icn3d 3.21.2 → 3.22.0

package/icn3d.js

@@ -5986,11 +5986,23 @@ class ClickMenu {
            thisClass.setLogCmd("export pqr", true);
         });
 
-        me.myEventCls.onIds(["#" + me.pre + "delphipdbh", "#" + me.pre + "phipqr", "#" + me.pre + "phiurlpqr"], "click", async function(e) { me.icn3d; //e.preventDefault();
-            let bPdb = true;
-            await me.htmlCls.setHtmlCls.exportPqr(bPdb);
-            thisClass.setLogCmd("export pdbh", false);
-         });
+      //   me.myEventCls.onIds("#" + me.pre + "delphipqbh", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
+      //       let bPdb = true;
+      //       await me.htmlCls.setHtmlCls.exportPqr(bPdb);
+      //       thisClass.setLogCmd("export pdbh", false);
+      //    });
+
+        me.myEventCls.onIds("#" + me.pre + "profixpdb", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
+         let bHydrogen = false;
+         await ic.scapCls.exportPdbProfix(bHydrogen);
+         thisClass.setLogCmd("export pdb missing atoms", true);
+        });
+
+        me.myEventCls.onIds("#" + me.pre + "profixpdbh", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
+        let bHydrogen = true;
+        await ic.scapCls.exportPdbProfix(bHydrogen);
+        thisClass.setLogCmd("export pdb hydrogen", true);
+       });
 
         me.myEventCls.onIds("#" + me.pre + "mn1_exportStl", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
            thisClass.setLogCmd("export stl file", false);
@@ -7778,7 +7790,7 @@ 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',
@@ -8498,7 +8510,8 @@ class SetMenu {
         html += this.getLink('mn1_exportCounts', 'Residue Counts', undefined, 2);
 
         html += this.getLink('mn1_exportPdbRes', 'PDB', 1, 2);
-        html += this.getLink('delphipdbh', 'PDB with Hydrogens', undefined, 2);
+        html += this.getLink('profixpdb', 'PDB with Missing Atoms', undefined, 2);
+        html += this.getLink('profixpdbh', 'PDB with Hydrogens', undefined, 2);
 
         if(me.cfg.cid === undefined) {
             html += this.getLink('mn1_exportSecondary', 'Secondary Structure', undefined, 2);
@@ -9330,6 +9343,10 @@ 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 +9421,15 @@ 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 +10540,11 @@ 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>";
@@ -10893,11 +10920,14 @@ class SetDialog {
 
         html += me.htmlCls.divStr + "dl_realignbystruct' class='" + dialogClass + "'>";
 
-        html += me.htmlCls.divNowrapStr + "1. Select sets in two chains below <br>or use your current selection:</div><br>";
+        html += me.htmlCls.divNowrapStr + "<b>1</b>. Select sets in two chains below <br>or use your current selection:</div><br>";
         html += "<div style='text-indent:1.1em'><select id='" + me.pre + "atomsCustomRealignByStruct' multiple size='5' style='min-width:130px;'>";
         html += "</select></div><br>";
 
-        html += "<div>2. " + me.htmlCls.buttonStr + "applyRealignByStruct_tmalign'>Realign with TM-align</button>" + me.htmlCls.buttonStr + "applyRealignByStruct' style='margin-left:30px'>Realign with VAST</button></div><br>";
+        html += "<div><b>2a</b>. <div style='display:inline-block; width:80px'>MSA:</div> " + me.htmlCls.buttonStr + "applyRealignByStructMsa_tmalign'>Realign with TM-align</button>" + me.htmlCls.buttonStr + "applyRealignByStructMsa' style='margin-left:30px'>Realign with VAST</button></div><br>";
+
+        html += "<div>or <b>2b</b>. <div style='display:inline-block; width:65px'>Pairwise:</div> " + me.htmlCls.buttonStr + "applyRealignByStruct_tmalign'>Realign with TM-align</button>" + me.htmlCls.buttonStr + "applyRealignByStruct' style='margin-left:30px'>Realign with VAST</button></div><br>";
+
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_realigntwostru' class='" + dialogClass + "'>";
@@ -11570,6 +11600,32 @@ class Events {
        thisClass.setLogCmd('select ' + select + ' | name ' + commandname, true);
     }
 
+    async setRealign(alignType, bMsa) { let me = this.icn3dui, ic = me.icn3d, thisClass = this;
+        let nameArray = $("#" + me.pre + "atomsCustomRealignByStruct").val();
+        if(nameArray.length > 0) {
+            ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
+        }
+
+        me.cfg.aligntool = alignType;
+
+        if(bMsa) {
+            await ic.realignParserCls.realignOnStructAlignMsa(nameArray);
+        }
+        else {
+            await ic.realignParserCls.realignOnStructAlign();
+        }
+
+        let alignStr = (alignType == 'vast') ? 'structure align' : 'tmalign';
+        alignStr += (bMsa) ? ' msa' : '';
+
+        if(nameArray.length > 0) {
+            thisClass.setLogCmd("realign on " + alignStr + " | " + nameArray, true);
+        }
+        else {
+            thisClass.setLogCmd("realign on " + alignStr, true);
+        }
+    }
+
     readFile(bAppend, files, index, dataStrAll) { let me = this.icn3dui, ic = me.icn3d, thisClass = this;
         let file = files[index];
         let commandName = (bAppend) ? 'append': 'load';
@@ -11880,42 +11936,32 @@ class Events {
            }
         });
 
-        me.myEventCls.onIds("#" + me.pre + "applyRealignByStruct", "click", async function(e) { let ic = me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "applyRealignByStruct", "click", async function(e) { me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
-            let nameArray = $("#" + me.pre + "atomsCustomRealignByStruct").val();
-            if(nameArray.length > 0) {
-                ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
-            }
- 
-            me.cfg.aligntool = 'vast';
- 
-            await ic.realignParserCls.realignOnStructAlign();
-            if(nameArray.length > 0) {
-                thisClass.setLogCmd("realign on structure align | " + nameArray, true);
-            }
-            else {
-                thisClass.setLogCmd("realign on structure align", true);
-            }
+
+            await thisClass.setRealign('vast', false);
          });
 
-         me.myEventCls.onIds("#" + me.pre + "applyRealignByStruct_tmalign", "click", async function(e) { let ic = me.icn3d;
+         me.myEventCls.onIds("#" + me.pre + "applyRealignByStruct_tmalign", "click", async function(e) { me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
-            let nameArray = $("#" + me.pre + "atomsCustomRealignByStruct").val();
-            if(nameArray.length > 0) {
-                ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
-            }
 
-            me.cfg.aligntool = 'tmalign';
- 
-            await ic.realignParserCls.realignOnStructAlign();
-            if(nameArray.length > 0) {
-                thisClass.setLogCmd("realign on tmalign | " + nameArray, true);
-            }
-            else {
-                thisClass.setLogCmd("realign on tmalign", true);
-            }
+            await thisClass.setRealign('tmalign', false);
+         });
+
+         me.myEventCls.onIds("#" + me.pre + "applyRealignByStructMsa", "click", async function(e) { me.icn3d;
+            e.preventDefault();
+            if(!me.cfg.notebook) dialog.dialog( "close" );
+
+            await thisClass.setRealign('vast', true);
+         });
+
+         me.myEventCls.onIds("#" + me.pre + "applyRealignByStructMsa_tmalign", "click", async function(e) { me.icn3d;
+            e.preventDefault();
+            if(!me.cfg.notebook) dialog.dialog( "close" );
+
+            await thisClass.setRealign('tmalign', true);
          });
 
          me.myEventCls.onIds("#" + me.pre + "applyRealignByStruct_vastplus", "click", async function(e) { let ic = me.icn3d;
@@ -15002,7 +15048,7 @@ 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 +33101,7 @@ 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 +33139,7 @@ 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;
@@ -34000,7 +34046,7 @@ class AnnoCddSite {
     
                     let linkStr = (bCoordinates) ? 'icn3d-link icn3d-blue' : '';
 
-                    let htmlTmp2 = '<div class="icn3d-seqTitle ' + linkStr + '" site="site" posarray="' + adjustedResPosArray.toString() + '" shorttitle="' + title + '" setname="' + chnid + '_site_' + index + '" anno="sequence" chain="' + chnid + '" title="' + fulltitle + '">' + title + ' </div>';
+                    let htmlTmp2 = '<div class="icn3d-seqTitle ' + linkStr + '" site="site" posarray="' + resPosArray.toString() + '" shorttitle="' + title + '" setname="' + chnid + '_site_' + index + '" anno="sequence" chain="' + chnid + '" title="' + fulltitle + '">' + title + ' </div>';
                     let htmlTmp3 = '<span class="icn3d-residueNum" title="residue count">' + resCnt.toString() + ' Res</span>';
                     let htmlTmp = '<span class="icn3d-seqLine">';
                     html3 += htmlTmp2 + htmlTmp3 + '<br>';
@@ -34172,8 +34218,9 @@ class AnnoCddSite {
                     let from = parseInt(fromArray[i]), to = parseInt(toArray[i]);
                                        
                     for(let j = from; j <= to; ++j) {
-                        
-                        let resid = chnid + "_" + j;
+                        let resi = ic.ParserUtilsCls.getResi(chnid, j);
+                        //let resid = chnid + "_" + j;
+                        let resid = chnid + "_" + resi;
                         
                         if(ic.residues.hasOwnProperty(resid)) {
                             bCoordinates = true;
@@ -39925,7 +39972,7 @@ 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) {
@@ -41100,7 +41147,9 @@ class LineGraph {
         nodeArray2 = nodeArrays.nodeArray2;
         ic.lineGraphStr = '{\n';
 
-        let structureArray = ic.resid2specCls.atoms2structureArray(ic.hAtoms);
+        //let structureArray = ic.resid2specCls.atoms2structureArray(ic.hAtoms);
+        let structureArray = Object.keys(ic.structures);
+
         //if(Object.keys(ic.structures).length > 1) {
         if(structureArray.length > 1) {
 
@@ -41868,6 +41917,7 @@ class GetGraph {
 
     updateGraphColor() { let ic = this.icn3d, me = ic.icn3dui;
       // change graph color
+
       if(ic.graphStr !== undefined) {
           let graphJson = JSON.parse(ic.graphStr);
           let resid2color = {};
@@ -43991,7 +44041,7 @@ 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;
@@ -44531,7 +44581,8 @@ class ChainalignParser {
         }
     }
 
-    async downloadChainalignmentPart2b(chainresiCalphaHash2, chainidArray, hAtoms, dataArray, indexArray, mmdbid_t, struArray) { let ic = this.icn3d, me = ic.icn3dui;
+    async downloadChainalignmentPart2b(chainresiCalphaHash2, chainidArray, hAtoms, dataArray, 
+        indexArray, mmdbid_t, struArray) { let ic = this.icn3d, me = ic.icn3dui;
         //let bTargetTransformed = (ic.qt_start_end[0]) ? true : false;
 
         // modify the previous trans and rotation matrix
@@ -44876,7 +44927,7 @@ 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;
@@ -45062,11 +45113,16 @@ class ChainalignParser {
                 if(ic.afChainIndexHash.hasOwnProperty(index)) {
                     ++missedChainCnt;
 
-                    // need to pass C-alpha coords and get transformation matrix from backend
-                    ic.t_trans_add[index-1] = {"x":0, "y":0, "z":0};
-                    ic.q_trans_sub[index-1] = {"x":0, "y":0, "z":0};
+                    
 
-                    if(me.cfg.aligntool == 'tmalign') ic.q_trans_add[index-1] = {"x":0, "y":0, "z":0};
+                    if(me.cfg.aligntool == 'tmalign') {
+                        ic.q_trans_add[index-1] = {"x":0, "y":0, "z":0};
+                    }
+                    else {
+                        // need to pass C-alpha coords and get transformation matrix from backend
+                        ic.t_trans_add[index-1] = {"x":0, "y":0, "z":0};
+                        ic.q_trans_sub[index-1] = {"x":0, "y":0, "z":0};
+                    }
 
                     ic.q_rotation[index-1] = {"x1":1, "y1":0, "z1":0, "x2":0, "y2":1, "z2":0, "x3":0, "y3":0, "z3":1};
                     ic.qt_start_end[index-1] = undefined;
@@ -45123,10 +45179,14 @@ class ChainalignParser {
                 ic.q_rotation.push(align[0].q_rotation);
                 ic.qt_start_end.push(align[0].segs);
                 */
-                ic.t_trans_add[index] = align[0].t_trans_add;
-                ic.q_trans_sub[index] = align[0].q_trans_sub;
 
-                if(me.cfg.aligntool == 'tmalign') ic.q_trans_add[index] = align[0].q_trans_add;
+                if(me.cfg.aligntool == 'tmalign') {
+                    ic.q_trans_add[index] = align[0].q_trans_add;
+                }
+                else {
+                    ic.t_trans_add[index] = align[0].t_trans_add;
+                    ic.q_trans_sub[index] = align[0].q_trans_sub;
+                }
 
                 ic.q_rotation[index] = align[0].q_rotation;
                 ic.qt_start_end[index] = align[0].segs;
@@ -45673,11 +45733,11 @@ 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;
@@ -45737,7 +45797,7 @@ 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();
@@ -46834,7 +46894,7 @@ 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);
@@ -47039,20 +47099,22 @@ 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
@@ -47073,7 +47135,7 @@ 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();
         }
@@ -47895,6 +47957,8 @@ class RealignParser {
         let ajaxArray = [], chainidPairArray = [];
         let urlalign = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi";
         let urltmalign = me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
+
+        //let cnt = 0;
         let structArray = Object.keys(struct2domain);
         for(let s = 0, sl = structArray.length; s < sl; ++s) {
             let struct1 = structArray[s];
@@ -47907,13 +47971,13 @@ class RealignParser {
 
                 for(let i = 0, il = chainidArray1.length; i < il; ++i) {
                     let chainid1 = chainidArray1[i];
+                    let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(struct2domain[struct1][chainid1]);
                     for(let j = 0, jl = chainidArray2.length; j < jl; ++j) {
                         let chainid2 = chainidArray2[j];
 
                         let alignAjax;
 
                         if(me.cfg.aligntool != 'tmalign') {
-                            let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(struct2domain[struct1][chainid1]);
                             let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(struct2domain[struct2][chainid2]);
                         
                             let dataObj = {'domains1': jsonStr_q, 'domains2': jsonStr_t};
@@ -47931,7 +47995,8 @@ class RealignParser {
                         }
 
                         ajaxArray.push(alignAjax);
-                        chainidPairArray.push(chainid1 + ',' + chainid2); // chainid2 is target
+                        chainidPairArray.push(chainid1 + ',' + chainid2); 
+                        //++cnt;
                     }
                 }
             }
@@ -47948,6 +48013,87 @@ 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 chainid2domain = {};
+
+        for(let i = 0, il = nameArray.length; i < il; ++i) {
+            let chainid = nameArray[i];
+            let atoms = me.hashUtilsCls.intHash(ic.hAtoms, ic.chains[chainid]);               
+            let sseCnt = 0;
+            for(let serial in atoms) {
+                if(ic.atoms[serial].ssbegin) ++sseCnt;
+                if(sseCnt == minSseCnt) {
+                    chainid2domain[chainid] = atoms;
+                    break;
+                }
+            }
+        }
+
+        let ajaxArray = [], indexArray = [], struArray = [];
+        let urlalign = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi";
+        let urltmalign = me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
+
+        let chainid1 = nameArray[0];
+        let struct1 = chainid1.substr(0, chainid1.indexOf('_'));
+        let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(chainid2domain[chainid1]);
+
+        for(let i = 1, il = nameArray.length; i < il; ++i) {
+            let chainid2 = nameArray[i];
+            let struct2 = chainid2.substr(0, chainid2.indexOf('_'));
+
+            let alignAjax;
+
+            if(me.cfg.aligntool != 'tmalign') {
+                let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(chainid2domain[chainid2]);
+            
+                let dataObj = {'domains1': jsonStr_q, 'domains2': jsonStr_t};
+                alignAjax = me.getAjaxPostPromise(urlalign, dataObj);
+            }
+            else {
+                // let pdb_target = ic.saveFileCls.getAtomPDB(chainid2domain[chainid1], undefined, undefined, undefined, undefined, struct1);
+                // let pdb_query = ic.saveFileCls.getAtomPDB(chainid2domain[chainid2], undefined, undefined, undefined, undefined, struct2);
+
+                let pdb_target = ic.saveFileCls.getAtomPDB(ic.chains[chainid1], undefined, undefined, undefined, undefined, struct1);
+                let pdb_query = ic.saveFileCls.getAtomPDB(ic.chains[chainid2], undefined, undefined, undefined, undefined, struct2);
+
+                let dataObj = {'pdb_query': pdb_query, 'pdb_target': pdb_target};
+                alignAjax = me.getAjaxPostPromise(urltmalign, dataObj);                    
+            }
+
+            ajaxArray.push(alignAjax);
+            //chainidPairArray.push(chainid1 + ',' + chainid2); 
+
+            indexArray.push(i - 1);
+            struArray.push(struct2);
+
+            //++cnt;
+        }
+
+        let allPromise = Promise.allSettled(ajaxArray);
+        //try {
+            let dataArray = await allPromise;
+            //ic.qt_start_end = []; // reset the alignment
+            //await ic.chainalignParserCls.downloadChainalignmentPart2bRealignMsa(dataArray, chainidPairArray); 
+
+            // set trans and rotation matrix
+            ic.t_trans_add = [];
+            ic.q_trans_sub = [];
+
+            if(me.cfg.aligntool == 'tmalign') ic.q_trans_add = [];
+
+            ic.q_rotation = [];
+            ic.qt_start_end = [];
+
+            await ic.chainalignParserCls.downloadChainalignmentPart2b(undefined, nameArray, undefined, dataArray, 
+                indexArray, struct1, struArray);
+        // }
+        // catch(err) {
+        //     if(ic.bRender) var aaa = 1; //alert("These structures can NOT be aligned to each other...");
+        // }                   
+    }
+
     async realignChainOnSeqAlign(chainresiCalphaHash2, chainidArray, bRealign, bPredefined) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
@@ -49721,7 +49867,7 @@ 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'] = {};
@@ -49963,7 +50109,7 @@ 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('_'));
@@ -52144,7 +52290,7 @@ class LoadPDB {
 
         //let chainMissingResidueArray = {}
 
-        let id = (pdbid) ? pdbid : 'stru';
+        let id = (pdbid) ? pdbid : ic.defaultPdbId;
         let structure = id;
 
         let prevMissingChain = '';
@@ -52164,18 +52310,18 @@ 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();
                 }
 
@@ -52290,12 +52436,12 @@ 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();
                 }
 
@@ -52318,8 +52464,8 @@ 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();
                 }
 
@@ -53791,6 +53937,12 @@ class ApplyCommand {
       else if(command == 'export pdb') {
          me.htmlCls.setHtmlCls.exportPdb();
       }
+      else if(command == 'export pdb missing atoms') {
+        await ic.scapCls.exportPdbProfix(false);
+      }
+      else if(command == 'export pdb hydrogen') {
+        await ic.scapCls.exportPdbProfix(true);
+      }
       else if(command == 'export secondary structure') {
          me.htmlCls.setHtmlCls.exportSecondary();
       }
@@ -54964,21 +55116,23 @@ 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);
@@ -56179,6 +56333,17 @@ class LoadScript {
         await this.execCommandsBase(start, end, steps);
     }
 
+    getNameArray(command) { let ic = this.icn3d; ic.icn3dui;
+        let paraArray = command.split(' | ');
+        let nameArray = [];
+        if(paraArray.length == 2) {
+            nameArray = paraArray[1].split(',');
+            ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
+        }
+
+        return nameArray;
+    }
+
     async execCommandsBase(start, end, steps, bFinalStep) { let ic = this.icn3d, me = ic.icn3dui;
       let thisClass = this;
       let i;
@@ -56320,31 +56485,37 @@ class LoadScript {
             await ic.scapCls.applyCommandScap(command);
           }
           else if(command.indexOf('realign on seq align') == 0) {
-            let paraArray = command.split(' | ');
-            if(paraArray.length == 2) {
-                let nameArray = paraArray[1].split(',');
-                ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
-            }
+            this.getNameArray(command);
 
             await thisClass.applyCommandRealign(command);
           }
+          else if(command.indexOf('realign on structure align msa') == 0) {
+            let nameArray = this.getNameArray(command);
+
+            me.cfg.aligntool = 'vast';
+
+            await ic.realignParserCls.realignOnStructAlignMsa(nameArray);
+          }
           else if(command.indexOf('realign on structure align') == 0) {
-            let paraArray = command.split(' | ');
-            if(paraArray.length == 2) {
-                let nameArray = paraArray[1].split(',');
-                ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
-            }
+            this.getNameArray(command);
 
             me.cfg.aligntool = 'vast';
 
-            await thisClass.applyCommandRealignByStruct(command);
+            await ic.realignParserCls.realignOnStructAlign();
+          }
+          else if(command.indexOf('realign on tmalign msa') == 0) {
+            let nameArray = this.getNameArray(command);
+
+            me.cfg.aligntool = 'tmalign';
+
+            await ic.realignParserCls.realignOnStructAlignMsa(nameArray);
           }
           else if(command.indexOf('realign on tmalign') == 0) {
-            thisClass.getHAtoms(ic.commands[i]);
+            this.getNameArray(command);
 
             me.cfg.aligntool = 'tmalign';
 
-            await thisClass.applyCommandRealignByStruct(ic.commands[i]);
+            await ic.realignParserCls.realignOnStructAlign();
           }
           else if(command.indexOf('realign on vastplus') == 0) {
             thisClass.getHAtoms(ic.commands[i]);
@@ -59344,7 +59515,7 @@ 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
@@ -59391,16 +59562,17 @@ 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
 
@@ -59435,20 +59607,19 @@ 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);
@@ -59459,18 +59630,19 @@ 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;
@@ -59479,9 +59651,12 @@ 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(',');
@@ -59493,6 +59668,7 @@ 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;
                 }
@@ -59512,12 +59688,13 @@ 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;
@@ -59537,7 +59714,7 @@ 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];
@@ -59807,11 +59984,12 @@ console.log("free energy: " + energy + " kcal/mol");
 
           // get the full mutatnt PDB
           let pdbDataMutant = ic.saveFileCls.getAtomPDB(ic.atoms, false, false, false, chainResi2pdb);
+
           ic.hAtoms = {};
           let bMutation = true;
           ic.loadPDBCls.loadPDB(pdbDataMutant, pdbid, false, false, bMutation, bAddition);
           //let allAtoms2 = me.hashUtilsCls.cloneHash(ic.hAtoms);
-          
+
           ic.setStyleCls.setAtomStyleByOptions(ic.opts);
           ic.setColorCls.setColorByOptions(ic.opts, ic.hAtoms);
 
@@ -59866,11 +60044,10 @@ console.log("free energy: " + energy + " kcal/mol");
           }
 
           if(bPdb) {
-              //let pdbStr = '';
-              //pdbStr += ic.saveFileCls.getAtomPDB(ic.hAtoms);
+              // let file_pref =(ic.inputid) ? ic.inputid : "custom";
+              // ic.saveFileCls.saveFile(file_pref + '_' + snpStr + '.pdb', 'text', [pdbDataMutant]);
 
-              let file_pref =(ic.inputid) ? ic.inputid : "custom";
-              ic.saveFileCls.saveFile(file_pref + '_' + snpStr + '.pdb', 'text', [pdbDataMutant]);
+              await thisClass.exportPdbProfix(false, pdbDataMutant, snpStr); 
 
               ic.drawCls.draw();
           }
@@ -59921,7 +60098,40 @@ console.log("free energy: " + energy + " kcal/mol");
 
             /// if(ic.deferredScap !== undefined) ic.deferredScap.resolve();
             return;
-        }    }
+        }
+    }
+
+    async exportPdbProfix(bHydrogen, pdb, snpStr) { let ic = this.icn3d, me = ic.icn3dui;
+      let pdbStr;
+
+      if(pdb) {
+        pdbStr = pdb;
+      }
+      else {
+        let atoms = me.hashUtilsCls.intHash(ic.dAtoms, ic.hAtoms);
+        pdbStr += ic.saveFileCls.getAtomPDB(atoms);
+      }
+
+      let url = me.htmlCls.baseUrl + "scap/scap.cgi";
+      let hydrogenStr = (bHydrogen) ? '1' : '0';
+      let dataObj = {'pdb': pdbStr, 'profix': '1', 'hydrogen': hydrogenStr};
+
+      let data;
+       
+      try {
+        data = await me.getAjaxPostPromise(url, dataObj, undefined, undefined, undefined, undefined, 'text');
+      }
+      catch(err) {
+        var aaa = 1; //alert("There are some problems in adding missing atoms or hydrogens...");
+        return;
+      }
+
+      let file_pref =(ic.inputid) ? ic.inputid : "custom";
+      let postfix = (bHydrogen) ? "add_hydrogen" : "add_missing_atoms";
+      if(snpStr) postfix = snpStr;
+
+      ic.saveFileCls.saveFile(file_pref + '_icn3d_' + postfix + '.pdb', 'text', [data]);
+   }
 }
 
 /**
@@ -63765,10 +63975,11 @@ class SaveFile {
         }
 
 //        if(!bNoSs) {
-            let prevResi, stru;
+            let prevResi, stru, chainid;
             for(let i in calphaHash) {
                 let atom = ic.atoms[i];
                 stru = atom.structure;
+                chainid = atom.structure + '_' + atom.chain;
 
                 if(atom.ssbegin) {
                     if(atom.ss == 'helix') {
@@ -63789,7 +64000,9 @@ class SaveFile {
                 if(atom.ssend) {
                     if(atom.ss == 'helix') {
                         bHelixEnd = true;
-                        let helixLen = ic.resid2ncbi[atom.resi] - ic.resid2ncbi[prevResi];
+                        let residEnd = ic.resid2ncbi[chainid + '_' + atom.resi];
+                        let residStart = ic.resid2ncbi[chainid + '_' + prevResi];
+                        let helixLen = (residEnd && residStart) ? parseInt(residEnd.substr(residEnd.lastIndexOf('_') + 1)) - parseInt(residStart.substr(residStart.lastIndexOf('_') + 1)) : 0;
                         let helixType = 1;
                         if(bHelixBegin) stru2header[stru] += atom.resn.padStart(5, ' ') + atom.chain.replace(/_/gi, '').substr(0, 2).padStart(2, ' ')
                             + atom.resi.toString().padStart(5, ' ') + '  ' + helixType + helixLen.toString().padStart(36, ' ') + '\n';
@@ -63870,7 +64083,7 @@ class SaveFile {
             }
 
             let chainResi = atom.chain + '_' + atom.resi;
-            if(chainResi2pdb && chainResi2pdb.hasOwnProperty(chainResi)) {
+            if(chainResi2pdb && chainResi2pdb.hasOwnProperty(chainResi)) {    
                 if(!addedChainResiHash.hasOwnProperty(chainResi)) {
                     pdbStr += chainResi2pdb[chainResi];
                     addedChainResiHash[chainResi] = 1;
@@ -64035,7 +64248,7 @@ class SaveFile {
         }
 
         pdbStr += connStr;
-
+        
         if(bMulStruc) pdbStr += '\nENDMDL\n';
 
         return pdbStr;
@@ -64189,13 +64402,23 @@ 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;
@@ -64281,7 +64504,7 @@ 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;
             }
@@ -66833,6 +67056,7 @@ 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) { 
@@ -67416,7 +67640,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.21.1';
+    this.REVISION = '3.22.0';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -67887,7 +68111,7 @@ 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);
@@ -67916,7 +68140,7 @@ 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);