icn3d 3.13.0 → 3.14.3

package/icn3d.module.js

@@ -5127,7 +5127,11 @@ class UtilsCls {
         let dz = atom0.coord.z - atom1.coord.z;
         let distSq = dx*dx + dy*dy + dz*dz;
 
-        return distSq < 1.3 * r * r;
+        // r(N) = 0.71, r(H) = 0.31, N-H in residues are about 1.5
+        // factor = (1.5 / 1.02) * (1.5 / 1.02) = 2.16
+        let factor = ((atom0.elem == 'N' && atom1.elem.substr(0,1) == 'H') || (atom1.elem == 'N' && atom0.elem.substr(0,1) == 'H')) ? 2.2 : 1.3;
+
+        return distSq < factor * r * r;
     }
 
     //Convert a three-letter residue name to a one-letter residue abbreviation, e.g., 'LYS' to 'K', or ' A' to 'A' for nucleotides.
@@ -8383,15 +8387,16 @@ class Strand {
                 }
 
                 let maxDist = 6.0;
-                //let bBrokenSs = (prevCoorCA && Math.abs(currentCA.x - prevCoorCA.x) > maxDist) || (prevCoorCA && Math.abs(currentCA.y - prevCoorCA.y) > maxDist) || (prevCoorCA && Math.abs(currentCA.z - prevCoorCA.z) > maxDist);
-                let bBrokenSs = !atoms.hasOwnProperty(atom.serial) || (prevCoorCA && Math.abs(currentCA.x - prevCoorCA.x) > maxDist) || (prevCoorCA && Math.abs(currentCA.y - prevCoorCA.y) > maxDist) || (prevCoorCA && Math.abs(currentCA.z - prevCoorCA.z) > maxDist);
+                let bBrokenSs = (prevCoorCA && Math.abs(currentCA.x - prevCoorCA.x) > maxDist) || (prevCoorCA && Math.abs(currentCA.y - prevCoorCA.y) > maxDist) || (prevCoorCA && Math.abs(currentCA.z - prevCoorCA.z) > maxDist);
+                // The following code didn't work to select one residue
+                // let bBrokenSs = !atoms.hasOwnProperty(atom.serial) || (prevCoorCA && Math.abs(currentCA.x - prevCoorCA.x) > maxDist) || (prevCoorCA && Math.abs(currentCA.y - prevCoorCA.y) > maxDist) || (prevCoorCA && Math.abs(currentCA.z - prevCoorCA.z) > maxDist);
 
-                if(bBrokenSs && atom.ss === 'sheet') {
-                    bSheetSegment = true;
-                }
-                else if(bBrokenSs && atom.ss === 'helix') {
-                    bHelixSegment = true;
-                }
+                // if(bBrokenSs && atom.ss === 'sheet') {
+                //     bSheetSegment = true;
+                // }
+                // else if(bBrokenSs && atom.ss === 'helix') {
+                //     bHelixSegment = true;
+                // }
 
                 if ((atom.ssbegin || atom.ssend || (drawnResidueCount === totalResidueCount - 1) || bBrokenSs) && pnts[0].length > 0 && bSameChain) {
                     let atomName = 'CA';
@@ -14678,7 +14683,10 @@ class DefinedSets {
        ic.hAtoms = {};
        this.setHAtomsFromSets(orArray, 'or');
 
-       if(Object.keys(ic.hAtoms).length == 0) ic.hAtoms = me.hashUtilsCls.cloneHash(ic.atoms);
+       if(Object.keys(ic.hAtoms).length == 0) {
+           //ic.hAtoms = me.hashUtilsCls.cloneHash(ic.atoms);
+           ic.hAtoms = me.hashUtilsCls.cloneHash(ic.dAtoms);
+       }
        this.setHAtomsFromSets(andArray, 'and');
 
        this.setHAtomsFromSets(notArray, 'not');
@@ -18350,7 +18358,7 @@ class ShowInter {
                         for(let j = 0, jl = ic.atoms[atom.serial].bonds.length; j < jl; ++j) {
                             let serial = ic.atoms[atom.serial].bonds[j];
                             //if(ic.atoms[serial].name === 'H') {
-                            if(atom.elem.substr(0, 1) === 'H') {
+                            if(ic.atoms[serial].elem.substr(0, 1) === 'H') {
                                 ic.dAtoms[serial] = 1;
                                 ic.hAtoms[serial] = 1;
                             }
@@ -18359,11 +18367,29 @@ class ShowInter {
             }
         }
         else {
+            // for(let serial in ic.atoms) {
+            //     ic.dAtoms[serial] = 1;
+            //     ic.hAtoms[serial] = 1;
+            // }  
+
+            // add bonds in heavy atoms
+            //for(let serial in ic.hAtoms) {
             for(let serial in ic.atoms) {
-                ic.dAtoms[serial] = 1;
-                ic.hAtoms[serial] = 1;
-            }            
+                let atom = ic.atoms[serial];
+                //if(atom.name === 'H') {
+                if(atom.elem.substr(0, 1) === 'H') {                   
+                    if(ic.atoms[serial].bonds.length > 0) {
+                        let otherSerial = ic.atoms[serial].bonds[0];
+                        ic.atoms[otherSerial].bonds.push(atom.serial);
+                        if(ic.atoms[otherSerial].bondOrder) ic.atoms[otherSerial].bondOrder.push(1);
+                    }        
+                    
+                    ic.dAtoms[serial] = 1;
+                }
+            }
         }
+
+        ic.bShowHighlight = false;
     }
 
     hideHydrogens() { let ic = this.icn3d; ic.icn3dui;
@@ -18740,7 +18766,7 @@ class SetColor {
                 break;
 
             case 'chain':
-                if(ic.chainsColor !== undefined && Object.keys(ic.chainsColor).length > 0) { // mmdb input
+                if(ic.chainsColor !== undefined && Object.keys(ic.chainsColor).length > 0) { // mmdb input   
                     this.setMmdbChainColor();
                 }
                 else {
@@ -19844,7 +19870,7 @@ class Delphi {
 
        ic.loadPhiFrom = 'delphi';
 
-       let url = "https://www.ncbi.nlm.nih.gov/Structure/delphi/delphi.cgi";
+       let url = me.htmlCls.baseUrl + "delphi/delphi.cgi";
        let pdbid =(me.cfg.cid) ? me.cfg.cid : Object.keys(ic.structures).toString();
        let dataObj = {};
 
@@ -20656,7 +20682,7 @@ class Symd {
        let thisClass = this;
 
        //var url = "https://data.rcsb.org/rest/v1/core/assembly/" + pdbid + "/1";
-       let url = "https://www.ncbi.nlm.nih.gov/Structure/symd/symd.cgi";
+       let url = me.htmlCls.baseUrl + "symd/symd.cgi";
 
        let atomHash = me.hashUtilsCls.intHash(ic.dAtoms, ic.hAtoms);
 
@@ -21803,7 +21829,7 @@ class LoadPDB {
             }
 
             if(!(curChain === atom.chain && curResi === atom.resi)) {
-                // a new residue, add the residue-residue bond beides the regular bonds               
+                // a new residue, add the residue-residue bond besides the regular bonds               
                 this.refreshBonds(curResAtoms, prevCarbonArray[0]);
 
                 prevCarbonArray.splice(0, 1); // remove the first carbon
@@ -23534,7 +23560,7 @@ class Dssp {
 
           ic.pdbParserCls.loadPdbDataRender(bAppend);
 
-          if(ic.deferredMmdbaf !== undefined) ic.deferredMmdbaf.resolve();
+          //if(ic.deferredMmdbaf !== undefined) ic.deferredMmdbaf.resolve();
           if(ic.deferredSecondary !== undefined) ic.deferredSecondary.resolve();
       });
     }
@@ -23653,7 +23679,7 @@ class Dssp {
 
         ic.pdbParserCls.loadPdbDataRender(bAppend);
 
-        if(ic.deferredMmdbaf !== undefined) ic.deferredMmdbaf.resolve();
+        //if(ic.deferredMmdbaf !== undefined) ic.deferredMmdbaf.resolve();
         if(ic.deferredSecondary !== undefined) ic.deferredSecondary.resolve();
     }
 }
@@ -23674,7 +23700,7 @@ class PdbParser {
        let  url, dataType;
 
        if(bAf) {
-           url = "https://alphafold.ebi.ac.uk/files/AF-" + pdbid + "-F1-model_v2.pdb";
+           url = "https://alphafold.ebi.ac.uk/files/AF-" + pdbid + "-F1-model_v3.pdb";
            ic.ParserUtilsCls.setYourNote(pdbid.toUpperCase() + '(AlphaFold) in iCn3D');
        }
        else {
@@ -24818,13 +24844,13 @@ class OpmParser {
        });
     }
 
-    loadOpmData(data, pdbid, bFull, type, pdbid2) { let ic = this.icn3d; ic.icn3dui;
+    loadOpmData(data, pdbid, bFull, type, pdbid2) { let  ic = this.icn3d, me = ic.icn3dui;
         let  thisClass = this;
         let  url, dataType;
 
         if(!pdbid) pdbid = 'stru';
 
-        url = "https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdb_strview.cgi?v=2&program=icn3d&opm&uid=" + pdbid.toLowerCase();
+        url = me.htmlCls.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&opm&uid=" + pdbid.toLowerCase();
         dataType = "jsonp";
 
         $.ajax({
@@ -24965,7 +24991,7 @@ class MmdbParser {
 
         let  molid2rescount = data.moleculeInfor;
         let  molid2color = {}, chain2molid = {}, molid2chain = {};
-        let  chainNameHash = {};
+        let  chainNameHash = {};       
         for(let i in molid2rescount) {
           if(Object.keys(molid2rescount[i]).length === 0) continue;
 
@@ -24985,7 +25011,7 @@ class MmdbParser {
           chain2molid[chain] = i;
           molid2chain[i] = chain;
 
-          ic.chainsColor[chain] =(type !== undefined) ? me.parasCls.thr(me.htmlCls.GREY8) : me.parasCls.thr(color);
+          ic.chainsColor[chain] = (type !== undefined && !me.cfg.mmdbafid) ? me.parasCls.thr(me.htmlCls.GREY8) : me.parasCls.thr(color);
 
           let  geneId =(molid2rescount[i].geneId === undefined) ? '' : molid2rescount[i].geneId;
           let  geneSymbol =(molid2rescount[i].geneSymbol === undefined) ? '' : molid2rescount[i].geneSymbol;
@@ -26101,6 +26127,7 @@ class ChainalignParser {
                 let  ajaxArray = [], indexArray = [], struArray = [];
                 let urlalign = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi";
                 let urltmalign = me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
+                //let urltmalign = "https://test.ncbi.nlm.nih.gov/Structure/tmalign/tmalign.cgi";
 
                 for(let index in ic.afChainIndexHash) {
                     let idArray = ic.afChainIndexHash[index].split('_');
@@ -26556,7 +26583,7 @@ class ChainalignParser {
 
         let  url_t;
         if(ic.mmdbid_t.length > 5) {
-            url_t = "https://alphafold.ebi.ac.uk/files/AF-" + ic.mmdbid_t + "-F1-model_v2.pdb";
+            url_t = "https://alphafold.ebi.ac.uk/files/AF-" + ic.mmdbid_t + "-F1-model_v3.pdb";
 
             targetAjax = $.ajax({
                 url: url_t,
@@ -26594,7 +26621,7 @@ class ChainalignParser {
 
             let  url_q, queryAjax;
             if(ic.mmdbid_q.length > 5) {
-                url_q = "https://alphafold.ebi.ac.uk/files/AF-" + ic.mmdbid_q + "-F1-model_v2.pdb";
+                url_q = "https://alphafold.ebi.ac.uk/files/AF-" + ic.mmdbid_q + "-F1-model_v3.pdb";
 
                 queryAjax = $.ajax({
                     url: url_q,
@@ -26897,7 +26924,7 @@ class ChainalignParser {
             let structure = ic.structArray[i];
 
             if(isNaN(structure) && structure.length > 5) {
-                url_t = "https://alphafold.ebi.ac.uk/files/AF-" + ic.structArray[i] + "-F1-model_v2.pdb";
+                url_t = "https://alphafold.ebi.ac.uk/files/AF-" + ic.structArray[i] + "-F1-model_v3.pdb";
 
                 targetAjax = $.ajax({
                     url: url_t,
@@ -26962,6 +26989,8 @@ class ChainalignParser {
         let  hAtoms = {}, hAtomsTmp = {};
         let  bLastQuery = false;
 
+        ic.opts['color'] = (structArray.length == 1) ? 'chain' : 'structure';
+
         for(let i = 0, il = structArray.length; i < il; ++i) {
             if(i == structArray.length - 1) bLastQuery = true;
 
@@ -26974,10 +27003,11 @@ class ChainalignParser {
                 targetOrQuery = 'query';
                 bAppend = true; 
             }
-
+            
             //if(structArray[i].length > 4) {
             if(structArray[i].length > 5) {  // PDB ID plus postfix could be 5 
-                let bNoDssp = true;
+                //let bNoDssp = true;
+                let bNoDssp = false; // get secondary structure info
                 hAtomsTmp = ic.pdbParserCls.loadPdbData(queryDataArray[i], structArray[i], false, bAppend, targetOrQuery, bLastQuery, bNoDssp);
             }
             else {              
@@ -26990,7 +27020,7 @@ class ChainalignParser {
 
         // calculate secondary structures with applyCommandDssp
         if(bQuery && me.cfg.matchedchains) {
-            $.when(ic.pdbParserCls.applyCommandDssp(true)).then(function() {
+           // $.when(ic.pdbParserCls.applyCommandDssp(true)).then(function() {
                 let bRealign = true, bPredefined = true;
                 ic.realignParserCls.realignChainOnSeqAlign(undefined, ic.chainidArray, bRealign, bPredefined);
                 // reset annotations
@@ -26999,11 +27029,10 @@ class ChainalignParser {
                 if($('#' + ic.pre + 'dl_selectannotations').dialog( 'isOpen' )) {
                     $('#' + ic.pre + 'dl_selectannotations').dialog( 'close' );
                 }
-           });
-        }
-        else {
-            ic.pdbParserCls.applyCommandDssp(true);
+           //});
         }
+
+        if(ic.deferredMmdbaf !== undefined) ic.deferredMmdbaf.resolve();
     }
 }
 
@@ -28451,6 +28480,24 @@ class LoadScript {
 
               return;
           }
+          else if(ic.commands[i].trim().indexOf('set annotation ptm') == 0 ) { // the command may have "|||{"factor"...
+            let  strArray = ic.commands[i].split("|||");
+
+            if(Object.keys(ic.proteins).length > 0 &&(ic.bAjaxPTM === undefined || !ic.bAjaxPTM) ) {
+                $.when(thisClass.applyCommandPTM(strArray[0].trim())).then(function() {
+                    thisClass.execCommandsBase(i + 1, end, steps);
+                });
+            }
+            else {
+                if(Object.keys(ic.proteins).length > 0) {
+                    thisClass.applyCommandPTM(strArray[0].trim());
+                }
+
+                this.execCommandsBase(i + 1, end, steps);
+            }
+
+            return;
+          }
           else if(ic.commands[i].trim().indexOf('set annotation 3ddomain') == 0) { // the command may have "|||{"factor"...
               let  strArray = ic.commands[i].split("|||");
 
@@ -28681,6 +28728,8 @@ class LoadScript {
                 ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
             }
 
+            me.cfg.aligntool = 'vast';
+
             $.when(thisClass.applyCommandRealignByStruct(command)).then(function() {
                thisClass.execCommandsBase(i + 1, end, steps);
             });
@@ -28841,6 +28890,9 @@ class LoadScript {
                     else if(lastCommand.indexOf('set annotation snp') == 0) {
                         thisClass.applyCommandSnp(lastCommand);
                     }
+                    else if(lastCommand.indexOf('set annotation ptm') == 0) {
+                        thisClass.applyCommandPTM(lastCommand);
+                    }
                     else if(lastCommand.indexOf('set annotation 3ddomain') == 0) {
                         thisClass.applyCommand3ddomain(lastCommand);
                     }
@@ -28891,6 +28943,9 @@ class LoadScript {
                             let  nameArray = paraArray[1].split(',');
                             ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
                         }
+
+                        me.cfg.aligntool = 'vast';
+
                         thisClass.applyCommandRealignByStruct(lastCommand);
                     }
                     else if(lastCommand.indexOf('realign on tmalign') == 0) {
@@ -29296,6 +29351,25 @@ class LoadScript {
       return ic.deferredSnp.promise();
     }
 
+    applyCommandPTMBase(command) { let ic = this.icn3d; ic.icn3dui;
+        // chain functions together
+        let  pos = command.lastIndexOf(' '); // set annotation clinvar
+        command.substr(pos + 1);
+  
+        ic.annotationCls.setAnnoTabPTM();
+    }
+
+    applyCommandPTM(command) { let ic = this.icn3d; ic.icn3dui;
+        let  thisClass = this;
+  
+        // chain functions together
+        ic.deferredPTM = $.Deferred(function() {
+            thisClass.applyCommandPTMBase(command);
+        }); // end of me.deferred = $.Deferred(function() {
+  
+        return ic.deferredPTM.promise();
+    }
+
     applyCommand3ddomainBase(command) { let ic = this.icn3d; ic.icn3dui;
       // chain functions together
       let  pos = command.lastIndexOf(' ');
@@ -29640,7 +29714,7 @@ class ResizeCanvas {
         //let  itemArray = ['dl_selectannotations', 'dl_alignment', 'dl_2ddgm', 'dl_definedsets', 'dl_graph',
         //    'dl_linegraph', 'dl_scatterplot', 'dl_contactmap', 'dl_allinteraction', 'dl_copyurl',
         //    'dl_symmetry', 'dl_symd', 'dl_rmsd', 'dl_legend', 'dl_disttable'];
-        let itemArray = ['dl_2ddgm', 'dl_2dctn', 'dl_alignment', 'dl_sequence2', 'dl_definedsets', 'dl_setsmenu', 'dl_command', 'dl_setoperations', 'dl_vast', 'dl_foldseek', 'dl_mmtfid', 'dl_pdbid', 'dl_afid', 'dl_opmid', 'dl_pdbfile', 'dl_pdbfile_app', 'dl_rescolorfile', 'dl_customcolor', 'dl_align', 'dl_alignaf', 'dl_chainalign', 'dl_mutation', 'dl_mol2file', 'dl_sdffile', 'dl_xyzfile', 'dl_afmapfile', 'dl_urlfile', 'dl_mmciffile', 'dl_mmcifid', 'dl_mmdbid', 'dl_mmdbafid', 'dl_blast_rep_id', 'dl_yournote', 'dl_gi', 'dl_uniprotid', 'dl_cid', 'dl_pngimage', 'dl_state', 'dl_fixedversion', 'dl_selection', 'dl_dsn6', 'dl_dsn6url', 'dl_clr', 'dl_symmetry', 'dl_symd', 'dl_contact', 'dl_hbonds', 'dl_realign', 'dl_realignbystruct', 'dl_allinteraction', 'dl_interactionsorted', 'dl_linegraph', 'dl_linegraphcolor', 'dl_scatterplot', 'dl_scatterplotcolor', 'dl_contactmap', 'dl_alignerrormap', 'dl_elecmap2fofc', 'dl_elecmapfofc', 'dl_emmap', 'dl_aroundsphere', 'dl_adjustmem', 'dl_selectplane', 'dl_addlabel', 'dl_addlabelselection', 'dl_labelColor', 'dl_distance', 'dl_stabilizer', 'dl_disttwosets', 'dl_distmanysets', 'dl_stabilizer_rm', 'dl_thickness', 'dl_thickness2', 'dl_addtrack', 'dl_addtrack_tabs', 'dl_saveselection', 'dl_copyurl', 'dl_selectannotations', 'dl_annotations_tabs', 'dl_anno_view_tabs', 'dl_annotations', 'dl_graph', 'dl_svgcolor', 'dl_area', 'dl_colorbyarea', 'dl_rmsd', 'dl_buriedarea', 'dl_propbypercentout', 'dl_propbybfactor', 'dl_legend', 'dl_disttable'];
+        let itemArray = ['dl_2ddgm', 'dl_2dctn', 'dl_alignment', 'dl_sequence2', 'dl_definedsets', 'dl_setsmenu', 'dl_command', 'dl_setoperations', 'dl_vast', 'dl_foldseek', 'dl_mmtfid', 'dl_pdbid', 'dl_afid', 'dl_opmid', 'dl_pdbfile', 'dl_pdbfile_app', 'dl_rescolorfile', 'dl_customcolor', 'dl_align', 'dl_alignaf', 'dl_chainalign', 'dl_chainalign2', 'dl_chainalign3', 'dl_mutation', 'dl_mol2file', 'dl_sdffile', 'dl_xyzfile', 'dl_afmapfile', 'dl_urlfile', 'dl_mmciffile', 'dl_mmcifid', 'dl_mmdbid', 'dl_mmdbafid', 'dl_blast_rep_id', 'dl_yournote', 'dl_gi', 'dl_uniprotid', 'dl_cid', 'dl_pngimage', 'dl_state', 'dl_fixedversion', 'dl_selection', 'dl_dsn6', 'dl_dsn6url', 'dl_clr', 'dl_symmetry', 'dl_symd', 'dl_contact', 'dl_hbonds', 'dl_realign', 'dl_realignbystruct', 'dl_allinteraction', 'dl_interactionsorted', 'dl_linegraph', 'dl_linegraphcolor', 'dl_scatterplot', 'dl_scatterplotcolor', 'dl_contactmap', 'dl_alignerrormap', 'dl_elecmap2fofc', 'dl_elecmapfofc', 'dl_emmap', 'dl_aroundsphere', 'dl_adjustmem', 'dl_selectplane', 'dl_addlabel', 'dl_addlabelselection', 'dl_labelColor', 'dl_distance', 'dl_stabilizer', 'dl_disttwosets', 'dl_distmanysets', 'dl_stabilizer_rm', 'dl_thickness', 'dl_thickness2', 'dl_addtrack', 'dl_addtrack_tabs', 'dl_saveselection', 'dl_copyurl', 'dl_selectannotations', 'dl_annotations_tabs', 'dl_anno_view_tabs', 'dl_annotations', 'dl_graph', 'dl_svgcolor', 'dl_area', 'dl_colorbyarea', 'dl_rmsd', 'dl_buriedarea', 'dl_propbypercentout', 'dl_propbybfactor', 'dl_legend', 'dl_disttable'];
 
         for(let i in itemArray) {
             let  item = itemArray[i];
@@ -30837,7 +30911,8 @@ class ShowSeq {
         if(seqLength > ic.maxAnnoLength) {
             ic.maxAnnoLength = seqLength;
         }
-        let itemArray = ['giseq', 'cddsite', 'clinvar', 'snp', 'domain', 'interaction', 'custom', 'ssbond', 'crosslink', 'transmem'];
+        //let itemArray = ['giseq', 'cddsite', 'ptm', 'clinvar', 'snp', 'domain', 'interaction', 'custom', 'ssbond', 'crosslink', 'transmem'];
+        let itemArray = ['giseq', 'cddsite', 'clinvar', 'snp', 'ptm', 'ssbond', 'crosslink', 'transmem', 'domain', 'custom', 'interaction'];
         for(let i in itemArray) {
             let item = itemArray[i];
             if($("#" + ic.pre + item + "_" + chnid).length) $("#" + ic.pre + item + "_" + chnid).width(divLength);
@@ -32677,7 +32752,7 @@ class AnnoCddSite {
         let chnidArray = Object.keys(ic.protein_chainid);
         // show conserved domains and binding sites
         // live search
-        let url = me.htmlCls.baseUrl + "cdannots/cdannots.fcgi?fmt&frclive&live=lcl&queries=" + chnidBaseArray;
+        let url = me.htmlCls.baseUrl + "cdannots/cdannots.fcgi?fmt&frclive&live=lcl&queries=" + chnidBaseArray;     
         // precalculated
         //let url = me.htmlCls.baseUrl + "cdannots/cdannots.fcgi?fmt&live=lcl&queries=" + chnidBaseArray;
         // live search for AlphaFold structures
@@ -32723,7 +32798,7 @@ class AnnoCddSite {
 
                //url = me.htmlCls.baseUrl + "cdannots/cdannots.fcgi?fmt&live=lcl&queries=" + ic.giSeq[chnidArray[0]].join('');
                // live searchE
-               url = me.htmlCls.baseUrl + "cdannots/cdannots.fcgi?fmt&frclive&live=lcl&queries=" + seq;
+               url = me.htmlCls.baseUrl + "cdannots/cdannots.fcgi?fmt&frclive&live=lcl&queries=" + seq;             
                // precalculated
                //url = me.htmlCls.baseUrl + "cdannots/cdannots.fcgi?fmt&live=lcl&queries=" + seq;
 
@@ -33799,6 +33874,9 @@ class ApplyCommand {
       else if(command == 'set annotation interaction') {
           ic.annotationCls.setAnnoTabInteraction();
       }
+      else if(command == 'set annotation ptm') {
+        ic.annotationCls.setAnnoTabPTM();
+    }
       else if(command == 'set annotation cdd') {
           ic.annotationCls.setAnnoTabCdd();
       }
@@ -33845,6 +33923,9 @@ class ApplyCommand {
           else if(type == 'site') {
               ic.annotationCls.hideAnnoTabSite();
           }
+          else if(type == 'ptm') {
+            ic.annotationCls.hideAnnoTabPTM();
+        }
           else if(type == 'interaction') {
               ic.annotationCls.hideAnnoTabInteraction();
           }
@@ -34997,7 +35078,7 @@ class ApplyCommand {
         else if(cmd.indexOf('realign on seq align') == 0) return 'File > Realign Selection > on Sequence Alignment';
         else if(cmd.indexOf('realign') == 0) return 'File > Realign Selection > Residue by Residue';
         else if(cmd.indexOf('graph interaction pairs') == 0) return hbondIntStr + ' > 2D Graph(Force-Directed)';
-        else if(cmd.indexOf('export canvas') == 0) return 'File > Save Files > iCn3D PNG Image';
+        else if(cmd.indexOf('export canvas') == 0) return 'File > Save File > iCn3D PNG Image';
         else if(cmd == 'export stl file') return printStr + 'STL';
         else if(cmd == 'export vrml file') return printStr + 'VRML(Color)';
         else if(cmd == 'export stl stabilizer file') return printStr + 'STL W/ Stabilizers';
@@ -35043,6 +35124,7 @@ class ApplyCommand {
         else if(cmd== 'set view overview') return seqAnnoStr + ': "Summary" tab';
         else if(cmd == 'set annotation custom') return seqAnnoStr + ': "Custom" checkbox';
         else if(cmd == 'set annotation interaction') return seqAnnoStr + ': "Interactions" checkbox';
+        else if(cmd == 'set annotation ptm') return seqAnnoStr + ': "PTM" checkbox';
         else if(cmd == 'set annotation cdd') return seqAnnoStr + ': "Conserved Domains" checkbox';
         else if(cmd == 'set annotation site') return seqAnnoStr + ': "Functional Sites" checkbox';
         else if(cmd == 'set annotation ssbond') return seqAnnoStr + ': "Disulfide Bonds" checkbox';
@@ -35331,7 +35413,9 @@ class SelectByCommand {
                  bResidueId = true;
                }
                else {
-                 if(residueStrArray[j][0] === '3' && residueStrArray[j].length > 1 &&(residueStrArray[j].length - 1) % 3 === 0) { // three letter residue string, such as :3LysArg
+                 //if(residueStrArray[j].length > 1 && residueStrArray[j][0] === '3' && (residueStrArray[j].length - 1) % 3 === 0) { // three letter residue string, such as :3LysArg
+                 if(residueStrArray[j].length > 1 && residueStrArray[j][0] === '3' 
+                     && isNaN(residueStrArray[j][1]) && residueStrArray[j][0] !== '-') { // three letter residue string, such as :3LysArg or :3ZN, but not :30 neither :3-10
                    let  tmpStr = residueStrArray[j].toUpperCase();
                    threeLetterResidueStr = tmpStr.substr(1);
                    bResidueArrayThree = true;
@@ -35447,7 +35531,8 @@ class SelectByCommand {
                            }
                            else if(bResidueArrayThree) {
                                let  threeLetter = me.utilsCls.residueAbbr2Name(ic.chainsSeq[molecule_chain][s].name);
-                               chainSeq +=(threeLetter.length == 3) ? threeLetter : '   ';
+
+                               chainSeq +=(threeLetter.length == 3) ? threeLetter : threeLetter.padEnd(3, '_');
                            }
                            resiArray.push(ic.chainsSeq[molecule_chain][s].resi);
                        }
@@ -36345,7 +36430,8 @@ class SetSeqAlign {
               if(i > 0) {
                   let  index1 = alignIndex;
                   for(let j = prevIndex1 + 1, jl = start1; j < jl; ++j) {
-                      if(ic.chainsSeq[chainid1] === undefined) break;
+                      if(ic.chainsSeq[chainid1] === undefined || ic.chainsSeq[chainid1][j] === undefined) break;
+
                       let  resi = ic.chainsSeq[chainid1][j].resi;
                       let  resn = ic.chainsSeq[chainid1][j].name.toLowerCase();
 
@@ -36359,7 +36445,8 @@ class SetSeqAlign {
 
                   let  index2 = alignIndex;
                   for(let j = prevIndex2 + 1, jl = start2; j < jl; ++j) {
-                      if(ic.chainsSeq[chainid2] === undefined) break;
+                      if(ic.chainsSeq[chainid2] === undefined || ic.chainsSeq[chainid2] === undefined) break;
+                      
                       let  resi = ic.chainsSeq[chainid2][j].resi;
                       let  resn = ic.chainsSeq[chainid2][j].name.toLowerCase();
 
@@ -36505,11 +36592,15 @@ class SetSeqAlign {
         // start and end of MSA
         let start_t = 9999, end_t = -1;
 
+        let baseResi = ic.chainsSeq[chainid1][0].resi - 1;
+
         for(let index = 1, indexl = chainidArray.length; index < indexl; ++index) { 
             let chainIndex = index - 1;
+            if(!ic.qt_start_end[chainIndex]) continue;
+
             for(let i = 0, il = ic.qt_start_end[chainIndex].length; i < il; ++i) {
                 let  start1, end1;
-                if(bRealign) { // realresidue numbers are stored
+                if(bRealign) { // real residue numbers are stored
                     start1 = ic.qt_start_end[chainIndex][i].t_start;
                     end1 = ic.qt_start_end[chainIndex][i].t_end;
                 }
@@ -36517,9 +36608,9 @@ class SetSeqAlign {
                     start1 = ic.qt_start_end[chainIndex][i].t_start - 1;
                     end1 = ic.qt_start_end[chainIndex][i].t_end - 1;
                 }
-
                 for(let j = start1; j <= end1; ++j) {
-                    let resi = this.getResi(chainidArray[0], j, bRealign);
+                    let resiPos = j - baseResi;
+                    let resi = this.getResi(chainidArray[0], resiPos, bRealign);
                     resi2range_t[resi] = 1;
                     if(j < start_t) start_t = j;
                     if(j > end_t) end_t = j;
@@ -36527,6 +36618,9 @@ class SetSeqAlign {
             }
         }
 
+        // TM-align should use "start1 = ic.qt_start_end[chainIndex][i].t_start - 1", but the rest are the same as ""bRealign"
+        if(me.cfg.aligntool == 'tmalign') bRealign = true; // real residue numbers are stored
+
         let resi2rangeArray = Object.keys(resi2range_t);
         resi2rangeArray.sort(function(a, b) {
             return parseInt(a) - parseInt(b);
@@ -36573,7 +36667,7 @@ class SetSeqAlign {
         for(let j = 0, jl = ic.chainsSeq[chainid1].length; j < jl; ++j) { 
             let resi = ic.chainsSeq[chainid1][j].resi;
 
-            if((j < start_t || j > end_t) ) {
+            if((j + baseResi < start_t || j + baseResi > end_t) ) {
                 continue;
             }
 
@@ -37811,7 +37905,7 @@ class ParserUtils {
               if(me.cfg.showanno) {
                    let  cmd = "view annotations";
                    me.htmlCls.clickMenuCls.setLogCmd(cmd, true);
-                   ic.showAnnoCls.showAnnotations();
+                   ic.showAnnoCls.showAnnotations(); 
               }
               if(me.cfg.closepopup) {
                   ic.resizeCanvasCls.closeDialogs();
@@ -38302,8 +38396,8 @@ class HlSeq {
       if(me.bNode) return;
 
       let thisClass = this;
-      $("#" + ic.pre + "dl_sequence2").add("[id^=" + ic.pre + "dt_giseq]").add("[id^=" + ic.pre + "dt_custom]").add("[id^=" + ic.pre + "dt_site]").add("[id^=" + ic.pre + "dt_snp]").add("[id^=" + ic.pre + "dt_clinvar]").add("[id^=" + ic.pre + "dt_cdd]").add("[id^=" + ic.pre + "dt_domain]").add("[id^=" + ic.pre + "dt_interaction]").add("[id^=" + ic.pre + "dt_ssbond]").add("[id^=" + ic.pre + "dt_crosslink]").add("[id^=" + ic.pre + "dt_transmem]")
-      .add("[id^=" + ic.pre + "tt_giseq]").add("[id^=" + ic.pre + "tt_custom]").add("[id^=" + ic.pre + "tt_site]").add("[id^=" + ic.pre + "tt_snp]").add("[id^=" + ic.pre + "tt_clinvar]").add("[id^=" + ic.pre + "tt_cdd]").add("[id^=" + ic.pre + "tt_domain]").add("[id^=" + ic.pre + "tt_interaction]").add("[id^=" + ic.pre + "tt_ssbond]").add("[id^=" + ic.pre + "tt_crosslink]").add("[id^=" + ic.pre + "tt_transmem]")
+      $("#" + ic.pre + "dl_sequence2").add("[id^=" + ic.pre + "dt_giseq]").add("[id^=" + ic.pre + "dt_custom]").add("[id^=" + ic.pre + "dt_site]").add("[id^=" + ic.pre + "dt_ptm]").add("[id^=" + ic.pre + "dt_snp]").add("[id^=" + ic.pre + "dt_clinvar]").add("[id^=" + ic.pre + "dt_cdd]").add("[id^=" + ic.pre + "dt_domain]").add("[id^=" + ic.pre + "dt_interaction]").add("[id^=" + ic.pre + "dt_ssbond]").add("[id^=" + ic.pre + "dt_crosslink]").add("[id^=" + ic.pre + "dt_transmem]")
+      .add("[id^=" + ic.pre + "tt_giseq]").add("[id^=" + ic.pre + "tt_custom]").add("[id^=" + ic.pre + "tt_site]").add("[id^=" + ic.pre + "tt_ptm]").add("[id^=" + ic.pre + "tt_snp]").add("[id^=" + ic.pre + "tt_clinvar]").add("[id^=" + ic.pre + "tt_cdd]").add("[id^=" + ic.pre + "tt_domain]").add("[id^=" + ic.pre + "tt_interaction]").add("[id^=" + ic.pre + "tt_ssbond]").add("[id^=" + ic.pre + "tt_crosslink]").add("[id^=" + ic.pre + "tt_transmem]")
       .selectable({
           distance: 1, //Tolerance, in pixels, for when selecting should start. If specified, selecting will not start until the mouse has been dragged beyond the specified distance.
           stop: function() { let ic = thisClass.icn3d;
@@ -38356,11 +38450,11 @@ class HlSeq {
           }
       });
 
-      $("[id^=" + ic.pre + "ov_giseq]").add("[id^=" + ic.pre + "ov_custom]").add("[id^=" + ic.pre + "ov_site]").add("[id^=" + ic.pre + "ov_snp]").add("[id^=" + ic.pre + "ov_clinvar]").add("[id^=" + ic.pre + "ov_cdd]").add("[id^=" + ic.pre + "ov_domain]").add("[id^=" + ic.pre + "ov_interaction]").add("[id^=" + ic.pre + "ov_ssbond]").add("[id^=" + ic.pre + "ov_crosslink]").add("[id^=" + ic.pre + "ov_transmem]")
-      .add("[id^=" + ic.pre + "tt_giseq]").add("[id^=" + ic.pre + "tt_custom]").add("[id^=" + ic.pre + "tt_site]").add("[id^=" + ic.pre + "tt_snp]").add("[id^=" + ic.pre + "tt_clinvar]").add("[id^=" + ic.pre + "tt_cdd]").add("[id^=" + ic.pre + "tt_domain]").add("[id^=" + ic.pre + "tt_interaction]").add("[id^=" + ic.pre + "tt_ssbond]").add("[id^=" + ic.pre + "tt_crosslink]").add("[id^=" + ic.pre + "tt_transmem]")
+      $("[id^=" + ic.pre + "ov_giseq]").add("[id^=" + ic.pre + "ov_custom]").add("[id^=" + ic.pre + "ov_site]").add("[id^=" + ic.pre + "ov_ptm]").add("[id^=" + ic.pre + "ov_snp]").add("[id^=" + ic.pre + "ov_clinvar]").add("[id^=" + ic.pre + "ov_cdd]").add("[id^=" + ic.pre + "ov_domain]").add("[id^=" + ic.pre + "ov_interaction]").add("[id^=" + ic.pre + "ov_ssbond]").add("[id^=" + ic.pre + "ov_crosslink]").add("[id^=" + ic.pre + "ov_transmem]")
+      .add("[id^=" + ic.pre + "tt_giseq]").add("[id^=" + ic.pre + "tt_custom]").add("[id^=" + ic.pre + "tt_site]").add("[id^=" + ic.pre + "tt_ptm]").add("[id^=" + ic.pre + "tt_snp]").add("[id^=" + ic.pre + "tt_clinvar]").add("[id^=" + ic.pre + "tt_cdd]").add("[id^=" + ic.pre + "tt_domain]").add("[id^=" + ic.pre + "tt_interaction]").add("[id^=" + ic.pre + "tt_ssbond]").add("[id^=" + ic.pre + "tt_crosslink]").add("[id^=" + ic.pre + "tt_transmem]")
 
-      .add("#" + ic.pre + "dl_sequence2").add("[id^=" + ic.pre + "dt_giseq]").add("[id^=" + ic.pre + "dt_custom]").add("[id^=" + ic.pre + "dt_site]").add("[id^=" + ic.pre + "dt_snp]").add("[id^=" + ic.pre + "dt_clinvar]").add("[id^=" + ic.pre + "dt_cdd]").add("[id^=" + ic.pre + "dt_domain]").add("[id^=" + ic.pre + "dt_interaction]").add("[id^=" + ic.pre + "dt_ssbond]").add("[id^=" + ic.pre + "dt_crosslink]").add("[id^=" + ic.pre + "dt_transmem]")
-      .add("[id^=" + ic.pre + "tt_giseq]").add("[id^=" + ic.pre + "tt_custom]").add("[id^=" + ic.pre + "tt_site]").add("[id^=" + ic.pre + "tt_snp]").add("[id^=" + ic.pre + "tt_clinvar]").add("[id^=" + ic.pre + "tt_cdd]").add("[id^=" + ic.pre + "tt_domain]").add("[id^=" + ic.pre + "tt_interaction]").add("[id^=" + ic.pre + "tt_ssbond]").add("[id^=" + ic.pre + "tt_crosslink]").add("[id^=" + ic.pre + "tt_transmem]")
+      .add("#" + ic.pre + "dl_sequence2").add("[id^=" + ic.pre + "dt_giseq]").add("[id^=" + ic.pre + "dt_custom]").add("[id^=" + ic.pre + "dt_site]").add("[id^=" + ic.pre + "dt_ptm]").add("[id^=" + ic.pre + "dt_snp]").add("[id^=" + ic.pre + "dt_clinvar]").add("[id^=" + ic.pre + "dt_cdd]").add("[id^=" + ic.pre + "dt_domain]").add("[id^=" + ic.pre + "dt_interaction]").add("[id^=" + ic.pre + "dt_ssbond]").add("[id^=" + ic.pre + "dt_crosslink]").add("[id^=" + ic.pre + "dt_transmem]")
+      .add("[id^=" + ic.pre + "tt_giseq]").add("[id^=" + ic.pre + "tt_custom]").add("[id^=" + ic.pre + "tt_site]").add("[id^=" + ic.pre + "tt_ptm]").add("[id^=" + ic.pre + "tt_snp]").add("[id^=" + ic.pre + "tt_clinvar]").add("[id^=" + ic.pre + "tt_cdd]").add("[id^=" + ic.pre + "tt_domain]").add("[id^=" + ic.pre + "tt_interaction]").add("[id^=" + ic.pre + "tt_ssbond]").add("[id^=" + ic.pre + "tt_crosslink]").add("[id^=" + ic.pre + "tt_transmem]")
 
       .on('click', '.icn3d-seqTitle', function(e) { let ic = thisClass.icn3d;
           e.stopImmediatePropagation();
@@ -38401,7 +38495,7 @@ class HlSeq {
 
       let thisClass = this;
 
-      $("#" + ic.pre + "dl_sequence2").add("[id^=" + ic.pre + "giseq]").add("[id^=" + ic.pre + "custom]").add("[id^=" + ic.pre + "site]").add("[id^=" + ic.pre + "clinvar]").add("[id^=" + ic.pre + "snp]").add("[id^=" + ic.pre + "cdd]").add("[id^=" + ic.pre + "domain]").add("[id^=" + ic.pre + "interaction]").add("[id^=" + ic.pre + "ssbond]").add("[id^=" + ic.pre + "crosslink]").add("[id^=" + ic.pre + "transmem]").on('click', '.icn3d-residue', function(e) { let ic = thisClass.icn3d;
+      $("#" + ic.pre + "dl_sequence2").add("[id^=" + ic.pre + "giseq]").add("[id^=" + ic.pre + "custom]").add("[id^=" + ic.pre + "site]").add("[id^=" + ic.pre + "ptm]").add("[id^=" + ic.pre + "clinvar]").add("[id^=" + ic.pre + "snp]").add("[id^=" + ic.pre + "cdd]").add("[id^=" + ic.pre + "domain]").add("[id^=" + ic.pre + "interaction]").add("[id^=" + ic.pre + "ssbond]").add("[id^=" + ic.pre + "crosslink]").add("[id^=" + ic.pre + "transmem]").on('click', '.icn3d-residue', function(e) { let ic = thisClass.icn3d;
           e.stopImmediatePropagation();
 /*
           //if($(this).attr('id') === ic.pre + "dl_sequence2") {
@@ -38450,7 +38544,7 @@ class HlSeq {
 
       let thisClass = this;
 
-      $("#" + ic.pre + "dl_sequence2").add("[id^=" + ic.pre + "giseq]").add("[id^=" + ic.pre + "custom]").add("[id^=" + ic.pre + "site]").add("[id^=" + ic.pre + "feat]").add("[id^=" + ic.pre + "clinvar]").add("[id^=" + ic.pre + "snp]").add("[id^=" + ic.pre + "cdd]").add("[id^=" + ic.pre + "domain]").add("[id^=" + ic.pre + "interaction]").add("[id^=" + ic.pre + "ssbond]").add("[id^=" + ic.pre + "crosslink]").add("[id^=" + ic.pre + "transmem]").on('click', '.icn3d-seqTitle', function(e) { let ic = thisClass.icn3d;
+      $("#" + ic.pre + "dl_sequence2").add("[id^=" + ic.pre + "giseq]").add("[id^=" + ic.pre + "custom]").add("[id^=" + ic.pre + "site]").add("[id^=" + ic.pre + "ptm]").add("[id^=" + ic.pre + "feat]").add("[id^=" + ic.pre + "clinvar]").add("[id^=" + ic.pre + "snp]").add("[id^=" + ic.pre + "cdd]").add("[id^=" + ic.pre + "domain]").add("[id^=" + ic.pre + "interaction]").add("[id^=" + ic.pre + "ssbond]").add("[id^=" + ic.pre + "crosslink]").add("[id^=" + ic.pre + "transmem]").on('click', '.icn3d-seqTitle', function(e) { let ic = thisClass.icn3d;
           e.stopImmediatePropagation();
 
           //if($(this).attr('id') === ic.pre + "dl_sequence2") {
@@ -38647,7 +38741,7 @@ class HlSeq {
                             let residueid;
                             let structure = chainid.substr(0, chainid.indexOf('_'));
                             for(let i = 0, il = posArray.length; i < il; ++i) {
-                                if($(that).attr('site') !== undefined) {
+                                if($(that).attr('site') !== undefined || $(that).attr('ptm') !== undefined) {
                                     if(ic.bNCBI) {
                                         let residNCBI = chainid + '_' +(parseInt(posArray[i])+1).toString();
                                         // AlphaFold domains calculated on-the-fly have no conversion
@@ -38817,9 +38911,11 @@ class ShowAnno {
         }
 
         let nucleotide_chainid = {}, chemical_chainid = {}, chemical_set = {};
-        ic.protein_chainid = {};
+        //ic.protein_chainid = {};
 
         if(ic.bAnnoShown === undefined || !ic.bAnnoShown || ic.bResetAnno) { // ic.bResetAnno when loading another structure
+            ic.protein_chainid = {};
+
             let chainArray = Object.keys(ic.chains);
 
             if(ic.giSeq === undefined) ic.giSeq = {};
@@ -38860,6 +38956,7 @@ class ShowAnno {
                     chainidBase = chainArray[i];
                 }
                 //if(me.cfg.mmdbid !== undefined) { // protein and chemicals/ions are in different chains
+
                 if(ic.proteins.hasOwnProperty(atom.serial) && ic.chainsSeq[chainArray[i]].length > 1) {
                     ic.protein_chainid[chainArray[i]] = chainidBase;
                 }
@@ -39046,6 +39143,8 @@ class ShowAnno {
             ++i;
         }
         ic.interactChainbase = me.hashUtilsCls.unionHash(ic.interactChainbase, chemical_chainid);
+        ic.PTMChainbase = me.hashUtilsCls.unionHash(ic.PTMChainbase, ic.protein_chainid);
+
         ic.ssbondChainbase = me.hashUtilsCls.unionHash(ic.ssbondChainbase, ic.protein_chainid);
         ic.ssbondChainbase = me.hashUtilsCls.unionHash(ic.ssbondChainbase, chemical_chainid);
         ic.crosslinkChainbase = me.hashUtilsCls.unionHash(ic.crosslinkChainbase, ic.protein_chainid);
@@ -39077,8 +39176,10 @@ class ShowAnno {
             //if(proteinName.length > 40) proteinName = proteinName.substr(0, 40) + "...";
             let categoryStr =(index == 0) ? "<span class='icn3d-annoLargeTitle'><b>Proteins</b>: </span><br><br>" : "";
             let geneLink =(ic.chainsGene[chnid] && ic.chainsGene[chnid].geneId) ? "(Gene: <a href='https://www.ncbi.nlm.nih.gov/gene/" + ic.chainsGene[chnid].geneId + "' target='_blank' title='" + ic.chainsGene[chnid].geneDesc + "'>" + ic.chainsGene[chnid].geneSymbol + "</a>)" : '';
+            let structure = chnid.substr(0, chnid.indexOf('_'));
+            let chainLink = (structure.length > 5) ? '<a href="https://alphafold.ebi.ac.uk/entry/' + structure + '" target="_blank">' + chnid + '</a>' : chnid;
             let chainHtml = "<div id='" + ic.pre + "anno_" + chnid + "' class='icn3d-annotation'>" + categoryStr
-                + "<span style='font-weight:bold;'>Annotations of " + chnid
+                + "<span style='font-weight:bold;'>Annotations of " + chainLink
                 + "</span>: <a class='icn3d-blue' href='https://www.ncbi.nlm.nih.gov/protein?term="
                 + chnid + "' target='_blank' title='" + fullProteinName + "'>" + proteinName + "</a>"
                 + geneLink + "&nbsp;&nbsp;&nbsp;"
@@ -39091,7 +39192,8 @@ class ShowAnno {
                 + this.addButton(chnid, "icn3d-sheetsets", "Sheet Sets", "Define sets for each sheet in this chain and add them to the menu of \"Defined Sets\"", 60, buttonStyle) + "&nbsp;"
                 + this.addButton(chnid, "icn3d-coilsets", "Coil Sets", "Define sets for each coil in this chain and add them to the menu of \"Defined Sets\"", 60, buttonStyle);
             $("#" + ic.pre + "dl_annotations").append(chainHtml);
-            let itemArray = ['giseq', 'cdd', 'clinvar', 'snp', 'domain', 'site', 'interaction', 'custom', 'ssbond', 'crosslink', 'transmem'];
+            //let itemArray = ['giseq', 'cdd', 'clinvar', 'snp', 'domain', 'site', 'ptm', 'interaction', 'custom', 'ssbond', 'crosslink', 'transmem'];
+            let itemArray = ['giseq', 'cdd', 'clinvar', 'snp', 'site', 'ptm', 'ssbond', 'crosslink', 'transmem', 'domain', 'custom', 'interaction'];
             // dt: detailed view, hide by default; ov: overview, show by default
             for(let i in itemArray) {
                 let item = itemArray[i];
@@ -39519,6 +39621,286 @@ class ShowAnno {
 
 }
 
+/**
+ * @author Jiyao Wang <wangjiy@ncbi.nlm.nih.gov> / https://github.com/ncbi/icn3d
+ */
+
+class AnnoPTM {
+    constructor(icn3d) {
+        this.icn3d = icn3d;
+    }
+
+    //Show the annotations of CDD domains and binding sites.
+    showPTM(chnid, chnidBase) { let ic = this.icn3d; ic.icn3dui;
+        let thisClass = this;
+
+        // UniProt ID
+        let structure = chnid.substr(0, chnid.indexOf('_'));
+        let chain = chnid.substr(chnid.indexOf('_') + 1);
+
+        // UniProt ID
+        if( structure.length > 5 ) {
+            let url =  "https://www.ebi.ac.uk/proteins/api/features/" + structure;     
+            $.ajax({
+              url: url,
+              dataType: 'json',
+              cache: true,
+              tryCount : 0,
+              retryLimit : 0, //1
+              success: function(data) {
+                thisClass.parsePTM(data, chnid);
+                if(ic.deferredPTM !== undefined) ic.deferredPTM.resolve();
+              },
+              error : function(xhr, textStatus, errorThrown ) {
+                this.tryCount++;
+                if(this.tryCount <= this.retryLimit) {
+                    //try again
+                    $.ajax(this);
+                    return;
+                }
+
+                thisClass.getNoPTM(chnid);
+
+                return;
+              }
+            });
+        }
+        else { // PDB
+            // get PDB to UniProt mapping
+            // https://www.ebi.ac.uk/pdbe/api/doc/
+            let structLower = structure.substr(0, 4).toLowerCase();
+            let urlMap = "https://www.ebi.ac.uk/pdbe/api/mappings/uniprot/" + structLower;
+
+            $.ajax({
+              url: urlMap,
+              dataType: 'json',
+              cache: true,
+              success: function(dataMap) {
+                let UniProtID = '';
+                if(!ic.UPResi2ResiPosPerChain) ic.UPResi2ResiPosPerChain = {};
+                ic.UPResi2ResiPosPerChain[chnid] = {};
+                let mapping = dataMap[structLower].UniProt;
+
+                let bFound = false;
+                for(let up in mapping) {
+                    let chainArray = mapping[up].mappings;
+                    if(bFound) break;
+
+                    for(let i = 0, il = chainArray.length; i < il; ++i) {
+                    //"entity_id": 3, "end": { "author_residue_number": null, "author_insertion_code": "", "residue_number": 219 }, "chain_id": "A", "start": { "author_residue_number": 94, "author_insertion_code": "", "residue_number": 1 }, "unp_end": 312, "unp_start": 94, "struct_asym_id": "C"
+                        let chainObj = chainArray[i];
+                        if(chainObj.chain_id == chain) {
+                            let start = chainObj.unp_start;
+                            let end = chainObj.unp_end;
+                            let posStart = chainObj.start.residue_number;
+                            let posEnd = chainObj.end.residue_number;
+
+                            if(posEnd - posStart != end - start) {
+                                console.log("There might be some issues in the PDB to UniProt residue mapping.");
+                            }
+
+                            for(let j = 0; j <= end - start; ++j) {
+                                ic.UPResi2ResiPosPerChain[chnid][j + start] = j + posStart - 1; // 0-based
+                            }
+
+                            UniProtID = up;
+                            bFound = true;
+                            break;
+                        }
+                    }
+                }
+
+                if(UniProtID == '') {
+                    thisClass.getNoPTM(chnid);
+                }
+                else {
+                    let url =  "https://www.ebi.ac.uk/proteins/api/features/" + UniProtID;     
+                    $.ajax({
+                        url: url,
+                        dataType: 'json',
+                        cache: true,
+                        tryCount : 0,
+                        retryLimit : 0, //1
+                        success: function(data) {
+                            thisClass.parsePTM(data, chnid);
+                            if(ic.deferredPTM !== undefined) ic.deferredPTM.resolve();
+                        },
+                        error : function(xhr, textStatus, errorThrown ) {
+                            this.tryCount++;
+                            if(this.tryCount <= this.retryLimit) {
+                                //try again
+                                $.ajax(this);
+                                return;
+                            }
+
+                            thisClass.getNoPTM(chnid);
+
+                            return;
+                        }
+                    });
+                }
+              },
+              error : function(xhr, textStatus, errorThrown ) {
+                thisClass.getNoPTM(chnid);
+              }
+            });
+        }
+    }
+
+    parsePTM(data, chnid) { let ic = this.icn3d, me = ic.icn3dui;
+
+        if(me.bNode) {
+            //if(!ic.resid2ptm) ic.resid2ptm = {};
+            ic.resid2ptm = {};
+            ic.resid2ptm[chnid] = [];
+        }
+
+        let ptmHash = {};
+        for(let i = 0, il = data.features.length; i < il; ++i) {
+            let feature = data.features[i];
+
+            if(feature.category == 'PTM' && feature.type != 'DISULFID' && feature.type != 'CROSSLNK') {
+                let title = '';
+                if(feature.type == 'CARBOHYD') {
+                    //title = 'Glycosylation, ' + feature.description;
+                    title = 'Glycosylation';
+                }
+                else if(feature.type == 'LIPID') {
+                    title = 'Lipidation, ' + feature.description;
+                }
+                else if(feature.description.indexOf('Phospho') == 0) {
+                    title = 'Phosphorylation';
+                }
+                else if(feature.description) {
+                    title = feature.description;
+                }
+                else {
+                    title = feature.type;
+                }
+
+                if(!ptmHash[title]) ptmHash[title] = [];
+                ptmHash[title].push(feature);
+            }
+        }
+
+        let index = 0;
+        let html = '', html2 = '', html3 = ''; 
+        html += '<div id="' + ic.pre + chnid + '_ptmseq_sequence" class="icn3d-cdd icn3d-dl_sequence">';
+        html2 += html;
+        html3 += html;
+        let stucture = chnid.substr(0, chnid.indexOf('_'));
+
+        for(let ptm in ptmHash) {
+            let ptmArray = ptmHash[ptm];
+            //"type": "MOD_RES", "category": "PTM", "description": "4-hydroxyproline", "begin": "382", "end": "382",
+            let resPosArray = [];
+            let bCoordinates = false;
+            for(let i = 0, il = ptmArray.length; i < il; ++i) {
+                let begin = parseInt(ptmArray[i].begin);
+                let end = parseInt(ptmArray[i].end);
+
+
+                for(let j = begin; j <= end; ++j) {
+                    if(stucture.length > 5) { // UniProt
+                        resPosArray.push(j - 1); // 0-based
+                    } 
+                    else { // PDB                       
+                        if(ic.UPResi2ResiPosPerChain[chnid][j]) resPosArray.push(ic.UPResi2ResiPosPerChain[chnid][j]);
+                    }
+                    
+                    if(!bCoordinates && ic.residues.hasOwnProperty(chnid + '_' + j)) {
+                        bCoordinates = true;
+                    }
+                }
+            }
+
+            if(resPosArray.length == 0) continue;
+
+            let resCnt = resPosArray.length;
+            let title = 'PTM: ' + ptm;
+            if(title.length > 17) title = title.substr(0, 17) + '...';
+            let fulltitle = ptm;
+
+            let linkStr = (bCoordinates) ? 'icn3d-link icn3d-blue' : '';
+
+            let htmlTmp2 = '<div class="icn3d-seqTitle ' + linkStr + '" ptm="ptm" posarray="' + resPosArray.toString() + '" shorttitle="' + title + '" setname="' + chnid + '_ptm_' + index + '" anno="sequence" chain="' + chnid + '" title="' + fulltitle + '">' + title + ' </div>';
+            let htmlTmp3 = '<span class="icn3d-residueNum" title="residue count">' + resCnt.toString() + ' Res</span>';
+            let htmlTmp = '<span class="icn3d-seqLine">';
+            html3 += htmlTmp2 + htmlTmp3 + '<br>';
+            html += htmlTmp2 + htmlTmp3 + htmlTmp;
+            html2 += htmlTmp2 + htmlTmp3 + htmlTmp;
+            let pre = 'ptm' + index.toString();
+            //var widthPerRes = ic.seqAnnWidth / ic.maxAnnoLength;
+            let prevEmptyWidth = 0;
+            let prevLineWidth = 0;
+            let widthPerRes = 1;
+            for(let i = 0, il = ic.giSeq[chnid].length; i < il; ++i) {
+                html += ic.showSeqCls.insertGap(chnid, i, '-');
+                if(resPosArray.indexOf(i) != -1) {
+                    let cFull = ic.giSeq[chnid][i];
+                    let c = cFull;
+                    if(cFull.length > 1) {
+                        c = cFull[0] + '..';
+                    }
+                    let pos = ic.annoCddSiteCls.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] = 'PTM: ' + ptm;
+                        ic.resid2ptm[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;
+                    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="' + c + pos + '">&nbsp;</div>';
+                        prevEmptyWidth += emptyWidth;
+                        prevLineWidth += widthPerRes;
+                    }
+                }
+                else {
+                    html += '<span>-</span>'; //'<span>-</span>';
+                }
+            }
+            htmlTmp = '<span class="icn3d-residueNum" title="residue count">&nbsp;' + resCnt.toString() + ' Residues</span>';
+            htmlTmp += '</span>';
+            htmlTmp += '<br>';
+            html += htmlTmp;
+            html2 += htmlTmp;
+
+            ++index;
+        }
+
+        html += '</div>';
+        html2 += '</div>';
+        html3 += '</div>';
+
+        $("#" + ic.pre + "dt_ptm_" + chnid).html(html);
+        $("#" + ic.pre + "ov_ptm_" + chnid).html(html2);
+        $("#" + ic.pre + "tt_ptm_" + chnid).html(html3);
+
+        // add here after the ajax call
+        ic.showAnnoCls.enableHlSeq();
+        ic.bAjaxPTM = true;
+    }
+
+    getNoPTM(chnid) { let ic = this.icn3d; ic.icn3dui;
+        console.log( "No PTM data were found for the chain " + chnid + "..." );
+   
+        $("#" + ic.pre + "dt_ptm_" + chnid).html('');
+        $("#" + ic.pre + "ov_ptm_" + chnid).html('');
+        $("#" + ic.pre + "tt_ptm_" + chnid).html('');
+
+        // add here after the ajax call
+        ic.showAnnoCls.enableHlSeq();
+        ic.bAjaxPTM = true;
+        if(ic.deferredPTM !== undefined) ic.deferredPTM.resolve();
+    }
+}
+
 /**
  * @author Jiyao Wang <wangjiy@ncbi.nlm.nih.gov> / https://github.com/ncbi/icn3d
  */
@@ -40648,11 +41030,11 @@ class AnnoSnpClinVar {
             if(ic.deferredClinvar !== undefined) ic.deferredClinvar.resolve();
         }
     }
-    showClinvarPart2(chnid, chnidBase, gi) { let ic = this.icn3d; ic.icn3dui;
+    showClinvarPart2(chnid, chnidBase, gi) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
         //var url = "https://www.ncbi.nlm.nih.gov/projects/SNP/beVarSearch_mt.cgi?appname=iCn3D&format=bed&report=pdb2bed&acc=" + chnidBase;
         //var url = "https://www.ncbi.nlm.nih.gov/Structure/icn3d/clinvar.txt";
-        let url = "https://www.ncbi.nlm.nih.gov/Structure/vastdyn/vastdyn.cgi?chainid_clinvar=" + chnidBase;
+        let url = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi?chainid_clinvar=" + chnidBase;
         if(ic.chainsGene[chnid] && ic.chainsGene[chnid].geneSymbol) {
             url += "&gene=" + ic.chainsGene[chnid].geneSymbol;
         }
@@ -40687,7 +41069,7 @@ class AnnoSnpClinVar {
         });
     }
 
-    showSnpPart2(chnid, chnidBase, gi) { let ic = this.icn3d; ic.icn3dui;
+    showSnpPart2(chnid, chnidBase, gi) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
         if(gi !== undefined) {
       /*      
@@ -40706,7 +41088,7 @@ class AnnoSnpClinVar {
                 } //if(data3 != "") {
                 else {
        */             
-                    let url4 = "https://www.ncbi.nlm.nih.gov/Structure/vastdyn/vastdyn.cgi?chainid_snp=" + chnidBase;
+                    let url4 = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi?chainid_snp=" + chnidBase;
                     if(ic.chainsGene[chnid] && ic.chainsGene[chnid].geneSymbol) {
                         url4 += "&gene=" + ic.chainsGene[chnid].geneSymbol;
                     }
@@ -40835,7 +41217,8 @@ class Annotation {
         this.setAnnoSeqBase(false);
     }
     setAnnoSeqBase(bShow) {  let ic = this.icn3d; ic.icn3dui;
-        let itemArray = ['site', 'snp', 'clinvar', 'cdd', 'domain', 'interaction', 'ssbond', 'crosslink', 'transmem'];
+        //let itemArray = ['site', 'ptm', 'snp', 'clinvar', 'cdd', 'domain', 'interaction', 'ssbond', 'crosslink', 'transmem'];
+        let itemArray = ['cdd', 'clinvar', 'snp', 'site', 'ptm', 'ssbond', 'crosslink', 'transmem', 'domain', 'interaction'];
         for(let i in itemArray) {
             let item = itemArray[i];
             if(bShow) {
@@ -40847,7 +41230,8 @@ class Annotation {
         }
     }
     setAnnoTabBase(bChecked) {  let ic = this.icn3d; ic.icn3dui;
-        let itemArray = ['all', 'binding', 'snp', 'clinvar', 'cdd', '3dd', 'interact', 'custom', 'ssbond', 'crosslink', 'transmem'];
+        //let itemArray = ['all', 'binding', 'ptm', 'snp', 'clinvar', 'cdd', '3dd', 'interact', 'custom', 'ssbond', 'crosslink', 'transmem'];
+        let itemArray = ['all', 'cdd', 'clinvar', 'snp', 'binding', 'ptm', 'ssbond', 'crosslink', 'transmem', '3dd', 'custom', 'interact'];
         for(let i in itemArray) {
             let item = itemArray[i];
             if($("#" + ic.pre + "anno_" + item).length) $("#" + ic.pre + "anno_" + item)[0].checked = bChecked;
@@ -40859,10 +41243,11 @@ class Annotation {
         this.updateClinvar();
         this.updateSnp();
         this.updateDomain();
-        this.updateInteraction();
+        this.updatePTM();
         this.updateSsbond();
         this.updateCrosslink();
         this.updateTransmem();
+        this.updateInteraction();
     }
     hideAnnoTabAll() {  let ic = this.icn3d; ic.icn3dui;
         this.setAnnoTabBase(false);
@@ -40915,6 +41300,11 @@ class Annotation {
             ic.bInteractionShown = false;
             this.updateInteraction();
         }
+        if($("#" + ic.pre + "anno_ptm").length && $("#" + ic.pre + "anno_ptm")[0].checked) {
+            $("[id^=" + ic.pre + "ptm]").show();
+            ic.bPTMShown = false;
+            this.updatePTM();
+        }
         if($("#" + ic.pre + "anno_custom").length && $("#" + ic.pre + "anno_custom")[0].checked) {
             $("[id^=" + ic.pre + "custom]").show();
         }
@@ -40996,6 +41386,15 @@ class Annotation {
         $("[id^=" + ic.pre + "interaction]").hide();
         if($("#" + ic.pre + "anno_interact").length) $("#" + ic.pre + "anno_interact")[0].checked = false;
     }
+    setAnnoTabPTM() {  let ic = this.icn3d; ic.icn3dui;
+        $("[id^=" + ic.pre + "ptm]").show();
+        if($("#" + ic.pre + "anno_ptm").length) $("#" + ic.pre + "anno_ptm")[0].checked = true;
+        this.updatePTM();
+    }
+    hideAnnoTabPTM() {  let ic = this.icn3d; ic.icn3dui;
+        $("[id^=" + ic.pre + "ptm]").hide();
+        if($("#" + ic.pre + "anno_ptm").length) $("#" + ic.pre + "anno_ptm")[0].checked = false;
+    }
     setAnnoTabSsbond() {  let ic = this.icn3d; ic.icn3dui;
         $("[id^=" + ic.pre + "ssbond]").show();
         if($("#" + ic.pre + "anno_ssbond").length) $("#" + ic.pre + "anno_ssbond")[0].checked = true;
@@ -41107,6 +41506,17 @@ class Annotation {
         }
         });
 
+        me.myEventCls.onIds("#" + ic.pre + "anno_ptm", "click", function(e) {
+            if($("#" + ic.pre + "anno_ptm")[0].checked) {
+                thisClass.setAnnoTabPTM();
+                me.htmlCls.clickMenuCls.setLogCmd("set annotation ptm", true);
+            }
+            else {
+                thisClass.hideAnnoTabPTM();
+                me.htmlCls.clickMenuCls.setLogCmd("hide annotation ptm", true);
+            }
+        });
+
         //$("#" + ic.pre + "anno_custom", "click", function(e) {
         me.myEventCls.onIds("#" + ic.pre + "anno_custom", "click", function(e) {
         if($("#" + ic.pre + "anno_custom")[0].checked) {
@@ -41202,7 +41612,7 @@ class Annotation {
         }
     }
     setAnnoDisplay(display, prefix) { let ic = this.icn3d; ic.icn3dui;
-        let itemArray = ['giseq', 'custom', 'site', 'snp', 'clinvar', 'cdd', 'domain', 'interaction', 'ssbond', 'crosslink', 'transmem'];
+        let itemArray = ['giseq', 'custom', 'site', 'ptm', 'snp', 'clinvar', 'cdd', 'domain', 'interaction', 'ssbond', 'crosslink', 'transmem'];
         for(let i in itemArray) {
             let item = itemArray[i];
             $("[id^=" + ic.pre + prefix + "_" + item + "]").attr('style', display);
@@ -41273,6 +41683,15 @@ class Annotation {
         }
         ic.bInteractionShown = true;
     }
+    updatePTM() { let ic = this.icn3d; ic.icn3dui;
+        if(ic.bPTMShown === undefined || !ic.bPTMShown) {
+            for(let chainid in ic.PTMChainbase) {
+                let chainidBase = ic.PTMChainbase[chainid];
+                ic.annoPTMCls.showPTM(chainid, chainidBase);
+            }
+        }
+        ic.bPTMShown = true;
+    }
     updateSsbond() { let ic = this.icn3d; ic.icn3dui;
         if(ic.bSSbondShown === undefined || !ic.bSSbondShown) {
             for(let chainid in ic.ssbondChainbase) {
@@ -43006,9 +43425,12 @@ class Selection {
 
     //Show the selection.
     showSelection() { let  ic = this.icn3d, me = ic.icn3dui;
-        ic.dAtoms = {};
+        //ic.dAtoms = {};
 
-        if(Object.keys(ic.hAtoms).length == 0) this.selectAll_base();
+        if(Object.keys(ic.hAtoms).length == 0) {
+            //this.selectAll_base();
+            ic.hAtoms = me.hashUtilsCls.cloneHash(ic.dAtoms);
+        }
 
         ic.dAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
         ic.viewSelectionAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
@@ -43649,11 +44071,14 @@ class SetStyle {
             console.log("WebGL context was lost. Reset WebGLRenderer and launch iCn3D again.");
 
             ic.renderer = new THREE.WebGLRenderer({
-                canvas: ic.container.get(0),
-                antialias: true,
-                preserveDrawingBuffer: true,
-                alpha: true
+              canvas: ic.oriContainer.get(0), //this.container.get(0),
+              antialias: true,
+              preserveDrawingBuffer: true,
+              sortObjects: false,
+              alpha: true
             });
+            // Enable VR
+            ic.renderer.xr.enabled = true;
 
             ic.drawCls.draw();
 
@@ -44862,7 +45287,8 @@ class ApplySymd {
                 }
                 else { // bSymd, subset, and one chain
                     if(Object.keys(ic.hAtoms).length == 0) {
-                        ic.hAtoms = me.hashUtilsCls.cloneHash(ic.atoms);
+                        //ic.hAtoms = me.hashUtilsCls.cloneHash(ic.atoms);
+                        ic.hAtoms = me.hashUtilsCls.cloneHash(ic.dAtoms);
                     }
 
                     // pick the first 1/order of selection
@@ -45512,7 +45938,8 @@ class VRButton {
             button.style.display = '';
 
             button.style.cursor = 'pointer';
-            button.style.left = 'calc(50% - 50px)';
+            //button.style.left = 'calc(50% - 50px)';
+            button.style.left = 'calc(33% - 50px)';
             button.style.width = '100px';
 
             button.textContent = 'ENTER VR';
@@ -45566,7 +45993,7 @@ class VRButton {
             button.style.display = '';
 
             button.style.cursor = 'auto';
-            button.style.left = 'calc(50% - 75px)';
+            button.style.left = 'calc(33% - 75px)'; //'calc(50% - 75px)';
             button.style.width = '150px';
 
             button.onmouseenter = null;
@@ -45759,7 +46186,8 @@ class ARButton {
 			button.style.display = '';
 
 			button.style.cursor = 'pointer';
-			button.style.left = 'calc(50% - 50px)';
+			//button.style.left = 'calc(50% - 50px)';
+			button.style.left = 'calc(66% - 50px)';
 			button.style.width = '100px';
 
 			button.textContent = 'START AR';
@@ -45807,7 +46235,7 @@ class ARButton {
 			button.style.display = '';
 
 			button.style.cursor = 'auto';
-			button.style.left = 'calc(50% - 75px)';
+			button.style.left = 'calc(66% - 50px)'; //'calc(50% - 75px)';
 			button.style.width = '150px';
 
 			button.onmouseenter = null;
@@ -45904,7 +46332,7 @@ class ARButton {
 
 			}
 
-			message.style.left = 'calc(50% - 90px)';
+			message.style.left = 'calc(66% - 90px)'; //'calc(50% - 90px)';
 			message.style.width = '180px';
 			message.style.textDecoration = 'none';
 
@@ -54286,9 +54714,17 @@ class ClickMenu {
     //    },
     //    clkMn1_chainalign: function() {
         me.myEventCls.onIds("#" + me.pre + "mn1_chainalign", "click", function(e) { me.icn3d;
-           me.htmlCls.dialogCls.openDlg('dl_chainalign', 'Align multiple chains of 3D structures');
+           me.htmlCls.dialogCls.openDlg('dl_chainalign', 'Align multiple chains by structure alignment');
         });
 
+        me.myEventCls.onIds("#" + me.pre + "mn1_chainalign2", "click", function(e) { me.icn3d;
+            me.htmlCls.dialogCls.openDlg('dl_chainalign2', 'Align multiple chains by sequence alignment');
+         });
+
+        me.myEventCls.onIds("#" + me.pre + "mn1_chainalign3", "click", function(e) { me.icn3d;
+            me.htmlCls.dialogCls.openDlg('dl_chainalign3', 'Align multiple chains residue by residue');
+         });
+
         me.myEventCls.onIds("#" + me.pre + "mn1_mutation", "click", function(e) { me.icn3d;
            me.htmlCls.dialogCls.openDlg('dl_mutation', 'Show the mutations in 3D');
         });
@@ -54467,6 +54903,12 @@ class ClickMenu {
            thisClass.setLogCmd("export pqr", true);
         });
 
+        me.myEventCls.onIds(["#" + me.pre + "delphipdbh", "#" + me.pre + "phipqr", "#" + me.pre + "phiurlpqr"], "click", function(e) { me.icn3d;
+            let bPdb = true;
+            me.htmlCls.setHtmlCls.exportPqr(bPdb);
+            thisClass.setLogCmd("export pdbh", false);
+         });
+
     //    clkMn1_exportStl: function() {
         me.myEventCls.onIds("#" + me.pre + "mn1_exportStl", "click", function(e) { let ic = me.icn3d;
            thisClass.setLogCmd("export stl file", false);
@@ -56834,11 +57276,12 @@ class SetMenu {
 
         html += "<li><span>Retrieve by ID</span>";
         html += "<ul>";
+        
+        html += me.htmlCls.setHtmlCls.getLink('mn1_mmdbafid', 'PDB/MMDB/AlphaFold IDs' + me.htmlCls.wifiStr);
         html += me.htmlCls.setHtmlCls.getLink('mn1_mmdbid', 'MMDB ID ' + me.htmlCls.wifiStr);
         html += me.htmlCls.setHtmlCls.getLink('mn1_mmtfid', 'MMTF ID ' + me.htmlCls.wifiStr);
         html += me.htmlCls.setHtmlCls.getLink('mn1_pdbid', 'PDB ID ' + me.htmlCls.wifiStr);
         html += me.htmlCls.setHtmlCls.getLink('mn1_afid', 'AlphaFold UniProt ID ' + me.htmlCls.wifiStr);
-        html += me.htmlCls.setHtmlCls.getLink('mn1_mmdbafid', 'MMDB or AlphaFold IDs' + me.htmlCls.wifiStr);
         if(!me.cfg.simplemenu) {
             html += me.htmlCls.setHtmlCls.getLink('mn1_opmid', 'OPM PDB ID ' + me.htmlCls.wifiStr);
             html += me.htmlCls.setHtmlCls.getLink('mn1_mmcifid', 'mmCIF ID ' + me.htmlCls.wifiStr);
@@ -56881,15 +57324,22 @@ class SetMenu {
         html += "</li>";
         html += "<li><span>Align</span>";
         html += "<ul>";
-        html += me.htmlCls.setHtmlCls.getLink('mn1_blast_rep_id', 'Sequence to Structure');
-        //html += me.htmlCls.setHtmlCls.getLink('mn1_align', 'Structure to Structure ' + me.htmlCls.wifiStr);
+        
+        html += "<li><span>Multiple Chains</span>";
+        html += "<ul>";
+        html += me.htmlCls.setHtmlCls.getRadio('mn1_chainalignRad', 'mn1_chainalign', 'by Structure Alignment ' + me.htmlCls.wifiStr);
+        html += me.htmlCls.setHtmlCls.getRadio('mn1_chainalignRad', 'mn1_chainalign2', 'by Sequence Alignment ' + me.htmlCls.wifiStr);
+        html += me.htmlCls.setHtmlCls.getRadio('mn1_chainalignRad', 'mn1_chainalign3', 'Residue by Residue');
+        html += "</ul>";
+        html += "</li>";
+
         html += "<li><span>Structure to Structure</span>";
         html += "<ul>";
         html += me.htmlCls.setHtmlCls.getLink('mn1_align', 'Two PDB Structures ' + me.htmlCls.wifiStr);
         html += me.htmlCls.setHtmlCls.getLink('mn1_alignaf', 'Two AlphaFold Structures ' + me.htmlCls.wifiStr);
         html += "</ul>";
 
-        html += me.htmlCls.setHtmlCls.getLink('mn1_chainalign', 'Multiple Chains ' + me.htmlCls.wifiStr);
+        html += me.htmlCls.setHtmlCls.getLink('mn1_blast_rep_id', 'Sequence to Structure');
 
         html += "</ul>";
         html += "</li>";
@@ -56933,7 +57383,7 @@ class SetMenu {
         html += "</ul>";
         html += "</li>";
 
-        html += "<li><span>Save Files</span>";
+        html += "<li><span>Save File</span>";
         html += "<ul>";
         //html += me.htmlCls.setHtmlCls.getLink('mn1_exportCanvas', 'iCn3D PNG Image');
 
@@ -56965,6 +57415,7 @@ class SetMenu {
     */
 
         html += me.htmlCls.setHtmlCls.getLink('mn1_exportPdbRes', 'PDB');
+        html += me.htmlCls.setHtmlCls.getLink('delphipdbh', 'PDB with Hydrogens');
 
         if(me.cfg.cid === undefined) {
             html += me.htmlCls.setHtmlCls.getLink('mn1_exportSecondary', 'Secondary Structure');
@@ -57538,7 +57989,7 @@ class SetMenu {
 
         html += "<ul class='icn3d-mn-item'>";
 
-        html += "<li><span style='padding-left:1.5em;'>Unicolor</span>";
+        html += "<li><span style='padding-left:1.5em!important;'>Unicolor</span>";
         html += "<ul>";
 
         html += "<li><span>Red</span>";
@@ -57745,7 +58196,7 @@ class SetMenu {
 
         if(me.cfg.cid === undefined) {
             //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrRainbow', 'Rainbow (R-V)');
-            html += "<li><span style='padding-left:1.5em;'>Rainbow (R-V)</span>";
+            html += "<li><span style='padding-left:1.5em!important;'>Rainbow (R-V)</span>";
             html += "<ul>";
             html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrRainbow', 'for Selection');
             html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrRainbowChain', 'for Chains');
@@ -57754,7 +58205,7 @@ class SetMenu {
 
             if(!me.cfg.simplemenu) {
                 //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSpectrum', 'Spectrum (V-R)');
-                html += "<li><span style='padding-left:1.5em;'>Spectrum (V-R)</span>";
+                html += "<li><span style='padding-left:1.5em!important;'>Spectrum (V-R)</span>";
                 html += "<ul>";
                 html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSpectrum', 'for Selection');
                 html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSpectrumChain', 'for Chains');
@@ -57762,7 +58213,7 @@ class SetMenu {
                 html += "</ul>";
             }
 
-            html += "<li><span style='padding-left:1.5em;'>Secondary</span>";
+            html += "<li><span style='padding-left:1.5em!important;'>Secondary</span>";
             html += "<ul>";
             html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSSGreen', 'Sheet in Green');
             html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSSYellow', 'Sheet in Yellow');
@@ -57777,13 +58228,13 @@ class SetMenu {
 
             //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrHydrophobic', 'Wimley-White<br><span style="padding-left:1.5em;">Hydrophobicity</span>');
 
-            html += "<li><span style='padding-left:1.5em;'>Hydrophobicity</span>";
+            html += "<li><span style='padding-left:1.5em!important;'>Hydrophobicity</span>";
             html += "<ul>";
             html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrNormalizedHP', 'Normalized');
             html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrHydrophobic', 'Wimley-White');
             html += "</ul>";
 
-            html += "<li><span style='padding-left:1.5em;'>B-factor</span>";
+            html += "<li><span style='padding-left:1.5em!important;'>B-factor</span>";
             html += "<ul>";
             html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrBfactor', 'Original');
             html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrBfactorNorm', 'Percentile');
@@ -57806,7 +58257,7 @@ class SetMenu {
 
             if(me.cfg.cid === undefined) {
                 if(!me.cfg.simplemenu) {
-                    html += "<li><span style='padding-left:1.5em;'>Defined Sets</span>";
+                    html += "<li><span style='padding-left:1.5em!important;'>Defined Sets</span>";
                     html += "<ul>";
                     html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrsets', 'Rainbow for Selected Sets<br>in "Analysis > Defined Sets"');
                     html += "</ul>";
@@ -57815,7 +58266,7 @@ class SetMenu {
 
             //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrResidue', 'Residue');
 
-            html += "<li><span style='padding-left:1.5em;'>Residue</span>";
+            html += "<li><span style='padding-left:1.5em!important;'>Residue</span>";
             html += "<ul>";
             html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrResidue', 'Default');
             html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrResidueCustom', 'Custom');
@@ -58119,17 +58570,29 @@ class SetMenu {
         html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#about' target='_blank'>About iCn3D<span style='font-size:0.9em'> " + me.REVISION + "</span></a></li>";
 
         html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#gallery' target='_blank'>Live Gallery " + me.htmlCls.wifiStr + "</a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#videos' target='_blank'>iCn3D Videos</a></li>";
+
+        html += "<li><span>FAQ</span>";
 
-        html += "<li><span>Tutorial</span>";
         html += "<ul>";
-        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#useicn3d' target='_blank'>Use iCn3D</a></li>";
-        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#videos' target='_blank'>iCn3D Videos</a></li>";
-        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#parameters' target='_blank'>URL Parameters</a></li>";
-        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#commands' target='_blank'>Commands</a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#viewstru' target='_blank'><span>View structure</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#tfstru' target='_blank'><span>Transform Structure</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#selsubset' target='_blank'><span>Select Subsets</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#changestylecolor' target='_blank'><span>Change Style/Color</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#saveview' target='_blank'><span>Save Work</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#showanno' target='_blank'><span>Show Annotations</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#exportanno' target='_blank'><span>Export Annotations</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#interanalysis' target='_blank'><span>Interactions Analysis</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#mutationanalysis' target='_blank'><span>Mutation Analysis</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#elecpot' target='_blank'><span>Electrostatic Pot.</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#simivast' target='_blank'><span>Similar PDB</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#simifoldseek' target='_blank'><span>Similar AlphaFold/PDB</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#alignmul' target='_blank'><span>Align Multiple Structures</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#batchanalysis' target='_blank'><span>Batch Analysis</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#embedicn3d' target='_blank'><span>Embed iCn3D</span></a></li>";
         html += "</ul>";
-        html += "</li>";
 
-        html += liStr + "https://www.ncbi.nlm.nih.gov/structure' target='_blank'>Search Structure " + me.htmlCls.wifiStr + "</a></li>";
+        //html += liStr + "https://www.ncbi.nlm.nih.gov/structure' target='_blank'>Search Structure " + me.htmlCls.wifiStr + "</a></li>";
         html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#citing' target='_blank'>Citing iCn3D</a></li>";
 
         html += "<li><span>Source Code</span>";
@@ -58143,7 +58606,10 @@ class SetMenu {
         if(!me.cfg.simplemenu) {
             html += "<li><span>Develop</span>";
             html += "<ul>";
-            html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#HowToUse' target='_blank'>How to Embed</a></li>";
+            html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#HowToUse' target='_blank'>Embed iCn3D</a></li>";
+            html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#parameters' target='_blank'>URL Parameters</a></li>";
+            html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#commands' target='_blank'>Commands</a></li>";
+    
             html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#datastructure' target='_blank'>Data Structure</a></li>";
             html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#classstructure' target='_blank'>Class Structure</a></li>";
             html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#addclass' target='_blank'>Add New Classes</a></li>";
@@ -58911,8 +59377,8 @@ class SetDialog {
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_foldseek' class='" + dialogClass + "' style='max-width:500px'>";
-        html += 'Note: You can search similar PDB or AlphaFold structures for any structure at the fast <a href="https://search.foldseek.com/search" target="_blank">Foldseek</a> web server. <br><br>Once you see the structure neighbors, you can view the alignment in iCn3D by inputing a list of chain IDs below. <br><br>The PDB chain IDs are the same as the record names such as "1hho_A". The AlphaFold chain IDs are the UniProt ID plus "_A". For example, the UniProt ID for the record name "AF-P69905-F1-model_v2" is "P69905".<br><br>'; 
-        html += "Chain ID List: " + me.htmlCls.inputTextStr + "id='" + me.pre + "foldseekchainids' value='P69905_A,P01942_A,1HHO_A' size=30> ";
+        html += 'Note: You can search similar PDB or AlphaFold structures for any structure at the fast <a href="https://search.foldseek.com/search" target="_blank">Foldseek</a> web server. <br><br>Once you see the structure neighbors, you can view the alignment in iCn3D by inputing a list of PDB chain IDs or AlphaFold UniProt IDs below. <br><br>The PDB chain IDs are the same as the record names such as "1hho_A". The UniProt ID is the text between "AF-" and "-F1". For example, the UniProt ID for the record name "AF-P69905-F1-model_v3" is "P69905".<br><br>'; 
+        html += "Chain ID List: " + me.htmlCls.inputTextStr + "id='" + me.pre + "foldseekchainids' value='P69905,P01942,1hho_A' size=30> ";
         html += me.htmlCls.buttonStr + "reload_foldseek'>Align</button>";
         html += "</div>";
 
@@ -59002,25 +59468,51 @@ class SetDialog {
         html += "<div style='width:550px'>";
         html += "All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).<br/><br/>";
         html += "<b>Chain IDs</b>: " + me.htmlCls.inputTextStr + "id='" + me.pre + "chainalignids' value='P69905,P01942,1HHO_A' size=50><br/><br/>";
-        html += "<b>Optional 1</b>, full chains are used for structure alignment<br/><br/>";
-        html += "<b>Optional 2</b>, sequence alignment (followed by structure alignemnt) based on residue numbers in the First/Master chain: <br>" + me.htmlCls.inputTextStr + "id='" + me.pre + "resalignids' placeholder='1,5,10-50' size=50><br/><br/>";
-        html += "<b>Optional 3</b>, predefined alignment with the first chain as the master. The rest chains are aligned to the master chain. Each alignment is defined as \" | \"-separated residue lists in one line. \"10-50\" means a range of residues from 10 to 50.<br><textarea id='" + me.pre + "predefinedres' rows='5' style='width: 100%; height: " +(me.htmlCls.LOG_HEIGHT) + "px; padding: 0px; border: 0px;' placeholder='1,5,10-50 | 1,5,10-50     \n2,6,11-51 | 1,5,10-50'></textarea><br/><br/>";
-        //html += me.htmlCls.buttonStr + "reload_chainalign_asym'>Align Asymmetric Unit</button>" + me.htmlCls.buttonStr + "reload_chainalign' style='margin-left:30px'>Align Biological Unit</button><br/><br/>";
-        html += me.htmlCls.buttonStr + "reload_chainalign_tmalign'>Align with TM-align</button>" + me.htmlCls.buttonStr + "reload_chainalign_asym' style='margin-left:30px'>Align with VAST</button><br/><br/>";
+        html += me.htmlCls.buttonStr + "reload_chainalign_tmalign'><b>Align with TM-align</b></button>" + me.htmlCls.buttonStr + "reload_chainalign_asym' style='margin-left:30px'><b>Align with VAST</b></button><br/><br/>";
+
+        html += "(Note: To align chains in custom PDB files, you could load them in \"File > Open File > PDB Files (appendable)\" and click \"Analysis > Defined Sets\". Finally select multiple chains in Defined Sets and click \"File > Realign Selection\".)<br><br>";
+        html += "</div></div>";
+
+        html += me.htmlCls.divStr + "dl_chainalign2' class='" + dialogClass + "'>";
+        html += "<div style='width:550px'>";
+        html += "All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).<br/><br/>";
+        html += "<b>Chain IDs</b>: " + me.htmlCls.inputTextStr + "id='" + me.pre + "chainalignids2' value='P69905,P01942,1HHO_A' size=50><br/><br/>";
+
+        html += "The sequence alignment (followed by structure alignemnt) is based on residue numbers in the First/Master chain: <br>" + me.htmlCls.inputTextStr + "id='" + me.pre + "resalignids' value='1,5,10-50' size=50><br/>";
+        html += me.htmlCls.buttonStr + "reload_chainalign_asym2' style='margin-top:3px;'><b>Align by Sequence Alignment</b></button><br/><br/>";
+
+        html += "(Note: To align chains in custom PDB files, you could load them in \"File > Open File > PDB Files (appendable)\" and click \"Analysis > Defined Sets\". Finally select multiple chains in Defined Sets and click \"File > Realign Selection\".)<br><br>";
+        html += "</div></div>";
+
+        html += me.htmlCls.divStr + "dl_chainalign3' class='" + dialogClass + "'>";
+        html += "<div style='width:550px'>";
+        html += "All chains will be aligned to the first chain in the comma-separated chain IDs. Each chain ID has the form of PDBID_chain (e.g., 1HHO_A, case sensitive) or UniprotID (e.g., P69905 for AlphaFold structures).<br/><br/>";
+        html += "<b>Chain IDs</b>: " + me.htmlCls.inputTextStr + "id='" + me.pre + "chainalignids3' value='P69905,P01942,1HHO_A' size=50><br/><br/>";
+        
+        html += "Each alignment is defined as \" | \"-separated residue lists in one line. \"10-50\" means a range of residues from 10 to 50.<br><textarea id='" + me.pre + "predefinedres' rows='5' style='width: 100%; height: " +(me.htmlCls.LOG_HEIGHT) + "px; padding: 0px; border: 0px;'>1,5,10-50 | 1,5,10-50     \n2,6,11-51 | 1,5,10-50</textarea><br/>";
+        html += me.htmlCls.buttonStr + "reload_chainalign_asym3'><b>Align Residue by Residue</b></button><br/><br/>";
 
         html += "(Note: To align chains in custom PDB files, you could load them in \"File > Open File > PDB Files (appendable)\" and click \"Analysis > Defined Sets\". Finally select multiple chains in Defined Sets and click \"File > Realign Selection\".)<br><br>";
         html += "</div></div>";
 
         html += me.htmlCls.divStr + "dl_mutation' class='" + dialogClass + "'>";
         html += "<div style='width:500px'>";
-        html += 'Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[PDB ID]_[Chain ID]_[Residue Number]_[One Letter Mutatnt Residue]". E.g., the mutation of N501Y in the E chain of PDB 6M0J can be specified as "6M0J_E_501_Y". <br/><br/>';
+        html += 'Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[PDB ID or AlphaFold UniProt ID]_[Chain ID]_[Residue Number]_[One Letter Mutatnt Residue]". E.g., the mutation of N501Y in the E chain of PDB 6M0J can be specified as "6M0J_E_501_Y". For AlphaFold structures, the "Chain ID" is "A".<br/><br/>';
         html += "<div style='display:inline-block; width:110px'>Mutations: </div>" + me.htmlCls.inputTextStr + "id='" + me.pre + "mutationids' value='6M0J_E_484_K,6M0J_E_501_Y,6M0J_E_417_N' size=50><br/><br/>";
 
-        html += "<b>Data Source</b>: <select id='" + me.pre + "idsource'>";
-        html += "<option value='mmdbid' selected>PDB ID</option>";
-        html += "<option value='afid'>AlphaFold UniProt ID</option>";
-        html += "</select><br/><br/>";
-        
+        // html += "<b>Data Source</b>: <select id='" + me.pre + "idsource'>";
+        // html += "<option value='mmdbid' selected>PDB ID</option>";
+        // html += "<option value='afid'>AlphaFold UniProt ID</option>";
+        // html += "</select><br/><br/>";
+ 
+        html += '<b>ID Type</b>: ';
+        html += '<input type="radio" name="' + me.pre + 'idsource" id="' + me.pre + 'type_mmdbid" value="mmdbid" checked>PDB ID';
+        html += '<input type="radio" name="' + me.pre + 'idsource" id="' + me.pre + 'type_afid" value="afid" style="margin-left:20px">AlphaFold UniProt ID<br><br>';
+
+        html += '<b>Show Mutation in</b>: ';
+        html += '<input type="radio" name="' + me.pre + 'pdbsource" id="' + me.pre + 'showin_currentpage" value="currentpage">Current Page';
+        html += '<input type="radio" name="' + me.pre + 'pdbsource" id="' + me.pre + 'showin_newpage" value="newpage" style="margin-left:20px" checked>New Page<br><br>';
+
         html += me.htmlCls.buttonStr + "reload_mutation_3d' title='Show the mutations in 3D using the scap program'>3D with scap</button>";
         html += me.htmlCls.buttonStr + "reload_mutation_inter' style='margin-left:20px' title='Show the mutations in 3D and the change of interactions'>Interactions</button>";
         html += me.htmlCls.buttonStr + "reload_mutation_pdb' style='margin-left:20px' title='Show the mutations in 3D and export the PDB of the mutant within 10 angstrom'>PDB</button>";
@@ -59104,7 +59596,7 @@ class SetDialog {
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_yournote' class='" + dialogClass + "'>";
-        html += "Your note will be saved in the HTML file when you click \"File > Save Files > iCn3D PNG Image\".<br><br>";
+        html += "Your note will be saved in the HTML file when you click \"File > Save File > iCn3D PNG Image\".<br><br>";
         html += "<textarea id='" + me.pre + "yournote' rows='5' style='width: 100%; height: " +(me.htmlCls.LOG_HEIGHT) + "px; padding: 0px; border: 0px;' placeholder='Enter your note here'></textarea><br>";
         html += me.htmlCls.buttonStr + "applyyournote'>Save</button>";
         html += "</div>";
@@ -59859,10 +60351,17 @@ class SetDialog {
         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>";
+        
+        // if(me.cfg.mmdbid != undefined || me.cfg.pdbid != undefined || me.cfg.mmtfid != undefined || me.cfg.mmcifid != undefined) { // PDB
+        //     html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_ptm' disabled>PTM (UniProt)" + me.htmlCls.space2 + "</span></td>";
+        // }
+        // else {
+            html += tmpStr1 + me.htmlCls.inputCheckStr + "id='" + me.pre + "anno_ptm'>PTM (UniProt)" + 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_interact'>Interactions" + 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>";
@@ -59901,6 +60400,17 @@ class Events {
         }
     }
 
+    convertUniProtInChains(alignment) { let me = this.icn3dui; me.icn3d;
+        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 += ',';
+        }
+
+        return alignment_final;
+    }
+
     searchSeq() { let me = this.icn3dui, ic = me.icn3d;
        let select = $("#" + me.pre + "search_seq").val();
        if(isNaN(select) && select.indexOf('$') == -1 && select.indexOf('.') == -1 && select.indexOf(':') == -1 && select.indexOf('@') == -1) {
@@ -59997,7 +60507,7 @@ class Events {
 
     saveHtml(id) { let me = this.icn3dui, ic = me.icn3d;
         let html = '';
-        html += '<link rel="stylesheet" href="https:///structure.ncbi.nlm.nih.gov/icn3d/lib/jquery-ui-1.12.1.min.css">\n';
+        html += '<link rel="stylesheet" href="https:///structure.ncbi.nlm.nih.gov/icn3d/lib/jquery-ui-1.13.2.min.css">\n';
         html += '<link rel="stylesheet" href="https:///structure.ncbi.nlm.nih.gov/icn3d/icn3d_full_ui.css">\n';
         html += $("#" + id).html();
         let idArray = id.split('_');
@@ -60007,24 +60517,6 @@ class Events {
         ic.saveFileCls.saveFile(structureStr + '-' + idStr + '.html', 'html', encodeURIComponent(html));
     }
 
-    getAlignParas() { let me = this.icn3dui; me.icn3d;
-        let alignment = $("#" + me.pre + "chainalignids").val();
-        let idArray = alignment.split(',');
-        let alignment_final = '';
-        for(let i = 0, il = idArray.length; i < il; ++i) {
-            alignment_final += (idArray[i].indexOf('_') != -1) ? idArray[i] : idArray[i] + '_A'; // AlphaFold ID
-            if(i < il - 1) alignment_final += ',';
-        }
-        let resalign = $("#" + me.pre + "resalignids").val();
-        let predefinedres = $("#" + me.pre + "predefinedres").val().trim().replace(/\n/g, '; ');
-        if(predefinedres && alignment_final.split(',').length - 1 != predefinedres.split('; ').length) {
-            alert("Please make sure the number of chains and the lines of predefined residues are the same...");
-            return;
-        }
-
-        return {"alignment": alignment_final, "resalign": resalign, "predefinedres": predefinedres};
-    }
-
     //Hold all functions related to click events.
     allEventFunctions() { let me = this.icn3dui, ic = me.icn3d;
         let thisClass = this;
@@ -60181,6 +60673,8 @@ class Events {
     //    },
     //    clickRealignonseqalign: function() {
         me.myEventCls.onIds("#" + me.pre + "mn2_realignonseqalign", "click", function(e) { let ic = me.icn3d;
+            if(ic.bRender) me.htmlCls.dialogCls.openDlg('dl_realign', 'Please select two sets to realign');
+
             if(Object.keys(ic.structures).length < 2) {
                 alert("At least two structuresare required for alignment...");
                 return;
@@ -60196,15 +60690,14 @@ class Events {
             if($("#" + me.pre + "atomsCustomRealign").length) {
                 $("#" + me.pre + "atomsCustomRealign").html(definedAtomsHtml);
             }
-            //if($("#" + me.pre + "atomsCustomRealign2").length) {
-            //    $("#" + me.pre + "atomsCustomRealign2").html(definedAtomsHtml);
-            //}
-            if(ic.bRender) me.htmlCls.dialogCls.openDlg('dl_realign', 'Please select two sets to realign');
+            
             $("#" + me.pre + "atomsCustomRealign").resizable();
             //$("#" + me.pre + "atomsCustomRealign2").resizable();
         });
 
         me.myEventCls.onIds("#" + me.pre + "mn2_realignonstruct", "click", function(e) { let ic = me.icn3d;
+            if(ic.bRender) me.htmlCls.dialogCls.openDlg('dl_realignbystruct', 'Please select two sets to realign');
+
             if(Object.keys(ic.structures).length < 2) {
                 alert("At least two structuresare required for alignment...");
                 return;
@@ -60219,10 +60712,7 @@ class Events {
             if($("#" + me.pre + "atomsCustomRealignByStruct").length) {
                 $("#" + me.pre + "atomsCustomRealignByStruct").html(definedAtomsHtml);
             }
-            //if($("#" + me.pre + "atomsCustomRealign2").length) {
-            //    $("#" + me.pre + "atomsCustomRealign2").html(definedAtomsHtml);
-            //}
-            if(ic.bRender) me.htmlCls.dialogCls.openDlg('dl_realignbystruct', 'Please select two sets to realign');
+            
             $("#" + me.pre + "atomsCustomRealignByStruct").resizable();
             //$("#" + me.pre + "atomsCustomRealign2").resizable();
         });
@@ -60259,10 +60749,7 @@ class Events {
                 ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
             }
  
-            // save the current selection
-            //ic.selectionCls.saveSelectionPrep();
-            //let name = 'realignSetsByStruct';
-            //ic.selectionCls.saveSelection(name, name);
+            me.cfg.aligntool = 'vast';
  
             ic.realignParserCls.realignOnStructAlign();
             if(nameArray.length > 0) {
@@ -60394,8 +60881,16 @@ class Events {
         me.myEventCls.onIds("#" + me.pre + "reload_foldseek", "click", function(e) { me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
-            me.htmlCls.clickMenuCls.setLogCmd("load chainalignment " + $("#" + me.pre + "foldseekchainids").val(), true);
-            window.open(hostUrl + '?chainalign=' + $("#" + me.pre + "foldseekchainids").val(), '_self');
+
+            // me.htmlCls.clickMenuCls.setLogCmd("load chainalignment " + $("#" + me.pre + "foldseekchainids").val(), true);
+            // window.open(hostUrl + '?chainalign=' + $("#" + me.pre + "foldseekchainids").val(), '_self');
+
+
+            let alignment = $("#" + me.pre + "foldseekchainids").val();
+            let alignment_final = thisClass.convertUniProtInChains(alignment);
+
+            me.htmlCls.clickMenuCls.setLogCmd("load chainalignment " + alignment_final, true);
+            window.open(hostUrl + '?chainalign=' + alignment_final + '&aligntool=tmalign&showalignseq=1&bu=0', '_self');
          });
 
         me.myEventCls.onIds("#" + me.pre + "reload_mmtf", "click", function(e) { me.icn3d;
@@ -60531,85 +61026,197 @@ class Events {
           });
     //    },
     //    clickReload_chainalign: function() {
-        me.myEventCls.onIds("#" + me.pre + "reload_chainalign", "click", function(e) { me.icn3d;
+/*        
+        me.myEventCls.onIds("#" + me.pre + "reload_chainalign", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
 
-           let result = thisClass.getAlignParas();
+           let alignment = $("#" + me.pre + "chainalignids").val();
+           let alignment_final = thisClass.convertUniProtInChains(alignment);
+           let resalign = $("#" + me.pre + "resalignids").val();
+           let predefinedres = $("#" + me.pre + "predefinedres").val().trim().replace(/\n/g, '; ');
+           if(predefinedres && alignment_final.split(',').length - 1 != predefinedres.split('; ').length) {
+               alert("Please make sure the number of chains and the lines of predefined residues are the same...");
+               return;
+           }
 
-           me.htmlCls.clickMenuCls.setLogCmd("load chains " + result.alignment + " | residues " + result.resalign + " | resdef " + result.predefinedres, false);
-           window.open(hostUrl + '?chainalign=' + result.alignment + '&resnum=' + result.resalign + '&resdef=' + result.predefinedres + '&showalignseq=1', '_blank');
+           me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " | residues " + resalign + " | resdef " + predefinedres, false);
+           window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=' + resalign + '&resdef=' + predefinedres + '&showalignseq=1', '_blank');
         });
+*/
 
         me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym", "click", function(e) { me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
 
-           let result = thisClass.getAlignParas();
+           let alignment = $("#" + me.pre + "chainalignids").val();
+           let alignment_final = thisClass.convertUniProtInChains(alignment);
 
-           me.htmlCls.clickMenuCls.setLogCmd("load chains " + result.alignment + " on asymmetric unit | residues " + result.resalign + " | resdef " + result.predefinedres, false);
-           window.open(hostUrl + '?chainalign=' + result.alignment + '&resnum=' + result.resalign + '&resdef=' + result.predefinedres + '&showalignseq=1&bu=0', '_blank');
+           me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues | resdef ", false);
+           window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=&resdef=&showalignseq=1&bu=0', '_blank');
         });
 
+        me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym2", "click", function(e) { me.icn3d;
+            e.preventDefault();
+            if(!me.cfg.notebook) dialog.dialog( "close" );
+ 
+            let alignment = $("#" + me.pre + "chainalignids2").val();
+            let alignment_final = thisClass.convertUniProtInChains(alignment);
+            let resalign = $("#" + me.pre + "resalignids").val();
+ 
+            me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues " + resalign + " | resdef ", false);
+            window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=' + resalign + '&resdef=&showalignseq=1&bu=0', '_blank');
+         });
+
+         me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym3", "click", function(e) { me.icn3d;
+            e.preventDefault();
+            if(!me.cfg.notebook) dialog.dialog( "close" );
+ 
+            let alignment = $("#" + me.pre + "chainalignids3").val();
+            let alignment_final = thisClass.convertUniProtInChains(alignment);
+
+            let predefinedres = $("#" + me.pre + "predefinedres").val().trim().replace(/\n/g, '; ');
+            if(predefinedres && alignment_final.split(',').length - 1 != predefinedres.split('; ').length) {
+                alert("Please make sure the number of chains and the lines of predefined residues are the same...");
+                return;
+            }
+ 
+            me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues | resdef " + predefinedres, false);
+            window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=&resdef=' + predefinedres + '&showalignseq=1&bu=0', '_blank');
+         });
+
         me.myEventCls.onIds("#" + me.pre + "reload_chainalign_tmalign", "click", function(e) { me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
 
-            let result = thisClass.getAlignParas();
+            let alignment = $("#" + me.pre + "chainalignids").val();
+            let alignment_final = thisClass.convertUniProtInChains(alignment);
  
-            me.htmlCls.clickMenuCls.setLogCmd("load chains " + result.alignment + " on asymmetric unit | residues " + result.resalign + " | resdef " + result.predefinedres + " | align tmalign", false);
-            window.open(hostUrl + '?chainalign=' + result.alignment + '&aligntool=tmalign&resnum=' + result.resalign + '&resdef=' + result.predefinedres + '&showalignseq=1&bu=0', '_blank');
+            me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues | resdef | align tmalign", false);
+            window.open(hostUrl + '?chainalign=' + alignment_final + '&aligntool=tmalign&resnum=&resdef=&showalignseq=1&bu=0', '_blank');
          });
 
-        me.myEventCls.onIds("#" + me.pre + "reload_mutation_3d", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_mutation_3d", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
            let mutationids = $("#" + me.pre + "mutationids").val();
-           let idsource = $("#" + me.pre + "idsource").val();
-           let mmdbid = mutationids.substr(0, mutationids.indexOf('_'));           
-           me.htmlCls.clickMenuCls.setLogCmd("3d of mutation " + mutationids, false);
-           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmdbid=' + mmdbid + '&command=scap 3d ' + mutationids + '; select displayed set', '_blank');
-           window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap 3d ' + mutationids + '; select displayed set', '_blank');
+           //let idsource = $("#" + me.pre + "idsource").val();
+           let idsource, pdbsource;
+           if($("#" + me.pre + "type_mmdbid").is(":checked")) {
+                idsource = 'mmdbid';
+           }
+           else {
+                idsource = 'afid';
+           }
+           if($("#" + me.pre + "showin_currentpage").is(":checked")) {
+                pdbsource = 'currentpage';
+            }
+            else {
+                pdbsource = 'newpage';
+            }
+
+           if(pdbsource == 'currentpage') {
+                let snp = mutationids;
+
+                ic.scapCls.retrieveScap(snp);
+                me.htmlCls.clickMenuCls.setLogCmd('scap 3d ' + snp, true);
+                me.htmlCls.clickMenuCls.setLogCmd("select displayed set", true);
+           }
+           else {
+                let mmdbid = mutationids.substr(0, mutationids.indexOf('_'));           
+                me.htmlCls.clickMenuCls.setLogCmd("3d of mutation " + mutationids, false);
+                window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap 3d ' + mutationids + '; select displayed set', '_blank');
+           }
         });
 
-        me.myEventCls.onIds("#" + me.pre + "reload_mutation_pdb", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_mutation_pdb", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
            let mutationids = $("#" + me.pre + "mutationids").val();
-           let idsource = $("#" + me.pre + "idsource").val();
-           let mmdbid = mutationids.substr(0, mutationids.indexOf('_'));
-           me.htmlCls.clickMenuCls.setLogCmd("pdb of mutation " + mutationids, false);
-           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmdbid=' + mmdbid + '&command=scap pdb ' + mutationids + '; select displayed set', '_blank');
-           window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap pdb ' + mutationids + '; select displayed set', '_blank');
+           //let idsource = $("#" + me.pre + "idsource").val();
+           let idsource, pdbsource;
+           if($("#" + me.pre + "type_mmdbid").is(":checked")) {
+                idsource = 'mmdbid';
+           }
+           else {
+                idsource = 'afid';
+           }
+           if($("#" + me.pre + "showin_currentpage").is(":checked")) {
+                pdbsource = 'currentpage';
+            }
+            else {
+                pdbsource = 'newpage';
+            }
+
+           if(pdbsource == 'currentpage') {
+                let snp = mutationids;
+
+                let bPdb = true;
+                ic.scapCls.retrieveScap(snp, undefined, bPdb);
+                me.htmlCls.clickMenuCls.setLogCmd('scap pdb ' + snp, true);
+           }
+           else {
+                let mmdbid = mutationids.substr(0, mutationids.indexOf('_'));
+                me.htmlCls.clickMenuCls.setLogCmd("pdb of mutation " + mutationids, false);
+                window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap pdb ' + mutationids + '; select displayed set', '_blank');
+           }
         });
 
         me.myEventCls.onIds("#" + me.pre + "reload_mutation_inter", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
            let mutationids = $("#" + me.pre + "mutationids").val();
-           let idsource = $("#" + me.pre + "idsource").val();
-
-           let mutationArray = mutationids.split(',');
-           let residArray = [];
-           for(let i = 0, il = mutationArray.length; i < il; ++i) {
-               let pos = mutationArray[i].lastIndexOf('_');
-               let resid = mutationArray[i].substr(0, pos);
-               residArray.push(resid);
+           //let idsource = $("#" + me.pre + "idsource").val();
+           let idsource, pdbsource;
+           if($("#" + me.pre + "type_mmdbid").is(":checked")) {
+                idsource = 'mmdbid';
+           }
+           else {
+                idsource = 'afid';
            }
+           if($("#" + me.pre + "showin_currentpage").is(":checked")) {
+                pdbsource = 'currentpage';
+            }
+            else {
+                pdbsource = 'newpage';
+            }
 
-           let mmdbid = mutationids.substr(0, mutationids.indexOf('_'));
+           if(pdbsource == 'currentpage') {
+                let snp = mutationids;
 
-           // if no structures are loaded yet
-           if(!ic.structures) {
-               ic.structures = {};
-               ic.structures[mmdbid] = 1;
+                let bInteraction = true;
+                ic.scapCls.retrieveScap(snp, bInteraction);
+                me.htmlCls.clickMenuCls.setLogCmd('scap interaction ' + snp, true);
+
+                let idArray = snp.split('_'); //stru_chain_resi_snp
+                let select = '.' + idArray[1] + ':' + idArray[2];
+                let name = 'snp_' + idArray[1] + '_' + idArray[2];
+                me.htmlCls.clickMenuCls.setLogCmd("select " + select + " | name " + name, true);
+                me.htmlCls.clickMenuCls.setLogCmd("line graph interaction pairs | selected non-selected | hbonds,salt bridge,interactions,halogen,pi-cation,pi-stacking | false | threshold 3.8 6 4 3.8 6 5.5", true);
+                me.htmlCls.clickMenuCls.setLogCmd("adjust dialog dl_linegraph", true);
+                me.htmlCls.clickMenuCls.setLogCmd("select displayed set", true);
            }
-           ic.resid2specCls.residueids2spec(residArray);
+           else {
+                let mutationArray = mutationids.split(',');
+                let residArray = [];
+                for(let i = 0, il = mutationArray.length; i < il; ++i) {
+                    let pos = mutationArray[i].lastIndexOf('_');
+                    let resid = mutationArray[i].substr(0, pos);
+                    residArray.push(resid);
+                }
 
-           me.htmlCls.clickMenuCls.setLogCmd("interaction change of mutation " + mutationids, false);
-           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmdbid=' + mmdbid + '&command=scap interaction ' + mutationids + '; select ' + selectSpec + ' | name test; line graph interaction pairs | selected non-selected | hbonds,salt bridge,interactions,halogen,pi-cation,pi-stacking | false | threshold 3.8 6 4 3.8 6 5.5; adjust dialog dl_linegraph; select displayed set', '_blank');
-           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmdbid=' + mmdbid + '&command=scap interaction ' + mutationids, '_blank');
-           window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap interaction ' + mutationids, '_blank');
+                let mmdbid = mutationids.substr(0, mutationids.indexOf('_'));
+
+                // if no structures are loaded yet
+                if(!ic.structures) {
+                    ic.structures = {};
+                    ic.structures[mmdbid] = 1;
+                }
+                ic.resid2specCls.residueids2spec(residArray);
+
+                me.htmlCls.clickMenuCls.setLogCmd("interaction change of mutation " + mutationids, false);
+                window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap interaction ' + mutationids, '_blank');
+           }
         });
 
     //    },
@@ -61665,6 +62272,27 @@ class Events {
             let color = $("#" + me.pre + "colorcustom").val();
             picker.set('#' + color).enter();
         });
+
+        let picker2 = new CP(document.querySelector("#" + me.pre + "labelcolorall"));
+        picker2.on("change", function(color) {
+            this.target.value = color;
+        });
+        me.myEventCls.onIds("#" + me.pre + "labelcolorall", "input", function() {
+            let color = $("#" + me.pre + "labelcolorall").val();
+            picker2.set('#' + color).enter();
+        });
+        me.myEventCls.onIds("#" + me.pre + "labelcolorall", "keyup", function() {
+            let color = $("#" + me.pre + "labelcolorall").val();
+            picker2.set('#' + color).enter();
+        });
+        me.myEventCls.onIds("#" + me.pre + "labelcolorall", "paste", function() {
+            let color = $("#" + me.pre + "labelcolorall").val();
+            picker2.set('#' + color).enter();
+        });
+        me.myEventCls.onIds("#" + me.pre + "labelcolorall", "cut", function() {
+            let color = $("#" + me.pre + "labelcolorall").val();
+            picker2.set('#' + color).enter();
+        });    
     //    },
     //    clickApplypick_stabilizer_rm: function() {
         me.myEventCls.onIds("#" + me.pre + "applypick_stabilizer_rm", "click", function(e) { let ic = me.icn3d;
@@ -62939,7 +63567,7 @@ class SetHtml {
         return html;
     }
 
-    exportPqr() { let me = this.icn3dui, ic = me.icn3d;
+    exportPqr(bPdb) { let me = this.icn3dui, ic = me.icn3d;
        let ionHash = {};
        let atomHash = {};
     /*
@@ -62971,13 +63599,15 @@ class SetHtml {
            }
        }
 
+       let fileExt = (bPdb) ? 'pdb' : 'pqr';
        if(me.cfg.cid) {
           let pqrStr = '';
 ///          pqrStr += ic.saveFileCls.getPDBHeader();
-          pqrStr += ic.saveFileCls.getAtomPDB(atomHash, true) + ic.saveFileCls.getAtomPDB(ionHash, true);
+          let bPqr = (bPdb) ? false : true;
+          pqrStr += ic.saveFileCls.getAtomPDB(atomHash, bPqr) + ic.saveFileCls.getAtomPDB(ionHash, bPqr);
 
           let file_pref =(ic.inputid) ? ic.inputid : "custom";
-          ic.saveFileCls.saveFile(file_pref + '_icn3d.pqr', 'text', [pqrStr]);
+          ic.saveFileCls.saveFile(file_pref + '_icn3d.' + fileExt, 'text', [pqrStr]);
        }
        else {
            let bCalphaOnly = me.utilsCls.isCalphaPhosOnly(me.hashUtilsCls.hash2Atoms(atomHash, ic.atoms));
@@ -63013,8 +63643,40 @@ class SetHtml {
               success: function(data) {
                   let pqrStr = data;
 
+                  if(bPdb) {
+                    let lineArray = pqrStr.split('\n');
+
+                    let pdbStr = '';
+                    for(let i = 0, il = lineArray.length; i < il; ++i) {
+                        let line = lineArray[i];
+                        if(line.substr(0, 6) == 'ATOM  ' || line.substr(0, 6) == 'HETATM') {
+                            let atomName = line.substr(12, 4).trim();
+                            let elem;
+                            if(line.substr(0, 6) == 'ATOM  ') {
+                                elem = atomName.substr(0, 1);
+                            }
+                            else {
+                                let twochar = atomName.substr(0, 2);
+                                if(me.parasCls.vdwRadii.hasOwnProperty(twochar)) {
+                                    elem = twochar;
+                                }
+                                else {
+                                    elem = atomName.substr(0, 1);
+                                }
+                            }
+
+                            pdbStr += line.substr(0, 54) + '                      ' + elem.padStart(2, ' ') + '\n';
+                        }
+                        else {
+                            pdbStr += line + '\n';
+                        }
+                    }
+
+                    pqrStr = pdbStr;
+                  }
+
                   let file_pref =(ic.inputid) ? ic.inputid : "custom";
-                  ic.saveFileCls.saveFile(file_pref + '_icn3d_residues.pqr', 'text', [pqrStr]);
+                  ic.saveFileCls.saveFile(file_pref + '_icn3d_residues.' + fileExt, 'text', [pqrStr]);
               },
               error : function(xhr, textStatus, errorThrown ) {
                 this.tryCount++;
@@ -63379,7 +64041,8 @@ class Html {
     this.simulation = undefined;
 
     //this.baseUrl = "https://structure.ncbi.nlm.nih.gov/";
-    this.baseUrl = "https://www.ncbi.nlm.nih.gov/Structure/";
+    this.baseUrl = (window && window.location && window.location.hostname == 'structure.ncbi.nlm.nih.gov') 
+        ? "https://structure.ncbi.nlm.nih.gov/Structure/" : "https://www.ncbi.nlm.nih.gov/Structure/";
     this.divStr = "<div id='" + this.icn3dui.pre;
     this.divNowrapStr = "<div style='white-space:nowrap'>";
     this.spanNowrapStr = "<span style='white-space:nowrap'>";
@@ -66236,7 +66899,7 @@ class iCn3D {
         if(bWebGL){
             //https://discourse.threejs.org/t/three-js-r128-ext-frag-depth-and-angle-instanced-arrays-extensions-are-not-supported/26037
             //this.renderer = new THREE.WebGL1Renderer({
-            if ( bWebGL2 && bVR) { 
+            if ( bWebGL2 && bVR) {                
                 this.renderer = new THREE.WebGLRenderer({
                     canvas: this.oriContainer.get(0), //this.container.get(0),
                     antialias: true,
@@ -66603,6 +67266,7 @@ class iCn3D {
 
     this.annoCddSiteCls = new AnnoCddSite(this);
     this.annoContactCls = new AnnoContact(this);
+    this.annoPTMCls = new AnnoPTM(this);
     this.annoCrossLinkCls = new AnnoCrossLink(this);
     this.annoDomainCls = new AnnoDomain(this);
     this.annoSnpClinVarCls = new AnnoSnpClinVar(this);
@@ -66850,7 +67514,7 @@ iCn3D.prototype.resetConfig = function () { let ic = this, me = ic.icn3dui;
     }
 
     if(me.cfg.blast_rep_id !== undefined) this.opts['color'] = 'conservation';
-    if(me.cfg.mmdbafid !== undefined) this.opts['color'] = 'structure';
+    if(me.cfg.mmdbafid !== undefined && ic.structures) ic.opts['color'] = (Object.keys(ic.structures).length == 1) ? 'chain' : 'structure';
 
     if(me.cfg.options !== undefined) $.extend(this.opts, me.cfg.options);
 };
@@ -66867,7 +67531,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.13.0';
+    this.REVISION = '3.14.3';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;