icn3d 3.26.9 → 3.28.0

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>";
 
         
@@ -8829,9 +8834,9 @@ class SetMenu {
 
         html += this.getMenuText('mn2_rotate90', 'Rotate 90&deg;', undefined, undefined, 2);
         html += "<ul>";
-        html += this.getRadio('mn6_rotate90', 'mn6_rotatex', 'X-axis(Shift + Key M)', undefined, undefined, 2);
-        html += this.getRadio('mn6_rotate90', 'mn6_rotatey', 'Y-axis(Shift + Key J)', undefined, undefined, 2);
-        html += this.getRadio('mn6_rotate90', 'mn6_rotatez', 'Z-axis', undefined, undefined, 2);
+        html += this.getRadio('mn6_rotate90', 'mn6_rotatex', 'rotate x', undefined, undefined, 2);
+        html += this.getRadio('mn6_rotate90', 'mn6_rotatey', 'rotate y', undefined, undefined, 2);
+        html += this.getRadio('mn6_rotate90', 'mn6_rotatez', 'rotate z', undefined, undefined, 2);
         html += "</ul>";
         html += "</li>";
         html += this.getMenuText('mn2_rotateauto', 'Auto Rotation', undefined, 1, 2);
@@ -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 + "'>";
@@ -11559,9 +11567,10 @@ class SetDialog {
 
         html += me.htmlCls.divStr + "dl_addtrack_tabs' style='border:0px;'>";
         html += "<ul>";
+        html += "<li><a href='#" + me.pre + "tracktab2c'>Isoforms & Exons</a></li>";
+        html += "<li><a href='#" + me.pre + "tracktab2b'>MSA</a></li>";
         html += "<li><a href='#" + me.pre + "tracktab1'>NCBI gi/Accession</a></li>";
         html += "<li><a href='#" + me.pre + "tracktab2'>FASTA</a></li>";
-        html += "<li><a href='#" + me.pre + "tracktab2b'>FASTA Alignment</a></li>";
         html += "<li><a href='#" + me.pre + "tracktab3'>BED File</a></li>";
         html += "<li><a href='#" + me.pre + "tracktab4'>Custom</a></li>";
         html += "<li><a href='#" + me.pre + "tracktab5'>Current Selection</a></li>";
@@ -11577,10 +11586,16 @@ class SetDialog {
         html += "</div>";
 
         html += me.htmlCls.divStr + "tracktab2b'>";
-        html += "<div style='width:600px'>The full protein sequences with gaps are listed one by one. The sequence of the structure is listed at the top. If there are non-gap residues(e.g., from RefSeq) outside of the sequence of the structure, please remove them. Each sequence has a title line starting with \">\".</div><br>";
-        html += "<b>FASTA alignment sequences</b>:<br>";
+        // html += "<div style='width:600px'>The full protein sequences with gaps are listed one by one. The sequence of the structure is listed at the top. If there are non-gap residues(e.g., from RefSeq) outside of the sequence of the structure, please remove them. Each sequence has a title line starting with \">\".</div><br>";
+        html += "<div style='width:600px'>Note: The full protein sequences with gaps in MSA are listed one by one. The sequence of the structure is listed at the top. Each sequence has a title line starting with \">\".</div><br>";
+
+        html += "<b>Precalculated Multiple Sequence Alignment (MSA)</b>:<br>";
         html += "<textarea id='" + me.pre + "track_fastaalign' rows='5' style='width: 100%; height: " +(2*me.htmlCls.LOG_HEIGHT) + "px; padding: 0px; border: 0px;'></textarea><br><br>";
-        html += "Position of the first residue in Sequences & Annotations window: " + me.htmlCls.inputTextStr + "id='" + me.pre + "fasta_startpos' value='1' size=2> <br><br>";
+
+        // html += "<b>Opion 1. Precalculated Multiple Sequence Alignment (MSA)</b>:<br>";
+        // html += "<textarea id='" + me.pre + "track_fastaalign' rows='5' style='width: 100%; height: " +(2*me.htmlCls.LOG_HEIGHT) + "px; padding: 0px; border: 0px;'></textarea><br><br>";
+        // html += "<b>Opion 2. NCBI Protein Accessions</b>: "+ me.htmlCls.inputTextStr + "id='" + me.pre + "track_acclist' size=60> <br><br>";
+        html += "<b>Position of the first residue in Sequences & Annotations window</b>: " + me.htmlCls.inputTextStr + "id='" + me.pre + "fasta_startpos' value='1' size=2> <br><br>";
 
         html += "Color Sequence by: <select id='" + me.pre + "colorseqby'>";
         html += me.htmlCls.optionStr + "'identity' selected>Identity</option>";
@@ -11590,6 +11605,22 @@ class SetDialog {
         html += me.htmlCls.buttonStr + "addtrack_button2b'>Add Track(s)</button>";
         html += "</div>";
 
+        html += me.htmlCls.divStr + "tracktab2c'>";
+        html += "<div style='width:500px'>Note: Show exons for all isoforms of the protein in the same gene as specified below.</div><br>";
+
+        html += "<b><a href='https://www.ncbi.nlm.nih.gov/gene' target='_blank'>NCBI Gene</a> ID</b>: "+ me.htmlCls.inputTextStr + "id='" + me.pre + "track_geneid' size=20>" + me.htmlCls.space3 + me.htmlCls.buttonStr + "exons_table'>Exons & Introns in Gene Table</button><br><br>";
+
+        html += "<b>Position of the first residue in Sequences & Annotations window</b>: " + me.htmlCls.inputTextStr + "id='" + me.pre + "fasta_startpos2' value='1' size=2> <br><br>";
+
+        html += "Color Sequence by: <select id='" + me.pre + "colorseqby2'>";
+        html += me.htmlCls.optionStr + "'identity' selected>Identity</option>";
+        html += me.htmlCls.optionStr + "'conservation'>Conservation</option>";
+        html += "</select> <br><br>";
+
+        html += me.htmlCls.buttonStr + "addtrack_button2c'>Show Isoforms & Exons</button>";
+        html += "</div>";
+
+
         html += me.htmlCls.divStr + "tracktab3'>";
         html += "BED file: " + me.htmlCls.inputFileStr + "id='" + me.pre + "track_bed' size=16> <br><br>";
         html += me.htmlCls.buttonStr + "addtrack_button3'>Add Track</button>";
@@ -12879,12 +12910,19 @@ 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 +12931,8 @@ 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 +12941,13 @@ 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.bResetAnno = true;
+            
+            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 +12986,12 @@ 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;
@@ -14307,13 +14352,15 @@ class Events {
         });
 
 
-        $(document).on("click", ".icn3d-addtrack", function(e) { me.icn3d;
+        $(document).on("click", ".icn3d-addtrack", function(e) { let ic = me.icn3d;
           e.stopImmediatePropagation();
           $("#" + me.pre + "anno_custom")[0].checked = true;
           $("[id^=" + me.pre + "custom]").show();
           //e.preventDefault();
           let chainid = $(this).attr('chainid');
+          let geneid = ic.chainsGene[chainid].geneId;
           $("#" + me.pre + "track_chainid").val(chainid);
+          $("#" + me.pre + "track_geneid").val(geneid);
           me.htmlCls.dialogCls.openDlg('dl_addtrack', 'Add track for Chain: ' + chainid);
           $( "#" + me.pre + "track_gi" ).focus();
         });
@@ -14528,8 +14575,17 @@ 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 };
+                }
             }
         }
 
@@ -14721,7 +14777,7 @@ 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;
@@ -32260,6 +32316,8 @@ class Alternate {
     // change the display atom when alternating
     //Show structures one by one.
     alternateStructures() { let ic = this.icn3d, me = ic.icn3dui;
+        ic.bAlernate = true;
+
         //ic.transformCls.zoominSelection();
         
         // default ic.ALTERNATE_STRUCTURE = -1
@@ -32374,11 +32432,11 @@ class Alternate {
 
         //ic.glycanCls.showGlycans();
 
+        ic.opts['rotationcenter'] = 'highlight center';
+        
         ic.drawCls.draw();
 
         ic.bShowHighlight = true;
-        //ic.opts['rotationcenter'] = 'molecule center';
-        ic.opts['rotationcenter'] = 'highlight center';
     }
 
     alternateWrapper() { let ic = this.icn3d; ic.icn3dui;
@@ -35560,13 +35618,13 @@ 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>";
             }
@@ -36004,6 +36062,10 @@ class AnnoCddSite {
                     let prevEmptyWidth = 0;
                     let prevLineWidth = 0;
                     let widthPerRes = 1;
+
+                    if(ic.seqStartLen && ic.seqStartLen[chnid]) html2 += ic.showSeqCls.insertMulGapOverview(chnid, ic.seqStartLen[chnid]);
+                    if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGap(ic.seqStartLen[chnid], '-');
+
                     for(let i = 0, il = ic.giSeq[chnid].length; i < il; ++i) {
                         html += ic.showSeqCls.insertGap(chnid, i, '-');
                         if(resPosArray.indexOf(i) != -1) {
@@ -36036,6 +36098,9 @@ class AnnoCddSite {
                             html += '<span>-</span>'; //'<span>-</span>';
                         }
                     }
+
+                    if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGap(ic.seqEndLen[chnid], '-');
+
                     htmlTmp = '<span class="icn3d-residueNum" title="residue count">&nbsp;' + resCnt.toString() + ' Residues</span>';
                     htmlTmp += '</span>';
                     htmlTmp += '<br>';
@@ -36193,6 +36258,9 @@ class AnnoCddSite {
                 html2 += '<div style="width:' + titleSpace + 'px!important;" class="icn3d-seqTitle ' + linkStr + '" ' + type + '="' + acc + '" from="' + fromArray + '" to="' + toArray + '" shorttitle="' + title + '" index="' + index + '" setname="' + setname + '" anno="sequence" chain="' + chnid + '" title="' + fulltitle + '">' + title + ' </div>';
                 html2 += htmlTmp3 + htmlTmp;
                 let pre = type + index.toString();
+
+                if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGap(ic.seqStartLen[chnid], '-');
+
                 for(let i = 0, il = ic.giSeq[chnid].length; i < il; ++i) {
                   html += ic.showSeqCls.insertGap(chnid, i, '-');
 
@@ -36220,9 +36288,15 @@ class AnnoCddSite {
                       html += '<span>-</span>'; //'<span>-</span>';
                   }
                 }
+
+                if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGap(ic.seqEndLen[chnid], '-');
+
                 let atom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.chains[chnid]);
                 let colorStr =(atom.color === undefined || atom.color.getHexString() === 'FFFFFF') ? 'DDDDDD' : atom.color.getHexString();
                 let color =(atom.color !== undefined) ? colorStr : "CCCCCC";
+
+                if(ic.seqStartLen && ic.seqStartLen[chnid]) html2 += ic.showSeqCls.insertMulGapOverview(chnid, ic.seqStartLen[chnid]);
+
                 if(me.cfg.blast_rep_id != chnid) { // regular
                     for(let i = 0, il = fromArray.length; i < il; ++i) {
                         let emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray[i] - ic.baseResi[chnid] - 1) / ic.maxAnnoLength) : Math.round(ic.seqAnnWidth *(fromArray[i] - toArray[i-1] - 1) / ic.maxAnnoLength);
@@ -36299,6 +36373,10 @@ class AnnoCddSite {
         let prevEmptyWidth = 0;
         let prevLineWidth = 0;
         let widthPerRes = 1;
+
+        if(ic.seqStartLen && ic.seqStartLen[chnid]) html2 += ic.showSeqCls.insertMulGapOverview(chnid, ic.seqStartLen[chnid]);
+        if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGap(ic.seqStartLen[chnid], '-');
+
         for(let i = 0, il = ic.giSeq[chnid].length; i < il; ++i) {
           html += ic.showSeqCls.insertGap(chnid, i, '-');
           let resi = ic.ParserUtilsCls.getResi(chnid, i);
@@ -36374,6 +36452,9 @@ class AnnoCddSite {
             html += '<span>-</span>'; //'<span>-</span>';
           }
         }
+
+        if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGap(ic.seqEndLen[chnid], '-');
+
         htmlTmp = '<span class="icn3d-residueNum" title="residue count">&nbsp;' + resCnt.toString() + ' Residues</span>';
         htmlTmp += '</span>';
         htmlTmp += '<br>';
@@ -36538,6 +36619,9 @@ class AnnoContact {
             let prevLineWidth = 0;
             let widthPerRes = 1;
 
+            if(ic.seqStartLen && ic.seqStartLen[chnid]) html2 += ic.showSeqCls.insertMulGapOverview(chnid, ic.seqStartLen[chnid]);
+            if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGap(ic.seqStartLen[chnid], '-');
+
             for(let i = 0, il = ic.giSeq[chnid].length; i < il; ++i) {
               html += ic.showSeqCls.insertGap(chnid, i, '-');
               let resi = ic.ParserUtilsCls.getResi(chnid, i);           
@@ -36573,6 +36657,9 @@ class AnnoContact {
                 html += '<span>-</span>'; //'<span>-</span>';
               }
             }
+
+            if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGap(ic.seqEndLen[chnid], '-');
+
             htmlTmp = '<span class="icn3d-residueNum" title="residue count">&nbsp;' + resCnt.toString() + ' Residues</span>';
             htmlTmp += '</span>';
             htmlTmp += '<br>';
@@ -36825,6 +36912,10 @@ class AnnoPTM {
             let prevEmptyWidth = 0;
             let prevLineWidth = 0;
             let widthPerRes = 1;
+
+            if(ic.seqStartLen && ic.seqStartLen[chnid]) html2 += ic.showSeqCls.insertMulGapOverview(chnid, ic.seqStartLen[chnid]);
+            if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGap(ic.seqStartLen[chnid], '-');
+
             for(let i = 0, il = ic.giSeq[chnid].length; i < il; ++i) {
                 html += ic.showSeqCls.insertGap(chnid, i, '-');
                 if(resPosArray.indexOf(i) != -1) {
@@ -36857,6 +36948,9 @@ class AnnoPTM {
                     html += '<span>-</span>'; //'<span>-</span>';
                 }
             }
+
+            if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGap(ic.seqEndLen[chnid], '-');
+
             htmlTmp = '<span class="icn3d-residueNum" title="residue count">&nbsp;' + resCnt.toString() + ' Residues</span>';
             htmlTmp += '</span>';
             htmlTmp += '<br>';
@@ -37136,6 +37230,9 @@ class AnnoDomain {
             html += htmlTmp2 + htmlTmp3 + htmlTmp;
             html2 += htmlTmp2 + htmlTmp3 + htmlTmp;
             let pre = 'domain3d' + index.toString();
+
+            if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGap(ic.seqStartLen[chnid], '-');
+
             for(let i = 0, il = ic.giSeq[chnid].length; i < il; ++i) {
               html += ic.showSeqCls.insertGap(chnid, i, '-');
               //if(i >= domainFrom && i <= domainTo) {
@@ -37155,9 +37252,15 @@ class AnnoDomain {
                 html += '<span>-</span>'; //'<span>-</span>';
               }
             }
+
+            if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGap(ic.seqEndLen[chnid], '-');
+
             let atom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.chains[chnid]);
             let colorStr =(atom.color === undefined || atom.color.getHexString() === 'FFFFFF') ? 'DDDDDD' : atom.color.getHexString();
             let color =(atom.color !== undefined) ? colorStr : "CCCCCC";
+
+            if(ic.seqStartLen && ic.seqStartLen[chnid]) html2 += ic.showSeqCls.insertMulGapOverview(chnid, ic.seqStartLen[chnid]);
+
             if(me.cfg.blast_rep_id != chnid) { // regular
                 for(let i = 0, il = fromArray.length; i < il; ++i) {
                     let emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray[i] - ic.baseResi[chnid] - 1) / ic.maxAnnoLength) : Math.round(ic.seqAnnWidth *(fromArray[i] - toArray[i-1] - 1) / ic.maxAnnoLength);
@@ -37425,9 +37528,18 @@ class AnnoSnpClinVar {
         let prevEmptyWidth = 0;
         let prevLineWidth = 0;
         let widthPerRes = 1;
+
+        if(bOverview) {
+            if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGapOverview(chnid, ic.seqStartLen[chnid]);
+        }
+        else {
+            if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGap(ic.seqStartLen[chnid], '-');
+        }
+
         for(let i = 1, il = ic.giSeq[chnid].length; i <= il; ++i) {
             if(bOverview) {
                 if(resi2index[i] !== undefined) {
+                    
                     // get the mouse over text
                     let cFull = ic.giSeq[chnid][i-1];
                     let c = cFull;
@@ -37452,7 +37564,8 @@ class AnnoSnpClinVar {
                         }
                     }
                     html += ic.showSeqCls.insertGapOverview(chnid, i-1);
-                    let emptyWidth =(me.cfg.blast_rep_id == chnid) ? Math.round(ic.seqAnnWidth *(i-1) /(ic.maxAnnoLength + ic.nTotalGap) - prevEmptyWidth - prevLineWidth) : Math.round(ic.seqAnnWidth *(i-1) / ic.maxAnnoLength - prevEmptyWidth - prevLineWidth);
+                    let emptyWidth = Math.round(ic.seqAnnWidth *(i-1) /(ic.maxAnnoLength + ic.nTotalGap) - prevEmptyWidth - prevLineWidth);
+                    //let emptyWidth =(me.cfg.blast_rep_id == chnid) ? Math.round(ic.seqAnnWidth *(i-1) /(ic.maxAnnoLength + ic.nTotalGap) - prevEmptyWidth - prevLineWidth) : Math.round(ic.seqAnnWidth *(i-1) / ic.maxAnnoLength - prevEmptyWidth - prevLineWidth);
                     //if(emptyWidth < 0) emptyWidth = 0;
                     if(bClinvar) {
                         if(snpTypeHash[i] == 'icn3d-clinvar' || snpTypeHash[i] == 'icn3d-clinvar-path') {
@@ -37681,6 +37794,10 @@ class AnnoSnpClinVar {
               }
             } // if(bOverview) {
         } // for
+
+        if(!bOverview) {
+            if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGap(ic.seqEndLen[chnid], '-');
+        }
         
         //var end = bStartEndRes ? ic.chainsSeq[chnid][ic.giSeq[chnid].length - 1 - ic.matchedPos[chnid] ].resi : '';
         if(line == 1) {
@@ -39125,7 +39242,7 @@ 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 +39253,8 @@ 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)]);
@@ -39292,7 +39411,7 @@ class AddTrack {
            thisClass.alignSequenceToStructure(chainid, data, title);
         });
 
-        // FASTA Alignment
+        // MSA 
         me.myEventCls.onIds("#" + ic.pre + "addtrack_button2b", "click", async function(e) { let ic = thisClass.icn3d;
            e.stopImmediatePropagation();
            //e.preventDefault();
@@ -39300,159 +39419,47 @@ class AddTrack {
 
            let chainid = $("#" + ic.pre + "track_chainid").val();
            let startpos = $("#" + ic.pre + "fasta_startpos").val();
+           if(!startpos) startpos = 1;
+
            let colorseqby = $("#" + ic.pre + "colorseqby").val();
            let type =(colorseqby == 'identity') ? 'identity' : 'custom';
 
            let fastaList = $("#" + ic.pre + "track_fastaalign").val();
-           let fastaArray = fastaList.split('>');
-
-           // the first array item is empty
-           // the second array item is the sequence of the structure, start with i = 2
-           let posFirst = fastaArray[1].indexOf('\n');
-           fastaArray[1].substr(0, posFirst);
-           let seqFirst = fastaArray[1].substr(posFirst + 1).replace(/\n/g, '');
-
-           let trackTitleArray = [];
-           let trackSeqArray = [];
-           for(let i = 2, il = fastaArray.length; i < il; ++i) {
-               let pos = fastaArray[i].indexOf('\n');
-               let title = fastaArray[i].substr(0, pos);
-               trackTitleArray.push(title);
-               let seq = fastaArray[i].substr(pos + 1).replace(/\n/g, '');
-               trackSeqArray.push(seq);
-           }
-
-           let startposGiSeq = undefined;
-           for(let i = 0, il = ic.giSeq[chainid].length; i < il; ++i) {
-               //let pos =(i >= ic.matchedPos[chainid] && i - ic.matchedPos[chainid] < ic.chainsSeq[chainid].length) ? ic.chainsSeq[chainid][i - ic.matchedPos[chainid]].resi : ic.baseResi[chainid] + 1 + i;
-               let pos = ic.ParserUtilsCls.getResi(chainid, i);
-
-               if(pos != startpos) {
-                   continue;
-               }
-               else {
-                   startposGiSeq = i;
-               }
-           }
-
-           if(startposGiSeq === undefined) var aaa = 1; //alert("Please double check the start position before clicking \"Add Track\"");
-
-
-           // set up gap for the master seq
-           // don't count gaps in both ends
-           ic.targetGapHash = {};
-           let prevSeq = '-', prevPos = 0, from, to, cnt = 0, dashCnt = 0;
-           let bFound = false, seqStart = 0, seqEnd = 0;
-           for(let i = 0, il = seqFirst.length; i < il; ++i) {
-              if(seqFirst[i] == '-' && seqFirst[i] != prevSeq) { // start of gap
-                  from = cnt;
-                  dashCnt = 0;
-              }
-
-              if(prevSeq == '-' && seqFirst[i] != prevSeq && cnt > 0) { // end of gap
-                  to = prevPos;
-                  ic.targetGapHash[from + startposGiSeq] = {'from': from + startposGiSeq, 'to': to + dashCnt - 1 + startposGiSeq};
-              }
-
-              prevSeq = seqFirst[i];
-              prevPos = cnt;
-
-              if(seqFirst[i] != '-') {
-                  ++cnt;
-                  seqEnd = i;
-
-                  if(!bFound) {
-                      seqStart = i;
-                      bFound = true;
-                  }
-              }
-              else {
-                  ++dashCnt;
-              }
-           }
-
-           await ic.annotationCls.resetAnnoAll();
-
-           let targetGapHashStr = '';
-           let cntTmp = 0;
-           for(let i in ic.targetGapHash) {
-               if(cntTmp > 0) targetGapHashStr += ' ';
-               targetGapHashStr += i + '_' + ic.targetGapHash[i].from + '_' + ic.targetGapHash[i].to;
-               ++cntTmp;
-           }
-
-           me.htmlCls.clickMenuCls.setLogCmd("msa | " + targetGapHashStr, true);
-
-           // add tracks
-           let resi2cntSameRes = {}; // count of same residue at each position
-           for(let j = 0, jl = trackSeqArray.length; j < jl; ++j) {
-               let resi = startpos; //startposGiSeq + 1;
-               let text = '';
-               for(let k = 0; k < startposGiSeq; ++k) {
-                   if(ic.targetGapHash.hasOwnProperty(k)) {
-                       for(let m = 0; m < ic.targetGapHash[k].to - ic.targetGapHash[k].from + 1; ++m) {
-                           text += '-';
-                       }
-                   }
-
-                   text += '-';
-               }
-
-               for(let k = seqStart; k <= seqEnd; ++k) {
-                  //if(seqFirst[k] == '-') continue;
-
-                  if(j == 0) resi2cntSameRes[resi] = 0;
-
-                  text += trackSeqArray[j][k]; //ic.giSeq[chainid][i];
-
-                  if(seqFirst[k] != '-') {
-                      if(seqFirst[k] == trackSeqArray[j][k]) ++resi2cntSameRes[resi];
-                      ++resi;
-                  }
-               }
-
-               let title =(trackTitleArray[j].length < 20) ? trackTitleArray[j] : trackTitleArray[j].substr(0, 20) + '...';
-               let bMsa = true;
-               thisClass.showNewTrack(chainid, title, text, undefined, undefined, type, undefined, bMsa);
-
-               me.htmlCls.clickMenuCls.setLogCmd("add track | chainid " + chainid + " | title " + title + " | text " + thisClass.simplifyText(text)
-                + " | type " + type + " | color 0 | msa 1", true);
-           }
 
-           // set colot for the master seq
-           if(trackSeqArray.length > 0) {
-                if(ic.queryresi2score === undefined) ic.queryresi2score = {};
-                if(ic.queryresi2score[chainid] === undefined) ic.queryresi2score[chainid] = {};
-
-                let nSeq = trackSeqArray.length;
-                for(let resi in resi2cntSameRes) {
-                    let score = parseInt(resi2cntSameRes[resi] / nSeq * 100);
-                    ic.queryresi2score[chainid][resi] = score;
-                }
+           if(fastaList) {
+                await thisClass.addMsaTracks(chainid, startpos, type, fastaList);
+            }
+        });
 
-                let resiArray = Object.keys(resi2cntSameRes);
-                let start = Math.min.apply(null, resiArray);
-                let end = Math.max.apply(null, resiArray);
+        // Gene table
+        me.myEventCls.onIds("#" + ic.pre + "exons_table", "click", async function(e) { let ic = thisClass.icn3d;
+            e.stopImmediatePropagation();
+            //dialog.dialog( "close" );
 
-                let resiScoreStr = '';
-                for(let resi = start; resi <= end; ++resi) {
-                    if(resi2cntSameRes.hasOwnProperty(resi)) {
-                        resiScoreStr += Math.round(resi2cntSameRes[resi] / nSeq * 9); // max 9
-                    }
-                    else {
-                        resiScoreStr += '_';
-                    }
-                }
+            let geneid = $("#" + ic.pre + "track_geneid").val().trim();
+            window.open('https://www.ncbi.nlm.nih.gov/gene/' + geneid + '?report=gene_table', '_blank');
+        });
 
-                ic.opts['color'] = 'align custom';
-                ic.setColorCls.setColorByOptions(ic.opts, ic.hAtoms);
+        // Isoform Alignment
+        me.myEventCls.onIds("#" + ic.pre + "addtrack_button2c", "click", async function(e) { let ic = thisClass.icn3d;
+            e.stopImmediatePropagation();
+            //e.preventDefault();
+            dialog.dialog( "close" );
 
-                ic.hlUpdateCls.updateHlAll();
+            let chainid = $("#" + ic.pre + "track_chainid").val();    
+            let geneid = $("#" + ic.pre + "track_geneid").val();
+            if(!geneid) {
+                var aaa = 1; //alert("Please fill in the Gene ID...");
+                return;
+            }
 
-                ic.drawCls.draw();
+            let startpos = $("#" + ic.pre + "fasta_startpos2").val();
+            if(!startpos) startpos = 1;
 
-                me.htmlCls.clickMenuCls.setLogCmd('color align custom | ' + chainid + ' | range ' + start + '_' + end + ' | ' + resiScoreStr, true);
-           }
+            let colorseqby = $("#" + ic.pre + "colorseqby2").val();
+            let type =(colorseqby == 'identity') ? 'identity' : 'custom';
+    
+            await thisClass.addExonTracks(chainid, geneid, startpos, type);
         });
 
         // BED file
@@ -39638,7 +39645,7 @@ class AddTrack {
 
     }
 
-    showNewTrack(chnid, title, text, cssColorArray, inTarget2queryHash, type, color, bMsa, fromArray, toArray) {  let ic = this.icn3d, me = ic.icn3dui;
+    showNewTrack(chnid, title, text, cssColorArray, inTarget2queryHash, type, color, bMsa, fromArray, toArray, seqStartLen, exonArray) {  let ic = this.icn3d, me = ic.icn3dui;
         //if(ic.customTracks[chnid] === undefined) {
         //    ic.customTracks[chnid] = {}
         //}
@@ -39687,22 +39694,28 @@ class AddTrack {
         $("#" + ic.pre + "tt_custom_" + chnid + "_" + simpTitle).width(divLength);
 
         let html = '<div id="' + ic.pre + 'giseq_sequence" class="icn3d-dl_sequence">';
+        let htmlExon = html;
         let html2 = html;
         let html3 = html;
+        let html3Exon = html;
 
         //var htmlTmp2 = '<div class="icn3d-seqTitle icn3d-link icn3d-blue" gi="' + chnid + '" anno="sequence" chain="' + chnid + '"><span style="white-space:nowrap;">' + title + '</span></div>';
         //var htmlTmp2 = '<div class="icn3d-seqTitle" gi="' + chnid + '" anno="sequence" chain="' + chnid + '"><span style="white-space:nowrap;">' + title + '</span></div>';
         let index = parseInt(Math.random()*10);
         let htmlTmp2 = '<div class="icn3d-seqTitle icn3d-link icn3d-blue" custom="' +(index+1).toString() + '" from="' + fromArray + '" to="' + toArray + '" shorttitle="' + simpTitle + '" index="' + index + '" setname="' + chnid + '_custom_' +(index+1).toString() + '" anno="sequence" chain="' + chnid + '" title="' + title + '">' + simpTitle + ' </div>';
+        let htmlTmp2Exon = '<div class="icn3d-seqTitle" chain="' + chnid + '" title="Exons of ' + title + '">Exons </div>';
+
         let htmlTmp3 = '<span class="icn3d-residueNum" title="residue count">' + resCnt.toString() + ' Pos</span>';
 
         html3 += htmlTmp2 + htmlTmp3 + '<br>';
+        html3Exon += htmlTmp2Exon + htmlTmp3 + '<br>';
 
         let htmlTmp = '<span class="icn3d-seqLine">';
 
         html += htmlTmp2 + htmlTmp3 + htmlTmp;
+        htmlExon += htmlTmp2Exon + htmlTmp3 + htmlTmp;
         html2 += htmlTmp2 + htmlTmp3 + htmlTmp;
-
+        
         //var pre ='cst' + ic.customTracks[chnid].length;
         let posTmp = chnid.indexOf('_');
         //var pre ='cst' + chnid.substr(posTmp);
@@ -39717,10 +39730,34 @@ class AddTrack {
         let bIdentityColor =(type === 'identity') && text.indexOf('cannot-be-aligned') == -1 && text.indexOf('cannot be aligned') == -1 ? true : false;
 
         let parsedResn = {};
-        let gapCnt = 0, currResi = 1;
+        let gapCnt = 0;
         htmlTmp2 = '';
+
+        // if(ic.seqStartLen && ic.seqStartLen[chnid]) html2 += ic.showSeqCls.insertMulGapOverview(chnid, ic.seqStartLen[chnid]);
+        // if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGap(ic.seqStartLen[chnid], '-');
+
+        let pos2exonColor = {}, pos2genome = {}, pos2exonIndex = {};
+        let cnt = 0;
+        if(exonArray) {
+            for(let j = 0, jl = exonArray.length; j < jl; ++j) {
+                let start = exonArray[j].resStart, end = exonArray[j].resEnd;
+                let genStart = exonArray[j].genomeRange.split('-')[0];
+
+                for(let k = 0, kl = end - start + 1; k < kl; ++k) {
+                    let colorStr = this.getExonColor(start, end, cnt);
+
+                    pos2exonColor[cnt] = colorStr;
+                    pos2genome[cnt] = (genStart + ic.exonOrder * k*3) + '-' + (genStart + ic.exonOrder * k*3 + ic.exonOrder * 2); // reverse order from large to small
+                    pos2exonIndex[cnt] = j;
+
+                    ++cnt;
+                }
+            }
+        }
+
+        cnt = 0;
         for(let i = 0, il = text.length; i < il; ++i) {
-          let resNum = i-gapCnt;
+          let resNum = i - gapCnt - ((ic.seqStartLen && ic.seqStartLen[chnid]) ? ic.seqStartLen[chnid] : 0);
 
           if(!bMsa) {
               html += ic.showSeqCls.insertGap(chnid, i, '-');
@@ -39741,7 +39778,8 @@ class AddTrack {
               let identityColorStr =(c == resName) ? 'FF0000' : '0000FF';
 
               //var pos =(resNum >= ic.matchedPos[chnid] && resNum - ic.matchedPos[chnid] < ic.chainsSeq[chnid].length) ? ic.chainsSeq[chnid][resNum - ic.matchedPos[chnid]].resi : ic.baseResi[chnid] + 1 + resNum;
-              let pos = ic.baseResi[chnid] + currResi;
+              //   let pos = ic.baseResi[chnid] + currResi;
+              let pos = ic.baseResi[chnid] + (i+1) - ((ic.seqStartLen && ic.seqStartLen[chnid]) ? ic.seqStartLen[chnid] : 0);
 
               if(inTarget2queryHash !== undefined) pos = ic.baseResi[chnid] + inTarget2queryHash[i] + 1; // 0-based
 
@@ -39772,9 +39810,13 @@ class AddTrack {
 
               html += '<span id="' + pre + '_' + ic.pre + chnid + '_' + pos + '" title="' + c + pos + '" class="icn3d-residue" ' + tmpStr + '>' + c + '</span>';
 
+              let tmpStrExon = 'style="background-color:' + pos2exonColor[cnt] + '"';
+              htmlExon += '<span id="' + pre + '_' + ic.pre + chnid + '_' + pos + '" title="' + c + pos + ', Exon ' + (pos2exonIndex[cnt] + 1) + ': ' + pos2genome[cnt] + '" class="icn3d-residue" ' + tmpStrExon + '>&nbsp;</span>';
+
               htmlTmp2 += 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);
+            //   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);
+              let emptyWidth = Math.round(ic.seqAnnWidth * i /(ic.maxAnnoLength + ic.nTotalGap) - prevEmptyWidth - prevLineWidth);
               if(emptyWidth < 0) emptyWidth = 0;
 
               htmlTmp2 += '<div style="display:inline-block; width:' + emptyWidth + 'px;">&nbsp;</div>';
@@ -39795,19 +39837,21 @@ class AddTrack {
 
               prevEmptyWidth += emptyWidth;
               prevLineWidth += widthPerRes;
-
-              ++currResi;
+              ++cnt;
           }
           else {
               if(bErrorMess) {
-                  html += '<span>' + c + '</span>';
+                html += '<span>' + c + '</span>';
               }
               else {
                 html += '<span>-</span>';
+                htmlExon += '<span></span>';
               }
           }
         }
 
+        // if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGap(ic.seqEndLen[chnid], '-');
+
         if(fromArray !== undefined) {
             htmlTmp2 = '';
             let fromArray2 = [], toArray2 = [];
@@ -39833,13 +39877,77 @@ class AddTrack {
             let colorStr =(atom.color === undefined || atom.color.getHexString() === 'FFFFFF') ? 'DDDDDD' : atom.color.getHexString();
             let color =(atom.color !== undefined) ? colorStr : "CCCCCC";
 
+            let cnt, prevCntTotal = 0;
             for(let i = 0, il = fromArray2.length; i < il; ++i) {
                 htmlTmp2 += ic.showSeqCls.insertGapOverview(chnid, fromArray2[i]);
 
-                let emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray2[i] - ic.baseResi[chnid] - 1) /(ic.maxAnnoLength + ic.nTotalGap)) : Math.round(ic.seqAnnWidth *(fromArray2[i] - toArray2[i-1] - 1) /(ic.maxAnnoLength + ic.nTotalGap));
+                let initialPos = (seqStartLen) ? fromArray2[i] : fromArray2[i] - ic.baseResi[chnid] - 1;
+
+                let emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth * initialPos /(ic.maxAnnoLength + ic.nTotalGap)) : Math.round(ic.seqAnnWidth *(fromArray2[i] - toArray2[i-1] - 1) /(ic.maxAnnoLength + ic.nTotalGap));
+                if(emptyWidth < 0) emptyWidth = 0;
+
                 htmlTmp2 += '<div style="display:inline-block; width:' + emptyWidth + 'px;">&nbsp;</div>';
 
-                htmlTmp2 += '<div style="display:inline-block; color:white!important; font-weight:bold; background-color:#' + color + '; width:' + Math.round(ic.seqAnnWidth *(toArray2[i] - fromArray2[i] + 1) /(ic.maxAnnoLength + ic.nTotalGap)) + 'px;" class="icn3d-seqTitle icn3d-link icn3d-blue" custom="' +(index+1).toString() + '" from="' + fromArray2 + '" to="' + toArray2 + '" shorttitle="' + simpTitle + '" index="' + index + '" setname="' + chnid + '_custom_' +(index+1).toString() + '" id="' + chnid + '_custom_' + index + '" anno="sequence" chain="' + chnid + '" title="' + title + '">' + title + '</div>';
+                if(!exonArray) {
+                    htmlTmp2 += '<div style="display:inline-block; color:white!important; font-weight:bold; background-color:#' + color + '; width:' + Math.round(ic.seqAnnWidth *(toArray2[i] - fromArray2[i] + 1) /(ic.maxAnnoLength + ic.nTotalGap)) + 'px;" class="icn3d-seqTitle icn3d-link icn3d-blue" custom="' +(index+1).toString() + '" from="' + fromArray2 + '" to="' + toArray2 + '" shorttitle="' + simpTitle + '" index="' + index + '" setname="' + chnid + '_custom_' +(index+1).toString() + '" id="' + chnid + '_custom_' + index + '" anno="sequence" chain="' + chnid + '" title="' + title + '">' + title + '</div>';
+                }
+                else {
+                    // determine how this range sits in the exon ranges in exonArray
+                    let startExon, endExon;
+                    
+                    cnt = toArray[i] - fromArray[i] + 1;
+                    let from = prevCntTotal, to = prevCntTotal + cnt - 1;
+
+                    prevCntTotal += cnt;
+
+                    // fromArray2 was adjusted with gaps, no gaps in this case
+                    // let offset = fromArray2[i] - fromArray[i];
+                    // let emptyWidth = Math.round(ic.seqAnnWidth * offset /(ic.maxAnnoLength + ic.nTotalGap));
+                    // htmlTmp2 += '<div style="display:inline-block; width:' + emptyWidth + 'px;">&nbsp;</div>';
+
+                    for(let j = 0, jl = exonArray.length; j < jl; ++j) {
+                        let start = exonArray[j].resStart, end = exonArray[j].resEnd;
+
+                        if(from >= start && from <= end) {
+                            startExon = {exonIndex: j, rangeStart: start, rangeEnd: end, from: from, genomeRange: exonArray[j].genomeRange};
+                        }
+
+                        if(to >= start && to <= end) {
+                            endExon = {exonIndex: j, rangeStart: start, rangeEnd: end, to: to, genomeRange: exonArray[j].genomeRange};
+                        }
+                    }
+
+                    let startColorStr, endColorStr, colorGradient;
+                    if(startExon && endExon && startExon.exonIndex == endExon.exonIndex) { // 
+                        startColorStr = this.getExonColor(startExon.rangeStart, startExon.rangeEnd, from);
+                        endColorStr = this.getExonColor(startExon.rangeStart, startExon.rangeEnd, to);
+
+                        colorGradient = startColorStr + ' 0%, #FFF 50%, ' + endColorStr + ' 100%';
+                        htmlTmp2 += this.getExonHtml(startExon.exonIndex, colorGradient, startExon.from, endExon.to, startExon.genomeRange);
+                    }
+                    else {
+                        if(startExon) {
+                            startColorStr = this.getExonColor(startExon.rangeStart, startExon.rangeEnd, from);
+
+                            colorGradient = startColorStr + ' 0%, #FFF 50%, #00F 100%';
+                            htmlTmp2 += this.getExonHtml(startExon.exonIndex, colorGradient, startExon.from, startExon.rangeEnd, startExon.genomeRange);
+                        }
+
+                        if(startExon && endExon) {
+                            for(let j = startExon.exonIndex + 1; j < endExon.exonIndex; ++j) {
+                                colorGradient = '#F00 0%, #FFF 50%, #00F 100%';
+                                htmlTmp2 += this.getExonHtml(j, colorGradient, exonArray[j].resStart, exonArray[j].resEnd, exonArray[j].genomeRange);
+                            }
+
+                            endColorStr = this.getExonColor(endExon.rangeStart, endExon.rangeEnd, to);
+
+                            colorGradient = '#F00 0%, #FFF 50%, ' + endColorStr + ' 100%';
+                            htmlTmp2 += this.getExonHtml(endExon.exonIndex, colorGradient, endExon.rangeStart, endExon.to, endExon.genomeRange);
+                        }
+                    }
+
+                    //htmlTmp2 += '<div style="display:inline-block; color:white!important; font-weight:bold; background-color:#' + color + '; width:' + Math.round(ic.seqAnnWidth *(toArray2[i] - fromArray2[i] + 1) /(ic.maxAnnoLength + ic.nTotalGap)) + 'px;" class="icn3d-seqTitle icn3d-link icn3d-blue" custom="' +(index+1).toString() + '" from="' + fromArray2 + '" to="' + toArray2 + '" shorttitle="' + simpTitle + '" index="' + index + '" setname="' + chnid + '_custom_' +(index+1).toString() + '" id="' + chnid + '_custom_' + index + '" anno="sequence" chain="' + chnid + '" title="' + title + '">' + title + '</div>';
+                }
             }
         }
 
@@ -39851,12 +39959,37 @@ class AddTrack {
 
         html += htmlTmp;
         html2 += htmlTmp2 + htmlTmp;
+        htmlExon += htmlTmp;
 
         html3 += '</div>';
+        html3Exon += '</div>';
 
-        $("#" + ic.pre + "dt_custom_" + chnid + "_" + simpTitle).html(html);
-        $("#" + ic.pre + "ov_custom_" + chnid + "_" + simpTitle).html(html2);
-        $("#" + ic.pre + "tt_custom_" + chnid + "_" + simpTitle).html(html3);
+        if(!exonArray) {
+            $("#" + ic.pre + "dt_custom_" + chnid + "_" + simpTitle).html(html);
+            $("#" + ic.pre + "ov_custom_" + chnid + "_" + simpTitle).html(html2);
+            $("#" + ic.pre + "tt_custom_" + chnid + "_" + simpTitle).html(html3);
+        }
+        else {
+            $("#" + ic.pre + "dt_custom_" + chnid + "_" + simpTitle).html(htmlExon + html);
+            $("#" + ic.pre + "ov_custom_" + chnid + "_" + simpTitle).html(html2);
+            $("#" + ic.pre + "tt_custom_" + chnid + "_" + simpTitle).html(html3Exon + html3);      
+        }
+    }
+
+    getExonHtml(exonIndex, colorGradient, from, to, genomeRange) { let ic = this.icn3d; ic.icn3dui;
+        return '<div style="display:inline-block; color:white!important; width:' + Math.round(ic.seqAnnWidth *(to - from + 1) /(ic.maxAnnoLength + ic.nTotalGap)) + 'px;" class="icn3d-seqTitle icn3d-link icn3d-blue" title="Exon ' + (exonIndex + 1) + ': ' + genomeRange + ' genomic interval" anno="sequence" title="' + (exonIndex + 1) + '"><div style="height: 12px; border: 1px solid #000; background: linear-gradient(to right, ' + colorGradient + ');"></div></div>';
+    }
+
+    getExonColor(start, end, pos) { let ic = this.icn3d; ic.icn3dui;
+        let middle = ( start + end) * 0.5;
+        if(pos < middle) {
+            let gb = parseInt((pos - start) / (middle - start) * 255);
+            return "rgb(255, " + gb + ", " + gb + ")";
+        }
+        else {
+            let rg = parseInt((end - pos) / (end - middle) * 255);
+            return "rgb(" + rg + ", " + rg + ", 255)";
+        }
     }
 
     alignSequenceToStructure(chainid, data, title) { let ic = this.icn3d, me = ic.icn3dui;
@@ -40164,6 +40297,7 @@ class AddTrack {
             let result = this.getFullText(text);
             text = result.text;
             this.showNewTrack(chainid, title, text, undefined, undefined, type, color, bMsa);
+
             return false;
         }
 
@@ -40286,6 +40420,722 @@ class AddTrack {
        }
     }
 
+    async getMsa(acclist, firstAcc, chainSeq) { let ic = this.icn3d, me = ic.icn3dui;
+        let trackTitleArray = [firstAcc], trackSeqArray = [];
+        // get all seq
+        let url = me.htmlCls.baseUrl + "/vastdyn/vastdyn.cgi?chainlist=" + acclist;
+        let data = await me.getAjaxPromise(url, 'jsonp');
+        let maxLen = 0, maxIndex = 0, index = 0;
+        //let seqArray = [];
+        for(let acc in data) {
+            let seq = data[acc];
+            //seqArray.push(seq);
+
+            let pos = acc.indexOf('.');
+            if(pos != -1) {
+                acc = acc.substr(0, pos);
+            }
+            trackTitleArray.push(acc);
+
+            if(seq.length > maxLen) {
+                maxLen = seq.length;
+                maxIndex = index;
+            }
+            ++index;
+        }
+        
+        // pairwise align each seq to the one with maxIndex
+        url = me.htmlCls.baseUrl + 'pwaln/pwaln.fcgi?from=msa';
+
+        let accArray = acclist.split(',');
+        // oroginal index, chain as the first one
+        let acc2index = {};
+        acc2index[firstAcc] = 0;
+        for(let i = 0, il = accArray.length; i < il; ++i) {
+            acc2index[accArray[i]] = i + 1;
+        }
+        let targetId = accArray[maxIndex];
+        accArray.splice(maxIndex, 1);
+
+        let queries = (chainSeq) ? chainSeq : firstAcc;
+        if(accArray.length > 0) queries += ',' + accArray.join(',');
+
+        let dataObj = {'targets': targetId, 'queries': queries};
+        let alignData = await me.getAjaxPostPromise(url, dataObj);
+
+        if(!alignData.data) {
+            console.log("The protein accessions " + targetId + "," + queries + " can not be aligned...");
+            return;
+        }
+
+        // get aligned length for each pair
+        let index_alignLen = [];
+        ic.qt_start_end = {};
+        // target: targetId
+        // queries: accArray
+        let accArrayFound = [], querySeqArray = [];
+        let firstKey = Object.keys(alignData.targets)[0];
+        let targetSeq = alignData.targets[firstKey].seqdata;
+
+        //add firstAcc to accArray
+        accArray.splice(0, 0, firstAcc);
+        
+        for(let index = 0, indexl = accArray.length; index < indexl; ++index) {
+            let query, target;
+
+            if(!alignData.data[index]) {
+                continue;
+            }
+        
+            query = alignData.data[index].query;
+            let acc;
+            if(query.acc.length <= 5) { // PDB
+                acc = query.acc.substr(0, 4) + '_' + query.acc.substr(4, 1);
+            }
+            else {
+                acc = query.acc;
+            }
+
+            if(index == 0) acc = firstAcc;
+
+            accArrayFound.push(acc);
+
+            firstKey = Object.keys(alignData.data[index].targets)[0];
+            target = alignData.data[index].targets[firstKey];
+
+            target = target.hsps[0];
+
+            querySeqArray.push(query.seqdata);
+            let alignLen = target.scores.num_ident * 100 + query.sz; // order by aligned seq length, then seq length
+
+            ic.qt_start_end[index] = [];
+
+            let segArray = target.segs;
+            for(let i = 0, il = segArray.length; i < il; ++i) {
+                let seg = segArray[i];
+                let qt_start_end = {t_start: seg.orifrom, t_end: seg.orito, q_start: seg.from, q_end: seg.to};
+                ic.qt_start_end[index].push(qt_start_end);
+            }
+
+            index_alignLen.push({index: index, alignLen: alignLen});
+        }
+
+        accArray = accArrayFound;
+
+        index_alignLen.sort(function(a,b){
+            return b.alignLen - a.alignLen;
+        });
+
+        // start and end of MSA
+        let start_t = 9999, end_t = -1;
+        for(let index = 0, indexl = accArray.length; index < indexl; ++index) { 
+            if(!ic.qt_start_end[index]) continue;
+
+            for(let i = 0, il = ic.qt_start_end[index].length; i < il; ++i) {
+                let start1, end1;
+                
+                start1 = ic.qt_start_end[index][i].t_start;
+                end1 = ic.qt_start_end[index][i].t_end;
+
+                for(let j = start1; j <= end1; ++j) {
+                    if(j < start_t) start_t = j;
+                    if(j > end_t) end_t = j;
+                }
+            }
+        }
+
+        // N- and C-terminal residues
+        let maxNtermLen = start_t, maxCtermLen = targetSeq.length - (end_t + 1);
+        let startArray = [], endArray = [];
+        for(let index = 0, indexl = accArray.length; index < indexl; ++index) { 
+            if(!ic.qt_start_end[index]) continue;
+
+            let qPos = ic.qt_start_end[index][0].q_start;
+            startArray.push(qPos);
+            if(maxNtermLen < qPos) maxNtermLen = qPos;
+
+            let lastIndex = ic.qt_start_end[index].length - 1;
+            qPos = ic.qt_start_end[index][lastIndex].q_end;
+            endArray.push(qPos);
+            let dist = querySeqArray[index].length - (qPos + 1);
+            if(maxCtermLen < dist) maxCtermLen = dist;
+        }
+
+        ic.msaSeq = {};
+        // assign the template
+        ic.msaSeq[targetId] = '';
+        
+        for(let i = start_t; i <= end_t; ++i) {
+            ic.msaSeq[targetId] += targetSeq[i];           
+        }    
+
+        // progressively merge sequences, starting from most similar to least similar
+        let alignedChainIndice = [0];
+        for(let arrayIndex = 0, arrayIndexl = index_alignLen.length; arrayIndex < arrayIndexl; ++arrayIndex) { 
+            let index = index_alignLen[arrayIndex].index;
+            alignedChainIndice.push(index);
+
+            ic.msaSeq[accArray[index]] = '';
+
+            // some proteins may not be aligned
+            if(!querySeqArray[index]) continue;
+
+            ic.setSeqAlignCls.mergeTwoSeqForAllSimple(targetId, accArray, index, alignedChainIndice, start_t, end_t, querySeqArray);
+        }  
+
+        // add N-terminal seq
+        let seqN = '', cnt;
+        for(let i = 0; i < maxNtermLen - start_t; ++i) {
+            seqN += '-';
+        }
+        for(let i = 0; i < start_t; ++i) {
+            seqN += targetSeq[i];
+        }
+        ic.msaSeq[targetId] = seqN + ic.msaSeq[targetId];
+
+        for(let index = 0, indexl = accArray.length; index < indexl; ++index) { 
+            seqN = '';
+            for(let i = 0; i < maxNtermLen - startArray[index]; ++i) {
+                seqN += '-';
+            }
+            for(let i = 0; i < startArray[index]; ++i) {
+                seqN += querySeqArray[index][i];
+            }
+
+            ic.msaSeq[accArray[index]] = seqN + ic.msaSeq[accArray[index]];
+        }
+
+        // add C-terminal seq
+        for(let i = end_t + 1; i < targetSeq.length; ++i) {
+            ic.msaSeq[targetId] += targetSeq[i];
+        }
+
+        cnt = targetSeq.length - (end_t + 1);
+        for(let i = 0; i < maxCtermLen - cnt; ++i) {
+            ic.msaSeq[targetId] += '-';
+        }
+
+        for(let index = 0, indexl = accArray.length; index < indexl; ++index) {
+            for(let i = endArray[index] + 1; i < querySeqArray[index].length; ++i) {
+                ic.msaSeq[accArray[index]] += querySeqArray[index][i];
+            }
+
+            cnt = querySeqArray[index].length - (endArray[index] + 1);
+            for(let i = 0; i < maxCtermLen - cnt; ++i) {
+                ic.msaSeq[accArray[index]] += '-';
+            }
+        }
+
+        for(let acc in ic.msaSeq) {
+            let index = acc2index[acc];
+            trackSeqArray[index] = ic.msaSeq[acc];
+            trackTitleArray[index] = acc;
+        }
+
+        // some of the protein may not be aligned
+        let trackTitleArrayFinal = [], trackSeqArrayFinal = [];
+        for(let i = 0, il = trackSeqArray.length; i < il; ++i) {
+            if(trackSeqArray[i]) {
+                trackSeqArrayFinal.push(trackSeqArray[i]);
+                trackTitleArrayFinal.push(trackTitleArray[i]);
+            }
+        }
+
+        let seqFirst = trackSeqArrayFinal[0];
+
+        trackSeqArrayFinal.splice(0, 1);
+        trackTitleArrayFinal.splice(0, 1);
+
+        return {trackTitleArray: trackTitleArrayFinal, trackSeqArray: trackSeqArrayFinal, seqFirst: seqFirst};
+    }
+
+    async getIsoformMsa(acclist, acc2exons) { let ic = this.icn3d, me = ic.icn3dui;
+        let trackTitleArray = [], trackSeqArray = [];
+        // get all seq
+        let url = me.htmlCls.baseUrl + "/vastdyn/vastdyn.cgi?chainlist=" + acclist;
+        let data = await me.getAjaxPromise(url, 'jsonp');
+        let maxLen = 0, maxIndex = 0, index = 0;
+        let accArray = [], querySeqArray = [];
+        for(let acc in data) {
+            let seq = data[acc];
+            querySeqArray.push(seq);
+
+            let pos = acc.indexOf('.');
+            if(pos != -1) {
+                acc = acc.substr(0, pos);
+            }
+            accArray.push(acc);
+
+            if(seq.length > maxLen) {
+                maxLen = seq.length;
+                maxIndex = index;
+            }
+            ++index;
+        }
+
+        // get aligned length for each pair
+        ic.qt_start_end = {};
+
+        // use the genomic interval as the alignment template
+        let targetId = 'genomeRes';
+
+        let acc2index = {};
+        
+        for(let index = 0, indexl = accArray.length; index < indexl; ++index) {
+            let acc = accArray[index];
+
+            acc2index[acc] = index;
+
+            ic.qt_start_end[index] = [];
+
+            let segArray = acc2exons[acc];     
+
+            for(let i = 0, il = segArray.length; i < il; ++i) {
+                let seg = segArray[i];
+                
+                // mRNA has the reverse order, use negative to make the order right, then minus the offset
+                let qt_start_end = {t_start: ic.exonOrder * seg.genResStart, t_end: ic.exonOrder * seg.genResEnd, q_start: seg.resStart, q_end: seg.resEnd};
+                ic.qt_start_end[index].push(qt_start_end);
+            }
+        }
+
+        // start and end of MSA
+        let start_t = 999999999, end_t = -999999999;
+        for(let index = 0, indexl = accArray.length; index < indexl; ++index) { 
+            if(!ic.qt_start_end[index]) continue;
+
+            for(let i = 0, il = ic.qt_start_end[index].length; i < il; ++i) {
+                let start1, end1;
+                
+                start1 = ic.qt_start_end[index][i].t_start;
+                end1 = ic.qt_start_end[index][i].t_end;
+
+                for(let j = start1; j <= end1; ++j) {
+                    if(j < start_t) start_t = j;
+                    if(j > end_t) end_t = j;
+                }
+            }
+        }
+
+        // minus the offset start_t
+        for(let index = 0, indexl = accArray.length; index < indexl; ++index) {
+            let segArray = ic.qt_start_end[index];
+            for(let i = 0, il = segArray.length; i < il; ++i) {
+                let seg = segArray[i];
+                seg.t_start -= start_t;
+                seg.t_end -= start_t;
+            }
+        }
+
+        ic.msaSeq = {};
+        // assign the template
+        ic.msaSeq[targetId] = '';
+
+        let start_tFinal = 0;
+        let end_tFinal = end_t - start_t;
+
+        for(let i = start_tFinal; i <= end_tFinal; ++i) {
+            ic.msaSeq[targetId] += 'X';   // fake seq        
+        }    
+
+        // progressively merge sequences, starting from most similar to least similar
+        let alignedChainIndice = [0];
+        for(let index = 0, indexl = accArray.length; index < indexl; ++index) { 
+            alignedChainIndice.push(index);
+
+            ic.msaSeq[accArray[index]] = '';
+
+            // some proteins may not be aligned
+            if(!querySeqArray[index]) continue;
+            ic.setSeqAlignCls.mergeTwoSeqForAllSimple(targetId, accArray, index, alignedChainIndice, start_tFinal, end_tFinal, querySeqArray);
+        }  
+
+        for(let acc in ic.msaSeq) {
+            let index = acc2index[acc];
+
+            if(index !== undefined) {
+                trackSeqArray[index] = ic.msaSeq[acc];
+                trackTitleArray[index] = acc;
+            }
+        }
+
+        // remove introns in trackSeqArray
+        let trackSeqArrayFinal = [];
+        for(let i = 0, il = trackSeqArray.length; i < il; ++i) {
+            trackSeqArrayFinal[i] = '';
+        }
+
+        for(let j = 0, jl = trackSeqArray[maxIndex].length; j < jl; ++j) {
+            let seq = trackSeqArray[maxIndex][j];
+
+            let bExon = (seq != '-') ? true : false;
+            if(!bExon) {
+                for(let i = 0, il = trackSeqArray.length; i < il; ++i) {
+                    if(trackSeqArray[i][j] != '-') {
+                        bExon = true;
+                        break;
+                    }
+                }
+            }
+            
+            if(bExon) {
+                for(let i = 0, il = trackSeqArray.length; i < il; ++i) {
+                    trackSeqArrayFinal[i] += trackSeqArray[i][j];
+                }
+            }
+        }
+
+        return {trackTitleArray: trackTitleArray, trackSeqArray: trackSeqArrayFinal, maxIndex: maxIndex};
+    }
+
+    async showMsaTracks(chainid, seqFirst, trackTitleArray, trackSeqArray, startpos, type, acc2exons) { let ic = this.icn3d; ic.icn3dui;
+        //ic.startposGiSeq = undefined;
+        for(let i = 0, il = ic.giSeq[chainid].length; i < il; ++i) {
+            //let pos =(i >= ic.matchedPos[chainid] && i - ic.matchedPos[chainid] < ic.chainsSeq, [chainid].length) ? ic.chainsSeq[chainid][i - ic.matchedPos[chainid]].resi : ic.baseResi[chainid] + 1 + i;
+            let pos = ic.ParserUtilsCls.getResi(chainid, i);
+
+            if(pos != startpos) {
+                continue;
+            }
+            else {
+                ic.startposGiSeq = i;
+            }
+        }
+
+        if(ic.startposGiSeq === undefined) {
+            var aaa = 1; //alert("Please double check the start position before clicking \"Add Track\"");
+            return;
+        }
+
+        // set up gap for the master seq
+        // don't count gaps in both ends
+        ic.targetGapHash = {};
+        let prevSeq = '-', prevPos = 0, from, to, cnt = 0, dashCnt = 0;
+        let bFound = false, seqStart = 0, seqEnd = 0, seqLength = seqFirst.length;
+        // add gaps to the N- and C-terminal
+        if(!ic.seqStartLen) ic.seqStartLen = {};
+        if(!ic.seqEndLen) ic.seqEndLen = {};
+        for(let i = 0, il = seqFirst.length; i < il; ++i) {
+            if(seqFirst[i] == '-' && seqFirst[i] != prevSeq) { // start of gap
+                from = cnt;
+                dashCnt = 0;
+            }
+
+            if(prevSeq == '-' && seqFirst[i] != prevSeq && cnt > 0) { // end of gap
+                to = prevPos;
+                ic.targetGapHash[from + ic.startposGiSeq] = {'from': from + ic.startposGiSeq, 'to': to + dashCnt - 1 + ic.startposGiSeq};
+            }
+
+            prevSeq = seqFirst[i];
+            prevPos = cnt;
+
+            if(seqFirst[i] != '-') {
+                ++cnt;
+                seqEnd = i;
+                ic.seqEndLen[chainid] = seqLength - 1 - seqEnd;
+
+                if(!bFound) {
+                    seqStart = i;
+                    ic.seqStartLen[chainid] = seqStart;
+
+                    bFound = true;
+                }
+            }
+            else {
+                ++dashCnt;
+            }
+        }
+
+        // adjust the total length
+        if(ic.maxAnnoLength < ic.maxAnnoLengthOri + ic.seqStartLen[chainid] + ic.seqEndLen[chainid]) {
+                ic.maxAnnoLength = ic.maxAnnoLengthOri + ic.seqStartLen[chainid] + ic.seqEndLen[chainid];
+        }
+
+        await ic.annotationCls.resetAnnoAll();
+
+        let targetGapHashStr = '';
+        let cntTmp = 0;
+        for(let i in ic.targetGapHash) {
+            if(cntTmp > 0) targetGapHashStr += ' ';
+            targetGapHashStr += i + '_' + ic.targetGapHash[i].from + '_' + ic.targetGapHash[i].to;
+            ++cntTmp;
+        }
+
+        //me.htmlCls.clickMenuCls.setLogCmd("msa | " + targetGapHashStr, true);
+
+        // add tracks
+        let resi2cntSameRes = {}; // count of same residue at each position
+        for(let j = 0, jl = trackSeqArray.length; j < jl; ++j) {
+            let resi = startpos;
+            let text = '';
+            for(let k = 0; k < ic.startposGiSeq; ++k) {
+                if(ic.targetGapHash.hasOwnProperty(k)) {
+                    for(let m = 0; m < ic.targetGapHash[k].to - ic.targetGapHash[k].from + 1; ++m) {
+                        text += '-';
+                    }
+                }
+
+                text += '-';
+            }
+
+            let resn, prevResn = '-';
+            let fromArray = [], toArray = [];
+            let bFound = false;
+            let seqStartLen = 0;
+            //    for(let k = seqStart; k <= seqEnd; ++k) {
+            for(let k = 0; k < seqLength; ++k) {
+                //if(seqFirst[k] == '-') continue;
+
+                if(j == 0) resi2cntSameRes[resi] = 0;
+
+                resn = trackSeqArray[j][k];
+
+                if(prevResn == '-' && resn != '-') {
+                    fromArray.push(k);
+                }
+
+                if(prevResn != '-' && resn == '-') {
+                    toArray.push(k - 1);
+                }
+
+                if(resn != '-') {
+                    if(!bFound) {
+                        seqStartLen = k;
+                        bFound = true;
+                    }
+                }
+
+                text += resn; //ic.giSeq[chainid][i];
+
+                if(seqFirst[k] != '-') {
+                    if(seqFirst[k] == trackSeqArray[j][k]) ++resi2cntSameRes[resi];
+                    ++resi;
+                }
+
+                prevResn = resn;
+            }
+
+            // last one
+            if(prevResn != '-') {
+                toArray.push(seqLength - 1);
+            }
+
+            let title =(trackTitleArray[j].length < 20) ? trackTitleArray[j] : trackTitleArray[j].substr(0, 20) + '...';
+            let bMsa = true;
+            let exonArray = (acc2exons) ? acc2exons[trackTitleArray[j]] : undefined;
+            this.showNewTrack(chainid, title, text, undefined, undefined, type, undefined, bMsa, fromArray, toArray, seqStartLen, exonArray);
+        }
+
+        // set color for the master seq
+        if(trackSeqArray.length > 0) {
+            if(ic.queryresi2score === undefined) ic.queryresi2score = {};
+            if(ic.queryresi2score[chainid] === undefined) ic.queryresi2score[chainid] = {};
+
+            let nSeq = trackSeqArray.length;
+            for(let resi in resi2cntSameRes) {
+                let score = parseInt(resi2cntSameRes[resi] / nSeq * 100);
+                ic.queryresi2score[chainid][resi] = score;
+            }
+
+            let resiArray = Object.keys(resi2cntSameRes);
+            let start = Math.min.apply(null, resiArray);
+            let end = Math.max.apply(null, resiArray);
+
+            let resiScoreStr = '';
+            for(let resi = start; resi <= end; ++resi) {
+                if(resi2cntSameRes.hasOwnProperty(resi)) {
+                    resiScoreStr += Math.round(resi2cntSameRes[resi] / nSeq * 9); // max 9
+                }
+                else {
+                    resiScoreStr += '_';
+                }
+            }
+
+            ic.opts['color'] = 'align custom';
+            ic.setColorCls.setColorByOptions(ic.opts, ic.hAtoms);
+
+            ic.hlUpdateCls.updateHlAll();
+
+            ic.drawCls.draw();
+
+            //me.htmlCls.clickMenuCls.setLogCmd('color align custom | ' + chainid + ' | range ' + start + '_' + end + ' | ' + resiScoreStr, true);
+        }
+    }
+
+    processAccList(acclist) { let ic = this.icn3d; ic.icn3dui;
+        // remove version from acc
+        let accArray = acclist.split(',');
+        let accHash = {};
+        let acclistTmp = '';
+        for(let i = 0, il = accArray.length; i < il; ++i) {
+            let acc = accArray[i];
+
+            if(accHash.hasOwnProperty(acc)) {
+                continue;
+            }
+            else {
+                accHash[acc] = 1;
+            }
+            
+            let pos = acc.indexOf('.');
+            if(pos != -1) {
+                acclistTmp += acc.substr(0, pos);
+            }
+            else {
+                acclistTmp += acc;
+            }
+
+            if(i < accArray.length - 1) {
+                acclistTmp += ',';
+            }
+        }
+
+        return acclistTmp;
+    }
+
+    async addExonTracks(chainid, geneid, startpos, type) { let ic = this.icn3d, me = ic.icn3dui;
+        let seqFirst, trackTitleArray = [], trackSeqArray = [];
+
+        // get acclist from geneid
+        let url = me.htmlCls.baseUrl + "/vastdyn/vastdyn.cgi?geneid2isoforms=" + geneid;
+        let data = await me.getAjaxPromise(url, 'jsonp');
+        let accArray = data.acclist;
+        let exons = data.exons;
+        let acc2exons = {};
+
+        let acclist = '';
+        ic.exonOrder = 1; // 1: increasing bp order; -1 decreasing bp order
+        for(let i = 0, il = accArray.length; i < il; ++i) {
+            let accOri = accArray[i];
+            let pos = accOri.indexOf('.');
+            let acc = (pos != -1) ? accOri.substr(0, pos) : accOri;
+
+            let cntTotal = 0, prevCntTotal = 0, rangeArray = [];
+            for(let j = 0, jl = exons[accOri].length; j < jl; ++j) {
+                let itemArray = exons[accOri][j].split('-');
+                itemArray[0] = parseInt(itemArray[0]);
+                itemArray[1] = parseInt(itemArray[1]);
+                itemArray[2] = parseInt(itemArray[2]);
+
+                ic.exonOrder = (itemArray[0] < itemArray[1]) ? 1 : -1;
+
+                let genomeRange = itemArray[0] + '-' + itemArray[1];
+                let cnt = (j == jl - 1) ? itemArray[2] - 3 : itemArray[2]; // The last one is stop codeon
+                cntTotal += cnt;
+
+                let resStart = parseInt(prevCntTotal/3.0 + 0.5); // 0-based
+                let resEnd = parseInt(cntTotal/3.0 + 0.5) - 1; // 0-based
+
+                let genResStart = parseInt(itemArray[0] / 3.0 + 0.5);
+                
+                //let genResEnd = parseInt(itemArray[1] / 3.0 + 0.5); // some difference due to round
+                let genResEnd = genResStart + ic.exonOrder * (resEnd - resStart);
+
+                rangeArray.push({genomeRange: genomeRange, genResStart: genResStart, genResEnd: genResEnd, resStart: resStart, resEnd: resEnd});
+
+                prevCntTotal = cntTotal;
+            }
+            acc2exons[acc] = rangeArray;
+
+            acclist += acc;
+            if(i < il - 1) {
+                acclist += ',';
+            }
+        }
+
+        let result = await this.getIsoformMsa(acclist, acc2exons);
+        trackTitleArray = result.trackTitleArray;
+        trackSeqArray = result.trackSeqArray;
+        //seqFirst = result.seqFirst;
+        let maxIndex = result.maxIndex;
+
+        let acclist2 = trackTitleArray[maxIndex];
+        let structure = chainid.substr(0, chainid.indexOf('_'));
+        let firstAcc;
+        if(structure.length > 5) {
+            if(ic.uniprot2acc && ic.uniprot2acc[structure]) structure = ic.uniprot2acc[structure];
+            firstAcc = structure;
+        }
+        else {
+            firstAcc = chainid;
+        }
+
+        // get the sequence from iCn3D because a uniProt ID can not be retrieved in pwaln.fcgi
+        if(structure.length > 5) {
+            let chainSeq = '';
+            for(let i = 0, il = ic.chainsSeq.length; i < il; ++i) {
+                chainSeq += ic.chainsSeq[i].resn;
+            }
+
+            result = await this.getMsa(acclist2, firstAcc, chainSeq);
+        }
+        else {
+            result = await this.getMsa(acclist2, firstAcc);
+        }
+
+        result.trackTitleArray;
+        let trackSeqArray2 = result.trackSeqArray;
+        seqFirst = result.seqFirst;
+
+        // merge trackTitleArray2[0] with trackSeqArray[maxIndex]
+        let A = trackSeqArray[maxIndex], B = trackSeqArray2[0];
+        let i = 0, j = 0;
+
+        let ALen = trackSeqArray.length;
+
+        while (i < A.length && j < B.length) {
+            if(A[i] != B[j]) {
+                if(A[i] == '-') { 
+                    // inser "-" in B
+                    B = B.substr(0, j) + '-' + B.substr(j);
+                    seqFirst = seqFirst.substr(0, j) + '-' + seqFirst.substr(j);
+                }
+                else { //if(B[j] == '-') { 
+                    // inser "-" in A
+                    for(let k = 0; k < ALen; ++k) {
+                        trackSeqArray[k] = trackSeqArray[k].substr(0, i) + '-' + trackSeqArray[k].substr(i);
+                    }
+                }
+            }
+
+            ++i;
+            ++j;
+        }
+
+        await this.showMsaTracks(chainid, seqFirst, trackTitleArray, trackSeqArray, startpos, type, acc2exons);
+
+        me.htmlCls.clickMenuCls.setLogCmd("add exon track | chainid " + chainid + " | geneid " + geneid + " | startpos " + startpos + " | type " + type, true);
+    }
+
+    async addMsaTracks(chainid, startpos, type, fastaList) { let ic = this.icn3d, me = ic.icn3dui;
+        let seqFirst, trackTitleArray = [], trackSeqArray = [];
+
+        let fastaArray = fastaList.split('>');
+
+        // the first array item is empty
+        // the second array item is the sequence of the structure, start with i = 2
+        let posFirst = fastaArray[1].indexOf('\n');
+        //let titleFirst = fastaArray[1].substr(0, posFirst);
+        seqFirst = fastaArray[1].substr(posFirst + 1).replace(/\n/g, '');
+
+        for(let i = 2, il = fastaArray.length; i < il; ++i) {
+            let pos = fastaArray[i].indexOf('\n');
+            let title = fastaArray[i].substr(0, pos);
+            if(title.indexOf('|') != -1) {
+                title = title.split('|')[1];
+                //   if(title.indexOf('.') != -1) {
+                //     title = title.split('.')[0];
+                //   }
+            }
+            trackTitleArray.push(title);
+            let seq = fastaArray[i].substr(pos + 1).replace(/\n/g, '');
+            trackSeqArray.push(seq);
+        }
+
+        await this.showMsaTracks(chainid, seqFirst, trackTitleArray, trackSeqArray, startpos, type);
+
+        me.htmlCls.clickMenuCls.setLogCmd("add msa track | chainid " + chainid + " | startpos " + startpos + " | type " + type + " | fastaList " + fastaList , true);
+    }
 }
 
 /**
@@ -40936,13 +41786,14 @@ class ShowAnno {
                 } // if(me.cfg.mmdbid
             } // for(let i = 0
 
-            ic.maxAnnoLength = 1;
+            ic.maxAnnoLengthOri = 1;
             for(let chainid in ic.chainsSeq) {
                 // use protein or nucleotide as the max length
-                if(ic.chainsSeq[chainid].length > ic.maxAnnoLength && (ic.protein_chainid.hasOwnProperty(chainid) || nucleotide_chainid.hasOwnProperty(chainid)) ) {
-                    ic.maxAnnoLength = ic.chainsSeq[chainid].length;
+                if(ic.chainsSeq[chainid].length > ic.maxAnnoLengthOri && (ic.protein_chainid.hasOwnProperty(chainid) || nucleotide_chainid.hasOwnProperty(chainid)) ) {
+                    ic.maxAnnoLengthOri = ic.chainsSeq[chainid].length;
                 }
             }
+            ic.maxAnnoLength = ic.maxAnnoLengthOri;
         }
 
         return {'nucleotide_chainid': nucleotide_chainid, 'chemical_chainid': chemical_chainid, 'chemical_set': chemical_set};
@@ -40957,7 +41808,7 @@ class ShowAnno {
         let chemical_chainid = result.chemical_chainid;
         let chemical_set = result.chemical_set;
 
-        if(ic.bAnnoShown === undefined || !ic.bAnnoShown || ic.bResetAnno) { // ic.bResetAnno when loading another structure
+        if(!ic.bAnnoShown || ic.bResetAnno) { // ic.bResetAnno when loading another structure
             // assign early to avoid load annotations twice
             ic.bAnnoShown = true;
 
@@ -40993,7 +41844,7 @@ 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 +41875,7 @@ class ShowAnno {
                     idArray.push(me.cfg.query_id);
                 }
 
-                // get seqeunce
+                // get sequence
                 if(ic.blastAcxn) { 
                     let chainid = me.cfg.afid + '_A';
                     let seq = '';
@@ -41098,13 +41949,52 @@ class ShowAnno {
         let thisClass = this;
         let chnidBaseArray = $.map(ic.protein_chainid, function(v) { return v; });
         let index = 0;
+
+        // get geneid
+        if(!ic.chainsGene) ic.chainsGene = {};
+        for(let chnid in ic.protein_chainid) {
+            let structure = chnid.substr(0, chnid.indexOf('_'));
+            // UniProt or NCBI protein accession
+            if(structure.length > 5) {
+                let refseqid, url;
+                if(ic.uniprot2acc && ic.uniprot2acc[structure]) {
+                    refseqid = ic.uniprot2acc[structure];
+                }
+                else {
+                    try {
+                        if(!ic.uniprot2acc) ic.uniprot2acc = {};
+                        url = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi?uniprot2refseq=" + structure;
+                        let result = await me.getAjaxPromise(url, 'jsonp');
+                        refseqid = (result && result.refseq) ? result.refseq : structure;
+
+                        ic.uniprot2acc[structure] = refseqid;
+                    }
+                    catch {
+                        console.log("Problem in getting protein accession from UniProt ID...");
+                        refseqid = structure;
+                    }
+                }
+
+                // get Gene info from protein name
+                // url = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi?protein2gene=" + refseqid;
+                // ic.chainsGene[chnid] = await me.getAjaxPromise(url, 'jsonp');
+
+                // get Gene info from uniprot
+                url = "https://rest.uniprot.org/uniprotkb/search?format=json&fields=xref_geneid,gene_names&query=" + structure;
+                let geneData = await me.getAjaxPromise(url, 'json');
+                let geneId = (geneData.results[0] && geneData.results[0].uniProtKBCrossReferences[0]) ? geneData.results[0].uniProtKBCrossReferences[0].id : undefined;
+                let geneSymbol = (geneData.results[0] && geneData.results[0].genes[0] && geneData.results[0].genes[0].geneName) ? geneData.results[0].genes[0].geneName.value : undefined;
+                ic.chainsGene[chnid] = {geneId: geneId, geneSymbol: geneSymbol};
+            }
+        }
+
         for(let chnid in ic.protein_chainid) {
             let buttonStyle = me.utilsCls.isMobile() ? 'none' : 'button';
             let fullProteinName = ic.showSeqCls.getProteinName(chnid);
             let proteinName = fullProteinName;
             //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 geneLink =(ic.chainsGene[chnid] && ic.chainsGene[chnid].geneId) ? "(Gene: <a href='https://www.ncbi.nlm.nih.gov/gene/" + ic.chainsGene[chnid].geneId + "?report=gene_table' 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
@@ -41351,7 +42241,7 @@ 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 +42253,7 @@ 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;
@@ -41655,6 +42545,9 @@ class ShowSeq {
             html += htmlTmp + '<span class="icn3d-seqLine">';
             let helixCnt = 0, sheetCnt = 0;
             let savedSsName = '';
+
+            if(ic.seqStartLen && ic.seqStartLen[chnid]) html += this.insertMulGap(ic.seqStartLen[chnid], ' ');
+
             for(let i = 0, il = giSeq.length; i < il; ++i) {
               html += this.insertGap(chnid, i, '-');
               let currResi;
@@ -41712,18 +42605,25 @@ class ShowSeq {
               }
               html += '</span>';
             }
+
+            if(ic.seqStartLen && ic.seqStartLen[chnid]) html += this.insertMulGap(ic.seqEndLen[chnid], ' ');
+
             html += '<span class="icn3d-residueNum"></span>';
             html += '</span>';
             html += '<br>';
             html += '</div>';
             html3 += '</div>';
         }
+
         // html to display secondary structures
         htmlTmp = '<div class="icn3d-residueLine" style="white-space:nowrap;">';
         htmlTmp += '<div class="icn3d-annoTitle" anno="0"></div>';
         htmlTmp += '<span class="icn3d-residueNum"></span>';
         html3 += htmlTmp + '<br>';
         html += htmlTmp + '<span class="icn3d-seqLine">';
+
+        if(ic.seqStartLen && ic.seqStartLen[chnid]) html += this.insertMulGap(ic.seqStartLen[chnid], '-');
+
         for(let i = 0, il = giSeq.length; i < il; ++i) {
           html += this.insertGap(chnid, i, '-');
         //   let resi =(i >= ic.matchedPos[chnid] && i - ic.matchedPos[chnid] < ic.chainsSeq[chnid].length) ? ic.chainsSeq[chnid][i - ic.matchedPos[chnid]].resi : ic.baseResi[chnid] + 1 + i;
@@ -41771,6 +42671,9 @@ class ShowSeq {
             html += '<span>-</span>'; //'<span>-</span>';
           }
         }
+
+        if(ic.seqStartLen && ic.seqStartLen[chnid]) html += this.insertMulGap(ic.seqEndLen[chnid], '-');
+
         html += '<span class="icn3d-residueNum"></span>';
         html += '</span>';
         html += '<br>';
@@ -41802,6 +42705,9 @@ class ShowSeq {
         html += htmlTmp + htmlTmp2;
         html2 += htmlTmp + htmlTmp2;
         let pos, nGap = 0;
+
+        if(ic.seqStartLen && ic.seqStartLen[chnid]) html += this.insertMulGap(ic.seqStartLen[chnid], '-');
+
         for(let i = 0, il = giSeq.length; i < il; ++i) {
           html += this.insertGap(chnid, i, '-');
           if(ic.targetGapHash !== undefined && ic.targetGapHash.hasOwnProperty(i)) nGap += ic.targetGapHash[i].to - ic.targetGapHash[i].from + 1;
@@ -41831,6 +42737,9 @@ class ShowSeq {
               html += '<span id="giseq_' + ic.pre + chnid + '_' + pos + '" title="' + cFull + pos + '" class="icn3d-residue" style="color:#' + color + '">' + c + '</span>';
           }
         }
+
+        if(ic.seqStartLen && ic.seqStartLen[chnid]) html += this.insertMulGap(ic.seqEndLen[chnid], '-');
+
         if(me.cfg.blast_rep_id == chnid) {
           // change color in 3D
           ic.opts['color'] = (ic.blastAcxn) ? 'confidence' : 'conservation';
@@ -41841,8 +42750,11 @@ class ShowSeq {
         // sequence, overview
         let atom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.chains[chnid]);
         let color =(atom.color) ? atom.color.getHexString() : "CCCCCC";
-        let width = Math.round(ic.seqAnnWidth * giSeq.length / ic.maxAnnoLength);
+        let width = Math.round(ic.seqAnnWidth * giSeq.length / (ic.maxAnnoLength + ic.nTotalGap));
         if(width < 1) width = 1;
+
+        if(ic.seqStartLen && ic.seqStartLen[chnid]) html2 += this.insertMulGapOverview(chnid, ic.seqStartLen[chnid]);
+
         if(me.cfg.blast_rep_id != chnid) { // regular
             html2 += '<div id="giseq_summary_' + ic.pre + chnid + '" class="icn3d-seqTitle icn3d-link" gi chain="' + chnid + '" style="display:inline-block; color:white; font-weight:bold; background-color:#' + color + '; width:' + width + 'px;">' + chnid + '</div>';
         }
@@ -41856,7 +42768,9 @@ class ShowSeq {
                 }
             }
             toArray2.push(giSeq.length - 1);
+
             html2 += '<div id="giseq_summary_' + ic.pre + chnid + '" class="icn3d-seqTitle icn3d-link" gi chain="' + chnid + '" style="width:' + width + 'px;">';
+            
             for(let i = 0, il = fromArray2.length; i < il; ++i) {
                 html2 += this.insertGapOverview(chnid, fromArray2[i]);
                 html2 += '<div style="display:inline-block; color:white!important; font-weight:bold; background-color:#' + color + '; width:' + Math.round(ic.seqAnnWidth *(toArray2[i] - fromArray2[i] + 1) /(ic.maxAnnoLength + ic.nTotalGap)) + 'px;" class="icn3d-seqTitle icn3d-link icn3d-blue" anno="sequence" gi chain="' + chnid + '" title="' + chnid + '">' + chnid + '</div>';
@@ -41988,6 +42902,9 @@ class ShowSeq {
                 htmlTmp += '<span class="icn3d-residueNum"></span>';
                 html3 += htmlTmp + '<br>';
                 html += htmlTmp + '<span class="icn3d-seqLine">';
+
+                if(ic.seqStartLen && ic.seqStartLen[chnid]) html += this.insertMulGap(ic.seqStartLen[chnid], '-');
+
                 for(let i = 0, il = giSeq.length; i < il; ++i) {
                     html += this.insertGap(chnid, i, '-');
                     //if(i >= ic.matchedPos[chnid] && i - ic.matchedPos[chnid] < ic.chainsSeq[chnid].length) {
@@ -42011,6 +42928,9 @@ class ShowSeq {
                     //   html += '<span></span>';
                     // }
                 }
+
+                if(ic.seqStartLen && ic.seqStartLen[chnid]) html += this.insertMulGap(ic.seqEndLen[chnid], '-');
+
                 html += '<span class="icn3d-residueNum"></span>';
                 html += '</span>';
                 html += '<br>';
@@ -42658,26 +43578,43 @@ class ShowSeq {
       let html = '';
       //if(me.cfg.blast_rep_id == chnid && ic.targetGapHash!== undefined && ic.targetGapHash.hasOwnProperty(seqIndex)) {
       if(ic.targetGapHash!== undefined && ic.targetGapHash.hasOwnProperty(seqIndex)) {
-          for(let j = 0; j <(ic.targetGapHash[seqIndex].to - ic.targetGapHash[seqIndex].from + 1); ++j) {
-              if(bNohtml) {
-                 html += text;
-              }
-              else {
-                 html += '<span>' + text + '</span>';
-              }
-          }
+        html += this.insertMulGap(ic.targetGapHash[seqIndex].to - ic.targetGapHash[seqIndex].from + 1, text, bNohtml);
       }
       return html;
     }
-    insertGapOverview(chnid, seqIndex) {  let ic = this.icn3d, me = ic.icn3dui;
+
+    insertMulGap(n, text, bNohtml) {  let ic = this.icn3d; ic.icn3dui;
+        let html = '';
+        for(let j = 0; j < n; ++j) {
+            if(bNohtml) {
+                html += text;
+            }
+            else {
+                html += '<span>' + text + '</span>';
+            }
+        }
+        return html;
+    }
+
+    insertGapOverview(chnid, seqIndex) {  let ic = this.icn3d; ic.icn3dui;
       let html2 = '';
-      if(me.cfg.blast_rep_id == chnid && ic.targetGapHash!== undefined && ic.targetGapHash.hasOwnProperty(seqIndex)) {
-          let width = ic.seqAnnWidth *(ic.targetGapHash[seqIndex].to - ic.targetGapHash[seqIndex].from + 1) /(ic.maxAnnoLength + ic.nTotalGap);
-          html2 += '<div style="display:inline-block; background-color:#333; width:' + width + 'px; height:3px;">&nbsp;</div>';
+    //   if(me.cfg.blast_rep_id == chnid && ic.targetGapHash !== undefined && ic.targetGapHash.hasOwnProperty(seqIndex)) {
+      if(ic.targetGapHash !== undefined && ic.targetGapHash.hasOwnProperty(seqIndex)) {
+        html2 += this.insertMulGapOverview(chnid, ic.targetGapHash[seqIndex].to - ic.targetGapHash[seqIndex].from + 1);
       }
       return html2;
     }
 
+    insertMulGapOverview(chnid, n) {  let ic = this.icn3d; ic.icn3dui;
+        let html2 = '';
+        let width = ic.seqAnnWidth * n /(ic.maxAnnoLength + ic.nTotalGap);
+        width = parseInt(width);
+        
+        // html2 += '<div style="display:inline-block; background-color:#333; width:' + width + 'px; height:3px;">&nbsp;</div>';
+        html2 += '<div style="display:inline-block; width:' + width + 'px;">&nbsp;</div>';
+        return html2;
+    }
+
     setAlternativeSeq(chnid, chnidBase) { let ic = this.icn3d; ic.icn3dui;
         //if(ic.chainsSeq[chnid] !== undefined) {
         let resArray = ic.chainsSeq[chnid];
@@ -42807,7 +43744,7 @@ 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 +45332,22 @@ 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 +45359,8 @@ 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 +45440,9 @@ 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 +45452,19 @@ 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 +45543,7 @@ 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 +45571,15 @@ 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 +45588,63 @@ 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 +49061,7 @@ 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 +49121,7 @@ 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 +49601,7 @@ 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 +49786,14 @@ 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();
@@ -49445,6 +50415,8 @@ class MmdbParser {
 
         if(data && data.uniprot) {
             me.cfg.afid = data.uniprot;
+            if(!ic.uniprot2acc) ic.uniprot2acc = {};
+            ic.uniprot2acc[data.uniprot] = refseqid;
         }
         else {
             var aaa = 1; //alert('The accession ' + refseqid + ' can not be mapped to AlphaFold UniProt ID. It will be treated as a UniProt ID instead.');
@@ -49462,6 +50434,73 @@ 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 +51577,9 @@ 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 +52515,7 @@ 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 +52526,7 @@ 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 +52558,6 @@ class RealignParser {
                         let chainid2 = chainidArray2[j];
 
                         let alignAjax;
-
                         if(me.cfg.aligntool != 'tmalign') {
                             let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(struct2domain[struct2][chainid2]);
                         
@@ -51554,7 +52596,7 @@ 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 +52605,7 @@ 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 +54726,7 @@ 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 +56540,7 @@ 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);
@@ -55657,14 +56699,121 @@ class SetSeqAlign {
         result = this.getTemplatePosFromOriPos(chainid1, prevIndex1, end_t, bRealign);
         pos1 = result.pos1;
         pos2 = result.pos2;
-        //for(let i = pos1; i < pos2; ++i) {
-        for(let i = pos1; i <= pos2; ++i) {
+        for(let i = pos1; i < pos2; ++i) {
+        //for(let i = pos1; i <= pos2; ++i) {
             ic.alnChainsSeq[chainid2].push(gapResObject2);           
         }     
 
         return hAtoms;
     }
 
+    // used for seq MSA
+    mergeTwoSeqForAllSimple(targetId, chainidArray, index, alignedChainIndice, start_t, end_t, querySeqArray) { let ic = this.icn3d; ic.icn3dui;
+        let chainid1 = targetId;
+        let chainid2 = chainidArray[index];
+
+        let pos1, pos2, prevIndex1, prevIndex2;
+
+        for(let i = 0, il = ic.qt_start_end[index].length; i < il; ++i) {
+            let start1, start2, end1, end2, resiStart1, start1Pos, end1Pos;
+            
+            start1 = ic.qt_start_end[index][i].t_start;
+            start2 = ic.qt_start_end[index][i].q_start;
+            end1 = ic.qt_start_end[index][i].t_end;
+            end2 = ic.qt_start_end[index][i].q_end;  
+
+            // 1. before the mapped residues
+            //resiStart1 = ic.ParserUtilsCls.getResi(chainid1, start1);
+            resiStart1 = start1;
+            start1Pos = start1;
+            end1Pos = end1;
+
+            // if the mapping does not start from start_t, add gaps to the query seq
+            if(i == 0) {
+                pos1 = start_t;
+                pos2 = start1Pos;
+                
+                if(start1Pos > start_t) {
+                    for(let j = 0, jl = pos2 - pos1; j < jl; ++j) {
+                        ic.msaSeq[chainid2] += '-';
+                    }
+                }
+            }
+            else {
+                pos1 = prevIndex1;
+                pos2 = start1;
+                let notAlnLen1 = pos2 - (pos1 + 1);
+                let notAlnLen2 = start2 - (prevIndex2 + 1);
+                
+                // insert non-aligned residues in query seq
+                // this.insertNotAlignRes(chainid2, prevIndex2+1, notAlnLen2, bRealign);
+
+                for(let j = 0, jl = notAlnLen2; j < jl; ++j) {
+                    let resn = querySeqArray[index][prevIndex2+1 + j];
+                    ic.msaSeq[chainid2] += resn;
+                }
+
+                if(notAlnLen1 >= notAlnLen2) {
+                    // add gaps before the query sequence
+                    for(let j = 0, jl = notAlnLen1 - notAlnLen2; j < jl; ++j) {
+                        ic.msaSeq[chainid2] += '-';
+                    }                       
+                }
+                else {
+                    // check the number of gaps before resiStart1 (n), and insert 'notAlnLen2 - notAlnLen1 - n' gaps
+                    // this.addGapAllAlnChains(chainidArray, alignedChainIndice, chainid1, resiStart1, notAlnLen2 - notAlnLen1);
+
+                    // let result = this.getResiPosInTemplate(chainid1, resi_t);
+                    // let nGap = result.ngap, pos_t = result.pos;
+
+                    let pos_t = resiStart1; // position to add gap
+            
+                    // add gaps for all previously aligned sequences, not the current sequence, which is the last one
+                    for(let j = 0, jl = alignedChainIndice.length - 1; j < jl; ++j) {
+                        let chainidTmp = (j == 0) ? chainid1 : chainidArray[alignedChainIndice[j]];
+
+                        for(let k = 0, kl = notAlnLen2 - notAlnLen1; k < kl; ++k) {
+                            //ic.msaSeq[chainidTmp].splice(pos_t, 0, '-');
+                            ic.msaSeq[chainidTmp] = ic.msaSeq[chainidTmp].substr(0, pos_t) + '-' + ic.msaSeq[chainidTmp].substr(pos_t);
+                        }
+                    }
+                }                           
+            }
+
+            // 2. In the mapped residues
+            pos1 = start1Pos;
+            pos2 = end1Pos;
+            
+            let k = 0;    
+            for(let j = pos1; j <= pos2; ++j) {
+                // inherit the gaps from the template
+                if(ic.msaSeq[chainid1][j] == '-') {
+                    ic.msaSeq[chainid2] += '-';
+                }
+                else {
+                    //let resn1 = targetSeq[start1 + k];
+                    let resn2 = querySeqArray[index][start2 + k];
+                    //let resn2 = (querySeqArray[index]) ? querySeqArray[index][start2 + k] : '?';
+                    
+                    ic.msaSeq[chainid2] += resn2;
+
+                    ++k;
+                }
+            }
+            
+            prevIndex1 = end1;
+            prevIndex2 = end2;  
+        } 
+
+        // add gaps at the end
+        pos1 = prevIndex1;
+        pos2 = end_t;
+        for(let i = pos1; i < pos2; ++i) {
+        //for(let i = pos1; i <= pos2; ++i) {
+            ic.msaSeq[chainid2] += '-';           
+        }
+    }
+
     setSeqAlignForRealign(chainid_t, chainid, chainIndex) { let ic = this.icn3d, me = ic.icn3dui;
           //var chainid_t = ic.chainidArray[0];
 
@@ -55893,7 +57042,7 @@ 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 +57110,7 @@ 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 +57271,11 @@ 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 +58166,7 @@ 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 +58243,7 @@ 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 +58252,7 @@ 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);
                     }
                 }
             }
@@ -60238,6 +61391,38 @@ class LoadScript {
     
             await ic.cartoon2dCls.draw2Dcartoon(type);
           }
+          else if(command.indexOf('add msa track') == 0) {
+            //add msa track | chainid " + chainid + " | startpos " + startpos + " | type " + type + " | fastaList " + fastaList 
+            let paraArray = command.split(' | ');
+    
+            let chainid = paraArray[1].substr(8);
+            let startpos = paraArray[2].substr(9);
+            let type = paraArray[3].substr(5);
+            let fastaList = paraArray[4].substr(10);
+
+            if($("#" + ic.pre + "anno_custom")[0]) {
+                $("#" + ic.pre + "anno_custom")[0].checked = true;
+            }
+            $("[id^=" + ic.pre + "custom]").show();
+
+            await ic.addTrackCls.addMsaTracks(chainid, startpos, type, fastaList);
+          }
+          else if(command.indexOf('add exon track') == 0) {
+            //add exon track | chainid " + chainid + " | geneid " + geneid + " | startpos " + startpos + " | type " + type
+            let paraArray = command.split(' | ');
+
+            let chainid = paraArray[1].substr(8);
+            let geneid = paraArray[2].substr(7);
+            let startpos = paraArray[3].substr(9);
+            let type = paraArray[4].substr(5);
+
+            if($("#" + ic.pre + "anno_custom")[0]) {
+                $("#" + ic.pre + "anno_custom")[0].checked = true;
+            }
+            $("[id^=" + ic.pre + "custom]").show();
+
+            await ic.addTrackCls.addExonTracks(chainid, geneid, startpos, type);
+          }
           else {
             await ic.applyCommandCls.applyCommand(ic.commands[i]);
           }
@@ -60484,6 +61669,10 @@ 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;
@@ -60946,12 +62135,18 @@ class SelectByCommand {
              residueStr = "*";
            }
            else if(colonPos2 != -1) {
-            refResStr = testStr.substr(colonPos2 + 5);
-            testStr = testStr.substr(0, colonPos2);
+              refResStr = testStr.substr(colonPos2 + 5);
+              testStr = testStr.substr(0, colonPos2);
+
+              // somehow sometimes refResStr or residueStr is rmpty
+              if(!refResStr) continue;
            }
            else if(colonPos != -1) {
-             residueStr = testStr.substr(colonPos + 1);
-             testStr = testStr.substr(0, colonPos);
+              residueStr = testStr.substr(colonPos + 1);
+              testStr = testStr.substr(0, colonPos);
+
+              // somehow sometimes refResStr or residueStr is rmpty
+              if(!residueStr) continue;
            }
 
            if(periodPos === -1) {
@@ -61579,6 +62774,8 @@ 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 +68015,7 @@ 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 +69149,13 @@ 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 +69175,38 @@ 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 +69232,7 @@ 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 +69258,12 @@ 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 +72535,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.26.0';
+    this.REVISION = '3.28.0';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -71619,6 +72828,14 @@ 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 +72843,7 @@ 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') {