icn3d 3.12.9 → 3.13.0

package/icn3d.js

@@ -24787,6 +24787,7 @@ 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 +24803,32 @@ 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 +25200,7 @@ 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";
 
                 for(let index in ic.afChainIndexHash) {
                     let idArray = ic.afChainIndexHash[index].split('_');
@@ -25191,17 +25209,31 @@ 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 +25365,9 @@ 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 +25512,37 @@ 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 +25727,8 @@ 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 +25762,8 @@ 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 +25781,9 @@ 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 +25829,9 @@ 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 +25854,8 @@ 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 +25888,20 @@ 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 +27787,24 @@ 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 +27993,17 @@ 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 +28135,20 @@ 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
@@ -36199,7 +36292,7 @@ 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 +36662,7 @@ 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;
@@ -55639,10 +55732,10 @@ 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 +55782,7 @@ 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
@@ -55903,7 +55996,9 @@ class SetMenu {
 
         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>";
@@ -57687,10 +57782,10 @@ 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" };
@@ -58000,23 +58095,19 @@ 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_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 += "(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>";
 
@@ -58362,7 +58453,7 @@ 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 +58911,7 @@ 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 + "'>";
@@ -59016,6 +59107,24 @@ 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) {
+            var aaa = 1; //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;
@@ -59263,6 +59372,25 @@ 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;
@@ -59486,62 +59614,53 @@ 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;
            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 = '';
-           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) {
-               var aaa = 1; //alert("Please make sure the number of chains and the lines of predefined residues are the same...");
-               return;
-           }
+           let result = thisClass.getAlignParas();
 
-           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.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.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 = '';
-           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) {
-               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');
+           let result = thisClass.getAlignParas();
+
+           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.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();
+ 
+            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.myEventCls.onIds("#" + me.pre + "reload_mutation_3d", "click", function(e) { me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
@@ -65848,7 +65967,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.12.8';
+    this.REVISION = '3.13.0';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -66258,7 +66377,7 @@ 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);
     }