icn3d 3.26.9 → 3.27.0

package/icn3d.js

@@ -4456,23 +4456,23 @@ class ParasCls {
             //this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * ( + 0.81)/(1.14 + 0.81)),
             // hydrophobic
             // https://en.m.wikipedia.org/wiki/Hydrophobicity_scales#Wimley%E2%80%93White_whole_residue_hydrophobicity_scales
-            'TRP': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-1.85 + 1.85)/(0 + 1.85)),
-            'PHE': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-1.13 + 1.85)/(0 + 1.85)),
-            'TYR': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-0.94 + 1.85)/(0 + 1.85)),
-            'LEU': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-0.56 + 1.85)/(0 + 1.85)),
-            'ILE': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-0.31 + 1.85)/(0 + 1.85)),
-            'CYS': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-0.24 + 1.85)/(0 + 1.85)),
-            'MET': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-0.23 + 1.85)/(0 + 1.85)),
+            'TRP': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-2.09 + 2.09) / (0 + 2.09)),
+            'PHE': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-1.71 + 2.09) / (0 + 2.09)),
+            'LEU': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-1.25 + 2.09) / (0 + 2.09)),
+            'ILE': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-1.12 + 2.09) / (0 + 2.09)),
+            'TYR': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-0.71 + 2.09) / (0 + 2.09)),
+            'MET': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-0.67 + 2.09) / (0 + 2.09)),
+            'VAL': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-0.46 + 2.09) / (0 + 2.09)),
+            'CYS': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-0.02 + 2.09) / (0 + 2.09)),
 
             // polar
-            'GLY': this.thr().setHSL(1/6.0, 1, 0.5 + 0.5 * (-0.01 + 0.58)/(0 + 0.58)),
-            'VAL': this.thr().setHSL(1/6.0, 1, 0.5 + 0.5 * (-0.07 + 0.58)/(0 + 0.58)),
-            'SER': this.thr().setHSL(1/6.0, 1, 0.5 + 0.5 * (-0.13 + 0.58)/(0 + 0.58)),
-            'THR': this.thr().setHSL(1/6.0, 1, 0.5 + 0.5 * (-0.14 + 0.58)/(0 + 0.58)),
-            'ALA': this.thr().setHSL(1/6.0, 1, 0.5 + 0.5 * (-0.17 + 0.58)/(0 + 0.58)),
-            'ASN': this.thr().setHSL(1/6.0, 1, 0.5 + 0.5 * (-0.42 + 0.58)/(0 + 0.58)),
-            'PRO': this.thr().setHSL(1/6.0, 1, 0.5 + 0.5 * (-0.45 + 0.58)/(0 + 0.58)),
-            'GLN': this.thr().setHSL(1/6.0, 1, 0.5 + 0.5 * (-0.58 + 0.58)/(0 + 0.58))
+            'PRO': this.thr().setHSL(1/6.0, 1, 0.5 + 0.5 * (-0.14 + 1.15) / (0 + 1.15)),
+            'THR': this.thr().setHSL(1/6.0, 1, 0.5 + 0.5 * (-0.25 + 1.15) / (0 + 1.15)),
+            'SER': this.thr().setHSL(1/6.0, 1, 0.5 + 0.5 * (-0.46 + 1.15) / (0 + 1.15)),
+            'ALA': this.thr().setHSL(1/6.0, 1, 0.5 + 0.5 * (-0.50 + 1.15) / (0 + 1.15)),
+            'GLN': this.thr().setHSL(1/6.0, 1, 0.5 + 0.5 * (-0.77 + 1.15) / (0 + 1.15)),
+            'ASN': this.thr().setHSL(1/6.0, 1, 0.5 + 0.5 * (-0.85 + 1.15) / (0 + 1.15)),
+            'GLY': this.thr().setHSL(1/6.0, 1, 0.5 + 0.5 * (-1.15 + 1.15) / (0 + 1.15))
         };
 
         this.normalizedHPColors = {
@@ -4490,59 +4490,58 @@ class ParasCls {
             //this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * ( + 0.81)/(1.14 + 0.81)),
             // hydrophobic
             // https://en.m.wikipedia.org/wiki/Hydrophobicity_scales#Wimley%E2%80%93White_whole_residue_hydrophobicity_scales
-            // 0.65 ~ -1.85: white ~ green
-            'TRP': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-1.85 + 1.85)/2.5),
-            'PHE': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-1.13 + 1.85)/2.5),
-            'TYR': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-0.94 + 1.85)/2.5),
-            'LEU': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-0.56 + 1.85)/2.5),
-            'ILE': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-0.31 + 1.85)/2.5),
-            'CYS': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-0.24 + 1.85)/2.5),
-            'MET': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-0.23 + 1.85)/2.5),
+            // 1.15 ~ -2.09: white ~ green
+            'TRP': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-2.09 + 2.09) / 3.24),
+            'PHE': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-1.71 + 2.09) / 3.24),
+            'LEU': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-1.25 + 2.09) / 3.24),
+            'ILE': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-1.12 + 2.09) / 3.24),
+            'TYR': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-0.71 + 2.09) / 3.24),
+            'MET': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-0.67 + 2.09) / 3.24),
+            'VAL': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-0.46 + 2.09) / 3.24),
+            'CYS': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (-0.02 + 2.09) / 3.24),
 
             // polar
-            'GLY': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (0.01 + 1.85)/2.5),
-            'VAL': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (0.07 + 1.85)/2.5),
-            'SER': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (0.13 + 1.85)/2.5),
-            'THR': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (0.14 + 1.85)/2.5),
-            'ALA': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (0.17 + 1.85)/2.5),
-            'ASN': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (0.42 + 1.85)/2.5),
-            'PRO': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (0.45 + 1.85)/2.5),
-            'GLN': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (0.58 + 1.85)/2.5)
+            'PRO': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (0.14 + 2.09) / 3.24),
+            'THR': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (0.25 + 2.09) / 3.24),
+            'SER': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (0.46 + 2.09) / 3.24),
+            'ALA': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (0.50 + 2.09) / 3.24),
+            'GLN': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (0.77 + 2.09) / 3.24),
+            'ASN': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (0.85 + 2.09) / 3.24),
+            'GLY': this.thr().setHSL(1/3.0, 1, 0.5 + 0.5 * (1.15 + 2.09) / 3.24)
         };
 
         this.hydrophobicValues = {
-            // charged residues
+            // charged residues, larger than max polar (1.15)
             '  G': 3,     '  A': 3,     '  T': 3,
             '  C': 3,     '  U': 3,     ' DG': 3,
             ' DA': 3,     ' DT': 3,     ' DC': 3,
             ' DU': 3,       'G': 3,       'A': 3,
             'T': 3,         'C': 3,       'U': 3,
             'DG': 3,       'DA': 3,      'DT': 3,
-            'DC': 3,       'DU': 3,     'ARG': 1,
-            'LYS': 1,     'ASP': 3,     'GLU': 3,
+            'DC': 3,       'DU': 3,     'ARG': 1.5,
+            'LYS': 1.5,     'ASP': 3,     'GLU': 3,
             'HIS': 2,
 
-            // + 0.81)/(1.14 + 0.81)),
             // hydrophobic
             // https://en.m.wikipedia.org/wiki/Hydrophobicity_scales#Wimley%E2%80%93White_whole_residue_hydrophobicity_scales
-            // 0.65 ~ -1.85: white ~ green
-            'TRP': -1.85,
-            'PHE': -1.13,
-            'TYR': -0.94,
-            'LEU': -0.56,
-            'ILE': -0.31,
-            'CYS': -0.24,
-            'MET': -0.23,
+            // 1.15 ~ -2.09: white ~ green
+            'TRP': -2.09,
+            'PHE': -1.71,
+            'LEU': -1.25,
+            'ILE': -1.12,
+            'TYR': -0.71,
+            'MET': -0.67,
+            'VAL': -0.46,
+            'CYS': -0.02,
 
             // polar
-            'GLY': 0.01,
-            'VAL': 0.07,
-            'SER': 0.13,
-            'THR': 0.14,
-            'ALA': 0.17,
-            'ASN': 0.42,
-            'PRO': 0.45,
-            'GLN': 0.58
+            'PRO': 0.14,
+            'THR': 0.25,
+            'SER': 0.46,
+            'ALA': 0.50,
+            'GLN': 0.77,
+            'ASN': 0.85,
+            'GLY': 1.15
         };
 
         this.residueAbbrev = {
@@ -5928,8 +5927,8 @@ class ClickMenu {
            me.htmlCls.dialogCls.openDlg('dl_esmfold', 'Sequence to structure prediction with ESMFold');
         });
 
-        me.myEventCls.onIds("#" + me.pre + "mn1_gi", "click", function(e) { me.icn3d; //e.preventDefault();
-           me.htmlCls.dialogCls.openDlg('dl_gi', 'Please input protein gi');
+        me.myEventCls.onIds("#" + me.pre + "mn1_proteinname", "click", function(e) { me.icn3d; //e.preventDefault();
+           me.htmlCls.dialogCls.openDlg('dl_proteinname', 'Please input protein or gene name');
         });
 
         me.myEventCls.onIds("#" + me.pre + "mn1_cid", "click", function(e) { me.icn3d; //e.preventDefault();
@@ -8454,10 +8453,16 @@ class SetMenu {
         let html = "";
 
         html += "<ul class='icn3d-mn-item'>";
-        //html += "<li><a href='https://www.ncbi.nlm.nih.gov/structure' target='_blank'>Search Structure " + me.htmlCls.wifiStr + "</a></li>";
-        html += this.getMenuUrl('mn1_searchstru', "https://www.ncbi.nlm.nih.gov/structure", "Search Structure " + me.htmlCls.wifiStr, 1, 1);
+        
+        html += this.getMenuText('mn1_searchgrooup', 'Search Structure ' + me.htmlCls.wifiStr, undefined, 1, 1);
+        html += "<ul>";
+        html += this.getMenuUrl('mn1_searchstru', 'https://www.ncbi.nlm.nih.gov/structure', 'PDB Structures ' + me.htmlCls.wifiStr, undefined, 2);
+        html += this.getLink('mn1_proteinname', 'AlphaFold Structures ' + me.htmlCls.wifiStr, undefined, 2);
+        html += this.getMenuUrl('mn1_afdatabase', 'https://alphafold.ebi.ac.uk', 'AlphaFold UniProt Database ' + me.htmlCls.wifiStr, undefined, 2);
+        html += "</ul>";
+        html += "</li>";
 
-        html += this.getMenuText('mn1_searchsimilar', 'Search Similar', undefined, undefined, 1);
+        html += this.getMenuText('mn1_searchsimilar', 'Search Similar' + me.htmlCls.wifiStr, undefined, undefined, 1);
         html += "<ul>";
         html += this.getLink('mn1_vastplus', 'NCBI VAST+ (PDB Complex)' + me.htmlCls.wifiStr, undefined, 2);
         html += this.getLink('mn1_vast', 'NCBI VAST (PDB Chain)' + me.htmlCls.wifiStr, undefined, 2);
@@ -8478,7 +8483,6 @@ class SetMenu {
         
         html += this.getLink('mn1_afid', 'UniProt ID ' + me.htmlCls.wifiStr, undefined, 3);
         html += this.getLink('mn1_refseqid', 'NCBI Protein Accession ' + me.htmlCls.wifiStr, undefined, 3);
-        // html += this.getLink('mn1_proteinname', 'Protein Name ' + me.htmlCls.wifiStr, undefined, 3);
         html += "</ul>";
 
         
@@ -8520,10 +8524,11 @@ class SetMenu {
         html += "</ul>";
         html += "</li>";
 
-        html += this.getMenuText('mn1_fold', 'AlphaFold/ESM', undefined, undefined, 1);
+        //html += this.getMenuText('mn1_fold', 'AlphaFold/ESM', undefined, undefined, 1);
+        html += this.getMenuText('mn1_fold', 'Predict by Seq.', undefined, undefined, 1);
         html += "<ul>";
-        html += this.getLink('mn1_alphafold', 'AlphaFold2 via ColabFold', undefined, 2);
         html += this.getLink('mn1_esmfold', 'ESMFold', undefined, 2);
+        html += this.getLink('mn1_alphafold', 'AlphaFold2 via ColabFold', undefined, 2);
         html += "</ul>";
 
         
@@ -10341,6 +10346,9 @@ class Dialog {
                     if(me.cfg.align) {
                         position ={ my: "left top", at: "left top+90", of: "#" + me.pre + "canvas", collision: "none" };
                     }
+                    else if(id === me.pre + 'dl_mmdbafid') {
+                        position ={ my: "left top", at: "left top+130", of: "#" + me.pre + "canvas", collision: "none" };
+                    }
                     else {
                         position ={ my: "left top", at: "left top+50", of: "#" + me.pre + "canvas", collision: "none" };
                     }
@@ -10874,7 +10882,7 @@ class SetDialog {
 
         html += me.htmlCls.divStr + "dl_esmfold' style='max-width:600px;' class='" + dialogClass + "'>";
         html += this.addNotebookTitle('dl_esmfold', 'Sequence to structure prediction with ESMFold');
-        html += "The sequence to structure prediction is done via <a href='https://esmatlas.com/resources?action=fold' target='_blank'>ESM Metagenomic Atlas</a>. Generally the sequence should be less than 1024 characters. For any seqeunce longer than 1024, please see the discussion <a href='https://github.com/facebookresearch/esm/issues/21' target='_blank'>here</a>.<br><br> ";
+        html += "The sequence to structure prediction is done via <a href='https://esmatlas.com/resources?action=fold' target='_blank'>ESM Metagenomic Atlas</a>. The sequence should be less than 400 characters. For any sequence longer than 400, please see the discussion <a href='https://github.com/facebookresearch/esm/issues/21' target='_blank'>here</a>.<br><br> ";
         html += "FASTA sequence: <br><textarea id='" + me.pre + "esmfold_fasta' rows='5' style='width: 100%; height: " +(me.htmlCls.LOG_HEIGHT) + "px; padding: 0px; border: 0px;'></textarea><br><br>";
         html += me.htmlCls.buttonStr + "run_esmfold'>ESMFold</button> ";
         html += "</div>";
@@ -10886,10 +10894,10 @@ class SetDialog {
         html += me.htmlCls.buttonStr + "applyyournote'>Save</button>";
         html += "</div>";
 
-        html += me.htmlCls.divStr + "dl_gi' class='" + dialogClass + "'>";
-        html += this.addNotebookTitle('dl_gi', 'Please input an NCBI gi');
-        html += "Protein gi: " + me.htmlCls.inputTextStr + "id='" + me.pre + "gi' value='1310960' size=8> ";
-        html += me.htmlCls.buttonStr + "reload_gi'>Load</button>";
+        html += me.htmlCls.divStr + "dl_proteinname' class='" + dialogClass + "'>";
+        html += this.addNotebookTitle('dl_proteinname', 'Please input a protein/gene name');
+        html += "Protein/Gene name: " + me.htmlCls.inputTextStr + "id='" + me.pre + "proteinname' value='TP53' size=8> ";
+        html += me.htmlCls.buttonStr + "reload_proteinname'>Search</button>";
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_cid' class='" + dialogClass + "'>";
@@ -12879,12 +12887,19 @@ class Events {
             }
 
             let esmfold_fasta = $("#" + me.pre + "esmfold_fasta").val();
-            let pdbid;
+            let pdbid = 'stru--';
 
             if(esmfold_fasta.indexOf('>') != -1) { //FASTA with header
                 let pos = esmfold_fasta.indexOf('\n');
                 ic.esmTitle = esmfold_fasta.substr(1, pos - 1).trim();
-                pdbid = (ic.esmTitle.indexOf(' ') != -1) ? ic.esmTitle.substr(0, ic.esmTitle.indexOf(' ')) : ic.esmTitle;
+                if(ic.esmTitle.indexOf('|') != -1) { // uniprot
+                    let idArray = ic.esmTitle.split('|');
+                    pdbid = (idArray.length > 2) ? idArray[1] : ic.esmTitle;
+                }
+                else { // NCBI
+                    pdbid = (ic.esmTitle.indexOf(' ') != -1) ? ic.esmTitle.substr(0, ic.esmTitle.indexOf(' ')) : ic.esmTitle;
+                }
+
                 if(pdbid.length < 6) pdbid = pdbid.padEnd(6, '-');
 
                 esmfold_fasta = esmfold_fasta.substr(pos + 1);
@@ -12893,8 +12908,8 @@ class Events {
             // remove new lines
             esmfold_fasta = esmfold_fasta.replace(/\s/g, '');
 
-            if(esmfold_fasta.length > 1024) {
-                var aaa = 1; //alert("Your seqeunce is larger than 1024 characters. Please consider to split it as described at https://github.com/facebookresearch/esm/issues/21.");
+            if(esmfold_fasta.length > 400) {
+                var aaa = 1; //alert("Your sequence is larger than 400 characters. Please consider to split it as described at https://github.com/facebookresearch/esm/issues/21.");
                 return;
             }
 
@@ -12903,6 +12918,11 @@ class Events {
             thisClass.setLogCmd("Run ESMFold with the sequence " + esmfold_fasta, false);
 
             let esmData = await me.getAjaxPostPromise(esmUrl, esmfold_fasta, true, alertMess, undefined, true, 'text');
+            
+            ic.bInputfile = true;
+            ic.InputfileType = 'pdb';
+            ic.InputfileData = (ic.InputfileData) ? ic.InputfileData + '\nENDMDL\n' + esmData : esmData;
+
             ic.bEsmfold = true;
             let bAppend = true;
             await ic.pdbParserCls.loadPdbData(esmData, pdbid, undefined, bAppend, undefined, undefined, undefined, ic.bEsmfold);
@@ -12941,12 +12961,12 @@ class Events {
          });
 
 
-        me.myEventCls.onIds("#" + me.pre + "reload_gi", "click", function(e) { let ic = me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_proteinname", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
-           thisClass.setLogCmd("load gi " + $("#" + me.pre + "gi").val(), false);
+           thisClass.setLogCmd("load protein " + $("#" + me.pre + "proteinname").val(), false);
            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
-           window.open(hostUrl + '?gi=' + $("#" + me.pre + "gi").val(), urlTarget);
+           window.open(hostUrl + '?protein=' + $("#" + me.pre + "proteinname").val(), urlTarget);
         });
 
         me.myEventCls.onIds("#" + me.pre + "reload_refseq", "click", function(e) { let ic = me.icn3d;
@@ -14528,8 +14548,17 @@ class AlignSeq {
 
         let chainHash = {};
         if (alignChainArray !== undefined) {
+
             for (let i = 0, il = alignChainArray.length; i < il; ++i) {
-                chainHash[alignChainArray[i]] = 1;
+                let chainid = alignChainArray[i];
+
+                // make sure some residues are aligned
+                if(ic.alnChainsSeq[chainid] && ic.alnChainsSeq[chainid].length > 0) {
+                    chainHash[chainid] = 1;
+                }
+                else {
+                    return { "sequencesHtml": sequencesHtml, "maxSeqCnt": maxSeqCnt };
+                }
             }
         }
 
@@ -14544,7 +14573,7 @@ class AlignSeq {
         let bHighlightChain;
         let index = 0, prevResCnt2nd = 0;
         let firstChainid, oriChainid;
-
+console.log("alignChainArray.length: " + alignChainArray.length);
         //  for(let i in ic.alnChains) {
         for (let m = 0, ml = alignChainArray.length; m < ml; ++m) {
             let i = alignChainArray[m];
@@ -14721,7 +14750,7 @@ class AlignSeq {
                 //sequencesHtml += "<div class='icn3d-residueLine' style='white-space:nowrap;'><div class='icn3d-seqTitle' chain='" + i + "' anno='" + j + "'>" + annotitle + "</div>" + resiHtmlArray[j] + "<br/></div>";
                 sequencesHtml += "<div class='icn3d-residueLine' style='white-space:nowrap;'><div class='icn3d-seqTitle' anno='" + j + "'>" + annotitle + "</div>" + resiHtmlArray[j] + "<br/></div>";
             }
-
+            
             sequencesHtml += '<div class="icn3d-seqTitle icn3d-link icn3d-blue" chain="' + i + '" anno="sequence" title="' + title + '">' + chainidTmp + ' </div><span class="icn3d-seqLine">' + seqHtml + '</span><br/>';
 
             if (index > 0) prevResCnt2nd += seqLength;
@@ -35560,13 +35589,13 @@ class SetOption {
             html += "<div>";
             
             if(colorType == 'normalized hydrophobic') {
-                html += "Dark green (W, F, Y, L, I, C, M): Hydrophobic<br>";
-                html += "Light green (G, V, S, T, A, N, P, Q): Polar<br>";
+                html += "Dark green (W, F, L, I, Y, M, V, C): Hydrophobic<br>";
+                html += "Light green (P, T, S, A, Q, N, G): Polar<br>";
                 html += "Grey: Charged, not hydrophobic<br><br>";
             }
             else {
-                html += "Green (W, F, Y, L, I, C, M): Hydrophobic<br>";
-                html += "Yellow (G, V, S, T, A, N, P, Q): Polar<br>";
+                html += "Green (W, F, L, I, Y, M, V, C): Hydrophobic<br>";
+                html += "Yellow (P, T, S, A, Q, N, G): Polar<br>";
                 html += "Red: Negatively Charged<br>";
                 html += "Blue: Positively Charged<br><br>";
             }
@@ -39125,7 +39154,7 @@ class Domain3d {
 		return {subdomains: subdomains, substruct: substruct, pos2resi: pos2resi };
 	} // end c2b_NewSplitChain
 
-	getDomainJsonForAlign(atoms) { let ic = this.icn3d, me = ic.icn3dui;
+	getDomainJsonForAlign(atoms, bForceOneDomain) { let ic = this.icn3d, me = ic.icn3dui;
 		let result = this.c2b_NewSplitChain(atoms);
 
 		let subdomains = result.subdomains;
@@ -39136,6 +39165,8 @@ class Domain3d {
 		let residueArray = Object.keys(residueHash);
 		let chnid = residueArray[0].substr(0, residueArray[0].lastIndexOf('_'));
 
+		if(bForceOneDomain) subdomains = [];
+
 		//the whole structure is also considered as a large domain
 		//if(subdomains.length == 0) {
 			//subdomains.push([parseInt(ic.chainsSeq[chnid][0].resi), parseInt(ic.chainsSeq[chnid][ic.chainsSeq[chnid].length - 1].resi)]);
@@ -40993,7 +41024,7 @@ class ShowAnno {
                     dataObj['targets'] = me.cfg.blast_rep_id + ':' + target_from_to_array.join(':');
                 }
 
-                // get seqeunce
+                // get sequence
                 if(ic.blastAcxn) { 
                     let chainid = me.cfg.afid + '_A';
                     let seq = '';
@@ -41024,7 +41055,7 @@ class ShowAnno {
                     idArray.push(me.cfg.query_id);
                 }
 
-                // get seqeunce
+                // get sequence
                 if(ic.blastAcxn) { 
                     let chainid = me.cfg.afid + '_A';
                     let seq = '';
@@ -41351,7 +41382,7 @@ class ShowAnno {
                 let data = ic.seqStructAlignData;
                 if(data.data !== undefined) {
                     query = data.data[0].query;
-                    // if target is seqeunce, the key is not chnid
+                    // if target is sequence, the key is not chnid
                     //target = data.data[0].targets[chnid];
                     let keys = Object.keys(data.data[0].targets);
                     target = data.data[0].targets[keys[0]];
@@ -41363,7 +41394,7 @@ class ShowAnno {
                     evalue = target.scores.e_value.toPrecision(2);
                     if(evalue > 1e-200) evalue = parseFloat(evalue).toExponential();
                     target.scores.bit_score;
-                    // if target is seqeunce, the key is not chnid
+                    // if target is sequence, the key is not chnid
                     // targetSeq = data.targets[chnid].seqdata;
                     let keys = Object.keys(data.targets);
                     targetSeq = data.targets[keys[0]].seqdata;
@@ -42807,7 +42838,7 @@ class HlSeq {
            //});
 
             // remove possible text selection
-            // the following code caused the scroll of seqeunce window to the top, remove it for now
+            // the following code caused the scroll of sequence window to the top, remove it for now
             /*
             if(window.getSelection) {
               if(window.getSelection().empty) {  // Chrome
@@ -44395,26 +44426,22 @@ class LineGraph {
 
         let pdbAjaxArray = [];
         for(let k = 0, kl = ic.refpdbArray.length; k < kl; ++k) {
-            //let urlpdb = me.htmlCls.baseUrl + "icn3d/refpdb/" + ic.refpdbArray[k] + ".pdb";
-            let urlpdb = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi?refpdbid=" + ic.refpdbArray[k];
+            //let urlpdb = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi?refpdbid=" + ic.refpdbArray[k];
+            let urlpdb = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi?refjsonid=" + ic.refpdbArray[k];
 
             let pdbAjax = me.getAjaxPromise(urlpdb, 'text');
 
             pdbAjaxArray.push(pdbAjax);
         }
 
-        try {
+        // try {
             let allPromise = Promise.allSettled(pdbAjaxArray);
             ic.pdbDataArray = await allPromise;
             await thisClass.parseRefPdbData(ic.pdbDataArray);
-        }
-        catch(err) {
-            if(!me.bNode) var aaa = 1; //alert("Error in retrieveing reference PDB data...");
-            //var aaa = 1; //alert("Error in retrieveing reference PDB data...");
-            return;
-        }       
-
         // }
+        // catch(err) {
+        //     if(!me.bNode) var aaa = 1; //alert("Error in retrieveing reference PDB data...");
+        //     return;
         // }
     }
 
@@ -44426,7 +44453,8 @@ class LineGraph {
         let ajaxArray = [];
         let domainidpairArray = [];
 
-        let urltmalign = me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
+        me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
+        let urlalign = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi";
 
         if(!ic.resid2domainid) ic.resid2domainid = {};
         //ic.resid2domainid = {};
@@ -44506,6 +44534,9 @@ class LineGraph {
 
                 for(let k = 0, kl = domainAtomsArray.length; k < kl; ++k) {
                     let pdb_target = ic.saveFileCls.getAtomPDB(domainAtomsArray[k], undefined, undefined, undefined, undefined, struct);
+                    let bForceOneDomain = true;
+                    let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(domainAtomsArray[k], bForceOneDomain);
+
                     // ig strand for any subset will have the same k, use the number of residue to separate them
                     let atomFirst = ic.firstAtomObjCls.getFirstAtomObj(domainAtomsArray[k]);
                     let atomLast = ic.firstAtomObjCls.getLastAtomObj(domainAtomsArray[k]);
@@ -44515,14 +44546,19 @@ class LineGraph {
                     ic.domainid2pdb[domainid] = pdb_target;
 
                     for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
-                        let struct2 = ic.defaultPdbId + index;
-                        //let pdb_query = (me.bNode) ? dataArray[index] : dataArray[index].value; //[0];
-                        let pdb_query = dataArray[index].value; //[0];
-                        let header = 'HEADER                                                        ' + struct2 + '\n';
-                        pdb_query = header + pdb_query;
-
-                        let dataObj = {'pdb_query': pdb_query, 'pdb_target': pdb_target, "queryid": ic.refpdbArray[index]};
-                        let alignAjax = me.getAjaxPostPromise(urltmalign, dataObj);
+                        // let struct2 = ic.defaultPdbId + index;
+                        // let pdb_query = dataArray[index].value; //[0];
+                        // let header = 'HEADER                                                        ' + struct2 + '\n';
+                        // pdb_query = header + pdb_query;
+                        let jsonStr_q = dataArray[index].value; //[0];
+
+                        // TM-align is not good when you align a full structure with the strand-only structure. VAST is better in this case.
+                        // let dataObj = {'pdb_query': pdb_query, 'pdb_target': pdb_target, "queryid": ic.refpdbArray[index]};
+                        // let alignAjax = me.getAjaxPostPromise(urltmalign, dataObj);
+
+                        let dataObj = {'domains1': jsonStr_q, 'domains2': jsonStr_t};
+                        let alignAjax = me.getAjaxPostPromise(urlalign, dataObj);
+
                         ajaxArray.push(alignAjax);
                         
                         domainidpairArray.push(domainid + "|" + ic.refpdbArray[index]);
@@ -44601,6 +44637,7 @@ class LineGraph {
         let thisClass = this;
 
         let tmscoreThreshold = 0.4; // 0.4; //0.5;
+        let rmsdThreshold = 10;
 
         // find the best alignment for each chain
         let domainid2score = {}, domainid2segs = {}, chainid2segs = {};
@@ -44628,8 +44665,15 @@ class LineGraph {
 
             if(queryData.length == 0) continue;
             
-            if(queryData[0].score < tmscoreThreshold || queryData[0].num_res < minResidues) {
-                continue;
+            if(!bRound1) {
+                if(queryData[0].score < tmscoreThreshold || queryData[0].num_res < minResidues) {
+                    continue;
+                }
+            }
+            else {
+                if(queryData[0].super_rmsd > rmsdThreshold || queryData[0].num_res < minResidues) {
+                    continue;
+                }
             }
 
             //let domainid_index = domainidpairArray[i].split(',');
@@ -44638,44 +44682,63 @@ class LineGraph {
             let refpdbname = domainidpairArray[i].substr(domainidpairArray[i].indexOf('|') + 1);
             //let chainid = domainid.split('-')[0];
 
-            if(!me.bNode) console.log("refpdbname " + refpdbname + " TM-score: " + queryData[0].score);
+            if(!bRound1) {
+                if(!me.bNode) console.log("refpdbname " + refpdbname + " TM-score: " + queryData[0].score);
+            }
+            else {
+                if(!me.bNode) console.log("refpdbname " + refpdbname + " RMSD: " + queryData[0].super_rmsd);
+            }
 
             // Ig-like domains: B (2150, 2150a, 2150b), C (3150, 3250), E (7150, 7250), F (8150, 8250) strands
             // Ig domain may require G (7050). But we'll leave that out for now.
-            let bBstrand = false, bCstrand = false, bEstrand = false, bFstrand = false;
-            for(let i = 0, il = queryData[0].segs.length; i < il; ++i) {
-                let seg = queryData[0].segs[i];
+            if(!bRound1) {
+                let bBstrand = false, bCstrand = false, bEstrand = false, bFstrand = false;
+                for(let i = 0, il = queryData[0].segs.length; i < il; ++i) {
+                    let seg = queryData[0].segs[i];
 
-                if(seg.q_start.indexOf('2150') != -1 || seg.q_start.indexOf('2250') != -1) {
-                    bBstrand = true;
-                }
-                else if(seg.q_start.indexOf('3150') != -1 || seg.q_start.indexOf('3250') != -1) {
-                    bCstrand = true;
-                }
-                else if(seg.q_start.indexOf('7150') != -1 || seg.q_start.indexOf('7250') != -1) {
-                    bEstrand = true;
-                }
-                else if(seg.q_start.indexOf('8150') != -1 || seg.q_start.indexOf('8250') != -1) {
-                    bFstrand = true;
+                    if(seg.q_start.indexOf('2150') != -1 || seg.q_start.indexOf('2250') != -1) {
+                        bBstrand = true;
+                    }
+                    else if(seg.q_start.indexOf('3150') != -1 || seg.q_start.indexOf('3250') != -1) {
+                        bCstrand = true;
+                    }
+                    else if(seg.q_start.indexOf('7150') != -1 || seg.q_start.indexOf('7250') != -1) {
+                        bEstrand = true;
+                    }
+                    else if(seg.q_start.indexOf('8150') != -1 || seg.q_start.indexOf('8250') != -1) {
+                        bFstrand = true;
+                    }
+
+                    //if(bBstrand && bCstrand && bEstrand && bFstrand && bGstrand) break;
+                    if(bBstrand && bCstrand && bEstrand && bFstrand) break;
                 }
 
-                //if(bBstrand && bCstrand && bEstrand && bFstrand && bGstrand) break;
-                if(bBstrand && bCstrand && bEstrand && bFstrand) break;
+                //if(!(bBstrand && bCstrand && bEstrand && bFstrand && bGstrand)) continue;
+                if(!(bBstrand && bCstrand && bEstrand && bFstrand)) {
+                    if(!me.bNode) console.log("Some of the Ig strands B, C, E, F are missing in the domain " + domainid + "...");
+                    continue;
+                }
             }
 
-            //if(!(bBstrand && bCstrand && bEstrand && bFstrand && bGstrand)) continue;
-            if(!(bBstrand && bCstrand && bEstrand && bFstrand)) {
-                if(!me.bNode) console.log("Some of the Ig strands B, C, E, F are missing in the domain " + domainid + "...");
-                continue;
+            if(!bRound1) {
+                if(!domainid2score.hasOwnProperty(domainid) || queryData[0].score > domainid2score[domainid]) {
+                    domainid2score[domainid] = queryData[0].score;  
+        
+                    ic.domainid2refpdbname[domainid] = refpdbname;
+                    domainid2segs[domainid] = queryData[0].segs;
+                    ic.domainid2ig2kabat[domainid] = queryData[0].ig2kabat;
+                    ic.domainid2ig2imgt[domainid] = queryData[0].ig2imgt;
+                }
             }
-
-            if(!domainid2score.hasOwnProperty(domainid) || queryData[0].score > domainid2score[domainid]) {
-                domainid2score[domainid] = queryData[0].score;    
-
-                ic.domainid2refpdbname[domainid] = refpdbname;
-                domainid2segs[domainid] = queryData[0].segs;
-                ic.domainid2ig2kabat[domainid] = queryData[0].ig2kabat;
-                ic.domainid2ig2imgt[domainid] = queryData[0].ig2imgt;
+            else {
+                if(!domainid2score.hasOwnProperty(domainid) || queryData[0].super_rmsd < domainid2score[domainid]) {
+                    domainid2score[domainid] = queryData[0].super_rmsd;  
+        
+                    ic.domainid2refpdbname[domainid] = refpdbname;
+                    domainid2segs[domainid] = queryData[0].segs;
+                    ic.domainid2ig2kabat[domainid] = queryData[0].ig2kabat;
+                    ic.domainid2ig2imgt[domainid] = queryData[0].ig2imgt;
+                }                
             }
         }
 
@@ -48092,7 +48155,7 @@ class ChainalignParser {
         let hAtomsAll = {};
 
         if(ic.bFullUi && ic.q_rotation !== undefined && !me.cfg.resnum && !me.cfg.resdef) {
-            // set multiple seqeunce alignment from ic.qt_start_end
+            // set multiple sequence alignment from ic.qt_start_end
             hAtomsAll = this.setMsa(chainidArray);
         }
 
@@ -48152,7 +48215,7 @@ class ChainalignParser {
         ic.qt_start_end = [];
 
         let mmdbid2cnt = {}, mmdbidpairHash = {};
-             
+
         let bFoundAlignment = false;
         for(let i = 0, il = dataArray.length; i < il; ++i) {
             // let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
@@ -48632,6 +48695,7 @@ class ChainalignParser {
 
     processAlign(align, index, queryData, bEqualMmdbid, bEqualChain, bNoAlert) { let ic = this.icn3d, me = ic.icn3dui;
         let bAligned = false;
+
         if((!align || align.length == 0) && !bNoAlert) {
             let serverName = (me.cfg.aligntool == 'tmalign') ? 'TM-align' : 'VAST';
         
@@ -48816,14 +48880,14 @@ class ChainalignParser {
         ic.ParserUtilsCls.showLoading();
 
         let allPromise = Promise.allSettled(ajaxArray);
-        try {
+        // try {
             let dataArray = await allPromise;
             await thisClass.parseMMdbAfData(dataArray, structArray, bQuery, vastplusAtype);
             if(vastplusAtype === undefined) ic.ParserUtilsCls.hideLoading();
-        }
-        catch(err) {
-            var aaa = 1; //alert("There are some problems in retrieving the coordinates...");
-        }          
+        // }
+        // catch(err) {
+        //     var aaa = 1; //alert("There are some problems in retrieving the coordinates...");
+        // }          
     //   });
     
     //   return ic.deferredMmdbaf.promise();
@@ -49462,6 +49526,73 @@ class MmdbParser {
         //await ic.loadScriptCls.loadScript(me.cfg.command, undefined, true);
     }
 
+    async downloadProteinname(protein) { let ic = this.icn3d, me = ic.icn3dui;
+        me.icn3d.bCid = undefined;
+
+        // get RefSeq ID from protein name
+        let url = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi?protein2acc=" + protein;
+
+        let accJson = await me.getAjaxPromise(url, 'jsonp');
+
+        let accArray = accJson.acc;
+
+        if(accArray.length == 0) {
+            if(!me.bNode) var aaa = 1; //alert('The protein/gene name ' + protein + ' can not be mapped to RefSeq proteins...');
+            return;
+        }
+
+        let ajaxArray = [];
+        for(let index = 0, indexl = accArray.length; index < indexl; ++index) {
+            let refseqid = accArray[index];
+            url = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi?refseq2uniprot=" + refseqid;
+
+            let ajax = me.getAjaxPromise(url, 'jsonp');
+
+            ajaxArray.push(ajax);
+        }
+
+        let allPromise = Promise.allSettled(ajaxArray);
+        let dataArray = await allPromise;
+
+        ajaxArray = [];
+        let afidArray = [];
+        for(let i = 0, il = dataArray.length; i < il; ++i) {
+            let data = dataArray[i].value;
+
+            if(data && data.uniprot) {
+                let afid = data.uniprot;
+                url = "https://alphafold.ebi.ac.uk/files/AF-" + afid + "-F1-model_" + ic.AFUniprotVersion + ".pdb";
+                ic.ParserUtilsCls.setYourNote(me.cfg.protein + '(NCBI Protein/Gene) in iCn3D');
+
+                let ajax = me.getAjaxPromise(url, 'text', true);
+                ajaxArray.push(ajax);
+                afidArray.push(afid);
+            }
+        }
+        
+        allPromise = Promise.allSettled(ajaxArray);
+        dataArray = await allPromise;
+       
+        for(let i = 0, il = dataArray.length; i < il; ++i) {
+            let data = dataArray[i].value;
+            me.cfg.afid = afidArray[i];
+
+            if(data) {
+                // add UniProt ID into the header
+                let header = 'HEADER                                                        ' + me.cfg.afid + '\n';
+                data = header + data;          
+                await ic.opmParserCls.parseAtomData(data, me.cfg.afid, undefined, 'pdb', undefined);
+
+                break;
+            }
+        }
+
+        if(!me.cfg.afid) {
+            if(!me.bNode) var aaa = 1; //alert('The protein/gene name ' + protein + ' can not be mapped to AlphaFold structures...');
+            return;
+        }
+    }
+
     getNoData(mmdbid, bGi) { let ic = this.icn3d, me = ic.icn3dui;
         if(bGi) {
             var aaa = 1; //alert("This gi " + mmdbid + " has no corresponding 3D structure...");
@@ -50538,6 +50669,9 @@ class PdbParser {
             if(me.cfg.refseqid) {
                 ic.ParserUtilsCls.setYourNote(me.cfg.refseqid.toUpperCase() + '(NCBI Protein Acc.) in iCn3D');
             }
+            else if(me.cfg.protein) {
+                ic.ParserUtilsCls.setYourNote(me.cfg.protein + '(NCBI Protein/Gene) in iCn3D');
+            }
             else {
                 ic.ParserUtilsCls.setYourNote(pdbid.toUpperCase() + '(AlphaFold) in iCn3D');
             }
@@ -51473,6 +51607,7 @@ class RealignParser {
     async realignOnStructAlign(bReverse) { let ic = this.icn3d, me = ic.icn3dui;
         // each 3D domain should have at least 3 secondary structures
         let minSseCnt = (me.cfg.aligntool != 'tmalign') ? 3 : 0;
+
         let struct2domain = {};
         for(let struct in ic.structures) {
             struct2domain[struct] = {};
@@ -51483,7 +51618,7 @@ class RealignParser {
                 let sseCnt = 0;
                 for(let serial in atoms) {
                     if(ic.atoms[serial].ssbegin) ++sseCnt;
-                    if(sseCnt == minSseCnt) {
+                    if(sseCnt > minSseCnt) {
                         struct2domain[struct][chainid] = atoms;
                         break;
                     }
@@ -51515,7 +51650,6 @@ class RealignParser {
                         let chainid2 = chainidArray2[j];
 
                         let alignAjax;
-
                         if(me.cfg.aligntool != 'tmalign') {
                             let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(struct2domain[struct2][chainid2]);
                         
@@ -51554,7 +51688,7 @@ class RealignParser {
 
     async realignOnStructAlignMsa(nameArray) { let ic = this.icn3d, me = ic.icn3dui;
         // each 3D domain should have at least 3 secondary structures
-        let minSseCnt = 3;
+        let minSseCnt = (me.cfg.aligntool != 'tmalign') ? 3 : 0;
         let chainid2domain = {};
 
         for(let i = 0, il = nameArray.length; i < il; ++i) {
@@ -51563,7 +51697,7 @@ class RealignParser {
             let sseCnt = 0;
             for(let serial in atoms) {
                 if(ic.atoms[serial].ssbegin) ++sseCnt;
-                if(sseCnt == minSseCnt) {
+                if(sseCnt > minSseCnt) {
                     chainid2domain[chainid] = atoms;
                     break;
                 }
@@ -53684,7 +53818,7 @@ class ParserUtils {
                         if(ic.bAnnoShown) await ic.showAnnoCls.showAnnotations();
                     }
 
-                    // Realign by seqeunce alignment with the residues in "segment", i.e., transmembrane helix
+                    // Realign by sequence alignment with the residues in "segment", i.e., transmembrane helix
                     let segment = data.segment;   // e.g., " 361- 379 ( 359- 384)", the first range is trnasmembrane range, 
                                                 //the second range is the range of the helix
                     let range = segment.replace(/ /gi, '').split('(')[0]; //361-379
@@ -55498,7 +55632,7 @@ class SetSeqAlign {
 
         //mmdbid1 = ic.mmdbid_t; 
         mmdbid1 = chainidArray[0].substr(0, pos1); //.toUpperCase();
-        mmdbid2 = chainid.substr(0, pos2); //.toUpperCase();
+        mmdbid2 = chainid.substr(0, pos2); //.toUpperCase()mergeTwoSeqForAll;
 
         chain1 = chainidArray[0].substr(pos1 + 1);
         chain2 = chainid.substr(pos2 + 1);
@@ -55893,7 +56027,7 @@ class LoadPDB {
     getStructureId(id, moleculeNum, bMutation) { let ic = this.icn3d; ic.icn3dui;
         let structure = id;
     
-        if(id == ic.defaultPdbId || bMutation) { // bMutation: side chain prediction
+        if(id == ic.defaultPdbId || bMutation || ic.structures.hasOwnProperty(id)) { // bMutation: side chain prediction
             structure = (moleculeNum === 1) ? id : id + moleculeNum.toString();
         }
 
@@ -55961,7 +56095,7 @@ class LoadPDB {
         let prevMissingChain = '';
         let CSerial, prevCSerial, OSerial, prevOSerial;
         
-        let bHeader = false;
+        let bHeader = false, bFirstAtom = true;
 
         for (let i in lines) {
             let line = lines[i];
@@ -56122,7 +56256,11 @@ class LoadPDB {
                     ic.pmid = line.substr(19).trim();
                 }
             } else if (record === 'ATOM  ' || record === 'HETATM') {
-                structure = this.getStructureId(id, moleculeNum, bMutation);
+                if(bFirstAtom) {
+                    structure = this.getStructureId(id, moleculeNum, bMutation);
+
+                    bFirstAtom = false;
+                }
 
                 let alt = line.substr(16, 1);
                 //if (alt !== " " && alt !== "A") continue;
@@ -57013,7 +57151,7 @@ class Vastplus {
 
             // reinitialize the alignment
             $("#" + ic.pre + "dl_sequence2").html('');
-          
+
             for(let j = 0, jl = nodeArray.length; j < jl; ++j) {
                 let node = parseInt(nodeArray[j]);
                 let segs = queryDataArray[node][0].segs;
@@ -57090,7 +57228,7 @@ class Vastplus {
                         for(let j = 0, jl = nodeArray.length; j < jl; ++j) {
                             chainpairStr += chainidpairArray[parseInt(nodeArray[j])] + '; ';
                         }
-                        console.log("Selected the alignment: " + chainpairStr);
+                        if(!me.bNode) console.log("Selected the alignment: " + chainpairStr);
 
                         break;
                     }
@@ -57099,7 +57237,7 @@ class Vastplus {
                         for(let j = 0, jl = nodeArray.length; j < jl; ++j) {
                             chainpairStr += chainidpairArray[parseInt(nodeArray[j])] + '; ';
                         }
-                        console.log("skipped the alignment: " + chainpairStr);
+                        if(!me.bNode) console.log("skipped the alignment: " + chainpairStr);
                     }
                 }
             }
@@ -60484,6 +60622,10 @@ class LoadScript {
             me.cfg.refseqid = id;
             await ic.mmdbParserCls.downloadRefseq(id);
         }
+        else if(command.indexOf('load protein') !== -1) {
+            me.cfg.protein = id;
+            await ic.mmdbParserCls.downloadProteinname(id);
+        }
         else if(command.indexOf('load seq_struct_ids ') !== -1) {
           ic.bSmithwm = false;
           ic.bLocalSmithwm = false;
@@ -61579,6 +61721,8 @@ class Selection {
           ic.graphStr = this.getGraphDataForDisplayed();
         }
 
+        ic.saveFileCls.showTitle();
+
         // don not redraw graphs after the selection changes
         /*
         if(ic.bGraph) ic.drawGraphCls.drawGraph(ic.graphStr, ic.pre + 'dl_graph');
@@ -66818,7 +66962,7 @@ 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_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_refseqid', '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_allinteracton', 'dl_interactionsorted', 'dl_linegraph', 'dl_linegraphcolor', 'dl_scatterplot', 'dl_scatterploitcolor', '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_proteinname', 'dl_refseqid', '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_allinteracton', 'dl_interactionsorted', 'dl_linegraph', 'dl_linegraphcolor', 'dl_scatterplot', 'dl_scatterploitcolor', '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];
@@ -67952,13 +68096,13 @@ class SaveFile {
 
     //Show the title and PDB ID of the PDB structure at the beginning of the viewer.
     showTitle() {var ic = this.icn3d, me = ic.icn3dui;
-        if(ic.molTitle !== undefined && ic.molTitle !== '') {
-            let title = ic.molTitle;
+        // if(ic.molTitle !== undefined && ic.molTitle !== '') {
+            let title = (ic.molTitle) ? ic.molTitle : '';
 
             let titlelinkColor =(ic.opts['background'] == 'black') ?  me.htmlCls.GREYD : 'black';
 
             if(ic.inputid === undefined) {
-                if(ic.molTitle.length > 40) title = ic.molTitle.substr(0, 40) + "...";
+                if(title.length > 40) title = title.substr(0, 40) + "...";
 
                 $("#" + ic.pre + "title").html(title);
             }
@@ -67978,31 +68122,38 @@ class SaveFile {
 
                 $("#" + ic.pre + "title").html(title);
             }
-            else if(me.cfg.mmdbafid !== undefined) {
-                let structureArray = Object.keys(ic.structures); //me.cfg.mmdbafid.split(',');
+            else { //if(me.cfg.mmdbafid !== undefined) {
+                //let structureArray = Object.keys(ic.structures); //me.cfg.mmdbafid.split(',');
+                let structureArray = Object.keys(me.utilsCls.getStructures(ic.dAtoms));
+
                 if(structureArray.length > 1) {
-                    title = 'Multiple structures: ' + structureArray;
+                    title = 'Multiple structures: ';
+                    for(let i = 0, il = structureArray.length; i < il; ++i) {
+                        let url = (isNaN(structureArray[i]) && structureArray[i].length > 5) ? 'https://alphafold.ebi.ac.uk/entry/' + structureArray[i] : 'https://www.ncbi.nlm.nih.gov/structure/?term=' + structureArray[i];
+                        title += '<a href="' + url + '" style="color:' + titlelinkColor + '" target="_blank">' + structureArray[i] + '</a>';
+                        if(i < il - 1) title += ', ';
+                    }
                     $("#" + ic.pre + "title").html(title);
                 }
                 else if(structureArray.length == 1) {
                     //let url = this.getLinkToStructureSummary();
-                    let url = (isNaN(ic.inputid) && ic.inputid.length > 5) ? 'https://alphafold.ebi.ac.uk/entry/' + ic.inputid : 'https://www.ncbi.nlm.nih.gov/structure/?term=' + ic.inputid;
+                    let url = (isNaN(structureArray[0]) && structureArray[0].length > 5) ? 'https://alphafold.ebi.ac.uk/entry/' + structureArray[0] : 'https://www.ncbi.nlm.nih.gov/structure/?term=' + structureArray[0];
 
                     this.setStructureTitle(url, title, titlelinkColor);
                 }
             }
-            else {
-                let url = this.getLinkToStructureSummary();
-                this.setStructureTitle(url, title, titlelinkColor);
-            }
-        }
-        else {
-            $("#" + ic.pre + "title").html("");
-        }
+            // else {
+            //     let url = this.getLinkToStructureSummary();
+            //     this.setStructureTitle(url, title, titlelinkColor);
+            // }
+        // }
+        // else {
+        //     $("#" + ic.pre + "title").html("");
+        // }
     }
 
     setStructureTitle(url, title, titlelinkColor) {var ic = this.icn3d, me = ic.icn3dui;
-        if(ic.molTitle.length > 40) title = ic.molTitle.substr(0, 40) + "...";
+        if(title.length > 40) title = title.substr(0, 40) + "...";
 
         let inputid = ic.inputid;
 
@@ -68028,7 +68179,7 @@ class SaveFile {
             let structureidArray = Object.keys(idHash);
             inputid = structureidArray.join(',');
 
-            text = (me.cfg.refseqid) ? ic.inputid : inputid.toUpperCase();
+            text = (me.cfg.refseqid || me.cfg.protein) ? ic.inputid : inputid.toUpperCase();
 
             //idName = (isNaN(inputid) && inputid.length > 5) ? "AlphaFold ID" : "PDB ID";
             if(bPdb && bAlphaFold) {
@@ -68054,7 +68205,12 @@ class SaveFile {
             }
         }
 
-        if(me.cfg.refseqid) idName = 'NCBI Protein Acc.';
+        if(me.cfg.refseqid) {
+            idName = 'NCBI Protein Acc.';
+        }
+        else if(me.cfg.protein) {
+            idName = 'Protein/Gene Name';
+        }
 
         if(!inputid || inputid.substr(0, 4) == ic.defaultPdbId) {
             $("#" + ic.pre + "title").html(title);
@@ -71326,7 +71482,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.26.0';
+    this.REVISION = '3.27.0';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -71619,6 +71775,14 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
         me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
         await ic.mmdbParserCls.downloadRefseq(me.cfg.refseqid);
     }
+    else if(me.cfg.protein !== undefined) {
+        ic.inputid = me.cfg.protein;
+        
+        // ic.bNCBI = true;
+        ic.loadCmd = 'load protein ' + me.cfg.protein;
+        me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
+        await ic.mmdbParserCls.downloadProteinname(me.cfg.protein);
+    }
     else if(me.cfg.blast_rep_id !== undefined) {
        // ic.bNCBI = true;
        ic.inputid =  me.cfg.query_id + ',' + me.cfg.blast_rep_id;
@@ -71626,7 +71790,7 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
        me.cfg.oriQuery_id = me.cfg.query_id;
        me.cfg.oriBlast_rep_id = me.cfg.blast_rep_id;
 
-       // custom seqeunce has query_id such as "Query_78989" in BLAST
+       // custom sequence has query_id such as "Query_78989" in BLAST
        if(me.cfg.query_id.substr(0,5) !== 'Query' && me.cfg.rid === undefined) {
             // make it backward compatible for  figure 2 in iCn3D paper: https://academic.oup.com/bioinformatics/article/36/1/131/5520951
             if(me.cfg.from == 'icn3d' && me.cfg.blast_rep_id == '1TSR_A' && me.cfg.query_id == 'NP_001108451.1') {