icn3d 3.19.3 → 3.20.0

package/icn3d.js

@@ -22958,13 +22958,18 @@ class PdbParser {
     //Ajax call was used to get the atom data from the "pdbid". This function was deferred so that
     //it can be chained together with other deferred functions for sequential execution. A wrapper
     //was added to support both http and https.
-    downloadPdb(pdbid, bAf) { let ic = this.icn3d; ic.icn3dui;
+    downloadPdb(pdbid, bAf) { let  ic = this.icn3d, me = ic.icn3dui;
       ic.deferredOpm = $.Deferred(function() {
         let  url, dataType;
 
         if(bAf) {
             url = "https://alphafold.ebi.ac.uk/files/AF-" + pdbid + "-F1-model_" + ic.AFUniprotVersion + ".pdb";
-            ic.ParserUtilsCls.setYourNote(pdbid.toUpperCase() + '(AlphaFold) in iCn3D');
+            if(me.cfg.refseqid) {
+                ic.ParserUtilsCls.setYourNote(me.cfg.refseqid.toUpperCase() + '(RefSeq) in iCn3D');
+            }
+            else {
+                ic.ParserUtilsCls.setYourNote(pdbid.toUpperCase() + '(AlphaFold) in iCn3D');
+            }
         }
         else {
             url = "https://files.rcsb.org/view/" + pdbid + ".pdb";
@@ -24610,15 +24615,15 @@ class MmdbParser {
         }
     }
 
-    downloadUniprotid(uniprotid) { let ic = this.icn3d; ic.icn3dui;
+    downloadRefseq(refseqid) { let  ic = this.icn3d, me = ic.icn3dui;
        // get gis
-       let  url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=protein&retmode=json&id=" + uniprotid;
+       let  url = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi?refseq2uniprot=" + refseqid;
 
        ic.bCid = undefined;
 
        $.ajax({
           url: url,
-          dataType: 'json',
+          dataType: 'jsonp',
           cache: true,
           tryCount : 0,
           retryLimit : 0, //1
@@ -24629,10 +24634,12 @@ class MmdbParser {
               //ic.ParserUtilsCls.hideLoading();
           },
           success: function(data) {
-               let  giArray = data.result.uids;
+                me.cfg.afid = data.uniprot;
 
-               let  redirectUrl = "https://www.ncbi.nlm.nih.gov/structure?linkname=protein_structure&from_uid=" + giArray.join(',');
-               window.open(redirectUrl, '_self');
+                let bAf = true;
+                $.when(ic.pdbParserCls.downloadPdb(me.cfg.afid, bAf)).then(function() {
+                    ic.loadScriptCls.loadScript(me.cfg.command, undefined, true);
+                });
           },
           error : function(xhr, textStatus, errorThrown ) {
             this.tryCount++;
@@ -28551,6 +28558,14 @@ class LoadScript {
           me.cfg.gi = id;
           ic.mmdbParserCls.downloadGi(id);
         }
+        else if(command.indexOf('load refseq') !== -1) {
+            me.cfg.refseqid = id;
+            ic.mmdbParserCls.downloadRefseq(id);
+        }
+        // else if(command.indexOf('load proteinname') !== -1) {
+        //     me.cfg.proteinname = id;
+        //     ic.mmdbParserCls.downloadProteinname(id);
+        // }
         else if(command.indexOf('load seq_struct_ids ') !== -1) {
           ic.bSmithwm = false;
           ic.bLocalSmithwm = false;
@@ -29029,6 +29044,7 @@ class LoadScript {
         if(ic.bTransparentSurface && ic.bRender) ic.drawCls.render();
 
         if(me.deferred !== undefined) me.deferred.resolve(); if(ic.deferred2 !== undefined) ic.deferred2.resolve();
+        if(me.deferredMmdbaf !== undefined) me.deferredMmdbaf.resolve();
     }
 
     replayFirstStep(currentNumber) { let  ic = this.icn3d, me = ic.icn3dui;
@@ -29249,7 +29265,7 @@ class ResizeCanvas {
         //let  itemArray = ['dl_selectannotations', 'dl_alignment', 'dl_2ddgm', 'dl_definedsets', 'dl_graph',
         //    'dl_linegraph', 'dl_scatterplot', 'dl_contactmap', 'dl_allinteraction', 'dl_copyurl',
         //    'dl_symmetry', 'dl_symd', 'dl_rmsd', 'dl_legend', 'dl_disttable'];
-        let itemArray = ['dl_2ddgm', 'dl_2dctn', 'dl_alignment', 'dl_sequence2', 'dl_definedsets', 'dl_setsmenu', 'dl_command', 'dl_setoperations', 'dl_vast', 'dl_foldseek', 'dl_mmtfid', 'dl_pdbid', 'dl_afid', 'dl_opmid', 'dl_pdbfile', 'dl_pdbfile_app', 'dl_rescolorfile', 'dl_customcolor', 'dl_align', 'dl_alignaf', 'dl_chainalign', 'dl_chainalign2', 'dl_chainalign3', 'dl_mutation', 'dl_mol2file', 'dl_sdffile', 'dl_xyzfile', 'dl_afmapfile', 'dl_urlfile', 'dl_mmciffile', 'dl_mmcifid', 'dl_mmdbid', 'dl_mmdbafid', 'dl_blast_rep_id', 'dl_yournote', 'dl_gi', 'dl_uniprotid', 'dl_cid', 'dl_pngimage', 'dl_state', 'dl_fixedversion', 'dl_selection', 'dl_dsn6', 'dl_dsn6url', 'dl_clr', 'dl_symmetry', 'dl_symd', 'dl_contact', 'dl_hbonds', 'dl_realign', 'dl_realignbystruct', 'dl_allinteraction', 'dl_interactionsorted', 'dl_linegraph', 'dl_linegraphcolor', 'dl_scatterplot', 'dl_scatterplotcolor', 'dl_contactmap', 'dl_alignerrormap', 'dl_elecmap2fofc', 'dl_elecmapfofc', 'dl_emmap', 'dl_aroundsphere', 'dl_adjustmem', 'dl_selectplane', 'dl_addlabel', 'dl_addlabelselection', 'dl_labelColor', 'dl_distance', 'dl_stabilizer', 'dl_disttwosets', 'dl_distmanysets', 'dl_stabilizer_rm', 'dl_thickness', 'dl_thickness2', 'dl_addtrack', 'dl_addtrack_tabs', 'dl_saveselection', 'dl_copyurl', 'dl_selectannotations', 'dl_annotations_tabs', 'dl_anno_view_tabs', 'dl_annotations', 'dl_graph', 'dl_svgcolor', 'dl_area', 'dl_colorbyarea', 'dl_rmsd', 'dl_buriedarea', 'dl_propbypercentout', 'dl_propbybfactor', 'dl_legend', 'dl_disttable'];
+        let itemArray = ['dl_2ddgm', 'dl_2dctn', 'dl_alignment', 'dl_sequence2', 'dl_definedsets', 'dl_setsmenu', 'dl_command', 'dl_setoperations', 'dl_vast', 'dl_foldseek', 'dl_mmtfid', 'dl_pdbid', 'dl_afid', 'dl_opmid', 'dl_pdbfile', 'dl_pdbfile_app', 'dl_rescolorfile', 'dl_customcolor', 'dl_align', 'dl_alignaf', 'dl_chainalign', 'dl_chainalign2', 'dl_chainalign3', 'dl_mutation', 'dl_mol2file', 'dl_sdffile', 'dl_xyzfile', 'dl_afmapfile', 'dl_urlfile', 'dl_mmciffile', 'dl_mmcifid', 'dl_mmdbid', 'dl_mmdbafid', 'dl_blast_rep_id', 'dl_yournote', 'dl_gi', 'dl_refseqid', 'dl_cid', 'dl_pngimage', 'dl_state', 'dl_fixedversion', 'dl_selection', 'dl_dsn6', 'dl_dsn6url', 'dl_clr', 'dl_symmetry', 'dl_symd', 'dl_contact', 'dl_hbonds', 'dl_realign', 'dl_realignbystruct', 'dl_allinteracton', 'dl_interactionsorted', 'dl_linegraph', 'dl_linegraphcolor', 'dl_scatterplot', 'dl_scatterploitcolor', 'dl_contactmap', 'dl_alignerrormap', 'dl_elecmap2fofc', 'dl_elecmapfofc', 'dl_emmap', 'dl_aroundsphere', 'dl_adjustmem', 'dl_selectplane', 'dl_addlabel', 'dl_addlabelselection', 'dl_labelColor', 'dl_distance', 'dl_stabilizer', 'dl_disttwosets', 'dl_distmanysets', 'dl_stabilizer_rm', 'dl_thickness', 'dl_thickness2', 'dl_addtrack', 'dl_addtrack_tabs', 'dl_saveselection', 'dl_copyurl', 'dl_selectannotations', 'dl_annotations_tabs', 'dl_anno_view_tabs', 'dl_annotations', 'dl_graph', 'dl_svgcolor', 'dl_area', 'dl_colorbyarea', 'dl_rmsd', 'dl_buriedarea', 'dl_propbypercentout', 'dl_propbybfactor', 'dl_legend', 'dl_disttable'];
 
         for(let i in itemArray) {
             let  item = itemArray[i];
@@ -29738,7 +29754,7 @@ class Domain3d {
 	//list< pair< pair< int, let >, let > >
 	//c2b_AlphaContacts(let n0, let* x0, let* y0, let* z0,
 	//	const let incr = 4, const let dcut = 8.0) { let ic = this.icn3d, me = ic.icn3dui;
-	c2b_AlphaContacts(n0, x0, y0, z0, dcut) { let ic = this.icn3d; ic.icn3dui;
+	c2b_AlphaContacts(n0, x0, y0, z0, dcut, resiArray) { let ic = this.icn3d; ic.icn3dui;
 		//if(!incr) incr = 4;
 		if(!dcut) dcut = this.dcut;
 
@@ -29752,7 +29768,8 @@ class Domain3d {
 
 			//ResRec rr0;
 			let rr0 = {};
-			rr0.rnum = i + 1;
+			//rr0.rnum = i + 1;
+			rr0.rnum = resiArray[i];
 			rr0.x = x0[i];
 			rr0.y = y0[i];
 			rr0.z = z0[i];
@@ -29780,7 +29797,7 @@ class Domain3d {
 			for (j = i + 1; j < len; ++j) {	
 				//ResRec rr2 = *rrit2;
 				let rr2 = list_rr[j];
-				if ((rr1.rnum - rr2.rnum <= 3) && (rr2.rnum - rr1.rnum <= 3)) continue;
+				if ((parseInt(rr1.rnum) - parseInt(rr2.rnum) <= 3) && (parseInt(rr2.rnum) - parseInt(rr1.rnum) <= 3)) continue;
 				let x2 = rr2.x;
 				let y2 = rr2.y;
 				let z2 = rr2.z;
@@ -29798,7 +29815,7 @@ class Domain3d {
 				//pair< int, let > rpair;
 				let lpair = {}, rpair = {};
 
-				if (rr1.rnum < rr2.rnum) {
+				if (parseInt(rr1.rnum) < parseInt(rr2.rnum)) {
 					rpair.first = rr1.rnum;
 					rpair.second = rr2.rnum;
 				}
@@ -29888,7 +29905,7 @@ class Domain3d {
 	// x0, y0, z0: array of x,y,z coordinates of C-alpha atoms
 	//c2b_NewSplitChain(chnid, dcut) { let ic = this.icn3d, me = ic.icn3dui;
 	c2b_NewSplitChain(atoms, dcut) { let ic = this.icn3d; ic.icn3dui;
-		let x0 = [], y0 = [], z0 = [];
+		let x0 = [], y0 = [], z0 = [], resiArray = [];
 
 		//substruct: array of secondary structures, each of which has the keys: From (1-based), To (1-based), Sheet (0 or 1), also add these paras: x1, y1, z1, x2, y2, z2
 		let substruct = [];
@@ -29903,11 +29920,11 @@ class Domain3d {
 		residueArray[0].substr(0, residueArray[0].lastIndexOf('_'));
 
 		let substructItem = {};
-		let resiOffset = 0;
 		for(let i = 0; i < residueArray.length; ++i) {
 			let resid = residueArray[i];
 
             let resi = resid.substr(resid.lastIndexOf('_') + 1);
+/*			
 			if(i == 0) {
 				resiOffset = resi - 1;
 
@@ -29917,10 +29934,13 @@ class Domain3d {
 					z0.push(undefined);					
 				}
 			}
+*/
 
 			//let resid = chnid + "_" + resi;
 			let atom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.residues[resid]);
 
+			if(!atom) continue;    
+/*
 			if(atom) {
 				x0.push(atom.coord.x);
 				y0.push(atom.coord.y);
@@ -29931,8 +29951,13 @@ class Domain3d {
 				y0.push(undefined);
 				z0.push(undefined);
 			}
-
-			if(!atom) continue;           
+*/
+			//if(!atom) continue;   
+			
+			x0.push(atom.coord.x);
+			y0.push(atom.coord.y);
+			z0.push(atom.coord.z);
+			resiArray.push(resi);
 
 			if(atom.ssend) {
 				substructItem.To = parseInt(resi);
@@ -29966,12 +29991,13 @@ class Domain3d {
 			return {subdomains: subdomains, substruct: substruct};
 		}
 
-		let seqLen = residueArray.length + resiOffset;
+		let seqLen = residueArray.length; // + resiOffset;
+		let lastResi = resiArray[seqLen - 1];
 
 		// get a list of Calpha-Calpha contacts
 		///list< pair< pair< int, let >, let > >
-		let cts = this.c2b_AlphaContacts(seqLen, x0, y0, z0, dcut);
-
+		let cts = this.c2b_AlphaContacts(seqLen, x0, y0, z0, dcut, resiArray);
+		
 		//
 		// Produce a "map" of the SSEs, i.e. vec_sse[i] = 0 means residue i + 1
 		// is in a loop, and vec_sse[i] = k means residue i + 1 belongs to SSE
@@ -30216,13 +30242,17 @@ class Domain3d {
 			let prts = list_parts[index];
 			//vector<int> resflags;
 			//resflags.clear();
-			let resflags = [];
+
+			//let resflags = [];
+			let resflags = {};
 
 			// a domain must have at least 3 SSEs...
 			if (prts.length <= 2) continue;
 
-			for (let i = 0; i < seqLen; i++)
-				resflags.push(0);
+			for (let i = 0; i < seqLen; i++) {
+				//resflags.push(0);
+				resflags[resiArray[i]] = 0;
+			}
 
 			for (let i = 0; i < prts.length; i++) {
 				let k = prts[i] - 1;
@@ -30236,8 +30266,10 @@ class Domain3d {
 				let From = sserec.From;
 				let To = sserec.To;
 
-				for (let j = From; j <= To; j++)
-					resflags[j - 1] = 1;
+				for (let j = From; j <= To; j++) {
+					//resflags[j - 1] = 1;
+					resflags[j] = 1;
+				}
 
 				if ((k == 0) && (From > 1)) {
 					// residues with negative residue numbers will not be included
@@ -30245,17 +30277,21 @@ class Domain3d {
 						//resflags[j - 1] = 1;
 						// include at most 10 residues
 						if(From - j <= 10) {
-							resflags[j - 1] = 1;
+							//resflags[j - 1] = 1;
+							resflags[j] = 1;
 						}
 					}
 				}
 
-				if ((k == substruct.length - 1) && (To < seqLen)) {
-					for (let j = To + 1; j <= seqLen; j++) {
+				//if ((k == substruct.length - 1) && (To < seqLen)) {
+				if ((k == substruct.length - 1) && (To < parseInt(lastResi))) {
+					//for (let j = To + 1; j <= seqLen; j++) {
+					for (let j = To + 1; j <= parseInt(lastResi); j++) {
 						//resflags[j - 1] = 1;
 						// include at most 10 residues
 						if(j - To <= 10) {
-							resflags[j - 1] = 1;
+							//resflags[j - 1] = 1;
+							resflags[j] = 1;
 						}
 					}
 				}
@@ -30269,8 +30305,10 @@ class Domain3d {
 					let ll = parseInt(0.5 * (From - To1 - 1));
 
 					if (ll > 0) {
-						for (let j = From - ll; j <= From - 1; j++)
-							resflags[j - 1] = 1;
+						for (let j = From - ll; j <= From - 1; j++) {
+							//resflags[j - 1] = 1;
+							resflags[j] = 1;
+						}
 					}
 				}
 
@@ -30286,8 +30324,10 @@ class Domain3d {
 					let ll = parseInt(0.5 * (From1 - To - 1) + 0.5);
 
 					if (ll > 0) {
-						for (let j = To + 1; j <= To + ll; j++)
-							resflags[j - 1] = 1;
+						for (let j = To + 1; j <= To + ll; j++) {
+							//resflags[j - 1] = 1;
+							resflags[j] = 1;
+						}
 					}
 				}
 			}
@@ -30300,11 +30340,13 @@ class Domain3d {
 			let segments = [];
 
 			for (let i = 0; i < seqLen; i++) {
-				let rf = resflags[i];
+				//let rf = resflags[i];
+				let rf = resflags[resiArray[i]];
 
 				if (!inseg && (rf == 1)) {
 					// new segment starts here
-					startseg = i + 1;
+					//startseg = i + 1;
+					startseg = resiArray[i];
 					inseg = true;
 					continue;
 				}
@@ -30312,7 +30354,8 @@ class Domain3d {
 				if (inseg && (rf == 0)) {
 					// segment ends
 					segments.push(startseg);
-					segments.push(i);
+					//segments.push(i);
+					segments.push(resiArray[i]);
 					inseg = false;
 				}
 			}
@@ -30320,7 +30363,8 @@ class Domain3d {
 			// check for the last segment
 			if (inseg) {
 				segments.push(startseg);
-				segments.push(seqLen);
+				//segments.push(seqLen);
+				segments.push(lastResi);
 			}
 
 			subdomains.push(segments);
@@ -34423,7 +34467,8 @@ class ApplyCommand {
         let  paraArray = command.split(' | ');
         let  url = paraArray[1];
 
-        window.open(url, '_blank');
+        let urlTarget = '_blank';
+        window.open(url, urlTarget);
       }
       else if(commandOri.indexOf('your note') == 0) {
         let  paraArray = commandOri.split(' | ');
@@ -37710,7 +37755,7 @@ class ParserUtils {
           ic.selectionCls.saveSelectionIfSelected();
           ic.drawCls.draw();
       }
-
+      
 //      if(ic.bInitial && me.cfg.command !== undefined && me.cfg.command !== '') {
       if(!ic.bCommandLoad && ic.bInitial && me.cfg.command !== undefined && me.cfg.command !== '') {
           if(Object.keys(ic.structures).length == 1) {
@@ -37718,11 +37763,13 @@ class ParserUtils {
               me.cfg.command = me.cfg.command.replace(new RegExp('!','g'), id + '_');
           }
           // final step resolved ic.deferred
-          if(me.cfg.mmdbafid === undefined && me.cfg.afid === undefined) ic.loadScriptCls.loadScript(me.cfg.command, undefined, true);
+          //if(me.cfg.mmdbafid === undefined && me.cfg.afid === undefined) ic.loadScriptCls.loadScript(me.cfg.command, undefined, true);
+          ic.loadScriptCls.loadScript(me.cfg.command, undefined, true);
           //ic.loadScriptCls.loadScript(me.cfg.command);
       }
       else {
           if(me.deferred !== undefined) me.deferred.resolve(); if(ic.deferred2 !== undefined) ic.deferred2.resolve();
+          if(me.deferredMmdbaf !== undefined) me.deferredMmdbaf.resolve();
       }
       //if(me.cfg.align !== undefined || me.cfg.chainalign !== undefined || ic.bRealign ||( ic.bInputfile && ic.InputfileType == 'pdb' && Object.keys(ic.structures).length >= 2) ) {
       if(Object.keys(ic.structures).length >= 2) {
@@ -54551,13 +54598,14 @@ class SaveFile {
         }
     }
 
-    setStructureTitle(url, title, titlelinkColor) {var ic = this.icn3d; ic.icn3dui;
+    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 idName = (isNaN(ic.inputid) && ic.inputid.length > 5) ? "AlphaFold ID" : "PDB ID";
+        if(me.cfg.refseqid) idName = 'NCBI RefSeq ID';
 
         $("#" + ic.pre + "title").html(idName + " <a id='" + ic.pre + "titlelink' href='" + url + "' style='color:" + titlelinkColor + "' target='_blank'>" + ic.inputid.toUpperCase() + "</a>" + asymmetricStr + ": " + title);
     }
@@ -54568,6 +54616,9 @@ class SaveFile {
        if(me.cfg.cid !== undefined) {
            url = "https://www.ncbi.nlm.nih.gov/pccompound/?term=";
        }
+       else if(me.cfg.refseqid !== undefined) {
+        url = "https://www.ncbi.nlm.nih.gov/protein/";
+       }
        else if(me.cfg.afid !== undefined) {
            url = "https://alphafold.ebi.ac.uk/search/text/";
        }
@@ -54613,12 +54664,14 @@ class SaveFile {
       if(structArray.length === 1) {
           url = "https://www.ncbi.nlm.nih.gov/" + db + "/?term=" + structArray[0];
           me.htmlCls.clickMenuCls.setLogCmd("Entrez " + db + " about PDB " + structArray[0] + ": " + url, false);
-          window.open(url, '_blank');
+          let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+          window.open(url, urlTarget);
       }
       else if(structArray.length === 2) {
           url = "https://www.ncbi.nlm.nih.gov/" + db + "/?term=" + structArray[0] + " OR " + structArray[1];
           me.htmlCls.clickMenuCls.setLogCmd("Entrez " + db + " about PDB " + structArray[0] + " OR " + structArray[1] + ": " + url, false);
-          window.open(url, '_blank');
+          let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+          window.open(url, urlTarget);
       }
     }
 }
@@ -54813,6 +54866,14 @@ class ClickMenu {
            me.htmlCls.dialogCls.openDlg('dl_afid', 'Please input AlphaFold UniProt ID');
         });
 
+        me.myEventCls.onIds("#" + me.pre + "mn1_refseqid", "click", function(e) { me.icn3d; e.preventDefault();
+            me.htmlCls.dialogCls.openDlg('dl_refseqid', 'Please input NCBI RefSeq ID');
+         });
+
+        // me.myEventCls.onIds("#" + me.pre + "mn1_proteinname", "click", function(e) { let ic = me.icn3d; e.preventDefault();
+        //     me.htmlCls.dialogCls.openDlg('dl_proteinname', 'Please input protein name to search');
+        //  });
+
     //    },
     //    clkMn1_opmid: function() {
         me.myEventCls.onIds("#" + me.pre + "mn1_opmid", "click", function(e) { me.icn3d; e.preventDefault();
@@ -54885,11 +54946,12 @@ class ClickMenu {
         me.myEventCls.onIds("#" + me.pre + "mn1_fixedversion", "click", function(e) { me.icn3d; e.preventDefault();
            me.htmlCls.dialogCls.openDlg('dl_fixedversion', 'Open Share Link URL in the archived version of iCn3D');
         });
-        me.myEventCls.onIds("#" + me.pre + "reload_fixedversion", "click", function(e) { me.icn3d; e.preventDefault();
+        me.myEventCls.onIds("#" + me.pre + "reload_fixedversion", "click", function(e) { let ic = me.icn3d; e.preventDefault();
            let url = $("#" + me.pre + "sharelinkurl").val();
            thisClass.setLogCmd("open " + url, false);
            localStorage.setItem('fixedversion', '1');
-           window.open(url, '_blank');
+           let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+           window.open(url, urlTarget);
         });
     //    },
     //    clkMn1_mmciffile: function() {
@@ -54921,13 +54983,6 @@ class ClickMenu {
            me.htmlCls.dialogCls.openDlg('dl_gi', 'Please input protein gi');
         });
 
-        me.myEventCls.onIds("#" + me.pre + "mn1_refseq", "click", function(e) { me.icn3d; e.preventDefault();
-            me.htmlCls.dialogCls.openDlg('dl_grefseq', 'Please input protein RefSeq');
-         });
-
-        me.myEventCls.onIds("#" + me.pre + "mn1_uniprotid", "click", function(e) { me.icn3d; e.preventDefault();
-           me.htmlCls.dialogCls.openDlg('dl_uniprotid', 'Please input UniProt ID');
-        });
     //    },
     //    clkMn1_cid: function() {
         me.myEventCls.onIds("#" + me.pre + "mn1_cid", "click", function(e) { me.icn3d; e.preventDefault();
@@ -55268,14 +55323,16 @@ class ClickMenu {
     //    clkMn1_link_structure: function() {
         me.myEventCls.onIds("#" + me.pre + "mn1_link_structure", "click", function(e) { let ic = me.icn3d; e.preventDefault();
            let url = ic.saveFileCls.getLinkToStructureSummary(true);
-           window.open(url, '_blank');
+           let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+           window.open(url, urlTarget);
         });
     //    },
     //    clkMn1_link_bind: function() {
         me.myEventCls.onIds("#" + me.pre + "mn1_link_bind", "click", function(e) { let ic = me.icn3d; e.preventDefault();
            url = "https://www.ncbi.nlm.nih.gov/pccompound?LinkName=pccompound_structure&from_uid=" + ic.inputid;
            thisClass.setLogCmd("link to 3D protein structures bound to CID " + ic.inputid + ": " + url, false);
-           window.open(url, '_blank');
+           let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+           window.open(url, urlTarget);
         });
     //    },
     //    clkMn1_link_vast: function() {
@@ -55302,8 +55359,10 @@ class ClickMenu {
                        thisClass.setLogCmd("link to structures similar to " + idArray[0] + ": " + url, false);
                    }
                }
-               window.open(url, '_blank');
            }
+
+           let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+           window.open(url, urlTarget);
         });
     //    },
     //    clkMn1_link_pubmed: function() {
@@ -55312,7 +55371,8 @@ class ClickMenu {
                let url;
                url = "https://www.ncbi.nlm.nih.gov/pubmed/?term=" + ic.molTitle;
                thisClass.setLogCmd("link to literature about " + ic.molTitle + ": " + url, false);
-               window.open(url, '_blank');
+               let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+               window.open(url, urlTarget);
            }
            else if(ic.pmid) {
                let idArray = ic.pmid.toString().split('_');
@@ -55325,7 +55385,8 @@ class ClickMenu {
                    url = "https://www.ncbi.nlm.nih.gov/pubmed/?term=" + idArray[0] + " OR " + idArray[1];
                    thisClass.setLogCmd("link to PubMed IDs " + idArray[0] + ", " + idArray[1] + ": " + url, false);
                }
-               window.open(url, '_blank');
+               let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+               window.open(url, urlTarget);
            }
            else if(isNaN(ic.inputid)) {
                let idArray = ic.inputid.toString().split('_');
@@ -55338,7 +55399,8 @@ class ClickMenu {
                    url = "https://www.ncbi.nlm.nih.gov/pubmed/?term=" + idArray[0] + " OR " + idArray[1];
                    thisClass.setLogCmd("link to literature about PDB " + idArray[0] + " OR " + idArray[1] + ": " + url, false);
                }
-               window.open(url, '_blank');
+               let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+               window.open(url, urlTarget);
            }
            else {
                if(me.cfg.cid !== undefined) {
@@ -55365,7 +55427,8 @@ class ClickMenu {
           if(text.length > 0) text = text.substr(0, text.length - 4);
           let url = "https://www.ncbi.nlm.nih.gov/protein/?term=" + text;
           thisClass.setLogCmd("link to Entrez protein about PDB " + structArray + ": " + url, false);
-          window.open(url, '_blank');
+          let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+          window.open(url, urlTarget);
         });
     //    },
     }
@@ -56666,7 +56729,8 @@ class ClickMenu {
            //else {
                url = url.replace("full.html", "full2.html");
                url += '&closepopup=1';
-               window.open(url, '_blank');
+               let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+               window.open(url, urlTarget);
                thisClass.setLogCmd('side by side | ' + url, true);
            //}
         });
@@ -57056,7 +57120,8 @@ class ClickMenu {
 
             let template = "<!doctype html>\n<head>\n<title>Loading Foldseek</title>\n<style>\n  body {\n    background-color: #121212;\n    color: #fff;\n    font-family: system-ui, -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen, Ubuntu, Cantarell, 'Open Sans', 'Helvetica Neue', sans-serif;\n    height: 100vh;\n    display: flex;\n    flex-direction: column;\n    flex-wrap: wrap;\n    justify-content: center;\n    align-items: center;\n  }\n  .loader {\n    display: block;\n    width: 80px;\n    height: 80px;\n  }\n  .loader:after {\n    content: \" \";\n    display: block;\n    width: 64px;\n    height: 64px;\n    margin: 8px;\n    border-radius: 50%;\n    border: 6px solid #fff;\n    border-color: #fff transparent #fff transparent;\n    animation: loader 1.2s linear infinite;\n  }\n  @keyframes loader {\n    0% {\n      transform: rotate(0deg);\n    }\n    100% {\n      transform: rotate(360deg);\n    }\n  }\n</style>\n</head>\n<body>\n<div>Foldseek is loading...</div><div class=\"loader\"></div>\n</body>";
 
-            let w = window.open('', '_blank');
+            let urlTarget = '_blank';
+            let w = window.open('', urlTarget);
             w.document.body.innerHTML = template;
 
             $.ajax({
@@ -57644,13 +57709,20 @@ class SetMenu {
         html += me.htmlCls.setHtmlCls.getLink('mn1_mmdbid', 'NCBI MMDB ID (annotation) ' + me.htmlCls.wifiStr, undefined, 2);
         html += me.htmlCls.setHtmlCls.getLink('mn1_mmtfid', 'RCSB MMTF ID (fast) ' + me.htmlCls.wifiStr, undefined, 2);
         html += me.htmlCls.setHtmlCls.getLink('mn1_pdbid', 'RCSB PDB ID ' + me.htmlCls.wifiStr, undefined, 2);
-        html += me.htmlCls.setHtmlCls.getLink('mn1_afid', 'AlphaFold UniProt ID ' + me.htmlCls.wifiStr, undefined, 2);
+
+        html += me.htmlCls.setHtmlCls.getMenuText('mn1_afwrap', 'AlphaFold Structures', undefined, undefined, 2);
+        html += "<ul>";
+        
+        html += me.htmlCls.setHtmlCls.getLink('mn1_afid', 'UniProt ID ' + me.htmlCls.wifiStr, undefined, 3);
+        html += me.htmlCls.setHtmlCls.getLink('mn1_refseqid', 'NCBI RefSeq ID ' + me.htmlCls.wifiStr, undefined, 3);
+        // html += me.htmlCls.setHtmlCls.getLink('mn1_proteinname', 'Protein Name ' + me.htmlCls.wifiStr, undefined, 3);
+        html += "</ul>";
+
+        
         html += me.htmlCls.setHtmlCls.getLink('mn1_opmid', 'OPM PDB ID ' + me.htmlCls.wifiStr, undefined, 2);
         html += me.htmlCls.setHtmlCls.getLink('mn1_mmcifid', 'RCSB mmCIF ID ' + me.htmlCls.wifiStr, undefined, 2);
-        html += me.htmlCls.setHtmlCls.getLink('mn1_gi', 'NCBI gi ' + me.htmlCls.wifiStr, undefined, 2);
-        //html += me.htmlCls.setHtmlCls.getLink('mn1_refseq', 'NCBI RefSeq ' + me.htmlCls.wifiStr, undefined, 2);
+        //html += me.htmlCls.setHtmlCls.getLink('mn1_gi', 'NCBI gi ' + me.htmlCls.wifiStr, undefined, 2);
 
-        //html += me.htmlCls.setHtmlCls.getLink('mn1_uniprotid', 'UniProt ID ' + me.htmlCls.wifiStr);
         html += me.htmlCls.setHtmlCls.getLink('mn1_cid', 'PubChem CID ' + me.htmlCls.wifiStr, 1, 2);
         
         html += "</ul>";
@@ -59858,6 +59930,16 @@ class SetDialog {
             + me.htmlCls.buttonStr + "reload_afmapfull' style='margin-left:30px'>Load Full (slow)</button>";
         html += "</div>";
 
+        html += me.htmlCls.divStr + "dl_refseqid' class='" + dialogClass + "'>";
+        html += "NCBI RefSeq ID: " + me.htmlCls.inputTextStr + "id='" + me.pre + "refseqid' value='0308234A' size=8> ";
+        html += me.htmlCls.buttonStr + "reload_refseq'>Load</button>";
+        html += "</div>";
+
+        // html += me.htmlCls.divStr + "dl_proteinname' class='" + dialogClass + "'>";
+        // html += "PDB ID: " + me.htmlCls.inputTextStr + "id='" + me.pre + "proteinname' value='kinase' size=8> ";
+        // html += me.htmlCls.buttonStr + "reload_proteinname'>Load</button>";
+        // html += "</div>";
+
         html += me.htmlCls.divStr + "dl_opmid' class='" + dialogClass + "'>";
         html += "<a href='https://opm.phar.umich.edu' target='_blank'>Orientations of Proteins in Membranes(OPM)</a> PDB ID: " + me.htmlCls.inputTextStr + "id='" + me.pre + "opmid' value='6JXR' size=8> ";
         html += me.htmlCls.buttonStr + "reload_opm'>Load</button>";
@@ -60076,17 +60158,6 @@ class SetDialog {
         html += me.htmlCls.buttonStr + "reload_gi'>Load</button>";
         html += "</div>";
 
-        html += me.htmlCls.divStr + "dl_refseq' class='" + dialogClass + "'>";
-        html += "Protein RefSeq: " + me.htmlCls.inputTextStr + "id='" + me.pre + "refseq' value='0308234A' size=8> ";
-        html += me.htmlCls.buttonStr + "reload_refseq'>Load</button>";
-        html += "</div>";
-
-        html += me.htmlCls.divStr + "dl_uniprotid' class='" + dialogClass + "'>";
-        html += "Note: A list of structures will be shown. Click \"View in iCn3D\" to view each structure in 3D.<br><br>";
-        html += "UniProt ID: " + me.htmlCls.inputTextStr + "id='" + me.pre + "uniprotid' value='P0DTC2' size=8> ";
-        html += me.htmlCls.buttonStr + "reload_uniprotid'>Load</button>";
-        html += "</div>";
-
         html += me.htmlCls.divStr + "dl_cid' class='" + dialogClass + "'>";
         html += "PubChem CID: " + me.htmlCls.inputTextStr + "id='" + me.pre + "cid' value='2244' size=8> ";
         html += me.htmlCls.buttonStr + "reload_cid'>Load</button>";
@@ -61090,7 +61161,7 @@ class Events {
         $("#" + me.pre + id).resizable();
     }
 
-    launchMmdb(ids, bBiounit, hostUrl) { let me = this.icn3dui; me.icn3d;
+    launchMmdb(ids, bBiounit, hostUrl) { let me = this.icn3dui, ic = me.icn3d;
         let flag = bBiounit ? '1' : '0';
 
         ids = ids.replace(/,/g, ' ').replace(/\s+/g, ',').trim();
@@ -61103,11 +61174,13 @@ class Events {
         let idArray = ids.split(',');
         if(idArray.length == 1 && (idArray[0].length == 4 || !isNaN(idArray[0])) ) {
             me.htmlCls.clickMenuCls.setLogCmd("load mmdb" + flag + " " + ids, false);
-            window.open(hostUrl + '?mmdbid=' + ids + '&bu=' + flag, '_blank');
+            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+            window.open(hostUrl + '?mmdbid=' + ids + '&bu=' + flag, urlTarget);
         }
         else {
             me.htmlCls.clickMenuCls.setLogCmd("load mmdbaf" + flag + " " + ids, false);
-            window.open(hostUrl + '?mmdbafid=' + ids + '&bu=' + flag, '_blank');
+            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+            window.open(hostUrl + '?mmdbafid=' + ids + '&bu=' + flag, urlTarget);
         }
     }
 
@@ -61456,18 +61529,20 @@ class Events {
 
     //    },
     //    clickReload_mmtf: function() {
-        me.myEventCls.onIds("#" + me.pre + "reload_vastplus", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_vastplus", "click", function(e) { let ic = me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
             me.htmlCls.clickMenuCls.setLogCmd("vast+ search " + $("#" + me.pre + "vastpluspdbid").val(), false);
-            window.open('https://www.ncbi.nlm.nih.gov/Structure/vastplus/vastplus.cgi?uid=' + $("#" + me.pre + "vastpluspdbid").val(), '_blank');
+            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+            window.open('https://www.ncbi.nlm.nih.gov/Structure/vastplus/vastplus.cgi?uid=' + $("#" + me.pre + "vastpluspdbid").val(), urlTarget);
          });
 
-        me.myEventCls.onIds("#" + me.pre + "reload_vast", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_vast", "click", function(e) { let ic = me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
             me.htmlCls.clickMenuCls.setLogCmd("vast search " + $("#" + me.pre + "vastpdbid").val() + "_" + $("#" + me.pre + "vastchainid").val(), false);
-            window.open('https://www.ncbi.nlm.nih.gov/Structure/vast/vastsrv.cgi?pdbid=' + $("#" + me.pre + "vastpdbid").val() + '&chain=' + $("#" + me.pre + "vastchainid").val(), '_blank');
+            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+            window.open('https://www.ncbi.nlm.nih.gov/Structure/vast/vastsrv.cgi?pdbid=' + $("#" + me.pre + "vastpdbid").val() + '&chain=' + $("#" + me.pre + "vastchainid").val(), urlTarget);
          });
 
         me.myEventCls.onIds("#" + me.pre + "reload_foldseek", "click", function(e) { me.icn3d;
@@ -61485,50 +61560,55 @@ class Events {
             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;
+        me.myEventCls.onIds("#" + me.pre + "reload_mmtf", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
            me.htmlCls.clickMenuCls.setLogCmd("load mmtf " + $("#" + me.pre + "mmtfid").val(), false);
-           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmtfid=' + $("#" + me.pre + "mmtfid").val(), '_blank');
-           window.open(hostUrl + '?mmtfid=' + $("#" + me.pre + "mmtfid").val(), '_blank');
+           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmtfid=' + $("#" + me.pre + "mmtfid").val(), urlTarget);
+           let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+           window.open(hostUrl + '?mmtfid=' + $("#" + me.pre + "mmtfid").val(), urlTarget);
         });
 
-        me.myEventCls.onIds("#" + me.pre + "mmtfid", "keyup", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "mmtfid", "keyup", function(e) { let ic = me.icn3d;
            if (e.keyCode === 13) {
                e.preventDefault();
                if(!me.cfg.notebook) dialog.dialog( "close" );
                me.htmlCls.clickMenuCls.setLogCmd("load mmtf " + $("#" + me.pre + "mmtfid").val(), false);
-               //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmtfid=' + $("#" + me.pre + "mmtfid").val(), '_blank');
-               window.open(hostUrl + '?mmtfid=' + $("#" + me.pre + "mmtfid").val(), '_blank');
+               //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmtfid=' + $("#" + me.pre + "mmtfid").val(), urlTarget);
+               let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+               window.open(hostUrl + '?mmtfid=' + $("#" + me.pre + "mmtfid").val(), urlTarget);
            }
         });
 
     //    },
     //    clickReload_pdb: function() {
-        me.myEventCls.onIds("#" + me.pre + "reload_pdb", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_pdb", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
            me.htmlCls.clickMenuCls.setLogCmd("load pdb " + $("#" + me.pre + "pdbid").val(), false);
-           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?pdbid=' + $("#" + me.pre + "pdbid").val(), '_blank');
-           window.open(hostUrl + '?pdbid=' + $("#" + me.pre + "pdbid").val(), '_blank');
+           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?pdbid=' + $("#" + me.pre + "pdbid").val(), urlTarget);
+           let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+           window.open(hostUrl + '?pdbid=' + $("#" + me.pre + "pdbid").val(), urlTarget);
         });
 
-        me.myEventCls.onIds("#" + me.pre + "pdbid", "keyup", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "pdbid", "keyup", function(e) { let ic = me.icn3d;
            if (e.keyCode === 13) {
                e.preventDefault();
                if(!me.cfg.notebook) dialog.dialog( "close" );
                me.htmlCls.clickMenuCls.setLogCmd("load pdb " + $("#" + me.pre + "pdbid").val(), false);
-               //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?pdbid=' + $("#" + me.pre + "pdbid").val(), '_blank');
-               window.open(hostUrl + '?pdbid=' + $("#" + me.pre + "pdbid").val(), '_blank');
+               //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?pdbid=' + $("#" + me.pre + "pdbid").val(), urlTarget);
+               let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+               window.open(hostUrl + '?pdbid=' + $("#" + me.pre + "pdbid").val(), urlTarget);
            }
         });
 
-        me.myEventCls.onIds("#" + me.pre + "reload_af", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_af", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
            me.htmlCls.clickMenuCls.setLogCmd("load af " + $("#" + me.pre + "afid").val(), false);
-           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?afid=' + $("#" + me.pre + "afid").val(), '_blank');
-           window.open(hostUrl + '?afid=' + $("#" + me.pre + "afid").val(), '_blank');
+           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?afid=' + $("#" + me.pre + "afid").val(), urlTarget);
+           let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+           window.open(hostUrl + '?afid=' + $("#" + me.pre + "afid").val(), urlTarget);
         });
 
         me.myEventCls.onIds("#" + me.pre + "reload_afmap", "click", function(e) { let ic = me.icn3d;
@@ -61550,79 +61630,87 @@ class Events {
             ic.contactMapCls.afErrorMap(afid, true);
         });
 
-        me.myEventCls.onIds("#" + me.pre + "afid", "keyup", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "afid", "keyup", function(e) { let ic = me.icn3d;
            if (e.keyCode === 13) {
                e.preventDefault();
                if(!me.cfg.notebook) dialog.dialog( "close" );
                me.htmlCls.clickMenuCls.setLogCmd("load af " + $("#" + me.pre + "afid").val(), false);
-               //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?afid=' + $("#" + me.pre + "afid").val(), '_blank');
-               window.open(hostUrl + '?afid=' + $("#" + me.pre + "afid").val(), '_blank');
+               //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?afid=' + $("#" + me.pre + "afid").val(), urlTarget);
+               let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+               window.open(hostUrl + '?afid=' + $("#" + me.pre + "afid").val(), urlTarget);
            }
         });
 
     //    },
     //    clickReload_opm: function() {
-        me.myEventCls.onIds("#" + me.pre + "reload_opm", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_opm", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
            me.htmlCls.clickMenuCls.setLogCmd("load opm " + $("#" + me.pre + "opmid").val(), false);
-           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?opmid=' + $("#" + me.pre + "opmid").val(), '_blank');
-           window.open(hostUrl + '?opmid=' + $("#" + me.pre + "opmid").val(), '_blank');
+           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?opmid=' + $("#" + me.pre + "opmid").val(), urlTarget);
+           let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+           window.open(hostUrl + '?opmid=' + $("#" + me.pre + "opmid").val(), urlTarget);
         });
 
-        me.myEventCls.onIds("#" + me.pre + "opmid", "keyup", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "opmid", "keyup", function(e) { let ic = me.icn3d;
            if (e.keyCode === 13) {
                e.preventDefault();
                if(!me.cfg.notebook) dialog.dialog( "close" );
                me.htmlCls.clickMenuCls.setLogCmd("load opm " + $("#" + me.pre + "opmid").val(), false);
-               //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?opmid=' + $("#" + me.pre + "opmid").val(), '_blank');
-               window.open(hostUrl + '?opmid=' + $("#" + me.pre + "opmid").val(), '_blank');
+               //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?opmid=' + $("#" + me.pre + "opmid").val(), urlTarget);
+               let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+               window.open(hostUrl + '?opmid=' + $("#" + me.pre + "opmid").val(), urlTarget);
            }
         });
 
     //    },
     //    clickReload_align_refined: function() {
-        me.myEventCls.onIds("#" + me.pre + "reload_align_refined", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_align_refined", "click", function(e) { let ic = me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
             let alignment = $("#" + me.pre + "alignid1").val() + "," + $("#" + me.pre + "alignid2").val();
             me.htmlCls.clickMenuCls.setLogCmd("load alignment " + alignment + ' | parameters &atype=1&bu=1', false);
-            //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?align=' + alignment + '&showalignseq=1&atype=1', '_blank');
-            window.open(hostUrl + '?align=' + alignment + '&showalignseq=1&atype=1&bu=1', '_blank');
+            //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?align=' + alignment + '&showalignseq=1&atype=1', urlTarget);
+            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+            window.open(hostUrl + '?align=' + alignment + '&showalignseq=1&atype=1&bu=1', urlTarget);
          });
     //    },
     //    clickReload_align_ori: function() {
-        me.myEventCls.onIds("#" + me.pre + "reload_align_ori", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_align_ori", "click", function(e) { let ic = me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
             let alignment = $("#" + me.pre + "alignid1").val() + "," + $("#" + me.pre + "alignid2").val();
             me.htmlCls.clickMenuCls.setLogCmd("load alignment " + alignment + ' | parameters &atype=0&bu=1', false);
-            //window.open( me.htmlCls.baseUrl + 'icn3d/full.html?align=' + alignment + '&showalignseq=1&atype=0', '_blank');
-            window.open(hostUrl + '?align=' + alignment + '&showalignseq=1&atype=0&bu=1', '_blank');
+            //window.open( me.htmlCls.baseUrl + 'icn3d/full.html?align=' + alignment + '&showalignseq=1&atype=0', urlTarget);
+            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+            window.open(hostUrl + '?align=' + alignment + '&showalignseq=1&atype=0&bu=1', urlTarget);
          });
 
-        me.myEventCls.onIds("#" + me.pre + "reload_align_tmalign", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_align_tmalign", "click", function(e) { let ic = me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
             let alignment = $("#" + me.pre + "alignid1").val() + "," + $("#" + me.pre + "alignid2").val();
             me.htmlCls.clickMenuCls.setLogCmd("load alignment " + alignment + ' | parameters &atype=2&bu=1', false);
-            window.open(hostUrl + '?align=' + alignment + '&showalignseq=1&atype=2&bu=1', '_blank');
+            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+            window.open(hostUrl + '?align=' + alignment + '&showalignseq=1&atype=2&bu=1', urlTarget);
          });
 
-        me.myEventCls.onIds("#" + me.pre + "reload_alignaf", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_alignaf", "click", function(e) { let ic = me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
             let alignment = $("#" + me.pre + "alignafid1").val() + "_A," + $("#" + me.pre + "alignafid2").val() + "_A";
             me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment + " | residues | resdef ", false);
-            window.open(hostUrl + '?chainalign=' + alignment + '&resnum=&resdef=&showalignseq=1', '_blank');
+            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+            window.open(hostUrl + '?chainalign=' + alignment + '&resnum=&resdef=&showalignseq=1', urlTarget);
           });
 
-        me.myEventCls.onIds("#" + me.pre + "reload_alignaf_tmalign", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_alignaf_tmalign", "click", function(e) { let ic = me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
             let alignment = $("#" + me.pre + "alignafid1").val() + "_A," + $("#" + me.pre + "alignafid2").val() + "_A";
             me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment + " | residues | resdef | align tmalign", false);
-            window.open(hostUrl + '?chainalign=' + alignment + '&aligntool=tmalign&resnum=&resdef=&showalignseq=1', '_blank');
+            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+            window.open(hostUrl + '?chainalign=' + alignment + '&aligntool=tmalign&resnum=&resdef=&showalignseq=1', urlTarget);
           });
     //    },
     //    clickReload_chainalign: function() {
@@ -61641,11 +61729,11 @@ class Events {
            }
 
            me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " | residues " + resalign + " | resdef " + predefinedres, false);
-           window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=' + resalign + '&resdef=' + predefinedres + '&showalignseq=1', '_blank');
+           window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=' + resalign + '&resdef=' + predefinedres + '&showalignseq=1', urlTarget);
         });
 */
 
-        me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
 
@@ -61653,10 +61741,11 @@ class Events {
            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');
+           let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+           window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=&resdef=&showalignseq=1&bu=0', urlTarget);
         });
 
-        me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym2", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym2", "click", function(e) { let ic = me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
  
@@ -61665,10 +61754,11 @@ class Events {
             let resalign = $("#" + me.pre + "resalignids").val();
  
             me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues " + resalign + " | resdef ", false);
-            window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=' + resalign + '&resdef=&showalignseq=1&bu=0', '_blank');
+            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+            window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=' + resalign + '&resdef=&showalignseq=1&bu=0', urlTarget);
          });
 
-         me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym3", "click", function(e) { me.icn3d;
+         me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym3", "click", function(e) { let ic = me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
  
@@ -61682,7 +61772,8 @@ class Events {
             }
  
             me.htmlCls.clickMenuCls.setLogCmd("load chains " + alignment_final + " on asymmetric unit | residues | resdef " + predefinedres, false);
-            window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=&resdef=' + predefinedres + '&showalignseq=1&bu=0', '_blank');
+            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+            window.open(hostUrl + '?chainalign=' + alignment_final + '&resnum=&resdef=' + predefinedres + '&showalignseq=1&bu=0', urlTarget);
          });
 
          me.myEventCls.onIds("#" + me.pre + "reload_chainalign_asym4", "click", function(e) { let ic = me.icn3d;
@@ -61707,7 +61798,7 @@ class Events {
             me.htmlCls.clickMenuCls.setLogCmd("realign predefined " + alignment_final + " " + predefinedres, true);
          });
 
-        me.myEventCls.onIds("#" + me.pre + "reload_chainalign_tmalign", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_chainalign_tmalign", "click", function(e) { let ic = me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
 
@@ -61715,7 +61806,8 @@ class Events {
             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');
+            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+            window.open(hostUrl + '?chainalign=' + alignment_final + '&aligntool=tmalign&resnum=&resdef=&showalignseq=1&bu=0', urlTarget);
          });
 
         me.myEventCls.onIds("#" + me.pre + "reload_mutation_3d", "click", function(e) { let ic = me.icn3d;
@@ -61747,7 +61839,8 @@ class Events {
            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');
+                let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+                window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap 3d ' + mutationids + '; select displayed set', urlTarget);
            }
         });
 
@@ -61780,7 +61873,8 @@ class Events {
            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');
+                let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+                window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap pdb ' + mutationids + '; select displayed set', urlTarget);
            }
         });
 
@@ -61837,44 +61931,49 @@ class Events {
                 ic.resid2specCls.residueids2spec(residArray);
 
                 me.htmlCls.clickMenuCls.setLogCmd("interaction change of mutation " + mutationids, false);
-                window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap interaction ' + mutationids, '_blank');
+                let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+                window.open(hostUrl + '?' + idsource + '=' + mmdbid + '&command=scap interaction ' + mutationids, urlTarget);
            }
         });
 
     //    },
     //    clickReload_mmcif: function() {
-        me.myEventCls.onIds("#" + me.pre + "reload_mmcif", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_mmcif", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
            me.htmlCls.clickMenuCls.setLogCmd("load mmcif " + $("#" + me.pre + "mmcifid").val(), false);
-           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmcifid=' + $("#" + me.pre + "mmcifid").val(), '_blank');
-           window.open(hostUrl + '?mmcifid=' + $("#" + me.pre + "mmcifid").val(), '_blank');
+           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmcifid=' + $("#" + me.pre + "mmcifid").val(), urlTarget);
+           let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+           window.open(hostUrl + '?mmcifid=' + $("#" + me.pre + "mmcifid").val(), urlTarget);
         });
 
-        me.myEventCls.onIds("#" + me.pre + "mmcifid", "keyup", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "mmcifid", "keyup", function(e) { let ic = me.icn3d;
            if (e.keyCode === 13) {
                e.preventDefault();
                if(!me.cfg.notebook) dialog.dialog( "close" );
                me.htmlCls.clickMenuCls.setLogCmd("load mmcif " + $("#" + me.pre + "mmcifid").val(), false);
-               //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmcifid=' + $("#" + me.pre + "mmcifid").val(), '_blank');
-               window.open(hostUrl + '?mmcifid=' + $("#" + me.pre + "mmcifid").val(), '_blank');
+               //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmcifid=' + $("#" + me.pre + "mmcifid").val(), urlTarget);
+               let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+               window.open(hostUrl + '?mmcifid=' + $("#" + me.pre + "mmcifid").val(), urlTarget);
            }
         });
 
     //    },
     //    clickReload_mmdb: function() {
-        me.myEventCls.onIds("#" + me.pre + "reload_mmdb", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_mmdb", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            //if(!me.cfg.notebook) dialog.dialog( "close" );
            me.htmlCls.clickMenuCls.setLogCmd("load mmdb1 " + $("#" + me.pre + "mmdbid").val(), false);
-           window.open(hostUrl + '?mmdbid=' + $("#" + me.pre + "mmdbid").val() + '&bu=1', '_blank');
+           let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+           window.open(hostUrl + '?mmdbid=' + $("#" + me.pre + "mmdbid").val() + '&bu=1', urlTarget);
         });
 
-        me.myEventCls.onIds("#" + me.pre + "reload_mmdb_asym", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_mmdb_asym", "click", function(e) { let ic = me.icn3d;
             e.preventDefault();
             //if(!me.cfg.notebook) dialog.dialog( "close" );
             me.htmlCls.clickMenuCls.setLogCmd("load mmdb0 " + $("#" + me.pre + "mmdbid").val(), false);
-            window.open(hostUrl + '?mmdbid=' + $("#" + me.pre + "mmdbid").val() + '&bu=0', '_blank');
+            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+            window.open(hostUrl + '?mmdbid=' + $("#" + me.pre + "mmdbid").val() + '&bu=0', urlTarget);
         });
 
          me.myEventCls.onIds("#" + me.pre + "reload_mmdbaf", "click", function(e) { me.icn3d;
@@ -61896,12 +61995,13 @@ class Events {
             thisClass.launchMmdb(ids, 0, hostUrl);
         });
 
-        me.myEventCls.onIds("#" + me.pre + "mmdbid", "keyup", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "mmdbid", "keyup", function(e) { let ic = me.icn3d;
            if (e.keyCode === 13) {
                e.preventDefault();
                //if(!me.cfg.notebook) dialog.dialog( "close" );
                me.htmlCls.clickMenuCls.setLogCmd("load mmdb1 " + $("#" + me.pre + "mmdbid").val(), false);
-               window.open(hostUrl + '?mmdbid=' + $("#" + me.pre + "mmdbid").val() + '&bu=1', '_blank');
+               let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+               window.open(hostUrl + '?mmdbid=' + $("#" + me.pre + "mmdbid").val() + '&bu=1', urlTarget);
               }
         });
 
@@ -61916,7 +62016,7 @@ class Events {
 
     //    },
     //    clickReload_blast_rep_id: function() {
-        me.myEventCls.onIds("#" + me.pre + "reload_blast_rep_id", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_blast_rep_id", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
            let query_id = $("#" + me.pre + "query_id").val();
@@ -61925,13 +62025,14 @@ class Events {
            me.htmlCls.clickMenuCls.setLogCmd("load seq_struct_ids " + query_id + "," + blast_rep_id, false);
            query_id =(query_id !== '' && query_id !== undefined) ? query_id : query_fasta;
            //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?from=icn3d&blast_rep_id=' + blast_rep_id
+           let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
            window.open(hostUrl + '?from=icn3d&alg=blast&blast_rep_id=' + blast_rep_id
              + '&query_id=' + query_id
              + '&command=view annotations; set annotation cdd; set annotation site; set view detailed view; select chain '
-             + blast_rep_id + '; show selection', '_blank');
+             + blast_rep_id + '; show selection', urlTarget);
         });
 
-        me.myEventCls.onIds("#" + me.pre + "reload_alignsw", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_alignsw", "click", function(e) { let ic = me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
             let query_id = $("#" + me.pre + "query_id").val();
@@ -61940,13 +62041,14 @@ class Events {
             me.htmlCls.clickMenuCls.setLogCmd("load seq_struct_ids_smithwm " + query_id + "," + blast_rep_id, false);
             query_id =(query_id !== '' && query_id !== undefined) ? query_id : query_fasta;
             
+            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
             window.open(hostUrl + '?from=icn3d&alg=smithwm&blast_rep_id=' + blast_rep_id
               + '&query_id=' + query_id
               + '&command=view annotations; set annotation cdd; set annotation site; set view detailed view; select chain '
-              + blast_rep_id + '; show selection', '_blank');
+              + blast_rep_id + '; show selection', urlTarget);
          });
 
-         me.myEventCls.onIds("#" + me.pre + "reload_alignswlocal", "click", function(e) { me.icn3d;
+         me.myEventCls.onIds("#" + me.pre + "reload_alignswlocal", "click", function(e) { let ic = me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
             let query_id = $("#" + me.pre + "query_id").val();
@@ -61955,75 +62057,84 @@ class Events {
             me.htmlCls.clickMenuCls.setLogCmd("load seq_struct_ids_local_smithwm " + query_id + "," + blast_rep_id, false);
             query_id =(query_id !== '' && query_id !== undefined) ? query_id : query_fasta;
             
+            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
             window.open(hostUrl + '?from=icn3d&alg=local_smithwm&blast_rep_id=' + blast_rep_id
               + '&query_id=' + query_id
               + '&command=view annotations; set annotation cdd; set annotation site; set view detailed view; select chain '
-              + blast_rep_id + '; show selection', '_blank');
+              + blast_rep_id + '; show selection', urlTarget);
          });
 
     //    },
     //    clickReload_gi: function() {
-        me.myEventCls.onIds("#" + me.pre + "reload_gi", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_gi", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
            me.htmlCls.clickMenuCls.setLogCmd("load gi " + $("#" + me.pre + "gi").val(), false);
-           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?gi=' + $("#" + me.pre + "gi").val(), '_blank');
-           window.open(hostUrl + '?gi=' + $("#" + me.pre + "gi").val(), '_blank');
+           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?gi=' + $("#" + me.pre + "gi").val(), urlTarget);
+           let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+           window.open(hostUrl + '?gi=' + $("#" + me.pre + "gi").val(), urlTarget);
         });
 
-        me.myEventCls.onIds("#" + me.pre + "reload_refseq", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_refseq", "click", function(e) { let ic = me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
-            me.htmlCls.clickMenuCls.setLogCmd("load refseq " + $("#" + me.pre + "refseq").val(), false);
-            //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?gi=' + $("#" + me.pre + "gi").val(), '_blank');
-            window.open(hostUrl + '?refseq=' + $("#" + me.pre + "refseq").val(), '_blank');
+            me.htmlCls.clickMenuCls.setLogCmd("load refseq " + $("#" + me.pre + "refseqid").val(), false);
+            //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?gi=' + $("#" + me.pre + "gi").val(), urlTarget);
+            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+            window.open(hostUrl + '?refseqid=' + $("#" + me.pre + "refseqid").val(), urlTarget);
          });
 
-        me.myEventCls.onIds("#" + me.pre + "gi", "keyup", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "gi", "keyup", function(e) { let ic = me.icn3d;
            if (e.keyCode === 13) {
                e.preventDefault();
                if(!me.cfg.notebook) dialog.dialog( "close" );
                me.htmlCls.clickMenuCls.setLogCmd("load gi " + $("#" + me.pre + "gi").val(), false);
-               //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?gi=' + $("#" + me.pre + "gi").val(), '_blank');
-               window.open(hostUrl + '?gi=' + $("#" + me.pre + "gi").val(), '_blank');
+               //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?gi=' + $("#" + me.pre + "gi").val(), urlTarget);
+               let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+               window.open(hostUrl + '?gi=' + $("#" + me.pre + "gi").val(), urlTarget);
            }
         });
 
-        me.myEventCls.onIds("#" + me.pre + "reload_uniprotid", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_uniprotid", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
            me.htmlCls.clickMenuCls.setLogCmd("load uniprotid " + $("#" + me.pre + "uniprotid").val(), false);
-           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?uniprotid=' + $("#" + me.pre + "uniprotid").val(), '_blank');
-           window.open(hostUrl + '?uniprotid=' + $("#" + me.pre + "uniprotid").val(), '_blank');
+           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?uniprotid=' + $("#" + me.pre + "uniprotid").val(), urlTarget);
+           let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+           window.open(hostUrl + '?uniprotid=' + $("#" + me.pre + "uniprotid").val(), urlTarget);
         });
 
-        me.myEventCls.onIds("#" + me.pre + "uniprotid", "keyup", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "uniprotid", "keyup", function(e) { let ic = me.icn3d;
            if (e.keyCode === 13) {
                e.preventDefault();
                if(!me.cfg.notebook) dialog.dialog( "close" );
                me.htmlCls.clickMenuCls.setLogCmd("load uniprotid " + $("#" + me.pre + "uniprotid").val(), false);
-               //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?uniprotid=' + $("#" + me.pre + "uniprotid").val(), '_blank');
-               window.open(hostUrl + '?uniprotid=' + $("#" + me.pre + "uniprotid").val(), '_blank');
+               //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?uniprotid=' + $("#" + me.pre + "uniprotid").val(), urlTarget);
+               let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+               window.open(hostUrl + '?uniprotid=' + $("#" + me.pre + "uniprotid").val(), urlTarget);
            }
         });
 
     //    },
     //    clickReload_cid: function() {
-        me.myEventCls.onIds("#" + me.pre + "reload_cid", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre 
+        + "reload_cid", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
            me.htmlCls.clickMenuCls.setLogCmd("load cid " + $("#" + me.pre + "cid").val(), false);
-           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?cid=' + $("#" + me.pre + "cid").val(), '_blank');
-           window.open(hostUrl + '?cid=' + $("#" + me.pre + "cid").val(), '_blank');
+           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?cid=' + $("#" + me.pre + "cid").val(), urlTarget);
+           let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+           window.open(hostUrl + '?cid=' + $("#" + me.pre + "cid").val(), urlTarget);
         });
 
-        me.myEventCls.onIds("#" + me.pre + "cid", "keyup", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "cid", "keyup", function(e) { let ic = me.icn3d;
            if (e.keyCode === 13) {
                e.preventDefault();
                if(!me.cfg.notebook) dialog.dialog( "close" );
                me.htmlCls.clickMenuCls.setLogCmd("load cid " + $("#" + me.pre + "cid").val(), false);
-               //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?cid=' + $("#" + me.pre + "cid").val(), '_blank');
-               window.open(hostUrl + '?cid=' + $("#" + me.pre + "cid").val(), '_blank');
+               //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?cid=' + $("#" + me.pre + "cid").val(), urlTarget);
+               let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+               window.open(hostUrl + '?cid=' + $("#" + me.pre + "cid").val(), urlTarget);
            }
         });
 
@@ -67857,7 +67968,8 @@ class Vastplus {
 
                 let pdbAjaxArray = [];
                 for(let k = 0, kl = ic.refpdbArray.length; k < kl; ++k) {
-                    let urlpdb = me.htmlCls.baseUrl + "icn3d/refpdb/" + ic.refpdbArray[k] + ".pdb";
+                    //let urlpdb = me.htmlCls.baseUrl + "icn3d/refpdb/" + ic.refpdbArray[k] + ".pdb";
+                    let urlpdb = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi?refpdbid=" + ic.refpdbArray[k];
 
                     let pdbAjax = $.ajax({
                         url: urlpdb,
@@ -67906,7 +68018,7 @@ class Vastplus {
                 // align each 3D domain with reference structure
                 let result = ic.domain3dCls.c2b_NewSplitChain(ic.chains[chainid]);
                 let subdomains = result.subdomains;
-
+                
                 let domainAtomsArray = [];
                 if(subdomains.length <= 1) {
                     domainAtomsArray.push(ic.chains[chainid]);
@@ -67920,6 +68032,7 @@ class Vastplus {
                     for(let k = 0, kl = subdomains.length; k < kl; ++k) {
                         let domainAtoms = {};
                         let segArray = subdomains[k];
+
                         for(let m = 0, ml = segArray.length; m < ml; m += 2) {
                             let startResi = segArray[m];
                             let endResi = segArray[m+1];
@@ -67933,10 +68046,9 @@ class Vastplus {
                         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;
@@ -68028,14 +68140,14 @@ console.log(domainid + ' TM-score: ' + domainid2score[domainid] + ' matched ' +
                 ic.domainid2ig2kabat[domainid] = queryData[0].ig2kabat;
             }
         }
-
+        
         // combine domainid into chainid
         for(let domainid in domainid2segs) {
             let chainid = domainid.split('-')[0];
             if(!chainid2segs[chainid]) chainid2segs[chainid] = [];
             chainid2segs[chainid] = chainid2segs[chainid].concat(domainid2segs[domainid]);
         }
-
+        
         // assign ic.resid2refnum, ic.refnum2residArray, ic.chainsMapping
         if(!ic.resid2refnum) ic.resid2refnum = {};
         if(!ic.refnum2residArray) ic.refnum2residArray = {};
@@ -69798,7 +69910,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.19.1';
+    this.REVISION = '3.20.0';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -70087,11 +70199,20 @@ iCn3DUI.prototype.show3DStructure = function(pdbStr) { let me = this;
        me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
        ic.mmdbParserCls.downloadGi(me.cfg.gi);
     }
-    else if(me.cfg.uniprotid !== undefined) {
-       ic.loadCmd = 'load uniprotid ' + me.cfg.uniprotid;
-       me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
-       ic.mmdbParserCls.downloadUniprotid(me.cfg.uniprotid);
-    }
+    else if(me.cfg.refseqid !== undefined) {
+        ic.inputid = me.cfg.refseqid;
+        
+        ic.bNCBI = true;
+        ic.loadCmd = 'load refseq ' + me.cfg.refseqid;
+        me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
+        ic.mmdbParserCls.downloadRefseq(me.cfg.refseqid);
+     }
+    //  else if(me.cfg.proteinname !== undefined) {
+    //     ic.bNCBI = true;
+    //     ic.loadCmd = 'load proteinname ' + me.cfg.gi;
+    //     me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
+    //     ic.mmdbParserCls.downloadProteinname(me.cfg.proteinname);
+    //  }
     else if(me.cfg.blast_rep_id !== undefined) {
        ic.bNCBI = true;