icn3d 3.21.1 → 3.21.3

package/icn3d.js

@@ -7778,7 +7778,7 @@ class ClickMenu {
                 type: 'POST',
                 data: { 
                     q : pdbstr,
-                    database: ["afdb50", "afdb-swissprot", "gmgcl_id", "pdb100"],
+                    database: ["afdb50", "afdb-swissprot", "gmgcl_id", "pdb100", "afdb-proteome", "mgnify_esm30"],
                     mode: "3diaa"
                 },
                 dataType: 'text',
@@ -9330,6 +9330,10 @@ class SetMenu {
               html += this.getRadio('mn4_clr', 'mn4_clrIdentity', 'Identity', undefined, undefined, 2);
               html += this.getRadio('mn4_clr', 'mn4_clrConserved', 'Conservation', true, undefined, 2);
             }
+            else {
+              html += this.getRadio('mn4_clr', 'mn4_clrIdentity', 'Identity', undefined, undefined, 2);
+              html += this.getRadio('mn4_clr', 'mn4_clrConserved', 'Conservation', undefined, undefined, 2);
+            }
 
             //if(me.cfg.afid) html += this.getRadio('mn4_clr', 'mn4_clrConfidence', 'AF Confidence');
             //if(!me.cfg.mmtfid && !me.cfg.pdbid && !me.cfg.opmid && !me.cfg.mmdbid && !me.cfg.gi && !me.cfg.uniprotid && !me.cfg.blast_rep_id && !me.cfg.cid && !me.cfg.mmcifid && !me.cfg.align && !me.cfg.chainalign) {
@@ -9404,6 +9408,15 @@ class SetMenu {
 
             html += this.getLink('mn6_hbondsYes', 'Interactions', 1, 1);
 
+            html += this.getMenuText('mn1_window', 'Bring to Front', undefined, undefined, 1);
+            html += "<ul>";
+            html += this.getLink('mn1_window_table', 'Interaction Table', undefined, 2);
+            html += this.getLink('mn1_window_linegraph', '2D Interaction Network', undefined, 2);
+            html += this.getLink('mn1_window_scatterplot', '2D Interaction Map', undefined, 2);
+            html += this.getLink('mn1_window_graph', '2D Graph(Force-Directed)', undefined, 2);
+            html += "</ul>";
+            html += "</li>";
+
             html += this.getLink('mn6_contactmap', 'Contact Map', undefined, 1);
 
             if(!me.cfg.notebook) {
@@ -10514,10 +10527,11 @@ class SetDialog {
 
         html += me.htmlCls.divStr + "dl_customref' class='" + dialogClass + "'>";
         html += '<div style="width:550px;">You can define your own reference numbers in a custom file using Excel, and then export it as a CSV file. An example file is shown below with cells separated by commas.<br>';
-        html += '<pre>refnum,11,12,,21,22<br>';
-        html += '1TUP_A,100,101,,,132<br>';
-        html += '1TUP_B,110,111,,141,142</pre>';
-        html += 'The first row defines the reference residue numbers. The 1st cell could be anything. The rest cells are reference residue numbers (e.g., 11, 12, 21, 22) or empty cells. Each chain has a separate row. The first cell of the second row is the chain ID "1TUP_A". The rest cells are the corresponding real residue numbers for reference residue numbers in the first row. For example, the reference numbers for residues 100, 101, and 132 in the chain 1TUP_A are 11, 12, and 22, respectively. The thrid row shows the real residue numbers for the chain "1TUP_B".<br><br>';
+        html += '<pre>refnum,11,12,,21,22,,10C,11C,20C<br>';
+        html += '1TUP_A,100,101,,,132,,,,<br>';
+        html += '1TUP_B,110,111,,141,142,,,,</pre>';
+        html += '1TUP_C,,,,,,,200,201,230</pre>';
+        html += 'The first row defines the reference residue numbers, which could be any strings. The 1st cell could be anything. The rest cells are reference residue numbers (e.g., 11, 21, 10C, etc.) or empty cells. Each chain has a separate row. The first cell of the second row is the chain ID "1TUP_A". The rest cells are the corresponding real residue numbers for reference residue numbers in the first row. For example, the reference numbers for residues 100, 101, and 132 in the chain 1TUP_A are 11, 12, and 22, respectively. The fourth row shows another set of reference numners for the chain "1TUP_C". It could be a chain from a different structure.<br><br>';
         html += 'To select all residues corresponding to the reference numbers, you can simplay replace ":" with "%" in the <a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#selectb" target="_blank">Specification</a>. For example, "%12"  selects the residue 101 in 1TUP_A and the residue 111 in 1TUP_B. ".A%12" has the chain "A" filter and selects the residue 101 in 1TUP_A.<br>';
         html += '</div><br>';
         html += "Custom File: " + me.htmlCls.inputFileStr + "id='" + me.pre + "cstreffile' size=8> <br><br>";
@@ -15002,7 +15016,7 @@ class SetHtml {
        else if(pos != -1) {
            let url = imageStr.substr(pos + matchedStr.length);
            me.htmlCls.clickMenuCls.setLogCmd('load iCn3D PNG image ' + $("#" + me.pre + "pngimage").val(), false);
-           window.open(url);
+           window.open(url, '_self');
        }
        else if(posState != -1) {
            let matchedStrData = "Start of data file======\n";
@@ -33055,7 +33069,7 @@ class SetColor {
                         let b = atom.b;
 
                         // PDB
-                        b = (atom.structure.length < 6) ? 100 - b : b;
+                        b = (atom.structure.substr(0, 4) != ic.defaultPdbId && atom.structure.length < 6) ? 100 - b : b;
 
                         if(b >= 90) {
                             atom.color = me.parasCls.thr().setRGB(0, 0.325, 0.839);
@@ -33093,7 +33107,7 @@ class SetColor {
                         if(b > 100) b = 100;
 
                         // AlphaFold
-                        b = (atom.structure.length > 5) ? 100 - b : b;
+                        b = (atom.structure.substr(0, 4) != ic.defaultPdbId && atom.structure.length > 5) ? 100 - b : b;
 
                         let s1 = (ic.middB - b) * ic.spanBinv1;
                         let s2 = (b - ic.middB) * ic.spanBinv2;
@@ -34138,7 +34152,7 @@ class AnnoCddSite {
                 for(let s = 0, sl = segArray.length; s < sl; ++s) {
                     let domainFrom = Math.round(segArray[s].from);
                     let domainTo = Math.round(segArray[s].to);
-                    
+
                     // if(ic.bNCBI) {
                     //     fromArray.push(domainFrom);
                     //     toArray.push(domainTo);
@@ -34148,8 +34162,11 @@ class AnnoCddSite {
                     //     toArray.push(thisClass.getAdjustedResi(domainTo, chnid, ic.matchedPos, ic.chainsSeq, ic.baseResi) - 1);
                     // }
 
-                    fromArray.push(ic.ParserUtilsCls.getResi(chnid, domainFrom));
-                    toArray.push(ic.ParserUtilsCls.getResi(chnid, domainTo));
+                    // fromArray.push(ic.ParserUtilsCls.getResi(chnid, domainFrom));
+                    // toArray.push(ic.ParserUtilsCls.getResi(chnid, domainTo));
+
+                    fromArray.push(domainFrom);
+                    toArray.push(domainTo);
 
                     for(let i = domainFrom; i <= domainTo; ++i) {
                         resiHash[i] = 1;
@@ -38859,7 +38876,8 @@ class ShowAnno {
             if(me.cfg.blast_rep_id === undefined) {
                if(ic.bFullUi) {
                     if(me.cfg.mmtfid !== undefined) { // mmtf data do NOT have the missing residues
-                        let id = chainArray[0].substr(0, chainArray[0].indexOf('_'));
+                        //let id = chainArray[0].substr(0, chainArray[0].indexOf('_'));
+                        let id = Object.keys(ic.structures)[0];
 
                         await ic.mmcifParserCls.downloadMmcifSymmetry(id, 'mmtfid');
                     }
@@ -39921,7 +39939,7 @@ class ShowSeq {
 
                     //if(ic.resid2refnum.hasOwnProperty(residueid)) {
                     let refnumLabel = ic.resid2refnum[residueid];
-                    if(refnumLabel) {
+                    if(refnumLabel) {                        
                         let refnumStr_ori = refnumLabel.replace(/'/g, '').substr(1);
                         let refnumStr;
                         if(bCustom) {
@@ -40408,7 +40426,7 @@ class HlSeq {
                                 to = parseInt(toArray[i]);
 
                                 for(let j = from; j <= to; ++j) {
-                                    // if(ic.bNCBI && ($(that).attr('domain') !== undefined || $(that).attr('feat') !== undefined || $(that).attr('3ddomain') !== undefined) ) {
+                                    /*
                                     if( ($(that).attr('domain') !== undefined || $(that).attr('feat') !== undefined || $(that).attr('3ddomain') !== undefined) ) {
                                         let residNCBI = chainid + '_' + (j+1).toString();
                                         // AlphaFold domains calculated on-the-fly have no conversion
@@ -40424,6 +40442,12 @@ class HlSeq {
 
                                         residueid = ic.ncbi2resid[residNCBI];
                                     }
+                                    */
+                                    
+                                    if(($(that).attr('domain') !== undefined || $(that).attr('feat') !== undefined) || $(that).attr('3ddomain') !== undefined) {
+                                        let residNCBI = chainid + '_' + (j+1).toString();
+                                        residueid = ic.ncbi2resid[residNCBI];
+                                    }
                                     else {
                                         residueid = chainid + '_' + (j+1).toString();
                                     }
@@ -40861,7 +40885,7 @@ class HlUpdate {
        // update annotation windows and alignment sequences
        let chainHash = {};
        for(let i = 0, il = residueArray.length; i < il; ++i) {
-           let pickedResidue = residueArray[i];
+           let pickedResidue = residueArray[i].trim();
            //[id$= is expensive to search id ending with
            //var resElem = $("[id$=" + ic.pre + pickedResidue + "]");
            let resElem = $("[id=giseq_" + ic.pre + pickedResidue + "]");
@@ -43981,7 +44005,7 @@ class ContactMap {
 
         let graphStr = '{\n';
 
-        let struc1 = (ic.structures.length > 0) ? ic.structures[0] : 'stru';
+        let struc1 = (ic.structures.length > 0) ? ic.structures[0] : ic.defaultPdbId;
         let len1 = nodeArray1.length,
             len2 = nodeArray2.length;
         let factor = 1;
@@ -44866,7 +44890,7 @@ class ChainalignParser {
             let chainid = chainidArray[i];
             let pos = chainid.indexOf('_');
             let struct = chainid.substr(0, pos); 
-            if(struct != 'stru') struct = struct.toUpperCase();
+            if(struct != ic.defaultPdbId) struct = struct.toUpperCase();
 
             if(!struct2cnt.hasOwnProperty(struct)) {
                 struct2cnt[struct] = 1;
@@ -45663,11 +45687,11 @@ class MmcifParser {
 
         //ic.bCid = undefined;
  
-        let data1 = await me.getAjaxPromise(url, 'text', false, 'The structure " + mmcifid + " was not found...');
+        let data1 = await me.getAjaxPromise(url, 'text', false, "The structure " + mmcifid + " was not found...");
 
         url = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi";
         let dataObj = {'mmcifheader': data1};
-        let data = await me.getAjaxPostPromise(url, dataObj, false, 'The mmCIF data of " + mmcifid + " can not be parsed...');
+        let data = await me.getAjaxPostPromise(url, dataObj, false, "The mmCIF data of " + mmcifid + " can not be parsed...");
 
         if(data.emd !== undefined) ic.emd = data.emd;
         if(data.organism !== undefined) ic.organism = data.organism;
@@ -45727,7 +45751,7 @@ class MmcifParser {
     //loadAtomDataIn. The deferred parameter was resolved after the parsing so that other javascript code can be executed.
     async loadMmcifData(data, mmcifid) { let ic = this.icn3d; ic.icn3dui;
         if(!mmcifid) mmcifid = data.mmcif;
-        if(!mmcifid) mmcifid = 'stru';
+        if(!mmcifid) mmcifid = ic.defaultPdbId;
 
         if(data.atoms !== undefined) {
             ic.init();
@@ -45814,6 +45838,16 @@ class MmdbParser {
         }
     }
 
+        //Ajax call was used to get the atom data from the NCBI "gi". This function was deferred so that
+    //it can be chained together with other deferred functions for sequential execution. Note that
+    //only one structure corresponding to the gi will be shown. If there is no structures available
+    //for the gi, a warning message will be shown.
+    async downloadGi(gi) { let ic = this.icn3d; ic.icn3dui;
+        ic.bCid = undefined;
+        let bGi = true;
+        await this.downloadMmdb(gi, bGi);
+    }
+
     //Ajax call was used to get the atom data from "sequence_id_comma_structure_id", comma-separated
     //NCBI protein accessions of a protein sequence and a chain of a 3D structure (e.g., 23491729,1TUP_A).
     //This function was deferred so that it can be chained together with other deferred functions for
@@ -46814,7 +46848,7 @@ class OpmParser {
 
     async loadOpmData(data, pdbid, bFull, type, pdbid2) { let ic = this.icn3d, me = ic.icn3dui;
         try {
-             if(!pdbid) pdbid = 'stru';
+             if(!pdbid) pdbid = ic.defaultPdbId;
             let url = me.htmlCls.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&opm&uid=" + pdbid.toLowerCase();
     
             let opmdata = await me.getAjaxPromise(url, 'jsonp', false);
@@ -47019,20 +47053,22 @@ class PdbParser {
         if(me.cfg.opmid === undefined) ic.ParserUtilsCls.transformToOpmOri(pdbid);
 
         if(ic.biomtMatrices !== undefined && ic.biomtMatrices.length > 1) {
-          $("#" + ic.pre + "assemblyWrapper").show();
+          if(!me.bNode) $("#" + ic.pre + "assemblyWrapper").show();
 
           ic.asuCnt = ic.biomtMatrices.length;
         }
 
-        if(ic.emd !== undefined) {
-            $("#" + ic.pre + "mapWrapper1").hide();
-            $("#" + ic.pre + "mapWrapper2").hide();
-            $("#" + ic.pre + "mapWrapper3").hide();
-        }
-        else {
-            $("#" + ic.pre + "emmapWrapper1").hide();
-            $("#" + ic.pre + "emmapWrapper2").hide();
-            $("#" + ic.pre + "emmapWrapper3").hide();
+        if(!me.bNode) {
+            if(ic.emd !== undefined) {
+                $("#" + ic.pre + "mapWrapper1").hide();
+                $("#" + ic.pre + "mapWrapper2").hide();
+                $("#" + ic.pre + "mapWrapper3").hide();
+            }
+            else {
+                $("#" + ic.pre + "emmapWrapper1").hide();
+                $("#" + ic.pre + "emmapWrapper2").hide();
+                $("#" + ic.pre + "emmapWrapper3").hide();
+            }
         }
 
         // calculate secondary structures if not available
@@ -47053,7 +47089,7 @@ class PdbParser {
         else {
             await this.loadPdbDataRender(bAppend);
 
-            await ic.ParserUtilsCls.checkMemProteinAndRotate();
+            if(!me.bNode) await ic.ParserUtilsCls.checkMemProteinAndRotate();
 
             /// if(ic.deferredOpm !== undefined) ic.deferredOpm.resolve();
         }
@@ -49701,7 +49737,7 @@ class ParserUtils {
 
       //var dxymax = npoint / 2.0 * step;
 
-      pdbid =(pdbid) ? pdbid.toUpperCase() : 'stru';
+      pdbid =(pdbid) ? pdbid.toUpperCase() : ic.defaultPdbId;
 
       ic.structures[pdbid].push(pdbid + '_MEM');
       ic.chains[pdbid + '_MEM'] = {};
@@ -49943,7 +49979,7 @@ class ParserUtils {
                     let afMemdata = await me.getAjaxPromise(url2, 'text');
 
                     ic.bAfMem = true;
-                    $("#" + me.pre + "togglememli").show(); // show the menu "View > Toggle Membrane"
+                    if(!me.bNode) $("#" + me.pre + "togglememli").show(); // show the menu "View > Toggle Membrane"
 
                     // append the PDB
                     let pdbid = data.pdbid.substr(0, data.pdbid.indexOf('_'));
@@ -52124,13 +52160,12 @@ class LoadPDB {
 
         //let chainMissingResidueArray = {}
 
-        let id = (pdbid) ? pdbid : 'stru';
+        let id = (pdbid) ? pdbid : ic.defaultPdbId;
+        let structure = id;
 
         let prevMissingChain = '';
         let CSerial, prevCSerial, OSerial, prevOSerial;
-
-        let structure = "stru";
-
+        
         let bHeader = false;
 
         for (let i in lines) {
@@ -52145,18 +52180,18 @@ class LoadPDB {
 
                 if(id == '') {
                     if(bAppend) {
-                        id = "stru";
+                        id = ic.defaultPdbId;
                     }
                     else {
-                        //if(!ic.inputid) ic.inputid = 'stru';
-                        id = (ic.inputid && ic.inputid.indexOf('/') == -1) ? ic.inputid.substr(0, 10) : "stru"; //ic.filename.substr(0, 4);
+                        //if(!ic.inputid) ic.inputid = ic.defaultPdbId;
+                        id = (ic.inputid && ic.inputid.indexOf('/') == -1) ? ic.inputid.substr(0, 10) : ic.defaultPdbId; //ic.filename.substr(0, 4);
                     }
                 }
 
                 structure = id;
 
-                if(id == 'stru' || bMutation) { // bMutation: side chain prediction
-                //if(id == 'stru') {
+                if(id == ic.defaultPdbId || bMutation) { // bMutation: side chain prediction
+                //if(id == ic.defaultPdbId) {
                         structure = (moleculeNum === 1) ? id : id + moleculeNum.toString();
                 }
 
@@ -52181,7 +52216,7 @@ class LoadPDB {
 
                   if(j === startResi) helixStart.push(resid);
                   if(j === endResi) helixEnd.push(resid);
-                }               
+                }    
             } else if (record === 'SHEET ') {
                 //ic.bSecondaryStructure = true;
                 if(bOpm === undefined || !bOpm) ic.bSecondaryStructure = true;
@@ -52243,10 +52278,7 @@ class LoadPDB {
                     //let chain = line.substr(19, 1);
                     let chain = line.substr(18, 2).trim();
                     //let resi = parseInt(line.substr(21, 5));
-                    let resi = line.substr(21, 5);
-
-                    //var structure = parseInt(line.substr(13, 1));
-                    //if(line.substr(13, 1) == ' ') structure = 1;
+                    let resi = line.substr(21, 5).trim();
 
                     //var chainNum = structure + '_' + chain;
                     let chainNum = id + '_' + chain;
@@ -52274,12 +52306,12 @@ class LoadPDB {
                 ic.organism = ic.organism.substr(0, ic.organism.length - 1);
             } else if (record === 'ENDMDL') {
                 ++moleculeNum;
-                id = 'stru';
+                id = ic.defaultPdbId;
 
                 structure = id;
                 
-                if(id == 'stru' || bMutation) { // bMutation: side chain prediction
-                //if(id == 'stru') {
+                if(id == ic.defaultPdbId || bMutation) { // bMutation: side chain prediction
+                //if(id == ic.defaultPdbId) {
                         structure = (moleculeNum === 1) ? id : id + moleculeNum.toString();
                 }
 
@@ -52302,8 +52334,8 @@ class LoadPDB {
             } else if (record === 'ATOM  ' || record === 'HETATM') {
                 structure = id;
                 
-                if(id == 'stru' || bMutation) { // bMutation: side chain prediction
-                //if(id == 'stru') {
+                if(id == ic.defaultPdbId || bMutation) { // bMutation: side chain prediction
+                //if(id == ic.defaultPdbId) {
                         structure = (moleculeNum === 1) ? id : id + moleculeNum.toString();
                 }
 
@@ -52718,73 +52750,81 @@ class LoadPDB {
         for(let chainNum in ic.chainsSeq) {
             if(chainMissingResidueArray[chainNum] === undefined) continue;
 
-            //let A = ic.chainsSeq[chainNum];
-            //let B = chainMissingResidueArray[chainNum];
-
-            let A = chainMissingResidueArray[chainNum];
-            let B = ic.chainsSeq[chainNum];
-
-            let m = A.length;
-            let n = B.length;
-
-            let C = new Array(m + n);
-            //var C2 = new Array(m + n);
-            //var C3 = new Array(m + n);
-
-            // http://www.algolist.net/Algorithms/Merge/Sorted_arrays
-            // m - size of A
-            // n - size of B
-            // size of C array must be equal or greater than m + n
-              let i, j, k;
-              i = 0;
-              j = 0;
-              k = 0;
-              while (i < m && j < n) {
-                    if (parseInt(A[i].resi) <= parseInt(B[j].resi)) {
-                          C[k] = A[i];
-                          //C2[k] = A2[i];
-                          //C3[k] = A3[i];
-                          i++;
-                    } else {
-                          C[k] = B[j];
-                          //if(B[j].resi % 10 === 0) {
-                          //    C2[k] = B[j].resi.toString();
-                          //}
-                          //else {
-                          //    C2[k] = '';
-                          //}
-                          //C3[k] = '-';
-                          j++;
+            ic.chainsSeq[chainNum] = this.mergeTwoSequences(chainMissingResidueArray[chainNum], ic.chainsSeq[chainNum]);     
+        }
+
+        this.setResidMapping();
+    }
+
+    mergeTwoSequences(A, B) {
+        let m = A.length; // missing residues
+        let n = B.length; // residues with coord
+
+        // inserted domain such as PRK150 in the R chain of PDB 6WW2
+        let lastResiA = parseInt(A[m - 1].resi);
+        let lastResiB = parseInt(B[n - 1].resi);
+        let lastResi = (lastResiA >= lastResiB) ? lastResiA : lastResiB;
+
+        let C = new Array(m + n);
+        // http://www.algolist.net/Algorithms/Merge/Sorted_arrays
+        // m - size of A
+        // n - size of B
+        // size of C array must be equal or greater than m + n
+          let i = 0, j = 0, k = 0;
+          let bInsertion = false;
+
+          while (i < m && j < n) {
+                let aResi = parseInt(A[i].resi), bResi = parseInt(B[j].resi);
+                if(aResi > lastResi && bResi > lastResi) bInsertion = true;
+
+                if(aResi <= lastResi &&  bResi > lastResi) {
+                    if (aResi > bResi || bInsertion) {
+                        C[k] = B[j];
+                        j++;
                     }
-                    k++;
-              }
-              if (i < m) {
-                    for (let p = i; p < m; p++) {
-                          C[k] = A[p];
-                          //C2[k] = A2[p];
-                          //C3[k] = A3[p];
-                          k++;
+                    else  {
+                        C[k] = A[i];
+                        i++;
                     }
-              } else {
-                    for (let p = j; p < n; p++) {
-                          C[k] = B[p];
-                          //if(B[p].resi % 10 === 0) {
-                          //    C2[k] = B[p].resi.toString();
-                          //}
-                          //else {
-                          //    C2[k] = '';
-                          //}
-                          //C3[k] = '-';
-                          k++;
+                }
+                else if(aResi > lastResi &&  bResi <= lastResi) {
+                    if (aResi <= bResi || bInsertion) {
+                        C[k] = A[i];
+                        i++;
                     }
-              }
+                    else  {
+                        C[k] = B[j];
+                        j++;
+                    }
+                }
+                else {
+                    if (aResi <= bResi) {
+                        C[k] = A[i];
+                        i++;
+                    }
+                    else {
+                        C[k] = B[j];
+                        j++;
+                    }
+                }
 
-            ic.chainsSeq[chainNum] = C;
-            //ic.chainsAn[chainNum][0] = C2;
-            //ic.chainsAn[chainNum][1] = C3;
-        }
+                k++;
+          }
 
-        this.setResidMapping();
+          if (i < m) {
+                for (let p = i; p < m; p++) {
+                      C[k] = A[p];
+                      k++;
+                }
+          } 
+          else {
+                for (let p = j; p < n; p++) {
+                      C[k] = B[p];
+                      k++;
+                }
+          }
+
+          return C;
     }
 
     setResidMapping() { let ic = this.icn3d; ic.icn3dui;
@@ -54940,21 +54980,23 @@ class ApplyCommand {
       else if(command.indexOf('window') == 0) {
         let secondPart = command.substr(command.indexOf(' ') + 1);
 
-        if(secondPart == "aligned sequences") {
+        setTimeout(function(){
+          if(secondPart == "aligned sequences") {
             me.htmlCls.dialogCls.openDlg('dl_alignment', 'Select residues in aligned sequences');
-        }
-        else if(secondPart == "interaction table") {
-            me.htmlCls.dialogCls.openDlg('dl_allinteraction', 'Show interactions');
-        }
-        else if(secondPart == "interaction graph") {
-            me.htmlCls.dialogCls.openDlg('dl_linegraph', 'Show interactions between two lines of residue nodes');
-        }
-        else if(secondPart == "interaction scatterplot") {
-            me.htmlCls.dialogCls.openDlg('dl_scatterplot', 'Show interactions as scatterplot');
-        }
-        else if(secondPart == "force-directed graph") {
-            me.htmlCls.dialogCls.openDlg('dl_graph', 'Force-directed graph');
-        }
+          }
+          else if(secondPart == "interaction table") {
+              me.htmlCls.dialogCls.openDlg('dl_allinteraction', 'Show interactions');
+          }
+          else if(secondPart == "interaction graph") {
+              me.htmlCls.dialogCls.openDlg('dl_linegraph', 'Show interactions between two lines of residue nodes');
+          }
+          else if(secondPart == "interaction scatterplot") {
+              me.htmlCls.dialogCls.openDlg('dl_scatterplot', 'Show interactions as scatterplot');
+          }
+          else if(secondPart == "force-directed graph") {
+              me.htmlCls.dialogCls.openDlg('dl_graph', 'Force-directed graph');
+          }
+        }, 1000);
       }
       else if(command.indexOf('set theme') == 0) {
         let color = command.substr(command.lastIndexOf(' ') + 1);
@@ -56582,6 +56624,10 @@ class LoadScript {
 
             await ic.chainalignParserCls.downloadMmdbAf(id);
         }
+        else if(command.indexOf('load gi') !== -1) {
+            me.cfg.gi = id;
+            await ic.mmdbParserCls.downloadGi(id);
+        }
         else if(command.indexOf('load refseq') !== -1) {
             me.cfg.refseqid = id;
             await ic.mmdbParserCls.downloadRefseq(id);
@@ -59316,7 +59362,7 @@ class Dssp {
     async showIgRefNum() { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
-        if(Object.keys(ic.resid2refnum).length > 0) {
+        if(ic.resid2refnum  && Object.keys(ic.resid2refnum).length > 0) {
             ic.bShowRefnum = true;
 
             // open sequence view
@@ -59363,16 +59409,17 @@ class Dssp {
         let ajaxArray = [];
         let domainidpairArray = [];
 
-        me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
+        let urltmalign = me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
 
         ic.resid2domainid = {};
 
         for(let i = 0, il = struArray.length; i < il; ++i) {
             let struct = struArray[i];
             let chainidArray = ic.structures[struct];
- 
+
             for(let j = 0, jl = chainidArray.length; j < jl; ++j) {
                 let chainid = chainidArray[j];
+
                 if(!ic.proteins.hasOwnProperty(ic.firstAtomObjCls.getFirstAtomObj(ic.chains[chainid]).serial)) continue;
                 if(ic.chainsSeq[chainid].length < 50) continue; // peptide
 
@@ -59407,20 +59454,19 @@ class Dssp {
                         domainAtomsArray.push(domainAtoms);
                     }
                 }
-                
+       
                 for(let k = 0, kl = domainAtomsArray.length; k < kl; ++k) {
+
                     let pdb_target = ic.saveFileCls.getAtomPDB(domainAtomsArray[k], undefined, undefined, undefined, undefined, struct);
                     let domainid = chainid + '-' + k;
                     for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
-                        let struct2 = "stru" + index;
+                        let struct2 = ic.defaultPdbId + index;
                         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(url, dataObj);
-
+                        let alignAjax = me.getAjaxPostPromise(urltmalign, dataObj);
                         ajaxArray.push(alignAjax);
                         
                         domainidpairArray.push(domainid + "," + index);
@@ -59431,18 +59477,19 @@ class Dssp {
 
         let allPromise = Promise.allSettled(ajaxArray);
         try {
-            let dataArray = await allPromise;
-            await thisClass.parseAlignData(dataArray, domainidpairArray);
+            let dataArray2 = await allPromise;
+            
+            await thisClass.parseAlignData(dataArray2, domainidpairArray);
 
             /// if(ic.deferredRefnum !== undefined) ic.deferredRefnum.resolve();
         }
         catch(err) {
-            console.log("Error in aligning with TM-align...");
+            if(!me.bNode) console.log("Error in aligning with TM-align...");
             return;
         }         
     }
 
-    async parseAlignData(dataArray, domainidpairArray) { let ic = this.icn3d; ic.icn3dui;
+    async parseAlignData(dataArray, domainidpairArray) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
         let tmscoreThreshold = 0.4; //0.5;
@@ -59451,9 +59498,12 @@ class Dssp {
         let domainid2score = {}, domainid2segs = {}, chainid2segs = {};
         ic.chainid2index = {};
         ic.domainid2ig2kabat = {};
+
         for(let i = 0, il = domainidpairArray.length; i < il; ++i) {
             let queryData = dataArray[i].value; //[0];
+         
             if(queryData.length == 0) continue;
+
             if(queryData[0].score < tmscoreThreshold || queryData[0].num_res < 50) continue;
 
             let domainid_index = domainidpairArray[i].split(',');
@@ -59465,6 +59515,7 @@ class Dssp {
             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('2050') != -1) {
                     bBstrand = true;
                 }
@@ -59484,12 +59535,13 @@ class Dssp {
                 //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)) continue;
 
             if(!domainid2score.hasOwnProperty(domainid) || queryData[0].score > domainid2score[domainid]) {
                 domainid2score[domainid] = queryData[0].score;
-console.log(domainid + ' TM-score: ' + domainid2score[domainid] + ' matched ' + ic.refpdbArray[domainid_index[1]]);                
+if(!me.bNode) console.log(domainid + ' TM-score: ' + domainid2score[domainid] + ' matched ' + ic.refpdbArray[domainid_index[1]]);                
                 ic.chainid2index[chainid] = domainid_index[1]; // could be several, just take the recent one for simplicity
                 domainid2segs[domainid] = queryData[0].segs;
                 ic.domainid2ig2kabat[domainid] = queryData[0].ig2kabat;
@@ -59509,7 +59561,7 @@ console.log(domainid + ' TM-score: ' + domainid2score[domainid] + ' matched ' +
         if(!ic.chainsMapping) ic.chainsMapping = {};
         for(let chainid in chainid2segs) {
             let segArray = chainid2segs[chainid];
-console.log("One of the reference PDBs for chain chainid: " + ic.refpdbArray[ic.chainid2index[chainid]]);
+if(!me.bNode) console.log("One of the reference PDBs for chain chainid: " + ic.refpdbArray[ic.chainid2index[chainid]]);
 
             for(let i = 0, il = segArray.length; i < il; ++i) {
                 let seg = segArray[i];
@@ -64161,13 +64213,23 @@ class SaveFile {
     setStructureTitle(url, title, titlelinkColor) {var ic = this.icn3d, me = ic.icn3dui;
         if(ic.molTitle.length > 40) title = ic.molTitle.substr(0, 40) + "...";
 
-        //var asymmetricStr =(ic.bAssemblyUseAsu) ? "(Asymmetric Unit)" : "";
-        let asymmetricStr = "";
+        let text = ic.inputid.toUpperCase();
 
         let idName = (isNaN(ic.inputid) && ic.inputid.length > 5) ? "AlphaFold ID" : "PDB ID";
+        if(ic.inputid.indexOf('http') != -1) {
+            idName = "Data from";
+            url = ic.inputid;
+            text = ic.inputid;
+        }
+
         if(me.cfg.refseqid) idName = 'NCBI Protein Acc.';
 
-        $("#" + ic.pre + "title").html(idName + " <a id='" + ic.pre + "titlelink' href='" + url + "' style='color:" + titlelinkColor + "' target='_blank'>" + ic.inputid.toUpperCase() + "</a>" + asymmetricStr + ": " + title);
+        if(!ic.inputid || ic.inputid.substr(0, 4) == ic.defaultPdbId) {
+            $("#" + ic.pre + "title").html(title);
+        }
+        else {
+            $("#" + ic.pre + "title").html(idName + " <a id='" + ic.pre + "titlelink' href='" + url + "' style='color:" + titlelinkColor + "' target='_blank'>" + text + "</a>: " + title);
+        }
     }
 
     getLinkToStructureSummary(bLog) {var ic = this.icn3d, me = ic.icn3dui;
@@ -64253,7 +64315,7 @@ class ShareLink {
         if(bPngHtml) url += "&random=" + parseInt(Math.random() * 1000); // generate a new shorten URL and thus image name everytime
         //var inputid =(ic.inputid) ? ic.inputid : "custom";
         let inputid = Object.keys(ic.structures).join('_');
-        if(inputid == 'stru') {
+        if(inputid == ic.defaultPdbId) {
             if(ic.filename) {
                 inputid = ic.filename;
             }
@@ -66805,6 +66867,7 @@ class iCn3D {
     this.transparentRenderOrder = false; // false: regular transparency; true: expensive renderOrder for each face
 
     this.AFUniprotVersion = 'v4';
+    this.defaultPdbId = 'stru';
 
     if(!this.icn3dui.bNode) {
         if ( bWebGL2 && bVR) { 
@@ -67388,7 +67451,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.21.0';
+    this.REVISION = '3.21.3';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -67665,6 +67728,12 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
        me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
        await ic.mmdbParserCls.downloadMmdb(me.cfg.mmdbid);
     }
+    else if(me.cfg.gi !== undefined) {
+        // ic.bNCBI = true;
+        ic.loadCmd = 'load gi ' + me.cfg.gi;
+        me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
+        await ic.mmdbParserCls.downloadGi(me.cfg.gi);
+    }
     else if(me.cfg.refseqid !== undefined) {
         ic.inputid = me.cfg.refseqid;
         
@@ -67853,7 +67922,7 @@ iCn3DUI.prototype.getAjaxPromise = function(url, dataType, beforeSend, alertMess
                 if(beforeSend) me.icn3d.ParserUtilsCls.showLoading();
             },
             complete: function() {
-                if(complete) ic.ParserUtilsCls.hideLoading();
+                if(complete) me.icn3d.ParserUtilsCls.hideLoading();
             },
             success: function(data) {
                 resolve(data);
@@ -67882,7 +67951,7 @@ iCn3DUI.prototype.getAjaxPostPromise = function(url, data, beforeSend, alertMess
                 if(beforeSend) me.icn3d.ParserUtilsCls.showLoading();
             },
             complete: function() {
-                if(complete) ic.ParserUtilsCls.hideLoading();
+                if(complete) me.icn3d.ParserUtilsCls.hideLoading();
             },
             success: function(data) {
                 resolve(data);