        html += me.htmlCls.buttonStr + "reload_alignaf_tmalign'>Align with TM-align</button>" + me.htmlCls.buttonStr + "reload_alignaf' style='margin-left:30px'>Align with VAST</button>";
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_chainalign' class='" + dialogClass + "'>";
-    /*
-        html += "Enter the PDB chain IDs in the form of pdbid_chain(e.g., 1HHO_A, case sensitive): <br/><br/>ID1: " + me.htmlCls.inputTextStr + "id='" + me.pre + "chainalignid1' value='1HHO_A' size=8>" + me.htmlCls.space3 + me.htmlCls.space3 + "ID2: " + me.htmlCls.inputTextStr + "id='" + me.pre + "chainalignid2' value='4N7N_A' size=8><br/><br/>";
-        html += me.htmlCls.buttonStr + "reload_chainalign'>Align</button><br/><br/>";
-        html += "<div style='width:450px'>(Note: To align chains in custom PDB files, you could concatenate PDB files in a single PDB file with the separation line \"ENDMDL\". Then load it in \"Open File > PDB File\" in the \"File\" menu and click \"View Sequences & Annotations\" in the \"Window\" menu. Finally select two chains in the sequence window and click \"Realign Selection\" in the \"File\" menu.)</div>";
-        html += "</div>";
-    */
         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'><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'>";
@@ -58362,7 +58528,7 @@ class SetDialog {
         html += "<div style='text-indent:1.1em'><select id='" + me.pre + "atomsCustomRealignByStruct' multiple size='5' style='min-width:130px;'>";
         html += "</select></div>";
 
-        html += "<div>2. " + me.htmlCls.buttonStr + "applyRealignByStruct'>Realign by Structure</button></div><br>";
+        html += "<div>2. " + me.htmlCls.buttonStr + "applyRealignByStruct_tmalign'>Realign with TM-align</button>" + me.htmlCls.buttonStr + "applyRealignByStruct' style='margin-left:30px'>Realign with VAST</button></div><br>";
         html += "</div>";
 
 
@@ -58820,7 +58986,7 @@ class SetDialog {
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_rmsd' class='" + dialogClass + "'>";
-        html += "<br><b>Alignment RMSD</b>: " + me.htmlCls.inputTextStr + "id='" + me.pre + "realignrmsd' value='35' size='10'>&#8491;<br><br>";
+        
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_buriedarea' class='" + dialogClass + "'>";
@@ -59006,7 +59172,7 @@ 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 += $("#" + id).html();
         let idArray = id.split('_');
@@ -59172,6 +59338,8 @@ class Events {
     //    },
     //    clickRealignonseqalign: function() {
         me.myEventCls.onIds("#" + me.pre + "mn2_realignonseqalign", "click", function(e) { let ic = me.icn3d;
+            if(ic.bRender) me.htmlCls.dialogCls.openDlg('dl_realign', 'Please select two sets to realign');
+
             if(Object.keys(ic.structures).length < 2) {
                 var aaa = 1; //alert("At least two structuresare required for alignment...");
                 return;
@@ -59187,15 +59355,14 @@ class Events {
             if($("#" + 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) {
                 var aaa = 1; //alert("At least two structuresare required for alignment...");
                 return;
@@ -59210,10 +59377,7 @@ 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();
         });
@@ -59263,6 +59427,25 @@ class Events {
                 me.htmlCls.clickMenuCls.setLogCmd("realign on structure align", true);
             }
          });
+
+         me.myEventCls.onIds("#" + me.pre + "applyRealignByStruct_tmalign", "click", function(e) { let ic = me.icn3d;
+            e.preventDefault();
+            if(!me.cfg.notebook) dialog.dialog( "close" );
+            let nameArray = $("#" + me.pre + "atomsCustomRealignByStruct").val();
+            if(nameArray.length > 0) {
+                ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
+            }
+
+            me.cfg.aligntool = 'tmalign';
+ 
+            ic.realignParserCls.realignOnStructAlign();
+            if(nameArray.length > 0) {
+                me.htmlCls.clickMenuCls.setLogCmd("realign on tmalign | " + nameArray, true);
+            }
+            else {
+                me.htmlCls.clickMenuCls.setLogCmd("realign on tmalign", true);
+            }
+         });
     //    },
 
         me.myEventCls.onIds("#" + me.pre + "applyColorSpectrumBySets", "click", function(e) { let ic = me.icn3d;
@@ -59486,19 +59669,28 @@ class Events {
             window.open(hostUrl + '?align=' + alignment + '&showalignseq=1&atype=0&bu=1', '_blank');
          });
 
-         me.myEventCls.onIds("#" + me.pre + "reload_alignaf", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_alignaf", "click", function(e) { me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
             let alignment = $("#" + me.pre + "alignafid1").val() + "_A," + $("#" + me.pre + "alignafid2").val() + "_A";
             me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment + " | residues | resdef ", false);
             window.open(hostUrl + '?chainalign=' + alignment + '&resnum=&resdef=&showalignseq=1', '_blank');
           });
+
+        me.myEventCls.onIds("#" + me.pre + "reload_alignaf_tmalign", "click", function(e) { me.icn3d;
+            e.preventDefault();
+            if(!me.cfg.notebook) dialog.dialog( "close" );
+            let alignment = $("#" + me.pre + "alignafid1").val() + "_A," + $("#" + me.pre + "alignafid2").val() + "_A";
+            me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment + " | residues | resdef | align tmalign", false);
+            window.open(hostUrl + '?chainalign=' + alignment + '&aligntool=tmalign&resnum=&resdef=&showalignseq=1', '_blank');
+          });
     //    },
     //    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 alignment = $("#" + me.pre + "chainalignid1").val() + "," + $("#" + me.pre + "chainalignid2").val();
+
            let alignment = $("#" + me.pre + "chainalignids").val();
            let idArray = alignment.split(',');
            let alignment_final = '';
@@ -59508,21 +59700,20 @@ class Events {
            }
            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) {
                var aaa = 1; //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 + " | residues " + resalign + " | resdef " + predefinedres, false);
-           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?chainalign=' + alignment + '&resnum=' + resalign + '&resdef=' + predefinedres + '&showalignseq=1', '_blank');
            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 alignment = $("#" + me.pre + "chainalignid1").val() + "," + $("#" + me.pre + "chainalignid2").val();
+
            let alignment = $("#" + me.pre + "chainalignids").val();
            let idArray = alignment.split(',');
            let alignment_final = '';
@@ -59530,18 +59721,66 @@ class Events {
                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) {
-               var aaa = 1; //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 " + resalign + " | resdef " + predefinedres, false);
-           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?chainalign=' + alignment + '&resnum=' + resalign + '&resdef=' + predefinedres + '&showalignseq=1&bu=0', '_blank');
-           window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=' + resalign + '&resdef=' + 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) {
+                var aaa = 1; //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 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 " + 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;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
@@ -60646,6 +60885,27 @@ 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;
@@ -61920,7 +62180,7 @@ 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 = {};
     /*
@@ -61952,13 +62212,15 @@ 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));
@@ -61994,8 +62256,40 @@ 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++;
@@ -62360,7 +62654,8 @@ 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'>";
@@ -65848,7 +66143,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.12.8';
+    this.REVISION = '3.13.2';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -66258,7 +66553,7 @@ iCn3DUI.prototype.show3DStructure = function(pdbStr) { let me = this;
 
         ic.bChainAlign = true;
         ic.inputid = me.cfg.chainalign;
-        ic.loadCmd = 'load chainalignment ' + me.cfg.chainalign + ' | resnum ' + me.cfg.resnum + ' | resdef ' + me.cfg.resdef + ' | parameters ' + me.cfg.inpara;
+        ic.loadCmd = 'load chainalignment ' + me.cfg.chainalign + ' | resnum ' + me.cfg.resnum + ' | resdef ' + me.cfg.resdef + ' | aligntool ' + me.cfg.aligntool + ' | parameters ' + me.cfg.inpara;
         me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
         ic.chainalignParserCls.downloadChainalignment(me.cfg.chainalign, me.cfg.resnum, me.cfg.resdef);
     }