icn3d 3.12.7 → 3.13.0

package/icn3d.module.js

@@ -14310,15 +14310,7 @@ class DefinedSets {
                 dAtoms = me.hashUtilsCls.unionHash(dAtoms, ic.alnChains[alignChain]);
             }
 
-            let  residuesHash = {}, chains = {};
-            for(let i in dAtoms) {
-                let  atom = ic.atoms[i];
-
-                let  chainid = atom.structure + '_' + atom.chain;
-                let  resid = chainid + '_' + atom.resi;
-                residuesHash[resid] = 1;
-                chains[chainid] = 1;
-            }
+            let  residuesHash = ic.firstAtomObjCls.getResiduesFromAtoms(dAtoms);
 
             let  commandname = 'protein_aligned';
             let  commanddescr = 'aligned protein and nucleotides';
@@ -23538,8 +23530,11 @@ class Dssp {
           thisClass.parseDsspData(dataArray, struArray, bAppend);
       })
       .fail(function() {
+          console.log("DSSP calculation had a problem with this structure " + struArray[0] + "...");
+
           ic.pdbParserCls.loadPdbDataRender(bAppend);
 
+          if(ic.deferredMmdbaf !== undefined) ic.deferredMmdbaf.resolve();
           if(ic.deferredSecondary !== undefined) ic.deferredSecondary.resolve();
       });
     }
@@ -23773,6 +23768,9 @@ class PdbParser {
                 thisClass.loadPdbData(data);
                 ic.loadScriptCls.loadScript(command);
             }
+            else if(type === 'mmcif') {
+                ic.mmcifParserCls.parseMmcifData(data, undefined, command);
+            }
             else if(type === 'mol2') {
                 ic.mol2ParserCls.loadMol2Data(data);
             }
@@ -25378,6 +25376,8 @@ class RealignParser {
 
         ic.selectionCls.saveSelection(name, name);
 
+        me.htmlCls.clickMenuCls.setLogCmd("realign", true);
+
         let  structHash = {}, struct2chain = {};
         ic.realignResid = {};
         let  lastStruResi = '';
@@ -25488,7 +25488,7 @@ class RealignParser {
 
       // align seq
       ic.hAtoms = ic.chainalignParserCls.setMsa(chainidArray);
-      
+
       ic.transformCls.zoominSelection();
 
       ic.chainalignParserCls.downloadChainalignmentPart3(undefined, chainidArray, ic.hAtoms);
@@ -25687,6 +25687,7 @@ 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];
@@ -25702,16 +25703,32 @@ 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
@@ -25792,6 +25809,8 @@ class RealignParser {
                     base_t = base;
                 }
                 else {
+                    let hAtoms = {};
+
                     predefinedResPair = predefinedResArray[i - 1].split(' | ');
 
                     let chainidpair = chainid_t + ',' + chainid;
@@ -25803,6 +25822,8 @@ class RealignParser {
                     resiArray = predefinedResPair[0].split(",");
                     result = thisClass.getSeqCoorResid(resiArray, chainid_t, base_t);
 
+                    hAtoms = me.hashUtilsCls.unionHash(hAtoms, result.hAtoms);
+
                     if(!struct2SeqHash[chainidpair][mmdbid_t]) struct2SeqHash[chainidpair][mmdbid_t] = '';
                     if(!struct2CoorHash[chainidpair][mmdbid_t]) struct2CoorHash[chainidpair][mmdbid_t] = [];
                     if(!struct2resid[chainidpair][mmdbid_t]) struct2resid[chainidpair][mmdbid_t] = [];
@@ -25814,6 +25835,7 @@ class RealignParser {
                     // slave
                     resiArray = predefinedResPair[1].split(",");
                     result = thisClass.getSeqCoorResid(resiArray, chainid, base); 
+                    hAtoms = me.hashUtilsCls.unionHash(hAtoms, result.hAtoms);
 
                     if(!struct2SeqHash[chainidpair][mmdbid]) struct2SeqHash[chainidpair][mmdbid] = '';
                     if(!struct2CoorHash[chainidpair][mmdbid]) struct2CoorHash[chainidpair][mmdbid] = [];
@@ -25822,6 +25844,18 @@ class RealignParser {
                     struct2SeqHash[chainidpair][mmdbid] += result.seq;
                     struct2CoorHash[chainidpair][mmdbid] = struct2CoorHash[chainidpair][mmdbid].concat(result.coor);
                     struct2resid[chainidpair][mmdbid] = struct2resid[chainidpair][mmdbid].concat(result.resid);
+
+                    // let  residueHash = ic.firstAtomObjCls.getResiduesFromAtoms(hAtoms);
+                    // let  residueArray = Object.keys(residueHash);
+        
+                    // let  commandname = chainidpair;
+                    // let  commanddescr = 'aligned ' + chainidpair;
+                    // let  select = "select " + ic.resid2specCls.residueids2spec(residueArray);
+        
+                    // ic.selectionCls.addCustomSelection(residueArray, commandname, commanddescr, select, true);
+        
+                    // me.htmlCls.clickMenuCls.setLogCmd(select + " | name " + commandname, true);
+                    // me.htmlCls.clickMenuCls.setLogCmd("realign", true);
                 }
             }
             else {
@@ -25921,6 +25955,7 @@ class RealignParser {
 
     getSeqCoorResid(resiArray, chainid, base) { let  ic = this.icn3d, me = ic.icn3dui;
         let seq = '', coorArray = [], residArray = [];
+        let hAtoms = {};
 
         for(let j = 0, jl = resiArray.length; j < jl; ++j) {
             if(resiArray[j].indexOf('-') != -1) {
@@ -25970,7 +26005,11 @@ class RealignParser {
             }
         }
 
-        return {seq: seq, coor: coorArray, resid: residArray};
+        for(let i = 0, il = residArray.length; i < il; ++i) {
+            hAtoms = me.hashUtilsCls.unionHash(hAtoms, ic.residues[residArray[i]]);
+        }
+
+        return {seq: seq, coor: coorArray, resid: residArray, hAtoms: hAtoms};
     }
 
     getResCoorArray(resid) { let ic = this.icn3d; ic.icn3dui;
@@ -26061,6 +26100,7 @@ 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('_');
@@ -26069,17 +26109,31 @@ 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);
@@ -26211,6 +26265,9 @@ 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 = [];
 
@@ -26355,30 +26412,37 @@ 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;
@@ -26410,17 +26474,12 @@ class ChainalignParser {
         //ic.hAtoms = hAtoms;
         ic.hAtoms = me.hashUtilsCls.cloneHash(hAtoms);
         ic.dAtoms = me.hashUtilsCls.cloneHash(hAtoms);
-
+        
         ic.ParserUtilsCls.renderStructure();
 
         //if(ic.chainidArray.length > 2) {
         if(chainidArray.length > 2) {
-            let  residuesHash = {};
-            for(let i in hAtoms) {
-                let  atom = ic.atoms[i];
-                let  resid = atom.structure + '_' + atom.chain + '_' + atom.resi;
-                residuesHash[resid] = 1;
-            }
+            let  residuesHash = ic.firstAtomObjCls.getResiduesFromAtoms(hAtoms);
 
             let  commandname = 'protein_aligned';
             let  commanddescr = 'protein aligned';
@@ -26456,18 +26515,10 @@ class ChainalignParser {
         //if(me.deferred !== undefined) me.deferred.resolve(); if(ic.deferred2 !== undefined) ic.deferred2.resolve();
     }
 
-    downloadChainalignment(chainalign, resnum, resdef) { let  ic = this.icn3d, me = ic.icn3dui;
-        let  thisClass = this;
-
-        ic.opts['proteins'] = 'c alpha trace';
-
-        let  alignArray = chainalign.split(',');
-        let domainArray = (me.cfg.domainids) ? me.cfg.domainids.split(',') : [];
-        if(domainArray.length < alignArray.length) domainArray = [];
-
+    addPostfixForChainids(chainidArray) { let ic = this.icn3d; ic.icn3dui;
         let struct2cnt = {};
-        for(let i = 0, il = alignArray.length; i < il; ++i) {
-            let  chainid = alignArray[i];
+        for(let i = 0, il = chainidArray.length; i < il; ++i) {
+            let  chainid = chainidArray[i];
             let  pos = chainid.indexOf('_');
             let struct = chainid.substr(0, pos).toUpperCase();
             if(!struct2cnt.hasOwnProperty(struct)) {
@@ -26479,10 +26530,22 @@ class ChainalignParser {
 
             struct = (struct2cnt[struct] == 1) ? struct : struct + struct2cnt[struct];
 
-            alignArray[i] = struct + chainid.substr(pos);
+            chainidArray[i] = struct + chainid.substr(pos);
         }
 
-        ic.chainidArray = alignArray;
+        return chainidArray;
+    }
+
+    downloadChainalignment(chainalign, resnum, resdef) { let  ic = this.icn3d, me = ic.icn3dui;
+        let  thisClass = this;
+
+        ic.opts['proteins'] = 'c alpha trace';
+
+        let  alignArray = chainalign.split(',');
+        let domainArray = (me.cfg.domainids) ? me.cfg.domainids.split(',') : [];
+        if(domainArray.length < alignArray.length) domainArray = [];
+
+        ic.chainidArray = this.addPostfixForChainids(alignArray);
 
         let  pos1 = alignArray[0].indexOf('_');
         ic.mmdbid_t = alignArray[0].substr(0, pos1).toUpperCase();
@@ -26564,7 +26627,8 @@ 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) {
@@ -26598,7 +26662,8 @@ class ChainalignParser {
           thisClass.parseChainAlignData(dataArray, alignArray, ic.mmdbid_t, ic.chain_t);
         })
         .fail(function() {
-            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';
+            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);
         });
     }
@@ -26616,6 +26681,9 @@ 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 = [];
 
@@ -26661,6 +26729,9 @@ 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;
                 }
@@ -26683,7 +26754,8 @@ 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) {
-            alert("These chains can not be aligned by VAST server.");
+            let serverName = (me.cfg.aligntool == 'tmalign') ? 'TM-align' : 'VAST';
+            alert("These chains can not be aligned by " + serverName + ".");
             return bAligned;
         }
 
@@ -26716,13 +26788,20 @@ 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;
@@ -26910,11 +26989,10 @@ class ChainalignParser {
         }
 
         // calculate secondary structures with applyCommandDssp
-        if(bQuery && me.cfg.masterchain) {
+        if(bQuery && me.cfg.matchedchains) {
             $.when(ic.pdbParserCls.applyCommandDssp(true)).then(function() {
                 let bRealign = true, bPredefined = true;
                 ic.realignParserCls.realignChainOnSeqAlign(undefined, ic.chainidArray, bRealign, bPredefined);
-
                 // reset annotations
                 $("#" + ic.pre + "dl_annotations").html("");
                 ic.bAnnoShown = false;
@@ -28609,6 +28687,24 @@ 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();
@@ -28797,6 +28893,17 @@ 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);
                     }
@@ -28892,6 +28999,21 @@ class LoadScript {
 
             ic.chainalignParserCls.downloadMmdbAf(id);
         }
+        /*
+        else if(command.indexOf('load vastsearch') !== -1) {
+            let idArray = loadStr.split(' || ');
+            let mmdbafid = idArray[1].substr(idArray[1].indexOf(' ') + 1);
+            ic.chainidArray = idArray[2].substr(idArray[2].indexOf(' ') + 1);
+            me.cfg.matchedchains = ic.chainidArray;
+
+            // load multiple PDBs
+            ic.bNCBI = true;
+            ic.bMmdbafid = true;
+
+            let bQuery = true;
+            ic.chainalignParserCls.downloadMmdbAf(mmdbafid, bQuery);
+        }
+        */
         else if(command.indexOf('load gi') !== -1) {
           me.cfg.gi = id;
           ic.mmdbParserCls.downloadGi(id);
@@ -28913,14 +29035,20 @@ 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
@@ -30720,6 +30848,7 @@ class ShowSeq {
         html3 += '<div class="icn3d-dl_sequence">';
         // html to display protein positions(10, 20, etc)
         //if(Object.keys(ic.chains[chnid]).length > 10) {
+
         if(ic.giSeq[chnid].length > 10) {
             htmlTmp = '<div class="icn3d-residueLine" style="white-space:nowrap;">';
             let atom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.chains[chnid]);
@@ -31095,6 +31224,56 @@ class ShowSeq {
                 html += '</div>';
                 html3 += '</div></div>';
             }
+/*            
+            else if(chnid == '4YHY_B') {
+                // test reference num
+                let resid2refnum = {};
+
+                let refData = {6: 'A1050', 22: 'B2050', 36: 'C3050', 48: 'C`3250', 61: 'C``3750', 70: 'D4050', 81: 'E5050', 96: 'F6050', 112: 'G7050'};
+
+                //ic.chainsMapping[chnid][chnid + '_' + resObject2.resi] = resObject1.resn + resObject1.resi;
+                for(let resi in refData) {
+                    let resid = chnid + '_' + resi;
+                    resid2refnum[resid] = refData[resi];
+                }
+
+
+                htmlTmp = '<div class="icn3d-dl_sequence">';
+                htmlTmp += '<div class="icn3d-residueLine" style="white-space:nowrap;">';
+                htmlTmp += '<div class="icn3d-annoTitle" anno="0" title="Ig Reference Numbers">Ig Reference Numbers</div>';
+                htmlTmp += '<span class="icn3d-residueNum"></span>';
+                html3 += htmlTmp + '<br>';
+                html += htmlTmp + '<span class="icn3d-seqLine">';
+                for(let i = 0, il = giSeq.length; i < il; ++i) {
+                    html += this.insertGap(chnid, i, '-');
+                    if(i >= ic.matchedPos[chnid] && i - ic.matchedPos[chnid] < ic.chainsSeq[chnid].length) {
+                      let currResi = ic.chainsSeq[chnid][i - ic.matchedPos[chnid]].resi;
+                      let residueid = chnid + '_' + currResi;
+                      if(!ic.residues.hasOwnProperty(residueid)) {
+                          html += '<span></span>';
+                      }
+                      else {
+                          let atom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.residues[residueid]);
+                          let resi_ori = atom.resi_ori;
+                          html += '<span>';
+                          if( resid2refnum.hasOwnProperty(residueid)) {
+                            html += resid2refnum[residueid] + ' ';
+                          }
+                          html += '</span>';
+                      }
+                    }
+                    else {
+                      html += '<span></span>';
+                    }
+                }
+                html += '<span class="icn3d-residueNum"></span>';
+                html += '</span>';
+                html += '<br>';
+                html += '</div>';
+                html += '</div>';
+                html3 += '</div></div>';
+            }
+*/
         }
         $("#" + ic.pre + 'dt_giseq_' + chnid).html(html);
         $("#" + ic.pre + 'ov_giseq_' + chnid).html(html2);
@@ -31220,12 +31399,24 @@ class AddTrack {
            //var title = 'fasta ' + fasta.substr(0, 5);
            let title = $("#" + ic.pre + "fasta_title").val();
 
+           let structure = chainid.substr(0, chainid.indexOf('_'));
+           let targets = chainid;
+           if(structure.length == 5) { // e.g., 1TUP2
+              targets = targets.substr(0,4);
+           }
+           else if(structure.length > 5) { // AlphaFold UniProt
+              targets = '';
+              for(let i = 0, il = ic.chainsSeq[chainid].length; i < il; ++i) {
+                targets += ic.chainsSeq[chainid][i].name;
+              }
+           }
+
            //var text = $("#" + ic.pre + "track_text").val();
            let url = 'https://www.ncbi.nlm.nih.gov/Structure/pwaln/pwaln.fcgi?from=track';
            $.ajax({
               url: url,
               type: 'POST',
-              data : {'targets': chainid, 'queries': fasta},
+              data : {'targets': targets, 'queries': fasta},
               dataType: 'jsonp',
               //dataType: 'json',
               tryCount : 0,
@@ -31811,12 +32002,14 @@ class AddTrack {
     }
 
     alignSequenceToStructure(chainid, data, title) { let ic = this.icn3d, me = ic.icn3dui;
-      let query, target;
+      let query, target, firstKey;
 
       if(data.data !== undefined) {
           query = data.data[0].query;
           //target = data.data[0].targets[chainid.replace(/_/g, '')];
-          target = data.data[0].targets[chainid];
+          //target = data.data[0].targets[chainid];
+          firstKey = Object.keys(data.data[0].targets)[0];
+          target = data.data[0].targets[firstKey];
 
           target = target.hsps[0];
       }
@@ -31832,7 +32025,8 @@ class AddTrack {
           target.scores.bit_score;
 
           //var targetSeq = data.targets[chainid.replace(/_/g, '')].seqdata;
-          let targetSeq = data.targets[chainid].seqdata;
+          //let targetSeq = data.targets[chainid].seqdata;
+          let targetSeq = data.targets[firstKey].seqdata;
           let querySeq = query.seqdata;
 
           let segArray = target.segs;
@@ -32563,6 +32757,10 @@ class AnnoCddSite {
 
         let chainWithData = {};
 
+        if(me.bNode) {
+            if(!ic.resid2cdd) ic.resid2cdd = {};
+            if(!ic.resid2site) ic.resid2site = {};
+        }
         for(let i = 0, il = dataArray.length; i < il; ++i) {
             let data = (bSeq) ? dataArray[i][0] : dataArray[i];
 
@@ -32578,6 +32776,7 @@ class AnnoCddSite {
                 let html2 = html;
                 let html3 = html;
                 let domainArray = cddData.doms;
+                if(me.bNode && !ic.resid2cdd[chnid]) ic.resid2cdd[chnid] = [];
                 let result = thisClass.setDomainFeature(domainArray, chnid, true, html, html2, html3);
 
                 ic.chainid2pssmid[chnid] = {pssmid2name: result.pssmid2name, pssmid2fromArray: result.pssmid2fromArray, pssmid2toArray: result.pssmid2toArray};
@@ -32596,6 +32795,7 @@ class AnnoCddSite {
 
                 // features
                 let featuteArray = cddData.motifs;
+                if(me.bNode && !ic.resid2site[chnid]) ic.resid2site[chnid] = [];
                 result = thisClass.setDomainFeature(featuteArray, chnid, false, html, html2, html3, acc2domain);
 
                 html = result.html; // + '</div>';
@@ -32660,6 +32860,12 @@ class AnnoCddSite {
                           let pos = thisClass.getAdjustedResi(i, chnid, ic.matchedPos, ic.chainsSeq, ic.baseResi);
 
                         html += '<span id="' + pre + '_' + ic.pre + chnid + '_' + pos + '" title="' + c + pos + '" class="icn3d-residue">' + cFull + '</span>';
+                        if(me.bNode) {
+                            let obj = {};
+                            obj[chnid + '_' + pos] = 'site: ' + siteArray[index].title;
+                            ic.resid2site[chnid].push(obj);
+                        }
+
                         html2 += ic.showSeqCls.insertGapOverview(chnid, i);
                         let emptyWidth =(me.cfg.blast_rep_id == chnid) ? Math.round(ic.seqAnnWidth * i /(ic.maxAnnoLength + ic.nTotalGap) - prevEmptyWidth - prevLineWidth) : Math.round(ic.seqAnnWidth * i / ic.maxAnnoLength - prevEmptyWidth - prevLineWidth);
                         //if(emptyWidth < 0) emptyWidth = 0;
@@ -32833,6 +33039,16 @@ class AnnoCddSite {
                       //var pos =(i >= ic.matchedPos[chnid] && i - ic.matchedPos[chnid] < ic.chainsSeq[chnid].length) ? ic.chainsSeq[chnid][i - ic.matchedPos[chnid]].resi : ic.baseResi[chnid] + 1 + i;
                       let pos = thisClass.getAdjustedResi(i, chnid, ic.matchedPos, ic.chainsSeq, ic.baseResi);
                       html += '<span id="' + pre + '_' + ic.pre + chnid + '_' + pos + '" title="' + c + pos + '" class="icn3d-residue">' + cFull + '</span>';
+                      if(me.bNode) {
+                        let obj = {};
+                        obj[chnid + '_' + pos] = fulltitle;
+                        if(bDomain) {
+                            ic.resid2cdd[chnid].push(obj);
+                        }
+                        else {
+                            ic.resid2site[chnid].push(obj);
+                        }
+                      }
                   }
                   else {
                       html += '<span>-</span>'; //'<span>-</span>';
@@ -32929,29 +33145,56 @@ class AnnoCddSite {
               let title = cFull +(i+1 + ic.baseResi[chnid]).toString();
               if(type == 'ssbond') {
                   title = 'Residue ' + resid + ' has disulfide bond with';
+                  let sstitle = '';
                   if(resid2resids[resid] !== undefined) {
                       for(let j = 0, jl = resid2resids[resid].length; j < jl; ++j) {
-                          title += ' residue ' + resid2resids[resid][j];
+                        sstitle += ' residue ' + resid2resids[resid][j];
                       }
                   }
+                  title += sstitle;
+
+                  if(me.bNode) {
+                    let obj = {};
+                    obj[resid] = 'disulfide bond with' + sstitle;
+                    ic.resid2ssbond[chnid].push(obj);
+                  }
               }
               else if(type == 'crosslink') {
                   title = 'Residue ' + resid + ' has cross-linkage with';
+                  let cltitle = '';
                   if(resid2resids[resid] !== undefined) {
                       for(let j = 0, jl = resid2resids[resid].length; j < jl; ++j) {
-                          title += ' residue ' + resid2resids[resid][j];
+                        cltitle += ' residue ' + resid2resids[resid][j];
                       }
                   }
+                  title += cltitle;
+
+                  if(me.bNode) {
+                    let obj = {};
+                    obj[resid] = 'cross-linkage with' + cltitle;
+                    ic.resid2crosslink[chnid].push(obj);
+                  }
               }
+              else {
+                title = 'Residue ' + resid + ' has connection with';
+                let cltitle = '';
+                if(resid2resids[resid] !== undefined) {
+                    for(let j = 0, jl = resid2resids[resid].length; j < jl; ++j) {
+                      cltitle += ' residue ' + resid2resids[resid][j];
+                    }
+                }
+                title += cltitle;
+              }
+
               html += '<span id="' + pre + '_' + ic.pre + chnid + '_' + pos + '" title="' + title + '" class="icn3d-residue">' + c + '</span>';
               html2 += ic.showSeqCls.insertGapOverview(chnid, i);
               let emptyWidth =(me.cfg.blast_rep_id == chnid) ? Math.round(ic.seqAnnWidth * i /(ic.maxAnnoLength + ic.nTotalGap) - prevEmptyWidth - prevLineWidth) : Math.round(ic.seqAnnWidth * i / ic.maxAnnoLength - prevEmptyWidth - prevLineWidth);
                 //if(emptyWidth < 0) emptyWidth = 0;
                 if(emptyWidth >= 0) {
-                html2 += '<div style="display:inline-block; width:' + emptyWidth + 'px;">&nbsp;</div>';
-                html2 += '<div style="display:inline-block; background-color:#000; width:' + widthPerRes + 'px;" title="' + title + '">&nbsp;</div>';
-                prevEmptyWidth += emptyWidth;
-                prevLineWidth += widthPerRes;
+                    html2 += '<div style="display:inline-block; width:' + emptyWidth + 'px;">&nbsp;</div>';
+                    html2 += '<div style="display:inline-block; background-color:#000; width:' + widthPerRes + 'px;" title="' + title + '">&nbsp;</div>';
+                    prevEmptyWidth += emptyWidth;
+                    prevLineWidth += widthPerRes;
                 }
           }
           else {
@@ -33017,7 +33260,12 @@ class AnnoSsbond {
             this.showSsbond_base(chnid, chnidBase);
         }
     }
-    showSsbond_base(chnid, chnidBase) { let ic = this.icn3d; ic.icn3dui;
+    showSsbond_base(chnid, chnidBase) { let ic = this.icn3d, me = ic.icn3dui;
+        if(me.bNode) {
+            if(!ic.resid2ssbond) ic.resid2ssbond = {};
+            if(!ic.resid2ssbond[chnid]) ic.resid2ssbond[chnid] = [];
+        }
+
         let chainid = chnidBase;
         let resid2resids = {};
         let structure = chainid.substr(0, chainid.indexOf('_'));
@@ -34038,12 +34286,11 @@ class ApplyCommand {
         let  bPosition = false;
         for(let i = 1, il = paraArray.length; i < il; ++i) {
             let  wordArray = paraArray[i].split(' ');
-
             if(wordArray[0] == 'x') {
                 bPosition = true;
-                x = wordArray[1];
-                y = wordArray[3];
-                z = wordArray[5];
+                x = parseFloat(wordArray[1]);
+                y = parseFloat(wordArray[3]);
+                z = parseFloat(wordArray[5]);
             }
             else if(wordArray[0] == 'size') {
                 size = paraArray[i].substr(paraArray[i].lastIndexOf(' ') + 1);
@@ -34061,9 +34308,9 @@ class ApplyCommand {
 
         if(!bPosition) {
           let  position = ic.applyCenterCls.centerAtoms(me.hashUtilsCls.hash2Atoms(ic.hAtoms, ic.atoms));
-          x = position.center.x;
-          y = position.center.y;
-          z = position.center.z;
+          x = parseFloat(position.center.x);
+          y = parseFloat(position.center.y);
+          z = parseFloat(position.center.z);
         }
 
         ic.analysisCls.addLabel(text, x,y,z, size, color, background, type);
@@ -34534,7 +34781,23 @@ class ApplyCommand {
         let  id = command.substr(command.lastIndexOf(' ') + 1);
         me.htmlCls.eventsCls.saveHtml(id);
       }
-
+      else if(command.indexOf('resdef') == 0) {
+        me.cfg.resdef = command.substr(command.indexOf(' ') + 1);
+      }
+      else if(command.indexOf('vast_search_chainid') == 0) {
+        ic.chainidArray = commandOri.substr(commandOri.indexOf(' ') + 1).split(',');
+
+        let bRealign = true, bPredefined = true;
+        ic.realignParserCls.realignChainOnSeqAlign(undefined, ic.chainidArray, bRealign, bPredefined);
+
+        // reset annotations
+        // $("#" + ic.pre + "dl_annotations").html("");
+        // ic.bAnnoShown = false;
+        // if($('#' + ic.pre + 'dl_selectannotations').dialog( 'isOpen' )) {
+        //     $('#' + ic.pre + 'dl_selectannotations').dialog( 'close' );
+        // }
+      }
+      
     // special, select ==========
 
       else if(command.indexOf('select displayed set') !== -1) {
@@ -34949,9 +35212,8 @@ class SelectByCommand {
            }
     }
 
-    selectBySpec(select, commandname, commanddesc, bDisplay) { let  ic = this.icn3d, me = ic.icn3dui;
+    selectBySpec(select, commandname, commanddesc, bDisplay, bNoUpdateAll) { let  ic = this.icn3d, me = ic.icn3dui;
        select =(select.trim().substr(0, 6) === 'select') ? select.trim().substr(7) : select.trim();
-
        ic.hAtoms = {};
 
        // selection definition is similar to Chimera: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html
@@ -35265,8 +35527,8 @@ class SelectByCommand {
        if(commandname != "") {
            ic.selectionCls.addCustomSelection(residueAtomArray, commandname, commanddesc, select, bSelectResidues);
 
-           let  nameArray = [commandname];
-           ic.definedSetsCls.changeCustomAtoms(nameArray);
+           let  nameArray = [commandname];          
+           if(!bNoUpdateAll) ic.definedSetsCls.changeCustomAtoms(nameArray);
        }
     }
 }
@@ -36930,7 +37192,7 @@ 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');
               }
 
@@ -36999,7 +37261,7 @@ class ParserUtils {
             resi2pos_q[resi] = i + 1;
         }
 
-        for(let i = 0, il = ic.realignResid[struct_t].length; i < il; ++i) {
+        for(let i = 0, il = ic.realignResid[struct_t].length; i < il && i < ic.realignResid[struct_q].length; ++i) {
             let resid_t = ic.realignResid[struct_t][i].resid;
             let pos_t = resid_t.lastIndexOf('_');
             let resi_t = parseInt(resid_t.substr(pos_t + 1));
@@ -37300,7 +37562,7 @@ 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;
@@ -37600,7 +37862,7 @@ class MmcifParser {
 
     //Ajax call was used to get the atom data from the "mmcifid". This function was deferred
     //so that it can be chained together with other deferred functions for sequential execution.
-    downloadMmcif(mmcifid) { let  ic = this.icn3d, me = ic.icn3dui;
+    downloadMmcif(mmcifid) { let ic = this.icn3d; ic.icn3dui;
        let  thisClass = this;
 
        let  url, dataType;
@@ -37626,34 +37888,7 @@ class MmcifParser {
               //ic.ParserUtilsCls.hideLoading();
           },
           success: function(data) {
-               url = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi";
-               $.ajax({
-                  url: url,
-                  type: 'POST',
-                  data : {'mmciffile': data},
-                  dataType: 'jsonp',
-                  cache: true,
-                  tryCount : 0,
-                  retryLimit : 0, //1
-                  beforeSend: function() {
-                      ic.ParserUtilsCls.showLoading();
-                  },
-                  complete: function() {
-                      //ic.ParserUtilsCls.hideLoading();
-                  },
-                  success: function(data) {
-                      thisClass.loadMmcifData(data, mmcifid);
-                  },
-                  error : function(xhr, textStatus, errorThrown ) {
-                    this.tryCount++;
-                    if(this.tryCount <= this.retryLimit) {
-                        //try again
-                        $.ajax(this);
-                        return;
-                    }
-                    return;
-                  }
-                });
+            thisClass.parseMmcifData(data, mmcifid);
           },
           error : function(xhr, textStatus, errorThrown ) {
             this.tryCount++;
@@ -37667,6 +37902,40 @@ class MmcifParser {
         });
     }
 
+    parseMmcifData(data, mmcifid, command) { let  ic = this.icn3d, me = ic.icn3dui;
+        let  thisClass = this;
+        
+        let url = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi";
+        $.ajax({
+           url: url,
+           type: 'POST',
+           data : {'mmciffile': data},
+           dataType: 'jsonp',
+           cache: true,
+           tryCount : 0,
+           retryLimit : 0, //1
+           beforeSend: function() {
+               ic.ParserUtilsCls.showLoading();
+           },
+           complete: function() {
+               //ic.ParserUtilsCls.hideLoading();
+           },
+           success: function(data) {
+               thisClass.loadMmcifData(data, mmcifid);
+               if(command) ic.loadScriptCls.loadScript(command);
+           },
+           error : function(xhr, textStatus, errorThrown ) {
+             this.tryCount++;
+             if(this.tryCount <= this.retryLimit) {
+                 //try again
+                 $.ajax(this);
+                 return;
+             }
+             return;
+           }
+         });
+    }
+
     downloadMmcifSymmetry(mmcifid, type) { let ic = this.icn3d; ic.icn3dui;
       let  thisClass = this;
 
@@ -38209,6 +38478,7 @@ class HlSeq {
 
       if($(that).hasClass('icn3d-seqTitle')) {
         let chainid = $(that).attr('chain');
+        let resn = $(that).attr('resn');
 
         if(ic.bAlignSeq) {
             ic.bSelectAlignResidue = false;
@@ -38233,20 +38503,24 @@ class HlSeq {
         }
 
         $(that).toggleClass('icn3d-highlightSeq');
-
         let commandname, commanddescr, position;
-        if(!ic.bAnnotations) {
-            if(ic.bAlignSeq) {
-                commandname = "align_" + chainid;
+        if(resn) {
+            commandname = resn; 
+        }
+        else {
+            if(!ic.bAnnotations) {
+                if(ic.bAlignSeq) {
+                    commandname = "align_" + chainid;
+                }
+                else {
+                    commandname = chainid;           
+                }
             }
             else {
-                commandname = chainid;
+                commandname = $(that).attr('setname');
+                commanddescr = $(that).attr('title');
             }
         }
-        else {
-            commandname = $(that).attr('setname');
-            commanddescr = $(that).attr('title');
-        }
 
         if($(that).hasClass('icn3d-highlightSeq')) {
             if(!ic.bAnnotations) {
@@ -38256,14 +38530,13 @@ class HlSeq {
                 }
                 else {
                     ic.currSelectedSets = [commandname];
-                    //ic.selectionCls.selectAChain(chainid, commandname, true);
                     ic.selectionCls.selectAChain(chainid, commandname, ic.bAlignSeq);
                 }
 
                 if(ic.bAlignSeq) {
                     me.htmlCls.clickMenuCls.setLogCmd('select alignChain ' + chainid, true);
                 }
-                else {
+                else {   
                     me.htmlCls.clickMenuCls.setLogCmd('select chain ' + chainid, true);
                 }
 
@@ -38278,14 +38551,35 @@ class HlSeq {
                     if($(that).attr('gi') !== undefined) {
                         if(ic.bCtrl || ic.bShift) {
                             ic.currSelectedSets.push(chainid);
-                            ic.selectionCls.selectAChain(chainid, chainid, false, true);
+                            if(resn) {
+                                let prevHAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
+                                let bNoUpdateAll = true;
+                                ic.selByCommCls.selectBySpec('select :3' + resn, commandname, commandname, false, bNoUpdateAll);
+                                ic.hAtoms = me.hashUtilsCls.unionHash(ic.hAtoms, prevHAtoms);
+                                ic.hlUpdateCls.updateHlAll(resn, undefined, true, true);
+                            }
+                            else {
+                                ic.selectionCls.selectAChain(chainid, chainid, false, true);
+                            }
                         }
                         else {
                             ic.currSelectedSets = [chainid];
-                            ic.selectionCls.selectAChain(chainid, chainid, false);
+                            if(resn) {
+                                let bNoUpdateAll = true;
+                                ic.selByCommCls.selectBySpec('select :3' + resn, commandname, commandname, false, bNoUpdateAll);
+                                ic.hlUpdateCls.updateHlAll(resn, undefined, true, true);
+                            }
+                            else {
+                                ic.selectionCls.selectAChain(chainid, chainid, false);
+                            }
                         }
 
-                        me.htmlCls.clickMenuCls.setLogCmd('select chain ' + chainid, true);
+                        if(resn) {
+                            me.htmlCls.clickMenuCls.setLogCmd('select :3' + resn, true);
+                        }
+                        else {
+                            me.htmlCls.clickMenuCls.setLogCmd('select chain ' + chainid, true);
+                        }
 
                         let setNames = ic.currSelectedSets.join(' or ');
                         //if(ic.currSelectedSets.length > 1) me.htmlCls.clickMenuCls.setLogCmd('select saved atoms ' + setNames, true);
@@ -38500,8 +38794,7 @@ class ShowAnno {
     }
 
     //show annotations such as SNPs, ClinVar, domains, binding sites, etc.
-    showAnnotations() { let ic = this.icn3d, me = ic.icn3dui;
-        let thisClass = this;
+    showAnnotations_part1() { let ic = this.icn3d, me = ic.icn3dui;
         me.htmlCls.dialogCls.openDlg('dl_selectannotations', 'Sequences and Annotations');
         // add note about assembly
         if((ic.bAssemblyNote === undefined || !ic.bAssemblyNote) && ic.asuCnt !== undefined ) {
@@ -38523,6 +38816,9 @@ class ShowAnno {
             ic.annotationCls.setAnnoView('overview');
         }
 
+        let nucleotide_chainid = {}, chemical_chainid = {}, chemical_set = {};
+        ic.protein_chainid = {};
+
         if(ic.bAnnoShown === undefined || !ic.bAnnoShown || ic.bResetAnno) { // ic.bResetAnno when loading another structure
             let chainArray = Object.keys(ic.chains);
 
@@ -38531,7 +38827,13 @@ class ShowAnno {
             if(ic.resi2disease_nonempty === undefined) ic.resi2disease_nonempty = {};
             if(ic.baseResi === undefined) ic.baseResi = {};
             if(ic.matchedPos === undefined) ic.matchedPos = {};
-            let dialogWidth =(me.cfg.notebook) ? me.htmlCls.WIDTH / 2 : $("#" + ic.pre + "dl_selectannotations").dialog( "option", "width" );
+            let dialogWidth;
+            if(me.bNode) { // no $().dialog
+                dialogWidth = 500;
+            }
+            else {
+                dialogWidth =(me.cfg.notebook) ? me.htmlCls.WIDTH / 2 : $("#" + ic.pre + "dl_selectannotations").dialog( "option", "width" );
+            }
             ic.seqAnnWidth = dialogWidth - 120 - 30*2 - 50; // title: 120px, start and end resi: 30px, extra space on the left and right: 50px
             ic.maxAnnoLength = 1;
             for(let chainid in ic.chainsSeq) {
@@ -38539,8 +38841,7 @@ class ShowAnno {
                     ic.maxAnnoLength = ic.chainsSeq[chainid].length;
                 }
             }
-            let nucleotide_chainid = {}, chemical_chainid = {}, chemical_set = {};
-            ic.protein_chainid = {};
+
             for(let i = 0, il = chainArray.length; i < il; ++i) {
                 Math.round(chainArray[i].indexOf('_'));
                 //if(pos > 4) continue; // NMR structures with structure id such as 2K042,2K043, ...
@@ -38598,7 +38899,21 @@ class ShowAnno {
                     } // for(let r = 0
                 } // if(me.cfg.mmdbid
             } // for(let i = 0
+        }
+
+        return {'nucleotide_chainid': nucleotide_chainid, 'chemical_chainid': chemical_chainid, 'chemical_set': chemical_set};
+    }
 
+    showAnnotations() { let ic = this.icn3d, me = ic.icn3dui;
+        let thisClass = this;
+
+        let result = this.showAnnotations_part1();
+
+        let nucleotide_chainid = result.nucleotide_chainid;
+        let chemical_chainid = result.chemical_chainid;
+        let chemical_set = result.chemical_set;
+            
+        if(ic.bAnnoShown === undefined || !ic.bAnnoShown || ic.bResetAnno) { // ic.bResetAnno when loading another structure
             if(me.cfg.blast_rep_id === undefined) {
                if(ic.bFullUi) {
                    if(me.cfg.mmtfid !== undefined) { // mmtf data do NOT have the missing residues
@@ -38714,8 +39029,10 @@ class ShowAnno {
         }
         ic.bAnnoShown = true;
     }
+
     showAnnoSeqData(nucleotide_chainid, chemical_chainid, chemical_set) { let ic = this.icn3d, me = ic.icn3dui;
-        this.getAnnotationData();
+        if(!me.bNode) this.getAnnotationData();
+
         let i = 0;
         for(let chain in nucleotide_chainid) {
             this.getSequenceData(chain, nucleotide_chainid[chain], 'nucleotide', i);
@@ -38738,12 +39055,15 @@ class ShowAnno {
             this.getCombinedSequenceData(name, chemical_set[name], i);
             ++i;
         }
-        this.enableHlSeq();
 
-        setTimeout(function(){
-          ic.annotationCls.hideAllAnno();
-          ic.annotationCls.clickCdd();
-        }, 0);
+        if(!me.bNode) {
+            this.enableHlSeq();
+
+            setTimeout(function(){
+            ic.annotationCls.hideAllAnno();
+            ic.annotationCls.clickCdd();
+            }, 0);
+        }
     }
 
     getAnnotationData() { let ic = this.icn3d, me = ic.icn3dui;
@@ -38780,15 +39100,17 @@ class ShowAnno {
             $("#" + ic.pre + "anno_" + chnid).append("<br><hr><br>");
             ++index;
         }
-        ic.annoCddSiteCls.setToolTip();
+        
+        if(!me.bNode) ic.annoCddSiteCls.setToolTip();
+
         // show the sequence and 3D structure
         //var url = "https://eme.utilsCls.ncbi.nlm.nih.gov/entrez/eUtilsCls/efetch.fcgi?db=protein&retmode=json&rettype=fasta&id=" + chnidBaseArray;
         let url = me.htmlCls.baseUrl + "/vastdyn/vastdyn.cgi?chainlist=" + chnidBaseArray;
 
-        if(ic.chainid_seq !== undefined) {
+        if(ic.chainid_seq !== undefined) {     
             this.processSeqData(ic.chainid_seq);
         }
-        else {
+        else {       
             $.ajax({
               url: url,
               dataType: 'jsonp', //'text',
@@ -38807,7 +39129,7 @@ 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);
@@ -38863,7 +39185,7 @@ class ShowAnno {
         let firstChainid = residArray[0].substr(0, pos);
         let sid =(me.cfg.mmdbid !== undefined && ic.chainid2sid !== undefined) ? ic.chainid2sid[firstChainid] : undefined;
         if(sid !== undefined) {
-            chemName = "<b><a class='icn3d-blue' href='https://pubchem.ncbi.nlm.nih.gov/substance/" + sid + "#section=2D-Structure' target='_blank'>" + name + " <img src='https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?sid=" + sid + "'></a></b>";
+            chemName = "<b>" + name + " <a class='icn3d-blue' href='https://pubchem.ncbi.nlm.nih.gov/substance/" + sid + "#section=2D-Structure' target='_blank'><img src='https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?sid=" + sid + "'></a></b>";
         }
         else {
             chemName = "<b>" + name + "</b>";
@@ -38875,7 +39197,8 @@ class ShowAnno {
         // sequence, detailed view
         let htmlTmp = '<div id="' + ic.pre + 'giseq_sequence" class="icn3d-dl_sequence">';
         let chainType = 'Chem.', chainTypeFull = 'Chemical';
-        htmlTmp += '<div class="icn3d-seqTitle2" anno="sequence"><span style="white-space:nowrap;" title="' + chainTypeFull + ' ' + name + '">' + chainType + ' ' + name + '</span></div>';
+        //htmlTmp += '<div class="icn3d-seqTitle2" anno="sequence"><span style="white-space:nowrap;" title="' + chainTypeFull + ' ' + name + '">' + chainType + ' ' + name + '</span></div>';
+        htmlTmp += '<div class="icn3d-seqTitle icn3d-link icn3d-blue" anno="sequence" gi="' + name + '" resn="' + name + '"><span style="white-space:nowrap;" title="' + chainTypeFull + ' ' + name + '">' + chainType + ' ' + name + '</span></div>';
         htmlTmp += '<span class="icn3d-residueNum" style="width:60px!important;" title="starting protein sequence number">Count: ' + residArray.length + '</span>';
         htmlTmp += '<span class="icn3d-seqLine">';
         // sequence, overview
@@ -38932,7 +39255,7 @@ 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) {
@@ -39121,9 +39444,12 @@ class ShowAnno {
               ic.hAtoms = me.hashUtilsCls.cloneHash(prevHAtoms);
             } // align seq to structure
         } // for loop
-        this.enableHlSeq();
-        // get CDD/Binding sites
-        ic.annoCddSiteCls.showCddSiteAll();
+        
+        if(!me.bNode) {
+            this.enableHlSeq();
+            // get CDD/Binding sites
+            ic.annoCddSiteCls.showCddSiteAll();
+        }
     }
 
     enableHlSeq() { let ic = this.icn3d, me = ic.icn3dui;
@@ -39216,6 +39542,10 @@ class AnnoContact {
         }
     }
     showInteraction_base(chnid, chnidBase) { let ic = this.icn3d, me = ic.icn3dui;
+        if(me.bNode) {
+            if(!ic.resid2contact) ic.resid2contact = {};
+            if(!ic.resid2contact[chnid]) ic.resid2contact[chnid] = [];
+        }
         // set interaction
         if(ic.chainname2residues === undefined) ic.chainname2residues = {};
         let radius = 4;
@@ -39325,6 +39655,12 @@ class AnnoContact {
     //            let pos = ic.chainsSeq[chnid][i - ic.matchedPos[chnid] ].resi;
                   let pos =(i >= ic.matchedPos[chnid] && i - ic.matchedPos[chnid] < ic.chainsSeq[chnid].length) ? ic.chainsSeq[chnid][i - ic.matchedPos[chnid]].resi : ic.baseResi[chnid] + 1 + i;
                   html += '<span id="' + pre + '_' + ic.pre + chnid + '_' + pos + '" title="' + cFull + pos + '" class="icn3d-residue">' + c + '</span>';
+                  if(me.bNode) {
+                      let obj = {};
+                      obj[chnid + '_' + pos] = fulltitle;
+                      ic.resid2contact[chnid].push(obj);
+                  }
+                  
                   html2 += ic.showSeqCls.insertGapOverview(chnid, i);
                   let emptyWidth =(me.cfg.blast_rep_id == chnid) ? Math.round(ic.seqAnnWidth * i /(ic.maxAnnoLength + ic.nTotalGap) - prevEmptyWidth - prevLineWidth) : Math.round(ic.seqAnnWidth * i / ic.maxAnnoLength - prevEmptyWidth - prevLineWidth);
                     //if(emptyWidth < 0) emptyWidth = 0;
@@ -39385,11 +39721,17 @@ class AnnoCrossLink {
             this.showCrosslink_base(chnid, chnidBase);
         }
     }
-    showCrosslink_base(chnid, chnidBase) { let ic = this.icn3d; ic.icn3dui;
+    showCrosslink_base(chnid, chnidBase) { let ic = this.icn3d, me = ic.icn3dui;
+        if(me.bNode) {
+            if(!ic.resid2crosslink) ic.resid2crosslink = {};
+            if(!ic.resid2crosslink[chnid]) ic.resid2crosslink[chnid] = [];
+        }
+
         let chainid = chnidBase;
         let resid2resids = {};
         let structure = chainid.substr(0, chainid.indexOf('_'));
         let clbondArray = ic.clbondpnts[structure];
+
         if(clbondArray === undefined) {
             $("#" + ic.pre + "dt_crosslink_" + chnid).html('');
             $("#" + ic.pre + "ov_crosslink_" + chnid).html('');
@@ -39426,16 +39768,16 @@ class AnnoDomain {
         this.icn3d = icn3d;
     }
 
-    showDomainPerStructure(index) { let ic = this.icn3d, me = ic.icn3dui;
+    showDomainPerStructure(index) { let ic = this.icn3d; ic.icn3dui;
         let thisClass = this;
         //var chnid = Object.keys(ic.protein_chainid)[0];
         //var pdbid = chnid.substr(0, chnid.indexOf('_'));
         let pdbArray = Object.keys(ic.structures);
         // show 3D domains
         let pdbid = pdbArray[index];
-        me.htmlCls.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&domain&molinfor&uid=" + pdbid;
+        //let url = me.htmlCls.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&domain&molinfor&uid=" + pdbid;
 
-        if(index == 0 && ic.mmdb_data !== undefined) {
+        if(index == 0 && ic.mmdb_data !== undefined) {      
             for(let chnid in ic.protein_chainid) {
                 if(chnid.indexOf(pdbid) !== -1) {
                     this.showDomainWithData(chnid, ic.mmdb_data);
@@ -39449,7 +39791,7 @@ class AnnoDomain {
                 }
             }
         }
-        else {                  
+        else {
             // calculate 3D domains on-the-fly
             //ic.protein_chainid[chainArray[i]] 
             let data = {};
@@ -39506,6 +39848,7 @@ class AnnoDomain {
         for(let i = 0, il = pdbArray.length; i < il; ++i) {
             ic.bAjaxDoneArray[i] = false;
         }
+
         for(let i = 0, il = pdbArray.length; i < il; ++i) {
             this.showDomainPerStructure(i);
         }
@@ -39550,6 +39893,7 @@ class AnnoDomain {
             let fromArray = [], toArray = [];
             let resiHash = {};
             let resCnt = 0;
+
             for(let i = 0, il = subdomainArray.length; i < il; ++i) {
                 let domainFrom = Math.round(subdomainArray[i][0]) - 1; // convert 1-based to 0-based
                 let domainTo = Math.round(subdomainArray[i][1]) - 1;
@@ -39576,6 +39920,25 @@ class AnnoDomain {
                     resiHash[j+1] = 1;
                 }
             }
+
+            // save 3D domain info for node.js script
+            if(me.bNode) {
+                let domainName = '3D domain ' +(index+1).toString();
+                            
+                if(!ic.resid2domain) ic.resid2domain = {};
+                if(!ic.resid2domain[chnid]) ic.resid2domain[chnid] = [];
+                for(let i = 0, il = fromArray.length; i < il; ++i) {
+                    let from = fromArray[i];
+                    let to = toArray[i];
+                    for(let j = from; j <= to; ++j) {
+                        // 0-based
+                        let obj = {};
+                        obj[chnid + '_' + (j+1).toString()] = domainName;
+                        ic.resid2domain[chnid].push(obj);
+                    }
+                }
+            }
+
             let htmlTmp2 = '<div class="icn3d-seqTitle icn3d-link icn3d-blue" 3ddomain="' +(index+1).toString() + '" from="' + fromArray + '" to="' + toArray + '" shorttitle="' + title + '" index="' + index + '" setname="' + chnid + '_3d_domain_' +(index+1).toString() + '" anno="sequence" chain="' + chnid + '" title="' + fulltitle + '">' + title + ' </div>';
             let htmlTmp3 = '<span class="icn3d-residueNum" title="residue count">' + resCnt.toString() + ' Res</span>';
             html3 += htmlTmp2 + htmlTmp3 + '<br>';
@@ -39655,6 +40018,59 @@ class AnnoSnpClinVar {
         this.icn3d = icn3d;
     }
 
+    showSnp(chnid, chnidBase) { let ic = this.icn3d; ic.icn3dui;
+        this.showSnpClinvar(chnid, chnidBase, true);
+    }
+    showClinvar(chnid, chnidBase) { let ic = this.icn3d; ic.icn3dui;
+        this.showSnpClinvar(chnid, chnidBase, false);
+    }
+
+    //Show the annotations of SNPs and ClinVar.
+    showSnpClinvar(chnid, chnidBase, bSnpOnly) { let ic = this.icn3d, me = ic.icn3dui;
+       let thisClass = this;
+
+       // get gi from acc
+       //var url2 = "https://www.ncbi.nlm.nih.gov/Structure/icn3d/chainid2repgi.txt";
+       let url2 = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi?chainid=" + chnidBase;
+       $.ajax({
+          url: url2,
+          dataType: 'jsonp', //'text',
+          cache: true,
+          tryCount : 0,
+          retryLimit : 0, //1
+          success: function(data2) {
+            //ic.chainid2repgi = JSON.parse(data2);
+            //var gi = ic.chainid2repgi[chnidBase];
+            let snpgi = data2.snpgi;
+            let gi = data2.gi;
+            if(bSnpOnly) {
+                thisClass.showSnpPart2(chnid, chnidBase, snpgi);
+            }
+            else {
+                let specialGiArray = [6137708,1942289,224510717,2624886,253723219,2554905,75765331,3660278,312207882,319443632,342350956,1827805,109157826,1065265,40889086,6730307,163931185,494469,163931091,60594093,55669745,18655489,17942684,6980537,166235465,6435586,4139398,4389047,364506122,78101667,262118402,20664221,2624640,158430173,494395,28948777,34810587,13399647,3660342,261278854,342350965,384482350,378792570,15988303,213424334,4558333,2098365,10835631,3318817,374074330,332639529,122919696,4389286,319443573,2781341,67464020,194709238,210061039,364506106,28949044,40889076,161172338,17943181,4557976,62738484,365813173,6137343,350610552,17942703,576308,223674070,15826518,1310997,93279697,4139395,255311799,157837067,361132363,357380836,146387678,383280379,1127268,299856826,13786789,1311054,46015217,3402130,381353319,30750059,218766885,340707375,27065817,355333104,2624634,62738384,241913553,304446010];
+                let giUsed = snpgi;
+                if(specialGiArray.includes(gi)) giUsed = gi;
+                thisClass.showClinvarPart2(chnid, chnidBase, giUsed);
+            }
+          },
+          error : function(xhr, textStatus, errorThrown ) {
+            this.tryCount++;
+            if(this.tryCount <= this.retryLimit) {
+                //try again
+                $.ajax(this);
+                return;
+            }
+            if(bSnpOnly) {
+                thisClass.processNoSnp(chnid);
+            }
+            else {
+                thisClass.processNoClinvar(chnid);
+            }
+            return;
+          }
+       });
+    }
+
     navClinVar(chnid) { let ic = this.icn3d; ic.icn3dui;
         let thisClass = this;
         ic.currClin[chnid] = - 1;
@@ -40090,7 +40506,7 @@ class AnnoSnpClinVar {
 
         return html;
     }
-    processSnpClinvar(data, chnid, chnidBase, bSnpOnly, bVirus) { let ic = this.icn3d; ic.icn3dui;
+    processSnpClinvar(data, chnid, chnidBase, bSnpOnly, bVirus) { let ic = this.icn3d, me = ic.icn3dui;
         let html = '<div id="' + ic.pre + chnid + '_snpseq_sequence" class="icn3d-dl_sequence">';
         let html2 = html;
         let html3 = html;
@@ -40107,6 +40523,16 @@ class AnnoSnpClinVar {
         let resi2clinAllele = {};
         let posHash = {}, posClinHash = {};
         let prevSnpStr = '';
+        if(me.bNode) {
+            if(bSnpOnly) {
+                if(!ic.resid2snp) ic.resid2snp = {};
+                if(!ic.resid2snp[chnid]) ic.resid2snp[chnid] = [];
+            }
+            else {
+                if(!ic.resid2clinvar) ic.resid2clinvar = {};
+                if(!ic.resid2clinvar[chnid]) ic.resid2clinvar[chnid] = [];
+            }
+        }
         for(let i = 0, il = lineArray.length; i < il; ++i) {
          //bSnpOnly: false
          //1310770    13    14    14Y>H    368771578    150500    Hereditary cancer-predisposing syndrome; Li-Fraumeni syndrome; not specified; Li-Fraumeni syndrome 1    Likely benign; Uncertain significance; Uncertain significance; Uncertain significance    1TSR_A    120407068    NP_000537.3
@@ -40120,6 +40546,19 @@ class AnnoSnpClinVar {
           prevSnpStr = snpStr;
           let resiStr = snpStr.substr(0, snpStr.length - 3);
           let resi = Math.round(resiStr);
+
+          if(me.bNode) {
+              let obj = {};
+              obj[chnid + '_' + resi] = snpStr;
+                
+              if(bSnpOnly) {
+                ic.resid2snp[chnid].push(obj);
+              }
+              else {
+                ic.resid2clinvar[chnid].push(obj);
+              }
+          }
+
           snpStr.substr(snpStr.length - 3, 1);
           let snpRes = snpStr.substr(snpStr.indexOf('>') + 1); //snpStr.substr(snpStr.length - 1, 1);
           //var rsnum = bSnpOnly ? '' : fieldArray[4];
@@ -40247,58 +40686,7 @@ class AnnoSnpClinVar {
           }
         });
     }
-    showSnp(chnid, chnidBase) { let ic = this.icn3d; ic.icn3dui;
-        this.showSnpClinvar(chnid, chnidBase, true);
-    }
-    showClinvar(chnid, chnidBase) { let ic = this.icn3d; ic.icn3dui;
-        this.showSnpClinvar(chnid, chnidBase, false);
-    }
-
-    //Show the annotations of SNPs and ClinVar.
-    showSnpClinvar(chnid, chnidBase, bSnpOnly) { let ic = this.icn3d, me = ic.icn3dui;
-       let thisClass = this;
 
-       // get gi from acc
-       //var url2 = "https://www.ncbi.nlm.nih.gov/Structure/icn3d/chainid2repgi.txt";
-       let url2 = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi?chainid=" + chnidBase;
-       $.ajax({
-          url: url2,
-          dataType: 'jsonp', //'text',
-          cache: true,
-          tryCount : 0,
-          retryLimit : 0, //1
-          success: function(data2) {
-            //ic.chainid2repgi = JSON.parse(data2);
-            //var gi = ic.chainid2repgi[chnidBase];
-            let snpgi = data2.snpgi;
-            let gi = data2.gi;
-            if(bSnpOnly) {
-                thisClass.showSnpPart2(chnid, chnidBase, snpgi);
-            }
-            else {
-                let specialGiArray = [6137708,1942289,224510717,2624886,253723219,2554905,75765331,3660278,312207882,319443632,342350956,1827805,109157826,1065265,40889086,6730307,163931185,494469,163931091,60594093,55669745,18655489,17942684,6980537,166235465,6435586,4139398,4389047,364506122,78101667,262118402,20664221,2624640,158430173,494395,28948777,34810587,13399647,3660342,261278854,342350965,384482350,378792570,15988303,213424334,4558333,2098365,10835631,3318817,374074330,332639529,122919696,4389286,319443573,2781341,67464020,194709238,210061039,364506106,28949044,40889076,161172338,17943181,4557976,62738484,365813173,6137343,350610552,17942703,576308,223674070,15826518,1310997,93279697,4139395,255311799,157837067,361132363,357380836,146387678,383280379,1127268,299856826,13786789,1311054,46015217,3402130,381353319,30750059,218766885,340707375,27065817,355333104,2624634,62738384,241913553,304446010];
-                let giUsed = snpgi;
-                if(specialGiArray.includes(gi)) giUsed = gi;
-                thisClass.showClinvarPart2(chnid, chnidBase, giUsed);
-            }
-          },
-          error : function(xhr, textStatus, errorThrown ) {
-            this.tryCount++;
-            if(this.tryCount <= this.retryLimit) {
-                //try again
-                $.ajax(this);
-                return;
-            }
-            if(bSnpOnly) {
-                thisClass.processNoSnp(chnid);
-            }
-            else {
-                thisClass.processNoClinvar(chnid);
-            }
-            return;
-          }
-       });
-    }
     showSnpPart2(chnid, chnidBase, gi) { let ic = this.icn3d; ic.icn3dui;
         let thisClass = this;
         if(gi !== undefined) {
@@ -43944,14 +44332,13 @@ class Label {
                     }
                     else {
                         let factor = (label.factor) ? oriFactor * label.factor : oriFactor;
-
                         bb = this.textSpriteCls.makeTextSprite(label.text, {fontsize: parseInt(labelsize), textColor: labelcolor, borderColor: labelbackground, backgroundColor: labelbackground, alpha: labelalpha, bSchematic: 0, factor: factor});
                     }
                 }
 
                 let labelOffset = (name == 'schematic' || name == 'residue') ? 0 : ic.coilWidth; // 0.3
-                bb.position.set(label.position.x + labelOffset, label.position.y + labelOffset, label.position.z + labelOffset);
-                ic.mdl.add(bb);
+                bb.position.set(parseFloat(label.position.x) + labelOffset, parseFloat(label.position.y) + labelOffset, parseFloat(label.position.z) + labelOffset);
+                ic.mdl.add(bb);          
                 // do not add labels to objects for pk
             }
         }
@@ -56245,10 +56632,10 @@ 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;';
 
@@ -56295,7 +56682,7 @@ 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
@@ -56509,7 +56896,9 @@ 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>";
@@ -58293,10 +58682,10 @@ 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" };
@@ -58606,23 +58995,19 @@ 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>";
 
@@ -58664,6 +59049,7 @@ class SetDialog {
         html += "File type: ";
         html += "<select id='" + me.pre + "filetype'>";
         html += me.htmlCls.optionStr + "'pdb' selected>PDB</option>";
+        html += me.htmlCls.optionStr + "'mmcif'>mmCIF</option>";
         html += me.htmlCls.optionStr + "'mol2'>Mol2</option>";
         html += me.htmlCls.optionStr + "'sdf'>SDF</option>";
         html += me.htmlCls.optionStr + "'xyz'>XYZ</option>";
@@ -58967,7 +59353,7 @@ 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>";
 
 
@@ -59341,31 +59727,7 @@ class SetDialog {
         html += "</div>";
         html += "</div>";
 
-        html += "<div class='icn3d-box' style='width:520px;'><b>Annotations:&nbsp;</b><br><table border=0><tr>";
-        let tmpStr1 = "<td style='min-width:110px;'><span style='white-space:nowrap'>";
-        let tmpStr2 = "<td style='min-width:130px;'><span style='white-space:nowrap'>";
-
-        html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_all'>All" + me.htmlCls.space2 + "</span></td>";
-        html += tmpStr2 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_cdd' checked>Conserved Domains" + me.htmlCls.space2 + "</span></td>";
-        html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_clinvar'>ClinVar" + me.htmlCls.space2 + "</span></td>";
-        html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_binding'>Functional Sites" + me.htmlCls.space2 + "</span></td>";
-        html += "</tr><tr>";
-        html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_custom'>Custom" + me.htmlCls.space2 + "</span></td>";
-        html += tmpStr2 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_3dd'>3D Domains" + me.htmlCls.space2 + "</span></td>";
-        html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_snp'>SNPs" + me.htmlCls.space2 + "</span></td>";
-        html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_interact'>Interactions" + me.htmlCls.space2 + "</span></td>";
-        html += "<td></td>";
-        html += "</tr><tr>";
-        html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_ssbond'>Disulfide Bonds" + me.htmlCls.space2 + "</span></td>";
-        html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_crosslink'>Cross-Linkages" + me.htmlCls.space2 + "</span></td>";
-        if(me.cfg.opmid !== undefined) {
-            html += "<td style='min-width:110px;'><span id='" + me.pre + "anno_transmemli' style='white-space:nowrap'>" + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_transmem'>Transmembrane" + me.htmlCls.space2 + "</span></td>";
-        }
-        else {
-            html += "<td style='min-width:110px;'><span id='" + me.pre + "anno_transmemli' style='display:none; white-space:nowrap'>" + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_transmem'>Transmembrane" + me.htmlCls.space2 + "</span></td>";
-        }
-        html += "<td></td>";
-        html += "</tr></table></div>";
+        html += this.getAnnoHeader();
 
         html += "<button style='white-space:nowrap; margin-left:5px;' id='" + me.pre + "showallchains'>Show All Chains</button><br>";
 
@@ -59449,7 +59811,7 @@ 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 + "'>";
@@ -59480,6 +59842,39 @@ class SetDialog {
 
         return html;
     }
+
+    getAnnoHeader() { let me = this.icn3dui; me.icn3d;
+        let html = '';
+
+        html += "<div id='" + me.pre + "annoHeaderSection' class='icn3d-box' style='width:520px;'><b>Annotations:&nbsp;</b><br>";
+        html += "<div id='" + me.pre + "annoHeader'><table border=0><tr>";
+        let tmpStr1 = "<td style='min-width:110px;'><span style='white-space:nowrap'>";
+        let tmpStr2 = "<td style='min-width:130px;'><span style='white-space:nowrap'>";
+
+        html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_all'>All" + me.htmlCls.space2 + "</span></td>";
+        html += tmpStr2 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_cdd' checked>Conserved Domains" + me.htmlCls.space2 + "</span></td>";
+        html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_clinvar'>ClinVar" + me.htmlCls.space2 + "</span></td>";
+        html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_binding'>Functional Sites" + me.htmlCls.space2 + "</span></td>";
+        html += "</tr><tr>";
+        html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_custom'>Custom" + me.htmlCls.space2 + "</span></td>";
+        html += tmpStr2 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_3dd'>3D Domains" + me.htmlCls.space2 + "</span></td>";
+        html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_snp'>SNPs" + me.htmlCls.space2 + "</span></td>";
+        html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_interact'>Interactions" + me.htmlCls.space2 + "</span></td>";
+        html += "<td></td>";
+        html += "</tr><tr>";
+        html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_ssbond'>Disulfide Bonds" + me.htmlCls.space2 + "</span></td>";
+        html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_crosslink'>Cross-Linkages" + me.htmlCls.space2 + "</span></td>";
+        if(me.cfg.opmid !== undefined) {
+            html += "<td style='min-width:110px;'><span id='" + me.pre + "anno_transmemli' style='white-space:nowrap'>" + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_transmem'>Transmembrane" + me.htmlCls.space2 + "</span></td>";
+        }
+        else {
+            html += "<td style='min-width:110px;'><span id='" + me.pre + "anno_transmemli' style='display:none; white-space:nowrap'>" + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_transmem'>Transmembrane" + me.htmlCls.space2 + "</span></td>";
+        }
+        html += "<td></td>";
+        html += "</tr></table></div></div>";
+
+        return html;
+    }
 }
 
 /**
@@ -59612,6 +60007,24 @@ 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) {
+            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;
@@ -59859,6 +60272,25 @@ 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;
@@ -60082,62 +60514,53 @@ 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) {
-               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) {
-               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" );
@@ -66444,7 +66867,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.12.5';
+    this.REVISION = '3.13.0';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -66628,6 +67051,8 @@ iCn3DUI.prototype.show3DStructure = function(pdbStr) { let me = this;
                     chainidArray.push(structureArray[i] + '_' + chainArray[i]);
                 }
                 
+                chainidArray = ic.chainalignParserCls.addPostfixForChainids(chainidArray);
+                
                 let bRealign = true, bPredefined = true;
                 ic.realignParserCls.realignChainOnSeqAlign(undefined, chainidArray, bRealign, bPredefined);
             }
@@ -66635,25 +67060,40 @@ iCn3DUI.prototype.show3DStructure = function(pdbStr) { let me = this;
         else if(me.cfg.resdef !== undefined && me.cfg.matchedchains !== undefined) {
             let stru_t = Object.keys(ic.structures)[0];
             let chain_t = stru_t + '_' + me.cfg.masterchain;
-            let chainidArray = me.cfg.matchedchains.split(',');
+            let domainidArray = me.cfg.matchedchains.split(',');
+            let chainidArray = [];
+            for(let i = 0, il = domainidArray.length; i  < il; ++i) {
+                let pos = domainidArray[i].lastIndexOf('_');
+                let lastId = domainidArray[i].substr(pos + 1);
+                if(!isNaN(lastId)) { // lastId is domain id
+                    chainidArray.push(domainidArray[i].substr(0, pos));
+                }
+                else {
+                    chainidArray.push(domainidArray[i]);
+                }
+            }
+
             let mmdbafid = '';
             for(let i = 0, il = chainidArray.length; i < il; ++i) {
                 if(i > 0) mmdbafid += ',';
                 mmdbafid += chainidArray[i].substr(0, chainidArray[i].indexOf('_'));
             }
+            
+            // realign
+            ic.chainidArray = [chain_t].concat(chainidArray);
+            ic.chainidArray = ic.chainalignParserCls.addPostfixForChainids(ic.chainidArray);
+
+            me.htmlCls.clickMenuCls.setLogCmd('resdef ' + me.cfg.resdef, true);
+
+            ic.loadCmd = 'vast_search_chainid ' + ic.chainidArray;
+            me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
 
             // load multiple PDBs
             ic.bNCBI = true;
             ic.bMmdbafid = true;
             
-            ic.loadCmd = 'load mmdbaf0 ' + mmdbafid;
-            me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
-
             let bQuery = true;
             ic.chainalignParserCls.downloadMmdbAf(mmdbafid, bQuery);
-
-            // realign
-            ic.chainidArray = [chain_t].concat(chainidArray);
         }
     }
     else if(me.cfg.url !== undefined) {
@@ -66837,7 +67277,7 @@ 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);
     }