icn3d 3.25.12 → 3.25.14

package/icn3d.js

@@ -6235,19 +6235,19 @@ class ClickMenu {
         });
 
         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;
+           let 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);
            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
            window.open(url, urlTarget);
         });
 
         me.myEventCls.onIds("#" + me.pre + "mn1_link_vast", "click", function(e) { let ic = me.icn3d; e.preventDefault();
-           if(ic.inputid === undefined) {
-                   url = "https://www.ncbi.nlm.nih.gov/pccompound?term=" + ic.molTitle;
-                   thisClass.setLogCmd("link to compounds " + ic.molTitle + ": " + url, false);
+         let url;  
+         if(ic.inputid === undefined) {
+               url = "https://www.ncbi.nlm.nih.gov/pccompound?term=" + ic.molTitle;
+               thisClass.setLogCmd("link to compounds " + ic.molTitle + ": " + url, false);
            }
            else {
-               let url;
                if(me.cfg.cid !== undefined) {
                        url = "https://www.ncbi.nlm.nih.gov/pccompound?LinkName=pccompound_pccompound_3d&from_uid=" + ic.inputid;
                        thisClass.setLogCmd("link to compounds with structure similar to CID " + ic.inputid + ": " + url, false);
@@ -6271,8 +6271,8 @@ class ClickMenu {
         });
 
         me.myEventCls.onIds("#" + me.pre + "mn1_link_pubmed", "click", function(e) { let ic = me.icn3d; e.preventDefault();
+           let url;
            if(ic.inputid === undefined) {
-               let url;
                url = "https://www.ncbi.nlm.nih.gov/pubmed/?term=" + ic.molTitle;
                thisClass.setLogCmd("link to literature about " + ic.molTitle + ": " + url, false);
                let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
@@ -6280,7 +6280,6 @@ class ClickMenu {
            }
            else if(ic.pmid) {
                let idArray = ic.pmid.toString().split('_');
-               let url;
                if(idArray.length === 1) {
                    url = "https://www.ncbi.nlm.nih.gov/pubmed/" + ic.pmid;
                    thisClass.setLogCmd("link to PubMed ID " + ic.pmid + ": " + url, false);
@@ -6294,7 +6293,6 @@ class ClickMenu {
            }
            else if(isNaN(ic.inputid)) {
                let idArray = ic.inputid.toString().split('_');
-               let url;
                if(idArray.length === 1) {
                    url = "https://www.ncbi.nlm.nih.gov/pubmed/?term=" + ic.inputid;
                    thisClass.setLogCmd("link to literature about PDB " + ic.inputid + ": " + url, false);
@@ -11008,11 +11006,11 @@ class SetDialog {
         
         html += "<div>4. " + me.htmlCls.buttonStr + "applyhbonds'>3D Display Interactions</button></div><br>";
 
-        html += "<div style='text-indent:1.1em'>" + me.htmlCls.buttonStr + "hbondWindow'>Highlight Interactions in Table</button><span style='margin-left:30px; font-wieght:bold'>Sort Interactions on</span>: " + me.htmlCls.buttonStr + "sortSet1'> Set 1</button>" + me.htmlCls.buttonStr + "sortSet2' style='margin-left:20px'>Set 2</button></div><br>";
+        html += "<div style='text-indent:1.1em'>" + me.htmlCls.buttonStr + "hbondWindow'>Highlight Interactions in Table</button><span style='margin-left:30px; font-wieght:bold'>Sort Interactions on</span>: " + me.htmlCls.buttonStr + "sortSet1'> Set 1</button>" + me.htmlCls.buttonStr + "sortSet2' style='margin-left:12px'>Set 2</button></div><br>";
 
-        html += "<div style='text-indent:1.1em'>" + me.htmlCls.buttonStr + "hbondLineGraph'>2D Interaction Network</button> to show interactions between two lines of residue nodes</div><br>";
+        html += "<div style='text-indent:1.1em'>" + me.htmlCls.buttonStr + "hbondLineGraph'>2D Interaction Network</button> " + me.htmlCls.buttonStr + "hbondLineGraph2' style='margin-left:12px'>2D Network with Reference Numbers</button> to show two lines of residue nodes</div><br>";
 
-        html += "<div style='text-indent:1.1em'>" + me.htmlCls.buttonStr + "hbondScatterplot'>2D Interaction Map</button> to show interactions as map</div><br>";
+        html += "<div style='text-indent:1.1em'>" + me.htmlCls.buttonStr + "hbondScatterplot'>2D Interaction Map</button> " + me.htmlCls.buttonStr + "hbondScatterplot2' style='margin-left:12px'>2D Map with Reference Numbers</button> to show map</div><br>";
 
         tmpStr = ': </td><td><input style="margin-left:-12px" type="text" id="';
 
@@ -13425,11 +13423,29 @@ class Events {
         me.myEventCls.onIds("#" + me.pre + "hbondLineGraph", "click", async function(e) { let ic = me.icn3d;
            e.preventDefault();
            
+           ic.bShownRefnum = false;
+           thisClass.setLogCmd("hide ref number", true);
            await ic.showInterCls.showInteractions('linegraph');
         });
+        me.myEventCls.onIds("#" + me.pre + "hbondLineGraph2", "click", async function(e) { let ic = me.icn3d;
+            e.preventDefault();
+            
+            ic.bShownRefnum = true;
+            thisClass.setLogCmd("show ref number", true);
+            await ic.showInterCls.showInteractions('linegraph');
+        });
         me.myEventCls.onIds("#" + me.pre + "hbondScatterplot", "click", async function(e) { let ic = me.icn3d;
+            e.preventDefault();
+            
+            ic.bShownRefnum = false;
+            thisClass.setLogCmd("hide ref number", true);
+            await ic.showInterCls.showInteractions('scatterplot');
+        });
+        me.myEventCls.onIds("#" + me.pre + "hbondScatterplot2", "click", async function(e) { let ic = me.icn3d;
            e.preventDefault();
            
+           ic.bShownRefnum = true;
+           thisClass.setLogCmd("show ref number", true);
            await ic.showInterCls.showInteractions('scatterplot');
         });
         // select residues
@@ -32147,7 +32163,7 @@ class Alternate {
 
         ic.dAtoms = {};
 
-        let bMutation = moleculeArray.length == 2 && moleculeArray[1].replace(moleculeArray[0], '') == '2';
+        let bMutation = ic.bScap; //moleculeArray.length == 2 && moleculeArray[1].replace(moleculeArray[0], '') == '2';
 
         for(let i = 0, il = moleculeArray.length; i < il; ++i) {
             let structure = moleculeArray[i];
@@ -35776,7 +35792,12 @@ class AnnoCddSite {
             || (Object.keys(ic.structures).length == 2 && me.cfg.align) ) {
                 let data = {};
                 try {
-                    data.value = await me.getAjaxPromise(url, 'jsonp');
+                    if(me.bNode) {
+                        data = await me.getAjaxPromise(url, 'jsonp');
+                    }
+                    else {
+                        data.value = await me.getAjaxPromise(url, 'jsonp');
+                    }
                  
                     thisClass.parseCddData([data], chnidArray);
                     /// if(ic.deferredAnnoCddSite !== undefined) ic.deferredAnnoCddSite.resolve();
@@ -35834,7 +35855,9 @@ class AnnoCddSite {
 
         for(let i = 0, il = dataArray.length; i < il; ++i) {
             //let data = (bSeq) ? dataArray[i][0] : dataArray[i];
-            let data = dataArray[i].value;
+            let data = (me.bNode) ? dataArray[i] : dataArray[i].value;
+
+            if(!data) continue;
 
             for(let chainI = 0, chainLen = data.data.length; chainI < chainLen; ++chainI) {
                 let cddData = data.data[chainI];
@@ -38576,49 +38599,48 @@ class Domain3d {
 		let residueArray = Object.keys(residueHash);
 		let chnid = residueArray[0].substr(0, residueArray[0].lastIndexOf('_'));
 
+		if(!ic.posid2resid) ic.posid2resid = {};
+
 		let substructItem = {};
 		let pos2resi = {};
 		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;
-
-				for(let j = 0; j < resiOffset; ++j) {
-					x0.push(undefined);
-					y0.push(undefined);
-					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);
 				z0.push(atom.coord.z);
 			}
 			else {
-				x0.push(undefined);
-				y0.push(undefined);
-				z0.push(undefined);
+				// x0.push(dummyCoord);
+				// y0.push(dummyCoord);
+				// z0.push(dummyCoord);
+
+				continue;
 			}
-*/
-			//if(!atom) continue;   
-			
-			x0.push(atom.coord.x);
-			y0.push(atom.coord.y);
-			z0.push(atom.coord.z);
+	
+			// if(!atom) {
+			// 	// continue;    
+			// }
+
+			// x0.push(atom.coord.x);
+			// y0.push(atom.coord.y);
+			// z0.push(atom.coord.z);
+
 			//resiArray.push(resi);
 			resiArray.push(i+1);
 			pos2resi[i+1] = resi;
 
+			ic.posid2resid[atom.structure + '_' + atom.chain + '_' + (i+1).toString()]  = resid;
+			// let residNCBI = ic.resid2ncbi[resid];
+			// let pos = residNCBI.substr(residNCBI.lastIndexOf('_') + 1);
+			// pos2resi[pos] = resi;
+
 			if(atom.ssend) {
 				//substructItem.To = parseInt(resi);
 				substructItem.To = i + 1;
@@ -39037,8 +39059,8 @@ class Domain3d {
 					ic.tddomains[domainName][resid] = 1;
 				}
 			}
-		}
-				
+		}			
+
 		return {subdomains: subdomains, substruct: substruct, pos2resi: pos2resi };
 	} // end c2b_NewSplitChain
 
@@ -39056,9 +39078,14 @@ class Domain3d {
 		//the whole structure is also considered as a large domain
 		//if(subdomains.length == 0) {
 			//subdomains.push([parseInt(ic.chainsSeq[chnid][0].resi), parseInt(ic.chainsSeq[chnid][ic.chainsSeq[chnid].length - 1].resi)]);
-			subdomains.push([parseInt(residueArray[0].substr(residueArray[0].lastIndexOf('_') + 1)), 
-			 	parseInt(residueArray[residueArray.length-1].substr(residueArray[residueArray.length-1].lastIndexOf('_') + 1))]);
-		//}
+
+			// subdomains.push([parseInt(residueArray[0].substr(residueArray[0].lastIndexOf('_') + 1)), 
+			//  	parseInt(residueArray[residueArray.length-1].substr(residueArray[residueArray.length-1].lastIndexOf('_') + 1))]);
+
+			// use position based
+			subdomains.push([1, residueArray.length]);
+				
+		//}	
 
 		// m_domains1: {"data": [ {"ss": [[1,20,30,x,y,z,x,y,z], [2,50,60,x,y,z,x,y,z]], "domain": [[1,43,x,y,z],[2,58,x,y,z], ...]}, {"ss": [[1,20,30,x,y,z,x,y,z], [2,50,60,x,y,z,x,y,z]],"domain": [[1,43,x,y,z],[2,58,x,y,z], ...]} ] }
 		let jsonStr = '{"data": [';
@@ -39078,6 +39105,10 @@ class Domain3d {
 					let from = pos2resi[substruct[k].From];
 					let to = pos2resi[substruct[k].To];
 
+					// 1-based residue numbers
+					let fromPos = substruct[k].From;
+					let toPos = substruct[k].To;
+
 					let residFrom = chnid + "_" + from;
 					let atomFrom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.residues[residFrom]);
 					if(!atomFrom || !ic.hAtoms.hasOwnProperty(atomFrom.serial)) continue;
@@ -39086,9 +39117,9 @@ class Domain3d {
 					let atomTo = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.residues[residTo]);
 					if(!atomTo || !ic.hAtoms.hasOwnProperty(atomTo.serial)) continue;
 
-					if(from >= start && to <= end) {
+					if(fromPos >= start && toPos <= end) {
 						if(ssCnt > 0) jsonStr += ', ';
-						jsonStr += '[' + sstype + ',' + from + ',' + to + ',' + substruct[k].x1.toFixed(2) + ',' + substruct[k].y1.toFixed(2) + ',' 
+						jsonStr += '[' + sstype + ',' + fromPos + ',' + toPos + ',' + substruct[k].x1.toFixed(2) + ',' + substruct[k].y1.toFixed(2) + ',' 
 							+ substruct[k].z1.toFixed(2) + ',' + substruct[k].x2.toFixed(2) + ',' + substruct[k].y2.toFixed(2) + ',' + substruct[k].z2.toFixed(2) + ']';
 						++ssCnt;
 					}
@@ -39106,7 +39137,10 @@ class Domain3d {
 				for(let k = 0, kl = residueArray.length; k < kl; ++k) {
 					let resid = residueArray[k];
 
-					let resi = resid.substr(resid.lastIndexOf('_') + 1);
+					// let resi = resid.substr(resid.lastIndexOf('_') + 1);
+					// let residNCBI = ic.resid2ncbi[resid];
+					// let pos = residNCBI.substr(residNCBI.lastIndexOf('_') + 1);
+					let pos = k + 1;
 		
 					//let resid = chnid + "_" + resi;
 					let atom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.residues[resid]);
@@ -39116,9 +39150,9 @@ class Domain3d {
 
 					//domain: resi, restype, x, y, z
 					let restype = me.parasCls.resn2restype[atom.resn];
-					if(restype !== undefined && resi >= start && resi <= end) {
+					if(restype !== undefined && pos >= start && pos <= end) {
 						if(domainCnt > 0) jsonStr += ', ';
-						jsonStr += '[' + resi + ',' + restype + ',' + atom.coord.x.toFixed(2) + ',' 
+						jsonStr += '[' + pos + ',' + restype + ',' + atom.coord.x.toFixed(2) + ',' 
 							+ atom.coord.y.toFixed(2) + ',' + atom.coord.z.toFixed(2) + ']';
 						++domainCnt;
 					}
@@ -39948,7 +39982,7 @@ class AddTrack {
         let bUnion = false, bUpdateHighlight = true;
 
         let strandCnt = 0, loopCnt = 0;
-        let setName, currStrand, prevStrand, prevStrandReal, currType, prevType;
+        let setName, currStrand, prevStrand, prevStrandReal = 'NT', currType, prevType;
 
         // clear selection
         ic.hAtoms = {};
@@ -40015,6 +40049,7 @@ class AddTrack {
         }
         else if(prevType == 'igloop') {
             ++loopCnt;
+            currStrand = 'CT';
             setName = 'Loop-' + prevStrandReal + '_' + currStrand + '-' + chainid + '-' + loopCnt.toString().padStart(3, '0');
             setName = setName.replace(/'/g, '`');
             if(type == 'igloop') ic.selectionCls.selectResidueList(selectedResidues, setName, setName, bUnion, bUpdateHighlight);
@@ -41093,7 +41128,7 @@ class ShowAnno {
             }
             catch(err) {
                 thisClass.enableHlSeq();
-                if(!me.bNode) console.log( "No data were found for the protein " + chnidBaseArray + "..." );
+                if(!me.bNode) console.log( "No sequence data were found for the protein " + chnidBaseArray + "..." );
                 for(let chnid in ic.protein_chainid) {
                     let chnidBase = ic.protein_chainid[chnid];
                     ic.showSeqCls.setAlternativeSeq(chnid, chnidBase);
@@ -41219,7 +41254,7 @@ class ShowAnno {
                 }
             }
             else {
-                if(!me.bNode) console.log( "No data were found for the chain " + chnid + "..." );
+                if(!me.bNode) console.log( "No sequence data were found for the chain " + chnid + "..." );
                 ic.showSeqCls.setAlternativeSeq(chnid, chnidBase);
             }
                      
@@ -42313,6 +42348,8 @@ class ShowSeq {
                     // assign the adjusted reference numbers
                     ic.resid2refnum[residueid] = refnumLabel;
 
+                    refnumStr = ic.refnumCls.rmStrandFromRefnumlabel(refnumLabel);
+
                     if(!ic.refnum2residArray.hasOwnProperty(refnumStr)) {
                         ic.refnum2residArray[refnumStr] = [residueid];
                     }
@@ -44301,6 +44338,11 @@ class GetGraph {
             if(!bVertical) adjusty += 4 * r;
         }
 
+        // show reference numbers
+        if(ic.bShownRefnum && ic.resid2refnum[resid]) {
+            nodeName = ic.resid2refnum[resid];
+        }
+
         let strokecolor = '#000';
         let strokewidth = '1';
         let textcolor = '#000';
@@ -44489,7 +44531,8 @@ class GetGraph {
         let complement = firstSetAtoms;
         if(Object.keys(complement).length > 0 && Object.keys(firstSetAtoms).length > 0) {
             let bSaltbridge = false;
-            ic.hBondCls.calculateChemicalHbonds(me.hashUtilsCls.intHash2Atoms(ic.dAtoms, complement, ic.atoms), me.hashUtilsCls.intHash2Atoms(ic.dAtoms, firstSetAtoms, ic.atoms), parseFloat(threshold), bSaltbridge, 'graph', true );
+            // let selectedAtoms = ic.hBondCls.calculateChemicalHbonds(me.hashUtilsCls.intHash2Atoms(ic.dAtoms, complement, ic.atoms), me.hashUtilsCls.intHash2Atoms(ic.dAtoms, firstSetAtoms, ic.atoms), parseFloat(threshold), bSaltbridge, 'graph', true );
+            ic.hBondCls.calculateChemicalHbonds(me.hashUtilsCls.hash2Atoms(complement, ic.atoms), me.hashUtilsCls.hash2Atoms(firstSetAtoms, ic.atoms), parseFloat(threshold), bSaltbridge, 'graph', true );
             resid2ResidhashHbond = me.hashUtilsCls.cloneHash(ic.resid2Residhash);
         }
 
@@ -44506,7 +44549,8 @@ class GetGraph {
         let complement = firstSetAtoms;
         if(Object.keys(complement).length > 0 && Object.keys(firstSetAtoms).length > 0) {
             let bSaltbridge = false;
-            ic.saltbridgeCls.calculateIonicInteractions(me.hashUtilsCls.intHash2Atoms(ic.dAtoms, complement, ic.atoms), me.hashUtilsCls.intHash2Atoms(ic.dAtoms, firstSetAtoms, ic.atoms), parseFloat(threshold), bSaltbridge, 'graph', true );
+            // let selectedAtoms = ic.saltbridgeCls.calculateIonicInteractions(me.hashUtilsCls.intHash2Atoms(ic.dAtoms, complement, ic.atoms), me.hashUtilsCls.intHash2Atoms(ic.dAtoms, firstSetAtoms, ic.atoms), parseFloat(threshold), bSaltbridge, 'graph', true );
+            ic.saltbridgeCls.calculateIonicInteractions(me.hashUtilsCls.hash2Atoms(complement, ic.atoms), me.hashUtilsCls.hash2Atoms(firstSetAtoms, ic.atoms), parseFloat(threshold), bSaltbridge, 'graph', true );
             resid2Residhash = me.hashUtilsCls.cloneHash(ic.resid2Residhash);
         }
         let ionicStr = this.getGraphLinks(resid2Residhash, resid2Residhash, me.htmlCls.ionicInsideColor, labelType, me.htmlCls.ionicInsideValue);
@@ -44519,19 +44563,22 @@ class GetGraph {
         let halogenpiStr = '', threshold;
         threshold = parseFloat($("#" + ic.pre + "halogenthreshold" ).val());
         if(Object.keys(complement).length > 0 && Object.keys(firstSetAtoms).length > 0) {
-            ic.piHalogenCls.calculateHalogenPiInteractions(me.hashUtilsCls.intHash2Atoms(ic.dAtoms, firstSetAtoms, ic.atoms), me.hashUtilsCls.intHash2Atoms(ic.dAtoms, complement, ic.atoms), parseFloat(threshold), 'graph', 'halogen', true );
+            // let selectedAtoms = ic.piHalogenCls.calculateHalogenPiInteractions(me.hashUtilsCls.intHash2Atoms(ic.dAtoms, firstSetAtoms, ic.atoms), me.hashUtilsCls.intHash2Atoms(ic.dAtoms, complement, ic.atoms), parseFloat(threshold), 'graph', 'halogen', true );
+            ic.piHalogenCls.calculateHalogenPiInteractions(me.hashUtilsCls.hash2Atoms(firstSetAtoms, ic.atoms), me.hashUtilsCls.hash2Atoms(complement, ic.atoms), parseFloat(threshold), 'graph', 'halogen', true );
             resid2Residhash = me.hashUtilsCls.cloneHash(ic.resid2Residhash);
         }
         halogenpiStr += this.getGraphLinks(resid2Residhash, resid2Residhash, me.htmlCls.halogenInsideColor, labelType, me.htmlCls.halogenInsideValue);
         threshold = parseFloat($("#" + ic.pre + "picationthreshold" ).val());
         if(Object.keys(complement).length > 0 && Object.keys(firstSetAtoms).length > 0) {
-            ic.piHalogenCls.calculateHalogenPiInteractions(me.hashUtilsCls.intHash2Atoms(ic.dAtoms, firstSetAtoms, ic.atoms), me.hashUtilsCls.intHash2Atoms(ic.dAtoms, complement, ic.atoms), parseFloat(threshold), 'graph', 'pi-cation', true );
+            // let selectedAtoms = ic.piHalogenCls.calculateHalogenPiInteractions(me.hashUtilsCls.intHash2Atoms(ic.dAtoms, firstSetAtoms, ic.atoms), me.hashUtilsCls.intHash2Atoms(ic.dAtoms, complement, ic.atoms), parseFloat(threshold), 'graph', 'pi-cation', true );
+            ic.piHalogenCls.calculateHalogenPiInteractions(me.hashUtilsCls.hash2Atoms(firstSetAtoms, ic.atoms), me.hashUtilsCls.hash2Atoms(complement, ic.atoms), parseFloat(threshold), 'graph', 'pi-cation', true );
             resid2Residhash = me.hashUtilsCls.cloneHash(ic.resid2Residhash);
         }
         halogenpiStr += this.getGraphLinks(resid2Residhash, resid2Residhash, me.htmlCls.picationInsideColor, labelType, me.htmlCls.picationInsideValue);
         threshold = parseFloat($("#" + ic.pre + "pistackingthreshold" ).val());
         if(Object.keys(complement).length > 0 && Object.keys(firstSetAtoms).length > 0) {
-            ic.piHalogenCls.calculateHalogenPiInteractions(me.hashUtilsCls.intHash2Atoms(ic.dAtoms, firstSetAtoms, ic.atoms), me.hashUtilsCls.intHash2Atoms(ic.dAtoms, complement, ic.atoms), parseFloat(threshold), 'graph', 'pi-stacking', true );
+            // let selectedAtoms = ic.piHalogenCls.calculateHalogenPiInteractions(me.hashUtilsCls.intHash2Atoms(ic.dAtoms, firstSetAtoms, ic.atoms), me.hashUtilsCls.intHash2Atoms(ic.dAtoms, complement, ic.atoms), parseFloat(threshold), 'graph', 'pi-stacking', true );
+            ic.piHalogenCls.calculateHalogenPiInteractions(me.hashUtilsCls.hash2Atoms(firstSetAtoms, ic.atoms), me.hashUtilsCls.hash2Atoms(complement, ic.atoms), parseFloat(threshold), 'graph', 'pi-stacking', true );
             resid2Residhash = me.hashUtilsCls.cloneHash(ic.resid2Residhash);
         }
         halogenpiStr += this.getGraphLinks(resid2Residhash, resid2Residhash, me.htmlCls.pistackingInsideColor, labelType, me.htmlCls.pistackingInsideValue);
@@ -44689,6 +44736,15 @@ class ShowInter {
     async showInteractions(type) { let ic = this.icn3d, me = ic.icn3dui;
        let nameArray = $("#" + ic.pre + "atomsCustomHbond").val();
        let nameArray2 = $("#" + ic.pre + "atomsCustomHbond2").val();
+
+       let atoms, atoms2;
+       atoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
+       atoms2 = ic.definedSetsCls.getAtomsFromNameArray(nameArray2);
+
+       // add the interacting atoms to display
+       ic.dAtoms = me.hashUtilsCls.unionHash(ic.dAtoms, atoms);
+       ic.dAtoms = me.hashUtilsCls.unionHash(ic.dAtoms, atoms2);
+
        if(nameArray2.length == 0) {
            var aaa = 1; //alert("Please select the first set");
        }
@@ -44774,7 +44830,8 @@ class ShowInter {
         ic.firstAtomObjCls.getFirstAtomObj(firstSetAtoms);
 
         if(Object.keys(complement).length > 0 && Object.keys(firstSetAtoms).length > 0) {
-            let selectedAtoms = ic.hBondCls.calculateChemicalHbonds(me.hashUtilsCls.intHash2Atoms(ic.dAtoms, complement, ic.atoms), me.hashUtilsCls.intHash2Atoms(ic.dAtoms, firstSetAtoms, ic.atoms), parseFloat(threshold), bSaltbridge );
+            // let selectedAtoms = ic.hBondCls.calculateChemicalHbonds(me.hashUtilsCls.intHash2Atoms(ic.dAtoms, complement, ic.atoms), me.hashUtilsCls.intHash2Atoms(ic.dAtoms, firstSetAtoms, ic.atoms), parseFloat(threshold), bSaltbridge );
+            let selectedAtoms = ic.hBondCls.calculateChemicalHbonds(me.hashUtilsCls.hash2Atoms(complement, ic.atoms), me.hashUtilsCls.hash2Atoms(firstSetAtoms, ic.atoms), parseFloat(threshold), bSaltbridge );
             let commanddesc;
             if(bSaltbridge) {
                 ic.resid2ResidhashSaltbridge = me.hashUtilsCls.cloneHash(ic.resid2Residhash);
@@ -44901,7 +44958,8 @@ class ShowInter {
         complement = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
         ic.firstAtomObjCls.getFirstAtomObj(firstSetAtoms);
         if(Object.keys(complement).length > 0 && Object.keys(firstSetAtoms).length > 0) {
-            let selectedAtoms = ic.saltbridgeCls.calculateIonicInteractions(me.hashUtilsCls.intHash2Atoms(ic.dAtoms, complement, ic.atoms), me.hashUtilsCls.intHash2Atoms(ic.dAtoms, firstSetAtoms, ic.atoms), parseFloat(threshold), bSaltbridge );
+            // let selectedAtoms = ic.saltbridgeCls.calculateIonicInteractions(me.hashUtilsCls.intHash2Atoms(ic.dAtoms, complement, ic.atoms), me.hashUtilsCls.intHash2Atoms(ic.dAtoms, firstSetAtoms, ic.atoms), parseFloat(threshold), bSaltbridge );
+            let selectedAtoms = ic.saltbridgeCls.calculateIonicInteractions(me.hashUtilsCls.hash2Atoms(complement, ic.atoms), me.hashUtilsCls.hash2Atoms(firstSetAtoms, ic.atoms), parseFloat(threshold), bSaltbridge );
             let commanddesc;
             ic.resid2ResidhashSaltbridge = me.hashUtilsCls.cloneHash(ic.resid2Residhash);
             commanddesc = 'all atoms that have ionic interactions with the selected atoms';
@@ -44936,7 +44994,8 @@ class ShowInter {
         complement = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
         ic.firstAtomObjCls.getFirstAtomObj(firstSetAtoms);
         if(Object.keys(complement).length > 0 && Object.keys(firstSetAtoms).length > 0) {
-            let selectedAtoms = ic.piHalogenCls.calculateHalogenPiInteractions(me.hashUtilsCls.intHash2Atoms(ic.dAtoms, firstSetAtoms, ic.atoms), me.hashUtilsCls.intHash2Atoms(ic.dAtoms, complement, ic.atoms), parseFloat(threshold), type, interactionType );
+            // let selectedAtoms = ic.piHalogenCls.calculateHalogenPiInteractions(me.hashUtilsCls.intHash2Atoms(ic.dAtoms, firstSetAtoms, ic.atoms), me.hashUtilsCls.intHash2Atoms(ic.dAtoms, complement, ic.atoms), parseFloat(threshold), type, interactionType );
+            let selectedAtoms = ic.piHalogenCls.calculateHalogenPiInteractions(me.hashUtilsCls.hash2Atoms(firstSetAtoms, ic.atoms), me.hashUtilsCls.hash2Atoms(complement, ic.atoms), parseFloat(threshold), type, interactionType );
             let commanddesc;
             if(interactionType == 'halogen') {
                 ic.resid2ResidhashHalogen = me.hashUtilsCls.cloneHash(ic.resid2Residhash);
@@ -45061,7 +45120,8 @@ class ShowInter {
     pickCustomSphere_base(radius, atomlistTarget, otherAtoms, bSphereCalc, bInteraction, type, select, bGetPairs, bIncludeTarget) {  let ic = this.icn3d, me = ic.icn3dui;  // ic.pAtom is set already
         let atoms;
         if(bInteraction) {
-            atoms = ic.contactCls.getAtomsWithinAtom(me.hashUtilsCls.intHash2Atoms(ic.dAtoms, otherAtoms, ic.atoms), me.hashUtilsCls.intHash2Atoms(ic.dAtoms, atomlistTarget, ic.atoms), parseFloat(radius), bGetPairs, bInteraction, undefined, bIncludeTarget);
+            // atoms = ic.contactCls.getAtomsWithinAtom(me.hashUtilsCls.intHash2Atoms(ic.dAtoms, otherAtoms, ic.atoms), me.hashUtilsCls.intHash2Atoms(ic.dAtoms, atomlistTarget, ic.atoms), parseFloat(radius), bGetPairs, bInteraction, undefined, bIncludeTarget);
+            atoms = ic.contactCls.getAtomsWithinAtom(me.hashUtilsCls.hash2Atoms(otherAtoms, ic.atoms), me.hashUtilsCls.hash2Atoms(atomlistTarget, ic.atoms), parseFloat(radius), bGetPairs, bInteraction, undefined, bIncludeTarget);
             ic.resid2ResidhashInteractions = me.hashUtilsCls.cloneHash(ic.resid2Residhash);
         }
         else {
@@ -46772,8 +46832,8 @@ class AlignParser {
             let dataArray = await allPromise;
 
             let data2 = data;
-            let data3 = dataArray[0].value; //v3[0];
-            let data4 = dataArray[1].value; //v4[0];
+            let data3 = (me.bNode) ? dataArray[0] : dataArray[0].value; //v3[0];
+            let data4 = (me.bNode) ? dataArray[1] : dataArray[1].value; //v4[0];
 
             if(data3.atoms !== undefined && data4.atoms !== undefined) {
                 // ic.deferredOpm = $.Deferred(function() {
@@ -46935,7 +46995,7 @@ class AlignParser {
             
             let bFound = false;
             for(let i = 0, il = dataArray.length; i < il; ++i) {
-                let opmdata = dataArray[i].value;
+                let opmdata = (me.bNode) ? dataArray[i] : dataArray[i].value;
 
                 if(!opmdata) continue;
 
@@ -47095,7 +47155,7 @@ class ChainalignParser {
 
         // modify the previous trans and rotation matrix
         for(let i = 0, il = dataArray.length; i < il; ++i) {
-            let align = dataArray[i].value;//[0];
+            let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
 
             let mmdbid_q = struArray[i];
             let index = indexArray[i];
@@ -47173,7 +47233,7 @@ class ChainalignParser {
         return hAtomsAll;
     }
 
-    downloadChainalignmentPart2bRealign(dataArray, chainidPairArray) { let ic = this.icn3d, me = ic.icn3dui;
+    downloadChainalignmentPart2bRealign(dataArray, chainidPairArray, bReverse) { let ic = this.icn3d, me = ic.icn3dui;
         // set trans and rotation matrix
         ic.t_trans_add = [];
         ic.q_trans_sub = [];
@@ -47187,7 +47247,7 @@ class ChainalignParser {
              
         let bFoundAlignment = false;
         for(let i = 0, il = dataArray.length; i < il; ++i) {
-            let align = dataArray[i].value;//[0];
+            let align = (me.bNode) ? dataArray[i] : dataArray[i].value;//[0];
 
             let bEqualMmdbid = false;
             let bEqualChain = false;
@@ -47215,9 +47275,16 @@ class ChainalignParser {
         }
 
         if(!bFoundAlignment) {
-            /// if(ic.deferredRealignByStruct !== undefined) ic.deferredRealignByStruct.resolve();
-            if(ic.bRender) var aaa = 1; //alert("These structures can NOT be aligned...");
-            return;
+            // sometimes VAST align works for the reversed pair
+            if(!bReverse) {
+                ic.realignParserCls.realignOnStructAlign(true);
+                return;
+            }
+            else {
+                /// if(ic.deferredRealignByStruct !== undefined) ic.deferredRealignByStruct.resolve();
+                if(ic.bRender) var aaa = 1; //alert("These structures can NOT be aligned...");
+                return;
+            }
         }
 
         // find the max aligned mmdbid as mmdbid_t
@@ -47572,7 +47639,7 @@ class ChainalignParser {
         // Each argument is an array with the following structure: [ data, statusText, jqXHR ]
         //var data2 = v2[0];
         // index = 0: the mmdb data of target
-        let targetData = dataArray[0].value; //[0];
+        let targetData = (me.bNode) ? dataArray[0] : dataArray[0].value; //[0];
         let header = 'HEADER                                                        ' + mmdbid_t + '\n';
         if(isNaN(mmdbid_t) && mmdbid_t.length > 5) targetData = header + targetData;
 
@@ -47590,7 +47657,7 @@ class ChainalignParser {
         let queryDataArray = [];
 
         for(let index = 1, indexl = chainidArray.length; index < indexl; ++index) {
-            let queryData = dataArray[index].value;//[0];
+            let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
 
             let pos = chainidArray[index].indexOf('_');
             let mmdbid_q = chainidArray[index].substr(0, pos).toUpperCase();
@@ -47636,7 +47703,7 @@ class ChainalignParser {
                     ic.qt_start_end[index-1] = undefined;
                 }
                 else {
-                    let align = dataArray[index2 - missedChainCnt].value;//[0];
+                    let align = (me.bNode) ? dataArray[index2 - missedChainCnt] : dataArray[index2 - missedChainCnt].value;//[0];
 
                     let bEqualMmdbid = (mmdbid_q == mmdbid_t);
                     let bEqualChain = (chain_q == chain_t);
@@ -47854,7 +47921,7 @@ class ChainalignParser {
 
         let queryDataArray = [];
         for(let index = 0, indexl = structArray.length; index < indexl; ++index) {
-            let queryData = dataArray[index].value;//[0];
+            let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
             let header = 'HEADER                                                        ' + structArray[index] + '\n';
             if(isNaN(structArray[index]) && structArray[index].length > 5) queryData = header + queryData;
 
@@ -50306,7 +50373,7 @@ class RealignParser {
       //var data2 = v2[0];
       for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
     //  for(let index = 1, indexl = dataArray.length; index < indexl; ++index) {
-          let data = dataArray[index].value;//[0];
+          let data = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
           if(!data) continue;
 
           let fromStruct = chainidArray[index + 1].substr(0, chainidArray[index + 1].indexOf('_')); //.toUpperCase();
@@ -50489,7 +50556,7 @@ class RealignParser {
         await this.realignChainOnSeqAlign(undefined, chainidArray, bRealign);
     }
 
-    async realignOnStructAlign() { let ic = this.icn3d, me = ic.icn3dui;
+    async realignOnStructAlign(bReverse) { let ic = this.icn3d, me = ic.icn3dui;
         // each 3D domain should have at least 3 secondary structures
         let minSseCnt = (me.cfg.aligntool != 'tmalign') ? 3 : 0;
         let struct2domain = {};
@@ -50516,6 +50583,8 @@ class RealignParser {
 
         //let cnt = 0;
         let structArray = Object.keys(struct2domain);
+        if(bReverse) structArray = structArray.reverse();
+
         for(let s = 0, sl = structArray.length; s < sl; ++s) {
             let struct1 = structArray[s];
             let chainidArray1 = Object.keys(struct2domain[struct1]);
@@ -50559,14 +50628,14 @@ class RealignParser {
         }
 
         let allPromise = Promise.allSettled(ajaxArray);
-        try {
+        // try {
             let dataArray = await allPromise;
             ic.qt_start_end = []; // reset the alignment
-            await ic.chainalignParserCls.downloadChainalignmentPart2bRealign(dataArray, chainidPairArray);  
-        }
-        catch(err) {
-            if(ic.bRender) var aaa = 1; //alert("These structures can NOT be aligned to each other...");
-        }                   
+            await ic.chainalignParserCls.downloadChainalignmentPart2bRealign(dataArray, chainidPairArray, bReverse);  
+        // }
+        // catch(err) {
+        //     if(ic.bRender) var aaa = 1; //alert("These structures can NOT be aligned to each other...");
+        // }                   
     }
 
     async realignOnStructAlignMsa(nameArray) { let ic = this.icn3d, me = ic.icn3dui;
@@ -50628,7 +50697,7 @@ class RealignParser {
         }
 
         let allPromise = Promise.allSettled(ajaxArray);
-        try {
+        // try {
             let dataArray = await allPromise;
 
             // set trans and rotation matrix
@@ -50642,10 +50711,10 @@ class RealignParser {
 
             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...");
-        }                   
+        // }
+        // 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;
@@ -52154,13 +52223,13 @@ class ParserUtils {
         let allPromise = Promise.allSettled([prms1, prms2]);
         let dataArray = await allPromise;
         
-        ic.interactionData1 = dataArray[0].value;
+        ic.interactionData1 = (me.bNode) ? dataArray[0] : dataArray[0].value;
         ic.html2ddgm = '';
         ic.diagram2dCls.draw2Ddgm(ic.interactionData1, mmdbid1, 0);
         if(me.cfg.show2d) me.htmlCls.dialogCls.openDlg('dl_2ddgm', 'Interactions');
 
 
-        ic.interactionData2 = dataArray[1].value;
+        ic.interactionData2 = (me.bNode) ? dataArray[1] : dataArray[1].value;
         ic.diagram2dCls.draw2Ddgm(ic.interactionData2, mmdbid2, 1);
 
         ic.html2ddgm += "<br>" + ic.diagram2dCls.set2DdgmNote(true);
@@ -52208,7 +52277,7 @@ class ParserUtils {
         // Each argument is an array with the following structure: [ data, statusText, jqXHR ]
         //var data2 = v2[0];
         for(let index = 0, indexl = chainidArray.length; index < indexl; ++index) {
-            let data = dataArray[index].value;//[0];
+            let data = (me.bNode) ? dataArray[index] : dataArray[index].value;//[0];
             let mmdbid = chainidArray[index].substr(0, chainidArray[index].indexOf('_'));
 
             ic.diagram2dCls.draw2Ddgm(data, mmdbid, 0);
@@ -53821,7 +53890,8 @@ class SetSeqAlign {
         return pos;
     }
 
-    getResnFromResi(chainid, resi) { let ic = this.icn3d, me = ic.icn3dui;
+    getResnFromResi(chainid, resi) { let ic = this.icn3d; ic.icn3dui;
+        /*
         let pos = this.getPosFromResi(chainid, resi);
         if(!pos) return '?';
 
@@ -53836,6 +53906,28 @@ class SetSeqAlign {
         }
 
         return resn;
+        */
+
+        let resid = chainid + '_' + resi;
+        return ic.residueId2Name[resid];
+    }
+
+    getResiAferAlign(chainid, bRealign, pos) { let ic = this.icn3d, me = ic.icn3dui;
+        let resi;
+        if(bRealign && me.cfg.aligntool == 'tmalign') {
+          resi = pos;
+        }
+        else {
+          if(ic.posid2resid) {
+              let resid = ic.posid2resid[chainid + '_' + pos];
+              resi = resid.substr(resid.lastIndexOf('_') + 1);
+          }
+          else {
+              resi = ic.chainsSeq[chainid][pos].resi;
+          }
+        }
+
+        return resi;
     }
 
     setSeqAlignChain(chainid, chainIndex, chainidArray) { let ic = this.icn3d, me = ic.icn3dui;
@@ -53943,10 +54035,10 @@ class SetSeqAlign {
           if(!ic.chainsMapping[chainid2]) ic.chainsMapping[chainid2] = {};
 
           let posChain1 = {}, posChain2 = {};
-         
+
           for(let i = 0, il = ic.qt_start_end[chainIndex].length; i < il; ++i) {
             let start1, start2, end1, end2;
-            if(bRealign) { // real residue numbers are stored, could be "100a"
+            if(bRealign && me.cfg.aligntool == 'tmalign') { // real residue numbers are stored, could be "100a"
                 start1 = parseInt(ic.qt_start_end[chainIndex][i].t_start);
                 start2 = parseInt(ic.qt_start_end[chainIndex][i].q_start);
                 end1 = parseInt(ic.qt_start_end[chainIndex][i].t_end);
@@ -53968,7 +54060,7 @@ class SetSeqAlign {
 
           for(let i = 0, il = ic.qt_start_end[chainIndex].length; i < il; ++i) {
               let start1, start2, end1, end2;
-              if(bRealign) { // real residue numbers are stored
+              if(bRealign && me.cfg.aligntool == 'tmalign') { // real residue numbers are stored
                 start1 = parseInt(ic.qt_start_end[chainIndex][i].t_start);
                 start2 = parseInt(ic.qt_start_end[chainIndex][i].q_start);
                 end1 = parseInt(ic.qt_start_end[chainIndex][i].t_end);
@@ -53990,8 +54082,9 @@ class SetSeqAlign {
 
                       if(ic.chainsSeq[chainid1] === undefined || ic.chainsSeq[chainid1][j] === undefined) break;
 
-                      let resi = (bRealign) ? j : ic.chainsSeq[chainid1][j].resi;
-                      let resn = (bRealign) ? this.getResnFromResi(chainid1, j).toLowerCase() : ic.chainsSeq[chainid1][j].name.toLowerCase();
+                      let resi = this.getResiAferAlign(chainid1, bRealign, j + 1);
+                      //   let resn = (bRealign && me.cfg.aligntool == 'tmalign') ? this.getResnFromResi(chainid1, j).toLowerCase() : ic.chainsSeq[chainid1][j].name.toLowerCase();
+                      let resn = this.getResnFromResi(chainid1, resi).toLowerCase();
                       
                       if(resn == '?') continue;
 
@@ -54009,11 +54102,11 @@ class SetSeqAlign {
                       posChain2[j] = 1;
 
                       if(ic.chainsSeq[chainid2] === undefined || ic.chainsSeq[chainid2] === undefined) break;
-                      
-                      //let resi = ic.chainsSeq[chainid2][j].resi;
-                      //let resn = ic.chainsSeq[chainid2][j].name.toLowerCase();
-                      let resi = (bRealign) ? j : ic.chainsSeq[chainid2][j].resi;
-                      let resn = (bRealign) ? this.getResnFromResi(chainid2, j).toLowerCase() : ic.chainsSeq[chainid2][j].name.toLowerCase();
+
+                      let resi = this.getResiAferAlign(chainid2, bRealign, j + 1);
+                      //   let resn = (bRealign && me.cfg.aligntool == 'tmalign') ? this.getResnFromResi(chainid2, j).toLowerCase() : ic.chainsSeq[chainid2][j].name.toLowerCase();
+                      let resn = this.getResnFromResi(chainid2, resi).toLowerCase();
+
 
                       if(resn == '?') continue;
 
@@ -54057,9 +54150,24 @@ class SetSeqAlign {
                   if(ic.chainsSeq[chainid1] === undefined || ic.chainsSeq[chainid2] === undefined) break;
 
                   let resi1, resi2, resn1, resn2;
+/*                 
                   if(bRealign) { // tmalign: just one residue in this for loop
-                    // resi1 = j + start1;
-                    // resi2 = j + start2;
+                    if(me.cfg.aligntool == 'tmalign') {
+                        resi1 = ic.qt_start_end[chainIndex][i].t_start;
+                        resi2 = ic.qt_start_end[chainIndex][i].q_start;
+                    }
+                    else {
+                        resi1 = j + start1;
+                        resi2 = j + start2;
+                    }
+
+                    resn1 = this.getResnFromResi(chainid1, resi1).toUpperCase();
+                    resn2 = this.getResnFromResi(chainid2, resi2).toUpperCase();
+
+                    if(resn1 == '?' || resn2 == '?') continue;
+                  }
+*/
+                  if(bRealign && me.cfg.aligntool == 'tmalign') { // tmalign: just one residue in this for loop
                     resi1 = ic.qt_start_end[chainIndex][i].t_start;
                     resi2 = ic.qt_start_end[chainIndex][i].q_start;
 
@@ -54071,10 +54179,15 @@ class SetSeqAlign {
                   else {
                     if(ic.chainsSeq[chainid1][j + start1] === undefined || ic.chainsSeq[chainid2][j + start2] === undefined) continue;
 
-                    resi1 = ic.chainsSeq[chainid1][j + start1].resi;
-                    resi2 = ic.chainsSeq[chainid2][j + start2].resi;
-                    resn1 = ic.chainsSeq[chainid1][j + start1].name.toUpperCase();
-                    resn2 = ic.chainsSeq[chainid2][j + start2].name.toUpperCase();
+                    // resi1 = ic.chainsSeq[chainid1][j + start1].resi;
+                    // resi2 = ic.chainsSeq[chainid2][j + start2].resi;
+                    // resn1 = ic.chainsSeq[chainid1][j + start1].name.toUpperCase();
+                    // resn2 = ic.chainsSeq[chainid2][j + start2].name.toUpperCase();
+
+                    resi1 =  this.getResiAferAlign(chainid1, bRealign, j + start1 + 1);
+                    resi2 =  this.getResiAferAlign(chainid2, bRealign, j + start2 + 1);
+                    resn1 = this.getResnFromResi(chainid1, resi1).toUpperCase();
+                    resn2 = this.getResnFromResi(chainid2, resi2).toUpperCase();
                   }
 
                   if(resn1 === resn2) {
@@ -54338,7 +54451,12 @@ class SetSeqAlign {
         resObject.mmdbid = chainid.substr(0, pos);
         resObject.chain = chainid.substr(pos+1);
         resObject.resi = (bGap) ? '' : resi; // resi will be empty if there is no coordinates
-        resObject.resn = (bGap) ? '-' : ((bAligned) ? resn.toUpperCase() : resn.toLowerCase());
+        if(!resn) {
+            resObject.resn = '-';
+        }
+        else {
+            resObject.resn = (bGap) ? '-' : ((bAligned) ? resn.toUpperCase() : resn.toLowerCase());
+        }
         resObject.aligned = (bGap) ? false : bAligned;
         resObject.color = (bGap || !bAligned) ? me.htmlCls.GREYC : ((resn == resn_t) ? "#FF0000" : "#0000FF"); // color by identity
         resObject.color2 = (bGap || !bAligned) ? me.htmlCls.GREYC : '#' + ic.showAnnoCls.getColorhexFromBlosum62(resn, resn_t); // color by conservation
@@ -54372,9 +54490,9 @@ class SetSeqAlign {
         return resn;
     }
 
-    getResnFromResid(resid) { let ic = this.icn3d; ic.icn3dui;
-        return ic.residueId2Name[resid];
-    }
+    // getResnFromResid(resid) { let ic = this.icn3d, me = ic.icn3dui;
+    //     return ic.residueId2Name[resid];
+    // }
 
     getResiPosInTemplate(chainid1, resi_t) { let ic = this.icn3d; ic.icn3dui;
         // check the number of gaps before resiStart1 (nGap), and insert 'notAlnLen2 - notAlnLen1 - nGap' gaps
@@ -54503,7 +54621,7 @@ class SetSeqAlign {
 
         for(let i = 0, il = ic.qt_start_end[chainIndex].length; i < il; ++i) {
             let start1, start2, end1, end2, resiStart1, start1Pos, end1Pos;
-            if(bRealign) { // real residue numbers are stored
+            if(bRealign && me.cfg.aligntool == 'tmalign') { // real residue numbers are stored
                 start1 = parseInt(ic.qt_start_end[chainIndex][i].t_start);
                 start2 = parseInt(ic.qt_start_end[chainIndex][i].q_start);
                 end1 = parseInt(ic.qt_start_end[chainIndex][i].t_end);
@@ -54587,8 +54705,8 @@ class SetSeqAlign {
                 else {                   
                     let resi1 = (bRealign) ? start1 + k : ic.ParserUtilsCls.getResi(chainid1, start1 + k);
                     let resi2 = (bRealign) ? start2 + k : ic.ParserUtilsCls.getResi(chainid2, start2 + k);
-                    let resn1 = this.getResnFromResid(chainid1 + '_' + resi1); //this.getResn(chainid1, start1 + k);
-                    let resn2 = this.getResnFromResid(chainid2 + '_' + resi2); //this.getResn(chainid2, start2 + k);
+                    let resn1 = this.getResnFromResi(chainid1, resi1); //this.getResn(chainid1, start1 + k);
+                    let resn2 = this.getResnFromResi(chainid2, resi2); //this.getResn(chainid2, start2 + k);
                     
                     let bAlign = true;
                     let resObject = this.getResObject(chainid2, false, bAlign, resi2, resn2, resn1);
@@ -55851,7 +55969,7 @@ class Vastplus {
 
         let queryDataArray = [];
         for(let index = 0, indexl = chainidpairArray.length; index < indexl; ++index) {
-            let queryData = dataArray[index].value; //[0];
+            let queryData = (me.bNode) ? dataArray[index] : dataArray[index].value; //[0];
 
             queryDataArray.push(queryData);
 /*
@@ -57819,6 +57937,12 @@ class ApplyCommand {
         let dataStr = paraArray[1].replace(/\\n/g, '\n');
         await ic.refnumCls.parseCustomRefFile(dataStr);
       }
+      else if(command.indexOf('show ref number') == 0) {
+        ic.bShownRefnum = true;
+      }
+      else if(command.indexOf('hide ref number') == 0) {
+        ic.bShownRefnum = false;
+      }
 
     // special, select ==========
 
@@ -59853,7 +59977,7 @@ class SelectByCommand {
            // $1,2,3: Structure
            // .A,B,C: chain
            // :5-10,K,chemicals: residues, could be 'proteins', 'nucleotides', 'chemicals', 'ions', and 'water'
-           // :refnum_1250,anchors,strands,loops: reference numbers 1250, anchor residues (e.g., 2250), residues in strands, residues in loops
+           // :ref_1250,anchors,strands,loops: reference numbers 1250, anchor residues (e.g., 2250), residues in strands, residues in loops
            // @CA,C,C*: atoms
            // wild card * can be used to select all
            //var currHighlightAtoms = {}
@@ -60001,7 +60125,7 @@ class SelectByCommand {
                      let residArray = [];
 
                      if(bRefnum) {
-                      let residArrayTmp = (ic.refnum2residArray[k]) ? ic.refnum2residArray[k] : [];
+                      let residArrayTmp = (ic.refnum2residArray[k.toString()]) ? ic.refnum2residArray[k.toString()] : [];
                       for(let m = 0, ml = residArrayTmp.length; m < ml; ++m) {
                         let residueId = residArrayTmp[m];
                         if(residueId.substr(0, residueId.lastIndexOf('_')) == molecule_chain) {
@@ -62059,14 +62183,14 @@ class Dssp {
         }
     }
 
-    async parseDsspData(dataArray, struArray, bAppend) { let ic = this.icn3d; ic.icn3dui;
+    async parseDsspData(dataArray, struArray, bAppend) { let ic = this.icn3d, me = ic.icn3dui;
         //var dataArray =(struArray.length == 1) ? [data] : data;
 
         // Each argument is an array with the following structure: [ data, statusText, jqXHR ]
         //var data2 = v2[0];
         for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
             //let ssHash = dataArray[index][0];
-            let ssHash = dataArray[index].value;
+            let ssHash = (me.bNode) ? dataArray[index] : dataArray[index].value;
 
             if(ssHash !== undefined && JSON.stringify(ssHash).indexOf('Oops there was a problem') === -1) {
               for(let chainNum in ic.chainsSeq) {
@@ -62192,8 +62316,19 @@ class Dssp {
         ic.bShowRefnum = false;
 
         ic.hAtoms = {};
-        ic.bResetAnno = true;
-        await ic.showAnnoCls.showAnnotations();
+        //ic.bResetAnno = true;
+
+        // await ic.showAnnoCls.showAnnotations();
+        if(ic.bAnnoShown) {
+            for(let chain in ic.protein_chainid) {
+                let chainidBase = ic.protein_chainid[chain];
+                ic.showSeqCls.showSeq(chain, chainidBase, 'protein');
+            }
+        }
+        else {
+            await ic.showAnnoCls.showAnnotations();
+        }
+
         ic.hlUpdateCls.updateHlAll();
     }
  
@@ -62230,7 +62365,7 @@ class Dssp {
         ic.refpdbArray = ['NaCaExchanger_2fwuA_dog_n2', 'C3_2qkiD_human_n1', 'Siglec3_5j0bB_human_C2-n2', 'ICOS_6x4gA_human_V', 'B2Microglobulin_7phrL_human_C1', 'VTCN1_Q7Z7D3_human_V-n2', 'Contactin1_2ee2A_human_FN3-n9', 'InsulinR_8guyE_human_FN3-n1', 'JAM1_1nbqA_human_VorIset-n2', 'LAG3_7tzgD_human_C2-n2', 'Palladin_2dm3A_human_Iset-n1', 'PD1_4zqkB_human_V', 'CD8a_1cd8A_human_V', 'VISTA_6oilA_human_V', 'LAG3_7tzgD_human_V-n1', 'TP47_1o75A_bacteria', 'TP34_2o6cA_bacteria', 'TEAD1_3kysC_human', 'RBPJ_6py8C_human_Unk-n2', 'TCRa_6jxrm_human_C1-n2', 'IsdA_2iteA_bacteria', 'LaminAC_1ifrA_human', 'CD19_6al5A_human_C2orV-n1'];
 
         // round 2
-        ic.refpdbHash = {};
+        ic.refpdbHash = {};      
         ic.refpdbHash['NaCaExchanger_2fwuA_dog_n2'] = ['NaCaExchanger_2fwuA_dog_n2', 'ORF7a_1xakA_virus', 'ECadherin_4zt1A_human_n2', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark'];
         ic.refpdbHash['C3_2qkiD_human_n1'] = ['C3_2qkiD_human_n1', 'RBPJ_6py8C_human_Unk-n1', 'BArrestin1_4jqiA_rat_n1'];
         ic.refpdbHash['Siglec3_5j0bB_human_C2-n2'] = ['Siglec3_5j0bB_human_C2-n2', 'CD2_1hnfA_human_C2-n2', 'GHR_1axiB_human_FN3-n1'];
@@ -62255,40 +62390,27 @@ class Dssp {
         ic.refpdbHash['LaminAC_1ifrA_human'] = ['LaminAC_1ifrA_human', 'MPT63_1lmiA_bacteria'];
         ic.refpdbHash['CD19_6al5A_human_C2orV-n1'] = ['CD19_6al5A_human_C2orV-n1'];
 */
-        // round 1
-        ic.refpdbArray = ['1FAB-HEAVY_5esv_V-n1', '1CD2_1hnfA_human_V-n1', '1LAG3_7tzgD_human_C2-n2', '1BTLA_2aw2A_human_Iset', '1JAM1_1nbqA_human_VorIset-n2', '1Palladin_2dm3A_human_Iset-n1', '1FAB-HEAVY_5esv_C1-n2', '1FAB-LIGHT_5esv_C1-n2', '1BArrestin1_4jqiA_rat_n1', '1IL6Rb_1bquB_human_FN3-n3', '1Contactin1_2ee2A_human_FN3-n9', '1InsulinR_8guyE_human_FN3-n1', '1NaCaExchanger_2fwuA_dog_n2', '1CuZnSuperoxideDismutase_1hl5C_human', '1CoAtomerGamma1_1r4xA_human', '1RBPJ_6py8C_human_Unk-n2', '1CD2_1hnfA_human_C2-n2', '1GHR_1axiB_human_FN3-n1', '1Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', '1ICOS_6x4gA_human_V', '1TCRa_6jxrm_human_C1-n2', '1LaminAC_1ifrA_human', '1IsdA_2iteA_bacteria', '1MPT63_1lmiA_bacteria', '1CD19_6al5A_human_C2orV-n1', '1ORF7a_1xakA_virus', '1ECadherin_4zt1A_human_n2', '1ASF1A_2iijA_human'];
+        // round 1, 16 templates
+        ic.refpdbArray = ['1InsulinR_8guyE_human_FN3-n1', '1Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', '1CoAtomerGamma1_1r4xA_human', '1C3_2qkiD_human_n1', '1CuZnSuperoxideDismutase_1hl5C_human', '1ASF1A_2iijA_human', '1FAB-LIGHT_5esv_C1-n2', '1CD2_1hnfA_human_C2-n2', '1NaCaExchanger_2fwuA_dog_n2', '1FAB-HEAVY_5esv_V-n1', '1PDL1_4z18B_human_V-n1', '1BTLA_2aw2A_human_Iset', '1LaminAC_1ifrA_human', '1IsdA_2iteA_bacteria', '1TCRa_6jxrm_human_C1-n2', '1CD19_6al5A_human_C2orV-n1'];
 
         // round 2
         ic.refpdbHash = {};
-        ic.refpdbHash['1FAB-HEAVY_5esv_V-n1'] = ['FAB-HEAVY_5esv_V-n1', 'CD8a_1cd8A_human_V', 'FAB-LIGHT_5esv_V-n1', 'VNAR_1t6vN_shark_V'];
-        ic.refpdbHash['1CD2_1hnfA_human_V-n1'] = ['CD2_1hnfA_human_V-n1', 'Contactin1_3s97C_human_C2-n2', 'LAG3_7tzgD_human_V-n1'];
-        ic.refpdbHash['1LAG3_7tzgD_human_C2-n2'] = ['LAG3_7tzgD_human_C2-n2', 'Siglec3_5j0bB_human_C2-n2'];
-        ic.refpdbHash['1BTLA_2aw2A_human_Iset'] = ['BTLA_2aw2A_human_Iset', 'PD1_4zqkB_human_V', 'TCRa_6jxrm_human_V-n1'];
-        ic.refpdbHash['1JAM1_1nbqA_human_VorIset-n2'] = ['JAM1_1nbqA_human_VorIset-n2', 'PDL1_4z18B_human_V-n1'];
-        ic.refpdbHash['1Palladin_2dm3A_human_Iset-n1'] = ['Palladin_2dm3A_human_Iset-n1', 'Titin_4uowM_human_Unk-n152', 'VISTA_6oilA_human_V'];
-        ic.refpdbHash['1FAB-HEAVY_5esv_C1-n2'] = ['FAB-HEAVY_5esv_C1-n2', 'B2Microglobulin_7phrL_human_C1', 'MHCIa_7phrH_human_C1'];
-        ic.refpdbHash['1FAB-LIGHT_5esv_C1-n2'] = ['FAB-LIGHT_5esv_C1-n2', 'VTCN1_Q7Z7D3_human_V-n2'];
-        ic.refpdbHash['1BArrestin1_4jqiA_rat_n1'] = ['BArrestin1_4jqiA_rat_n1', 'C3_2qkiD_human_n1', 'RBPJ_6py8C_human_Unk-n1'];
-        ic.refpdbHash['1IL6Rb_1bquB_human_FN3-n3'] = ['IL6Rb_1bquB_human_FN3-n3', 'Sidekick2_1wf5A_human_FN3-n7'];
-        ic.refpdbHash['1Contactin1_2ee2A_human_FN3-n9'] = ['Contactin1_2ee2A_human_FN3-n9', 'IL6Rb_1bquB_human_FN3-n2'];
-        ic.refpdbHash['1InsulinR_8guyE_human_FN3-n1'] = ['InsulinR_8guyE_human_FN3-n1', 'InsulinR_8guyE_human_FN3-n2'];
-        ic.refpdbHash['1NaCaExchanger_2fwuA_dog_n2'] = ['NaCaExchanger_2fwuA_dog_n2', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark'];
+        ic.refpdbHash['1InsulinR_8guyE_human_FN3-n1'] = ['InsulinR_8guyE_human_FN3-n1', 'IL6Rb_1bquB_human_FN3-n3', 'Sidekick2_1wf5A_human_FN3-n7', 'InsulinR_8guyE_human_FN3-n2', 'Contactin1_2ee2A_human_FN3-n9', 'IL6Rb_1bquB_human_FN3-n2'];
+        ic.refpdbHash['1Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'] = ['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', 'ICOS_6x4gA_human_V'];
+        ic.refpdbHash['1CoAtomerGamma1_1r4xA_human'] = ['CoAtomerGamma1_1r4xA_human', 'TP34_2o6cA_bacteria', 'RBPJ_6py8C_human_Unk-n2', 'TP47_1o75A_bacteria'];
+        ic.refpdbHash['1C3_2qkiD_human_n1'] = ['C3_2qkiD_human_n1', 'BArrestin1_4jqiA_rat_n1', 'RBPJ_6py8C_human_Unk-n1'];
         ic.refpdbHash['1CuZnSuperoxideDismutase_1hl5C_human'] = ['CuZnSuperoxideDismutase_1hl5C_human', 'TEAD1_3kysC_human'];
-        ic.refpdbHash['1CoAtomerGamma1_1r4xA_human'] = ['CoAtomerGamma1_1r4xA_human', 'TP34_2o6cA_bacteria'];
-        ic.refpdbHash['1RBPJ_6py8C_human_Unk-n2'] = ['RBPJ_6py8C_human_Unk-n2', 'TP47_1o75A_bacteria'];
-
-        ic.refpdbHash['1CD2_1hnfA_human_C2-n2'] = ['CD2_1hnfA_human_C2-n2'];
-        ic.refpdbHash['1GHR_1axiB_human_FN3-n1'] = ['GHR_1axiB_human_FN3-n1'];
-        ic.refpdbHash['1Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'] = ['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4'];
-        ic.refpdbHash['1ICOS_6x4gA_human_V'] = ['ICOS_6x4gA_human_V'];
-        ic.refpdbHash['1TCRa_6jxrm_human_C1-n2'] = ['TCRa_6jxrm_human_C1-n2'];
+        ic.refpdbHash['1ASF1A_2iijA_human'] = ['ASF1A_2iijA_human', 'MPT63_1lmiA_bacteria'];
+        ic.refpdbHash['1FAB-LIGHT_5esv_C1-n2'] = ['FAB-LIGHT_5esv_C1-n2', 'GHR_1axiB_human_FN3-n1', 'VTCN1_Q7Z7D3_human_V-n2', 'B2Microglobulin_7phrL_human_C1', 'FAB-HEAVY_5esv_C1-n2', 'MHCIa_7phrH_human_C1'];
+        ic.refpdbHash['1CD2_1hnfA_human_C2-n2'] = ['CD2_1hnfA_human_C2-n2', 'Siglec3_5j0bB_human_C2-n2'];
+        ic.refpdbHash['1NaCaExchanger_2fwuA_dog_n2'] = ['NaCaExchanger_2fwuA_dog_n2', 'ORF7a_1xakA_virus', 'ECadherin_4zt1A_human_n2', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark'];
+        ic.refpdbHash['1FAB-HEAVY_5esv_V-n1'] = ['FAB-HEAVY_5esv_V-n1', 'FAB-LIGHT_5esv_V-n1', 'VNAR_1t6vN_shark_V', 'TCRa_6jxrm_human_V-n1', 'VISTA_6oilA_human_V', 'CD8a_1cd8A_human_V', 'PD1_4zqkB_human_V'];
+        ic.refpdbHash['1PDL1_4z18B_human_V-n1'] = ['PDL1_4z18B_human_V-n1', 'CD2_1hnfA_human_V-n1', 'LAG3_7tzgD_human_V-n1'];
+        ic.refpdbHash['1BTLA_2aw2A_human_Iset'] = ['BTLA_2aw2A_human_Iset', 'Palladin_2dm3A_human_Iset-n1', 'Titin_4uowM_human_Unk-n152', 'LAG3_7tzgD_human_C2-n2', 'JAM1_1nbqA_human_VorIset-n2', 'Contactin1_3s97C_human_C2-n2'];
         ic.refpdbHash['1LaminAC_1ifrA_human'] = ['LaminAC_1ifrA_human'];
         ic.refpdbHash['1IsdA_2iteA_bacteria'] = ['IsdA_2iteA_bacteria'];
-        ic.refpdbHash['1MPT63_1lmiA_bacteria'] = ['MPT63_1lmiA_bacteria'];
-        ic.refpdbHash['1CD19_6al5A_human_C2orV-n1'] = ['CD19_6al5A_human_C2orV-n1'];
-        ic.refpdbHash['1ORF7a_1xakA_virus'] = ['ORF7a_1xakA_virus'];
-        ic.refpdbHash['1ECadherin_4zt1A_human_n2'] = ['ECadherin_4zt1A_human_n2'];
-        ic.refpdbHash['1ASF1A_2iijA_human'] = ['ASF1A_2iijA_human'];          
+        ic.refpdbHash['1TCRa_6jxrm_human_C1-n2'] = ['TCRa_6jxrm_human_C1-n2'];
+        ic.refpdbHash['1CD19_6al5A_human_C2orV-n1'] = ['CD19_6al5A_human_C2orV-n1'];         
 
         // use known ref structure
         ic.refpdbHash['5ESV'] = ['FAB-HEAVY_5esv_V-n1', 'FAB-LIGHT_5esv_V-n1', 'FAB-HEAVY_5esv_C1-n2', 'FAB-LIGHT_5esv_C1-n2'];
@@ -62432,15 +62554,16 @@ 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;
+                    // ig strand for any subset will have the same k, use the number of residue to separate them
+                    let domainid = chainid + '-' + k + '_' + domainAtomsArray[k].length; 
                     ic.domainid2pdb[domainid] = pdb_target;
 
                     for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
                         let struct2 = ic.defaultPdbId + index;
-                        let pdb_query = dataArray[index].value; //[0];
+                        let pdb_query = (me.bNode) ? dataArray[index] : dataArray[index].value; //[0];
                         let header = 'HEADER                                                        ' + struct2 + '\n';
                         pdb_query = header + pdb_query;
 
@@ -62448,7 +62571,7 @@ class Dssp {
                         let alignAjax = me.getAjaxPostPromise(urltmalign, dataObj);
                         ajaxArray.push(alignAjax);
                         
-                        domainidpairArray.push(domainid + "," + ic.refpdbArray[index]);
+                        domainidpairArray.push(domainid + "|" + ic.refpdbArray[index]);
                     }
                 }
             }
@@ -62474,7 +62597,7 @@ class Dssp {
     async parseAlignData(dataArray, domainidpairArray, bRound1) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
-        let tmscoreThreshold = 0.4; //0.5;
+        let tmscoreThreshold = 0.4; // 0.4; //0.5;
 
         // find the best alignment for each chain
         let domainid2score = {}, domainid2segs = {}, chainid2segs = {};
@@ -62492,7 +62615,7 @@ class Dssp {
         let minResidues = 20;
 
         for(let i = 0, il = domainidpairArray.length; i < il; ++i) {
-            let queryData = dataArray[i].value; //[0];
+            let queryData = (me.bNode) ? dataArray[i] : dataArray[i].value; //[0];
 
             if(!queryData) {
                 if(!me.bNode) console.log("The alignment data for " + domainidpairArray[i] + " is unavailable...");
@@ -62501,12 +62624,14 @@ class Dssp {
 
             if(queryData.length == 0) continue;
             
-            if(queryData[0].score < tmscoreThreshold || queryData[0].num_res < minResidues) continue;
+            if(queryData[0].score < tmscoreThreshold || queryData[0].num_res < minResidues) {
+                continue;
+            }
 
             //let domainid_index = domainidpairArray[i].split(',');
             //let domainid = domainid_index[0];
-            let domainid = domainidpairArray[i].substr(0, domainidpairArray[i].indexOf(','));
-            let refpdbname = domainidpairArray[i].substr(domainidpairArray[i].indexOf(',') + 1);
+            let domainid = domainidpairArray[i].substr(0, domainidpairArray[i].indexOf('|'));
+            let refpdbname = domainidpairArray[i].substr(domainidpairArray[i].indexOf('|') + 1);
             //let chainid = domainid.split('-')[0];
 
             // Ig-like domains: B (2150, 2150a, 2150b), C (3150, 3250), E (7150, 7250), F (8150, 8250) strands
@@ -62564,6 +62689,10 @@ class Dssp {
                     if(!me.bNode) console.log("Adjusted refpdbname for domainid " + domainid + ": " + refpdbname);   
                 }
 
+                if(!ic.refpdbHash[refpdbname]) {
+                    continue;
+                }
+
                 for(let k = 0, kl = ic.refpdbHash[refpdbname].length; k < kl; ++k) {
                     let urlpdb = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi?refpdbid=" + ic.refpdbHash[refpdbname][k];
 
@@ -62578,7 +62707,7 @@ class Dssp {
                 let pdb_target = ic.domainid2pdb[domainid];
                 for(let index = 0, indexl = ic.pdbDataArray.length; index < indexl; ++index) {
                     let struct2 = ic.defaultPdbId + index;
-                    let pdb_query = ic.pdbDataArray[index].value; //[0];
+                    let pdb_query = (me.bNode) ? ic.pdbDataArray[index] : ic.pdbDataArray[index].value; //[0];
                     let header = 'HEADER                                                        ' + struct2 + '\n';
                     pdb_query = header + pdb_query;
 
@@ -62587,7 +62716,7 @@ class Dssp {
                     ajaxArray.push(alignAjax);
                     
                     //domainidpairArray3.push(domainid + "," + refpdbname);
-                    domainidpairArray3.push(domainid + "," + ic.refpdbHash[refpdbname][index]);
+                    domainidpairArray3.push(domainid + "|" + ic.refpdbHash[refpdbname][index]);
                 }
             }
 
@@ -62675,8 +62804,17 @@ class Dssp {
 
             // open sequence view
             ic.hAtomsRefnum = {};
-            ic.bResetAnno = true;
-            await ic.showAnnoCls.showAnnotations();
+            //ic.bResetAnno = true;
+            if(ic.bAnnoShown) {
+                for(let chain in ic.protein_chainid) {
+                    let chainidBase = ic.protein_chainid[chain];
+                    ic.showSeqCls.showSeq(chain, chainidBase, 'protein');
+                }
+            }
+            else {
+                await ic.showAnnoCls.showAnnotations();
+            }
+
             ic.annotationCls.setAnnoViewAndDisplay('detailed view');
         }
         else {
@@ -62801,7 +62939,7 @@ class Dssp {
     }
 
     rmStrandFromRefnumlabel(refnumLabel) {
-        return refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').replace(/\+/g, '').replace(/\-/g, '').substr(1); // C', C''
+        return (!refnumLabel) ? refnumLabel : refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').replace(/\+/g, '').replace(/\-/g, '').substr(1); // C', C''
     }
  }
 
@@ -62862,6 +63000,8 @@ class Scap {
     async retrieveScap(snp, bInteraction, bPdb) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
+        ic.bScap = true;
+
         //snp: 6M0J_E_484_K,6M0J_E_501_Y,6M0J_E_417_N
         let snpStr = '';
         let snpArray = snp.split(','); //stru_chain_resi_snp
@@ -70785,7 +70925,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.25.1';
+    this.REVISION = '3.25.3';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;