icn3d 3.14.0 → 3.14.3

package/icn3d.js

@@ -7487,15 +7487,16 @@ class Strand {
                 }
 
                 let maxDist = 6.0;
-                //let bBrokenSs = (prevCoorCA && Math.abs(currentCA.x - prevCoorCA.x) > maxDist) || (prevCoorCA && Math.abs(currentCA.y - prevCoorCA.y) > maxDist) || (prevCoorCA && Math.abs(currentCA.z - prevCoorCA.z) > maxDist);
-                let bBrokenSs = !atoms.hasOwnProperty(atom.serial) || (prevCoorCA && Math.abs(currentCA.x - prevCoorCA.x) > maxDist) || (prevCoorCA && Math.abs(currentCA.y - prevCoorCA.y) > maxDist) || (prevCoorCA && Math.abs(currentCA.z - prevCoorCA.z) > maxDist);
+                let bBrokenSs = (prevCoorCA && Math.abs(currentCA.x - prevCoorCA.x) > maxDist) || (prevCoorCA && Math.abs(currentCA.y - prevCoorCA.y) > maxDist) || (prevCoorCA && Math.abs(currentCA.z - prevCoorCA.z) > maxDist);
+                // The following code didn't work to select one residue
+                // let bBrokenSs = !atoms.hasOwnProperty(atom.serial) || (prevCoorCA && Math.abs(currentCA.x - prevCoorCA.x) > maxDist) || (prevCoorCA && Math.abs(currentCA.y - prevCoorCA.y) > maxDist) || (prevCoorCA && Math.abs(currentCA.z - prevCoorCA.z) > maxDist);
 
-                if(bBrokenSs && atom.ss === 'sheet') {
-                    bSheetSegment = true;
-                }
-                else if(bBrokenSs && atom.ss === 'helix') {
-                    bHelixSegment = true;
-                }
+                // if(bBrokenSs && atom.ss === 'sheet') {
+                //     bSheetSegment = true;
+                // }
+                // else if(bBrokenSs && atom.ss === 'helix') {
+                //     bHelixSegment = true;
+                // }
 
                 if ((atom.ssbegin || atom.ssend || (drawnResidueCount === totalResidueCount - 1) || bBrokenSs) && pnts[0].length > 0 && bSameChain) {
                     let atomName = 'CA';
@@ -13782,7 +13783,10 @@ class DefinedSets {
        ic.hAtoms = {};
        this.setHAtomsFromSets(orArray, 'or');
 
-       if(Object.keys(ic.hAtoms).length == 0) ic.hAtoms = me.hashUtilsCls.cloneHash(ic.atoms);
+       if(Object.keys(ic.hAtoms).length == 0) {
+           //ic.hAtoms = me.hashUtilsCls.cloneHash(ic.atoms);
+           ic.hAtoms = me.hashUtilsCls.cloneHash(ic.dAtoms);
+       }
        this.setHAtomsFromSets(andArray, 'and');
 
        this.setHAtomsFromSets(notArray, 'not');
@@ -17862,7 +17866,7 @@ class SetColor {
                 break;
 
             case 'chain':
-                if(ic.chainsColor !== undefined && Object.keys(ic.chainsColor).length > 0) { // mmdb input
+                if(ic.chainsColor !== undefined && Object.keys(ic.chainsColor).length > 0) { // mmdb input   
                     this.setMmdbChainColor();
                 }
                 else {
@@ -22656,7 +22660,7 @@ class Dssp {
 
           ic.pdbParserCls.loadPdbDataRender(bAppend);
 
-          if(ic.deferredMmdbaf !== undefined) ic.deferredMmdbaf.resolve();
+          //if(ic.deferredMmdbaf !== undefined) ic.deferredMmdbaf.resolve();
           if(ic.deferredSecondary !== undefined) ic.deferredSecondary.resolve();
       });
     }
@@ -22775,7 +22779,7 @@ class Dssp {
 
         ic.pdbParserCls.loadPdbDataRender(bAppend);
 
-        if(ic.deferredMmdbaf !== undefined) ic.deferredMmdbaf.resolve();
+        //if(ic.deferredMmdbaf !== undefined) ic.deferredMmdbaf.resolve();
         if(ic.deferredSecondary !== undefined) ic.deferredSecondary.resolve();
     }
 }
@@ -22796,7 +22800,7 @@ class PdbParser {
        let  url, dataType;
 
        if(bAf) {
-           url = "https://alphafold.ebi.ac.uk/files/AF-" + pdbid + "-F1-model_v2.pdb";
+           url = "https://alphafold.ebi.ac.uk/files/AF-" + pdbid + "-F1-model_v3.pdb";
            ic.ParserUtilsCls.setYourNote(pdbid.toUpperCase() + '(AlphaFold) in iCn3D');
        }
        else {
@@ -24087,7 +24091,7 @@ class MmdbParser {
 
         let  molid2rescount = data.moleculeInfor;
         let  molid2color = {}, chain2molid = {}, molid2chain = {};
-        let  chainNameHash = {};
+        let  chainNameHash = {};       
         for(let i in molid2rescount) {
           if(Object.keys(molid2rescount[i]).length === 0) continue;
 
@@ -24107,7 +24111,7 @@ class MmdbParser {
           chain2molid[chain] = i;
           molid2chain[i] = chain;
 
-          ic.chainsColor[chain] =(type !== undefined) ? me.parasCls.thr(me.htmlCls.GREY8) : me.parasCls.thr(color);
+          ic.chainsColor[chain] = (type !== undefined && !me.cfg.mmdbafid) ? me.parasCls.thr(me.htmlCls.GREY8) : me.parasCls.thr(color);
 
           let  geneId =(molid2rescount[i].geneId === undefined) ? '' : molid2rescount[i].geneId;
           let  geneSymbol =(molid2rescount[i].geneSymbol === undefined) ? '' : molid2rescount[i].geneSymbol;
@@ -25679,7 +25683,7 @@ class ChainalignParser {
 
         let  url_t;
         if(ic.mmdbid_t.length > 5) {
-            url_t = "https://alphafold.ebi.ac.uk/files/AF-" + ic.mmdbid_t + "-F1-model_v2.pdb";
+            url_t = "https://alphafold.ebi.ac.uk/files/AF-" + ic.mmdbid_t + "-F1-model_v3.pdb";
 
             targetAjax = $.ajax({
                 url: url_t,
@@ -25717,7 +25721,7 @@ class ChainalignParser {
 
             let  url_q, queryAjax;
             if(ic.mmdbid_q.length > 5) {
-                url_q = "https://alphafold.ebi.ac.uk/files/AF-" + ic.mmdbid_q + "-F1-model_v2.pdb";
+                url_q = "https://alphafold.ebi.ac.uk/files/AF-" + ic.mmdbid_q + "-F1-model_v3.pdb";
 
                 queryAjax = $.ajax({
                     url: url_q,
@@ -26020,7 +26024,7 @@ class ChainalignParser {
             let structure = ic.structArray[i];
 
             if(isNaN(structure) && structure.length > 5) {
-                url_t = "https://alphafold.ebi.ac.uk/files/AF-" + ic.structArray[i] + "-F1-model_v2.pdb";
+                url_t = "https://alphafold.ebi.ac.uk/files/AF-" + ic.structArray[i] + "-F1-model_v3.pdb";
 
                 targetAjax = $.ajax({
                     url: url_t,
@@ -26085,6 +26089,8 @@ class ChainalignParser {
         let  hAtoms = {}, hAtomsTmp = {};
         let  bLastQuery = false;
 
+        ic.opts['color'] = (structArray.length == 1) ? 'chain' : 'structure';
+
         for(let i = 0, il = structArray.length; i < il; ++i) {
             if(i == structArray.length - 1) bLastQuery = true;
 
@@ -26097,10 +26103,11 @@ class ChainalignParser {
                 targetOrQuery = 'query';
                 bAppend = true; 
             }
-
+            
             //if(structArray[i].length > 4) {
             if(structArray[i].length > 5) {  // PDB ID plus postfix could be 5 
-                let bNoDssp = true;
+                //let bNoDssp = true;
+                let bNoDssp = false; // get secondary structure info
                 hAtomsTmp = ic.pdbParserCls.loadPdbData(queryDataArray[i], structArray[i], false, bAppend, targetOrQuery, bLastQuery, bNoDssp);
             }
             else {              
@@ -26113,7 +26120,7 @@ class ChainalignParser {
 
         // calculate secondary structures with applyCommandDssp
         if(bQuery && me.cfg.matchedchains) {
-            $.when(ic.pdbParserCls.applyCommandDssp(true)).then(function() {
+           // $.when(ic.pdbParserCls.applyCommandDssp(true)).then(function() {
                 let bRealign = true, bPredefined = true;
                 ic.realignParserCls.realignChainOnSeqAlign(undefined, ic.chainidArray, bRealign, bPredefined);
                 // reset annotations
@@ -26122,11 +26129,10 @@ class ChainalignParser {
                 if($('#' + ic.pre + 'dl_selectannotations').dialog( 'isOpen' )) {
                     $('#' + ic.pre + 'dl_selectannotations').dialog( 'close' );
                 }
-           });
-        }
-        else {
-            ic.pdbParserCls.applyCommandDssp(true);
+           //});
         }
+
+        if(ic.deferredMmdbaf !== undefined) ic.deferredMmdbaf.resolve();
     }
 }
 
@@ -34172,7 +34178,7 @@ class ApplyCommand {
         else if(cmd.indexOf('realign on seq align') == 0) return 'File > Realign Selection > on Sequence Alignment';
         else if(cmd.indexOf('realign') == 0) return 'File > Realign Selection > Residue by Residue';
         else if(cmd.indexOf('graph interaction pairs') == 0) return hbondIntStr + ' > 2D Graph(Force-Directed)';
-        else if(cmd.indexOf('export canvas') == 0) return 'File > Save Files > iCn3D PNG Image';
+        else if(cmd.indexOf('export canvas') == 0) return 'File > Save File > iCn3D PNG Image';
         else if(cmd == 'export stl file') return printStr + 'STL';
         else if(cmd == 'export vrml file') return printStr + 'VRML(Color)';
         else if(cmd == 'export stl stabilizer file') return printStr + 'STL W/ Stabilizers';
@@ -34507,7 +34513,9 @@ class SelectByCommand {
                  bResidueId = true;
                }
                else {
-                 if(residueStrArray[j][0] === '3' && residueStrArray[j].length > 1 &&(residueStrArray[j].length - 1) % 3 === 0) { // three letter residue string, such as :3LysArg
+                 //if(residueStrArray[j].length > 1 && residueStrArray[j][0] === '3' && (residueStrArray[j].length - 1) % 3 === 0) { // three letter residue string, such as :3LysArg
+                 if(residueStrArray[j].length > 1 && residueStrArray[j][0] === '3' 
+                     && isNaN(residueStrArray[j][1]) && residueStrArray[j][0] !== '-') { // three letter residue string, such as :3LysArg or :3ZN, but not :30 neither :3-10
                    let  tmpStr = residueStrArray[j].toUpperCase();
                    threeLetterResidueStr = tmpStr.substr(1);
                    bResidueArrayThree = true;
@@ -34623,7 +34631,8 @@ class SelectByCommand {
                            }
                            else if(bResidueArrayThree) {
                                let  threeLetter = me.utilsCls.residueAbbr2Name(ic.chainsSeq[molecule_chain][s].name);
-                               chainSeq +=(threeLetter.length == 3) ? threeLetter : '   ';
+
+                               chainSeq +=(threeLetter.length == 3) ? threeLetter : threeLetter.padEnd(3, '_');
                            }
                            resiArray.push(ic.chainsSeq[molecule_chain][s].resi);
                        }
@@ -42516,9 +42525,12 @@ class Selection {
 
     //Show the selection.
     showSelection() { let  ic = this.icn3d, me = ic.icn3dui;
-        ic.dAtoms = {};
+        //ic.dAtoms = {};
 
-        if(Object.keys(ic.hAtoms).length == 0) this.selectAll_base();
+        if(Object.keys(ic.hAtoms).length == 0) {
+            //this.selectAll_base();
+            ic.hAtoms = me.hashUtilsCls.cloneHash(ic.dAtoms);
+        }
 
         ic.dAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
         ic.viewSelectionAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
@@ -43159,11 +43171,14 @@ class SetStyle {
             console.log("WebGL context was lost. Reset WebGLRenderer and launch iCn3D again.");
 
             ic.renderer = new THREE.WebGLRenderer({
-                canvas: ic.container.get(0),
-                antialias: true,
-                preserveDrawingBuffer: true,
-                alpha: true
+              canvas: ic.oriContainer.get(0), //this.container.get(0),
+              antialias: true,
+              preserveDrawingBuffer: true,
+              sortObjects: false,
+              alpha: true
             });
+            // Enable VR
+            ic.renderer.xr.enabled = true;
 
             ic.drawCls.draw();
 
@@ -44372,7 +44387,8 @@ class ApplySymd {
                 }
                 else { // bSymd, subset, and one chain
                     if(Object.keys(ic.hAtoms).length == 0) {
-                        ic.hAtoms = me.hashUtilsCls.cloneHash(ic.atoms);
+                        //ic.hAtoms = me.hashUtilsCls.cloneHash(ic.atoms);
+                        ic.hAtoms = me.hashUtilsCls.cloneHash(ic.dAtoms);
                     }
 
                     // pick the first 1/order of selection
@@ -56360,11 +56376,12 @@ class SetMenu {
 
         html += "<li><span>Retrieve by ID</span>";
         html += "<ul>";
+        
+        html += me.htmlCls.setHtmlCls.getLink('mn1_mmdbafid', 'PDB/MMDB/AlphaFold IDs' + me.htmlCls.wifiStr);
         html += me.htmlCls.setHtmlCls.getLink('mn1_mmdbid', 'MMDB ID ' + me.htmlCls.wifiStr);
         html += me.htmlCls.setHtmlCls.getLink('mn1_mmtfid', 'MMTF ID ' + me.htmlCls.wifiStr);
         html += me.htmlCls.setHtmlCls.getLink('mn1_pdbid', 'PDB ID ' + me.htmlCls.wifiStr);
         html += me.htmlCls.setHtmlCls.getLink('mn1_afid', 'AlphaFold UniProt ID ' + me.htmlCls.wifiStr);
-        html += me.htmlCls.setHtmlCls.getLink('mn1_mmdbafid', 'MMDB or AlphaFold IDs' + me.htmlCls.wifiStr);
         if(!me.cfg.simplemenu) {
             html += me.htmlCls.setHtmlCls.getLink('mn1_opmid', 'OPM PDB ID ' + me.htmlCls.wifiStr);
             html += me.htmlCls.setHtmlCls.getLink('mn1_mmcifid', 'mmCIF ID ' + me.htmlCls.wifiStr);
@@ -56466,7 +56483,7 @@ class SetMenu {
         html += "</ul>";
         html += "</li>";
 
-        html += "<li><span>Save Files</span>";
+        html += "<li><span>Save File</span>";
         html += "<ul>";
         //html += me.htmlCls.setHtmlCls.getLink('mn1_exportCanvas', 'iCn3D PNG Image');
 
@@ -57653,17 +57670,29 @@ class SetMenu {
         html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#about' target='_blank'>About iCn3D<span style='font-size:0.9em'> " + me.REVISION + "</span></a></li>";
 
         html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#gallery' target='_blank'>Live Gallery " + me.htmlCls.wifiStr + "</a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#videos' target='_blank'>iCn3D Videos</a></li>";
+
+        html += "<li><span>FAQ</span>";
 
-        html += "<li><span>Tutorial</span>";
         html += "<ul>";
-        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#useicn3d' target='_blank'>Use iCn3D</a></li>";
-        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#videos' target='_blank'>iCn3D Videos</a></li>";
-        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#parameters' target='_blank'>URL Parameters</a></li>";
-        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#commands' target='_blank'>Commands</a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#viewstru' target='_blank'><span>View structure</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#tfstru' target='_blank'><span>Transform Structure</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#selsubset' target='_blank'><span>Select Subsets</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#changestylecolor' target='_blank'><span>Change Style/Color</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#saveview' target='_blank'><span>Save Work</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#showanno' target='_blank'><span>Show Annotations</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#exportanno' target='_blank'><span>Export Annotations</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#interanalysis' target='_blank'><span>Interactions Analysis</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#mutationanalysis' target='_blank'><span>Mutation Analysis</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#elecpot' target='_blank'><span>Electrostatic Pot.</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#simivast' target='_blank'><span>Similar PDB</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#simifoldseek' target='_blank'><span>Similar AlphaFold/PDB</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#alignmul' target='_blank'><span>Align Multiple Structures</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#batchanalysis' target='_blank'><span>Batch Analysis</span></a></li>";
+        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#embedicn3d' target='_blank'><span>Embed iCn3D</span></a></li>";
         html += "</ul>";
-        html += "</li>";
 
-        html += liStr + "https://www.ncbi.nlm.nih.gov/structure' target='_blank'>Search Structure " + me.htmlCls.wifiStr + "</a></li>";
+        //html += liStr + "https://www.ncbi.nlm.nih.gov/structure' target='_blank'>Search Structure " + me.htmlCls.wifiStr + "</a></li>";
         html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#citing' target='_blank'>Citing iCn3D</a></li>";
 
         html += "<li><span>Source Code</span>";
@@ -57677,7 +57706,10 @@ class SetMenu {
         if(!me.cfg.simplemenu) {
             html += "<li><span>Develop</span>";
             html += "<ul>";
-            html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#HowToUse' target='_blank'>How to Embed</a></li>";
+            html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#HowToUse' target='_blank'>Embed iCn3D</a></li>";
+            html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#parameters' target='_blank'>URL Parameters</a></li>";
+            html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#commands' target='_blank'>Commands</a></li>";
+    
             html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#datastructure' target='_blank'>Data Structure</a></li>";
             html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#classstructure' target='_blank'>Class Structure</a></li>";
             html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#addclass' target='_blank'>Add New Classes</a></li>";
@@ -58445,8 +58477,8 @@ class SetDialog {
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_foldseek' class='" + dialogClass + "' style='max-width:500px'>";
-        html += 'Note: You can search similar PDB or AlphaFold structures for any structure at the fast <a href="https://search.foldseek.com/search" target="_blank">Foldseek</a> web server. <br><br>Once you see the structure neighbors, you can view the alignment in iCn3D by inputing a list of chain IDs below. <br><br>The PDB chain IDs are the same as the record names such as "1hho_A". The AlphaFold chain IDs are the UniProt ID plus "_A". For example, the UniProt ID for the record name "AF-P69905-F1-model_v2" is "P69905".<br><br>'; 
-        html += "Chain ID List: " + me.htmlCls.inputTextStr + "id='" + me.pre + "foldseekchainids' value='P69905_A,P01942_A,1HHO_A' size=30> ";
+        html += 'Note: You can search similar PDB or AlphaFold structures for any structure at the fast <a href="https://search.foldseek.com/search" target="_blank">Foldseek</a> web server. <br><br>Once you see the structure neighbors, you can view the alignment in iCn3D by inputing a list of PDB chain IDs or AlphaFold UniProt IDs below. <br><br>The PDB chain IDs are the same as the record names such as "1hho_A". The UniProt ID is the text between "AF-" and "-F1". For example, the UniProt ID for the record name "AF-P69905-F1-model_v3" is "P69905".<br><br>'; 
+        html += "Chain ID List: " + me.htmlCls.inputTextStr + "id='" + me.pre + "foldseekchainids' value='P69905,P01942,1hho_A' size=30> ";
         html += me.htmlCls.buttonStr + "reload_foldseek'>Align</button>";
         html += "</div>";
 
@@ -58568,11 +58600,19 @@ class SetDialog {
         html += 'Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[PDB ID or AlphaFold UniProt ID]_[Chain ID]_[Residue Number]_[One Letter Mutatnt Residue]". E.g., the mutation of N501Y in the E chain of PDB 6M0J can be specified as "6M0J_E_501_Y". For AlphaFold structures, the "Chain ID" is "A".<br/><br/>';
         html += "<div style='display:inline-block; width:110px'>Mutations: </div>" + me.htmlCls.inputTextStr + "id='" + me.pre + "mutationids' value='6M0J_E_484_K,6M0J_E_501_Y,6M0J_E_417_N' size=50><br/><br/>";
 
-        html += "<b>Data Source</b>: <select id='" + me.pre + "idsource'>";
-        html += "<option value='mmdbid' selected>PDB ID</option>";
-        html += "<option value='afid'>AlphaFold UniProt ID</option>";
-        html += "</select><br/><br/>";
-        
+        // html += "<b>Data Source</b>: <select id='" + me.pre + "idsource'>";
+        // html += "<option value='mmdbid' selected>PDB ID</option>";
+        // html += "<option value='afid'>AlphaFold UniProt ID</option>";
+        // html += "</select><br/><br/>";
+ 
+        html += '<b>ID Type</b>: ';
+        html += '<input type="radio" name="' + me.pre + 'idsource" id="' + me.pre + 'type_mmdbid" value="mmdbid" checked>PDB ID';
+        html += '<input type="radio" name="' + me.pre + 'idsource" id="' + me.pre + 'type_afid" value="afid" style="margin-left:20px">AlphaFold UniProt ID<br><br>';
+
+        html += '<b>Show Mutation in</b>: ';
+        html += '<input type="radio" name="' + me.pre + 'pdbsource" id="' + me.pre + 'showin_currentpage" value="currentpage">Current Page';
+        html += '<input type="radio" name="' + me.pre + 'pdbsource" id="' + me.pre + 'showin_newpage" value="newpage" style="margin-left:20px" checked>New Page<br><br>';
+
         html += me.htmlCls.buttonStr + "reload_mutation_3d' title='Show the mutations in 3D using the scap program'>3D with scap</button>";
         html += me.htmlCls.buttonStr + "reload_mutation_inter' style='margin-left:20px' title='Show the mutations in 3D and the change of interactions'>Interactions</button>";
         html += me.htmlCls.buttonStr + "reload_mutation_pdb' style='margin-left:20px' title='Show the mutations in 3D and export the PDB of the mutant within 10 angstrom'>PDB</button>";
@@ -58656,7 +58696,7 @@ class SetDialog {
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_yournote' class='" + dialogClass + "'>";
-        html += "Your note will be saved in the HTML file when you click \"File > Save Files > iCn3D PNG Image\".<br><br>";
+        html += "Your note will be saved in the HTML file when you click \"File > Save File > iCn3D PNG Image\".<br><br>";
         html += "<textarea id='" + me.pre + "yournote' rows='5' style='width: 100%; height: " +(me.htmlCls.LOG_HEIGHT) + "px; padding: 0px; border: 0px;' placeholder='Enter your note here'></textarea><br>";
         html += me.htmlCls.buttonStr + "applyyournote'>Save</button>";
         html += "</div>";
@@ -59460,6 +59500,17 @@ class Events {
         }
     }
 
+    convertUniProtInChains(alignment) { let me = this.icn3dui; me.icn3d;
+        let idArray = alignment.split(',');
+        let alignment_final = '';
+        for(let i = 0, il = idArray.length; i < il; ++i) {
+            alignment_final += (idArray[i].indexOf('_') != -1) ? idArray[i] : idArray[i] + '_A'; // AlphaFold ID
+            if(i < il - 1) alignment_final += ',';
+        }
+
+        return alignment_final;
+    }
+
     searchSeq() { let me = this.icn3dui, ic = me.icn3d;
        let select = $("#" + me.pre + "search_seq").val();
        if(isNaN(select) && select.indexOf('$') == -1 && select.indexOf('.') == -1 && select.indexOf(':') == -1 && select.indexOf('@') == -1) {
@@ -59930,8 +59981,16 @@ class Events {
         me.myEventCls.onIds("#" + me.pre + "reload_foldseek", "click", function(e) { me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
-            me.htmlCls.clickMenuCls.setLogCmd("load chainalignment " + $("#" + me.pre + "foldseekchainids").val(), true);
-            window.open(hostUrl + '?chainalign=' + $("#" + me.pre + "foldseekchainids").val(), '_self');
+
+            // me.htmlCls.clickMenuCls.setLogCmd("load chainalignment " + $("#" + me.pre + "foldseekchainids").val(), true);
+            // window.open(hostUrl + '?chainalign=' + $("#" + me.pre + "foldseekchainids").val(), '_self');
+
+
+            let alignment = $("#" + me.pre + "foldseekchainids").val();
+            let alignment_final = thisClass.convertUniProtInChains(alignment);
+
+            me.htmlCls.clickMenuCls.setLogCmd("load chainalignment " + alignment_final, true);
+            window.open(hostUrl + '?chainalign=' + alignment_final + '&aligntool=tmalign&showalignseq=1&bu=0', '_self');
          });
 
         me.myEventCls.onIds("#" + me.pre + "reload_mmtf", "click", function(e) { me.icn3d;
@@ -60073,12 +60132,7 @@ class Events {
            if(!me.cfg.notebook) dialog.dialog( "close" );
 
            let alignment = $("#" + me.pre + "chainalignids").val();
-           let idArray = alignment.split(',');
-           let alignment_final = '';
-           for(let i = 0, il = idArray.length; i < il; ++i) {
-               alignment_final += (idArray[i].indexOf('_') != -1) ? idArray[i] : idArray[i] + '_A'; // AlphaFold ID
-               if(i < il - 1) alignment_final += ',';
-           }
+           let alignment_final = thisClass.convertUniProtInChains(alignment);
            let resalign = $("#" + me.pre + "resalignids").val();
            let predefinedres = $("#" + me.pre + "predefinedres").val().trim().replace(/\n/g, '; ');
            if(predefinedres && alignment_final.split(',').length - 1 != predefinedres.split('; ').length) {
@@ -60096,12 +60150,7 @@ class Events {
            if(!me.cfg.notebook) dialog.dialog( "close" );
 
            let alignment = $("#" + me.pre + "chainalignids").val();
-           let idArray = alignment.split(',');
-           let alignment_final = '';
-           for(let i = 0, il = idArray.length; i < il; ++i) {
-               alignment_final += (idArray[i].indexOf('_') != -1) ? idArray[i] : idArray[i] + '_A'; // AlphaFold ID
-               if(i < il - 1) alignment_final += ',';
-           }
+           let alignment_final = thisClass.convertUniProtInChains(alignment);
 
            me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues | resdef ", false);
            window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=&resdef=&showalignseq=1&bu=0', '_blank');
@@ -60112,12 +60161,7 @@ class Events {
             if(!me.cfg.notebook) dialog.dialog( "close" );
  
             let alignment = $("#" + me.pre + "chainalignids2").val();
-            let idArray = alignment.split(',');
-            let alignment_final = '';
-            for(let i = 0, il = idArray.length; i < il; ++i) {
-                alignment_final += (idArray[i].indexOf('_') != -1) ? idArray[i] : idArray[i] + '_A'; // AlphaFold ID
-                if(i < il - 1) alignment_final += ',';
-            }
+            let alignment_final = thisClass.convertUniProtInChains(alignment);
             let resalign = $("#" + me.pre + "resalignids").val();
  
             me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues " + resalign + " | resdef ", false);
@@ -60129,12 +60173,7 @@ class Events {
             if(!me.cfg.notebook) dialog.dialog( "close" );
  
             let alignment = $("#" + me.pre + "chainalignids3").val();
-            let idArray = alignment.split(',');
-            let alignment_final = '';
-            for(let i = 0, il = idArray.length; i < il; ++i) {
-                alignment_final += (idArray[i].indexOf('_') != -1) ? idArray[i] : idArray[i] + '_A'; // AlphaFold ID
-                if(i < il - 1) alignment_final += ',';
-            }
+            let alignment_final = thisClass.convertUniProtInChains(alignment);
 
             let predefinedres = $("#" + me.pre + "predefinedres").val().trim().replace(/\n/g, '; ');
             if(predefinedres && alignment_final.split(',').length - 1 != predefinedres.split('; ').length) {
@@ -60151,66 +60190,133 @@ class Events {
             if(!me.cfg.notebook) dialog.dialog( "close" );
 
             let alignment = $("#" + me.pre + "chainalignids").val();
-            let idArray = alignment.split(',');
-            let alignment_final = '';
-            for(let i = 0, il = idArray.length; i < il; ++i) {
-                alignment_final += (idArray[i].indexOf('_') != -1) ? idArray[i] : idArray[i] + '_A'; // AlphaFold ID
-                if(i < il - 1) alignment_final += ',';
-            }
+            let alignment_final = thisClass.convertUniProtInChains(alignment);
  
             me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues | resdef | align tmalign", false);
             window.open(hostUrl + '?chainalign=' + alignment_final + '&aligntool=tmalign&resnum=&resdef=&showalignseq=1&bu=0', '_blank');
          });
 
-        me.myEventCls.onIds("#" + me.pre + "reload_mutation_3d", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_mutation_3d", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
            let mutationids = $("#" + me.pre + "mutationids").val();
-           let idsource = $("#" + me.pre + "idsource").val();
-           let mmdbid = mutationids.substr(0, mutationids.indexOf('_'));           
-           me.htmlCls.clickMenuCls.setLogCmd("3d of mutation " + mutationids, false);
-           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmdbid=' + mmdbid + '&command=scap 3d ' + mutationids + '; select displayed set', '_blank');
-           window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap 3d ' + mutationids + '; select displayed set', '_blank');
+           //let idsource = $("#" + me.pre + "idsource").val();
+           let idsource, pdbsource;
+           if($("#" + me.pre + "type_mmdbid").is(":checked")) {
+                idsource = 'mmdbid';
+           }
+           else {
+                idsource = 'afid';
+           }
+           if($("#" + me.pre + "showin_currentpage").is(":checked")) {
+                pdbsource = 'currentpage';
+            }
+            else {
+                pdbsource = 'newpage';
+            }
+
+           if(pdbsource == 'currentpage') {
+                let snp = mutationids;
+
+                ic.scapCls.retrieveScap(snp);
+                me.htmlCls.clickMenuCls.setLogCmd('scap 3d ' + snp, true);
+                me.htmlCls.clickMenuCls.setLogCmd("select displayed set", true);
+           }
+           else {
+                let mmdbid = mutationids.substr(0, mutationids.indexOf('_'));           
+                me.htmlCls.clickMenuCls.setLogCmd("3d of mutation " + mutationids, false);
+                window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap 3d ' + mutationids + '; select displayed set', '_blank');
+           }
         });
 
-        me.myEventCls.onIds("#" + me.pre + "reload_mutation_pdb", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_mutation_pdb", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
            let mutationids = $("#" + me.pre + "mutationids").val();
-           let idsource = $("#" + me.pre + "idsource").val();
-           let mmdbid = mutationids.substr(0, mutationids.indexOf('_'));
-           me.htmlCls.clickMenuCls.setLogCmd("pdb of mutation " + mutationids, false);
-           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmdbid=' + mmdbid + '&command=scap pdb ' + mutationids + '; select displayed set', '_blank');
-           window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap pdb ' + mutationids + '; select displayed set', '_blank');
+           //let idsource = $("#" + me.pre + "idsource").val();
+           let idsource, pdbsource;
+           if($("#" + me.pre + "type_mmdbid").is(":checked")) {
+                idsource = 'mmdbid';
+           }
+           else {
+                idsource = 'afid';
+           }
+           if($("#" + me.pre + "showin_currentpage").is(":checked")) {
+                pdbsource = 'currentpage';
+            }
+            else {
+                pdbsource = 'newpage';
+            }
+
+           if(pdbsource == 'currentpage') {
+                let snp = mutationids;
+
+                let bPdb = true;
+                ic.scapCls.retrieveScap(snp, undefined, bPdb);
+                me.htmlCls.clickMenuCls.setLogCmd('scap pdb ' + snp, true);
+           }
+           else {
+                let mmdbid = mutationids.substr(0, mutationids.indexOf('_'));
+                me.htmlCls.clickMenuCls.setLogCmd("pdb of mutation " + mutationids, false);
+                window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap pdb ' + mutationids + '; select displayed set', '_blank');
+           }
         });
 
         me.myEventCls.onIds("#" + me.pre + "reload_mutation_inter", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
            let mutationids = $("#" + me.pre + "mutationids").val();
-           let idsource = $("#" + me.pre + "idsource").val();
-
-           let mutationArray = mutationids.split(',');
-           let residArray = [];
-           for(let i = 0, il = mutationArray.length; i < il; ++i) {
-               let pos = mutationArray[i].lastIndexOf('_');
-               let resid = mutationArray[i].substr(0, pos);
-               residArray.push(resid);
+           //let idsource = $("#" + me.pre + "idsource").val();
+           let idsource, pdbsource;
+           if($("#" + me.pre + "type_mmdbid").is(":checked")) {
+                idsource = 'mmdbid';
+           }
+           else {
+                idsource = 'afid';
            }
+           if($("#" + me.pre + "showin_currentpage").is(":checked")) {
+                pdbsource = 'currentpage';
+            }
+            else {
+                pdbsource = 'newpage';
+            }
 
-           let mmdbid = mutationids.substr(0, mutationids.indexOf('_'));
+           if(pdbsource == 'currentpage') {
+                let snp = mutationids;
 
-           // if no structures are loaded yet
-           if(!ic.structures) {
-               ic.structures = {};
-               ic.structures[mmdbid] = 1;
+                let bInteraction = true;
+                ic.scapCls.retrieveScap(snp, bInteraction);
+                me.htmlCls.clickMenuCls.setLogCmd('scap interaction ' + snp, true);
+
+                let idArray = snp.split('_'); //stru_chain_resi_snp
+                let select = '.' + idArray[1] + ':' + idArray[2];
+                let name = 'snp_' + idArray[1] + '_' + idArray[2];
+                me.htmlCls.clickMenuCls.setLogCmd("select " + select + " | name " + name, true);
+                me.htmlCls.clickMenuCls.setLogCmd("line graph interaction pairs | selected non-selected | hbonds,salt bridge,interactions,halogen,pi-cation,pi-stacking | false | threshold 3.8 6 4 3.8 6 5.5", true);
+                me.htmlCls.clickMenuCls.setLogCmd("adjust dialog dl_linegraph", true);
+                me.htmlCls.clickMenuCls.setLogCmd("select displayed set", true);
            }
-           ic.resid2specCls.residueids2spec(residArray);
+           else {
+                let mutationArray = mutationids.split(',');
+                let residArray = [];
+                for(let i = 0, il = mutationArray.length; i < il; ++i) {
+                    let pos = mutationArray[i].lastIndexOf('_');
+                    let resid = mutationArray[i].substr(0, pos);
+                    residArray.push(resid);
+                }
+
+                let mmdbid = mutationids.substr(0, mutationids.indexOf('_'));
 
-           me.htmlCls.clickMenuCls.setLogCmd("interaction change of mutation " + mutationids, false);
-           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmdbid=' + mmdbid + '&command=scap interaction ' + mutationids + '; select ' + selectSpec + ' | name test; line graph interaction pairs | selected non-selected | hbonds,salt bridge,interactions,halogen,pi-cation,pi-stacking | false | threshold 3.8 6 4 3.8 6 5.5; adjust dialog dl_linegraph; select displayed set', '_blank');
-           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmdbid=' + mmdbid + '&command=scap interaction ' + mutationids, '_blank');
-           window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap interaction ' + mutationids, '_blank');
+                // if no structures are loaded yet
+                if(!ic.structures) {
+                    ic.structures = {};
+                    ic.structures[mmdbid] = 1;
+                }
+                ic.resid2specCls.residueids2spec(residArray);
+
+                me.htmlCls.clickMenuCls.setLogCmd("interaction change of mutation " + mutationids, false);
+                window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap interaction ' + mutationids, '_blank');
+           }
         });
 
     //    },
@@ -65893,7 +65999,7 @@ class iCn3D {
         if(bWebGL){
             //https://discourse.threejs.org/t/three-js-r128-ext-frag-depth-and-angle-instanced-arrays-extensions-are-not-supported/26037
             //this.renderer = new THREE.WebGL1Renderer({
-            if ( bWebGL2 && bVR) { 
+            if ( bWebGL2 && bVR) {                
                 this.renderer = new THREE.WebGLRenderer({
                     canvas: this.oriContainer.get(0), //this.container.get(0),
                     antialias: true,
@@ -66508,7 +66614,7 @@ iCn3D.prototype.resetConfig = function () { let ic = this, me = ic.icn3dui;
     }
 
     if(me.cfg.blast_rep_id !== undefined) this.opts['color'] = 'conservation';
-    if(me.cfg.mmdbafid !== undefined) this.opts['color'] = 'structure';
+    if(me.cfg.mmdbafid !== undefined && ic.structures) ic.opts['color'] = (Object.keys(ic.structures).length == 1) ? 'chain' : 'structure';
 
     if(me.cfg.options !== undefined) $.extend(this.opts, me.cfg.options);
 };
@@ -66525,7 +66631,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.14.0';
+    this.REVISION = '3.14.3';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;