icn3d 3.28.9 → 3.28.11

package/icn3d.module.js

@@ -5062,6 +5062,17 @@ class UtilsCls {
 
       return this.getStructures(atoms);
     }
+
+    getDateDigitStr() { this.icn3dui;
+      let date = new Date();
+      let monthStr =(date.getMonth() + 1).toString();
+      if(date.getMonth() + 1 < 10) monthStr = '0' + monthStr;
+
+      let dateStr = date.getDate().toString();
+      if(date.getDate() < 10) dateStr = '0' + dateStr;
+
+      return date.getFullYear().toString() + monthStr + dateStr;
+    }
 }
 
 /**
@@ -7359,7 +7370,7 @@ class ClickMenu {
            ic.resid2specCls.selectProperty('polar');
         });
         me.myEventCls.onIds("#" + me.pre + "mn2_propBfactor", "click", function(e) { me.icn3d; //e.preventDefault();
-           me.htmlCls.dialogCls.openDlg('dl_propbybfactor', 'Select residue based on B-factor');
+           me.htmlCls.dialogCls.openDlg('dl_propbybfactor', 'Select residue based on B-factor/pLDDT');
         });
         me.myEventCls.onIds("#" + me.pre + "mn2_propSolAcc", "click", function(e) { me.icn3d; //e.preventDefault();
            me.htmlCls.dialogCls.openDlg('dl_propbypercentout', 'Select residue based on the percentage of solvent accessilbe surface area');
@@ -8174,24 +8185,24 @@ class ClickMenu {
            thisClass.setLogCmd('setoption phisurface nothing', true);
         });
 
-        me.myEventCls.onIds("#" + me.pre + "applymap2fofc", "click", function(e) { let ic = me.icn3d; 
+        me.myEventCls.onIds("#" + me.pre + "applymap2fofc", "click", async function(e) { let ic = me.icn3d; 
            e.preventDefault();
 
            //if(!me.cfg.notebook) dialog.dialog( "close" );
            let sigma2fofc = parseFloat($("#" + me.pre + "sigma2fofc" ).val());
            let type = '2fofc';
-           ic.dsn6ParserCls.dsn6Parser(ic.inputid, type, sigma2fofc);
+           await ic.dsn6ParserCls.dsn6Parser(ic.inputid, type, sigma2fofc);
            //ic.setOptionCls.setOption('map', '2fofc');
            thisClass.setLogCmd('set map 2fofc sigma ' + sigma2fofc, true);
         });
 
-        me.myEventCls.onIds("#" + me.pre + "applymapfofc", "click", function(e) { let ic = me.icn3d; 
+        me.myEventCls.onIds("#" + me.pre + "applymapfofc", "click", async function(e) { let ic = me.icn3d; 
            e.preventDefault();
 
            //if(!me.cfg.notebook) dialog.dialog( "close" );
            let sigmafofc = parseFloat($("#" + me.pre + "sigmafofc" ).val());
            let type = 'fofc';
-           ic.dsn6ParserCls.dsn6Parser(ic.inputid, type, sigmafofc);
+           await ic.dsn6ParserCls.dsn6Parser(ic.inputid, type, sigmafofc);
            //ic.setOptionCls.setOption('map', 'fofc');
            thisClass.setLogCmd('set map fofc sigma ' + sigmafofc, true);
         });
@@ -8216,7 +8227,7 @@ class ClickMenu {
            thisClass.setLogCmd('setoption emmap nothing', true);
         });
 
-        me.myEventCls.onIds("#" + me.pre + "applyemmap", "click", function(e) { let ic = me.icn3d; 
+        me.myEventCls.onIds("#" + me.pre + "applyemmap", "click", async function(e) { let ic = me.icn3d; 
            e.preventDefault();
 
            //if(!me.cfg.notebook) dialog.dialog( "close" );
@@ -8224,7 +8235,7 @@ class ClickMenu {
            let type = 'em';
            //ic.emd = 'emd-3906';
 
-           ic.densityCifParserCls.densityCifParser(ic.inputid, type, empercentage, ic.emd);
+           await ic.densityCifParserCls.densityCifParser(ic.inputid, type, empercentage, ic.emd);
            thisClass.setLogCmd('set emmap percentage ' + empercentage, true);
         });
 
@@ -8272,6 +8283,18 @@ class ClickMenu {
             // }
          });
 
+        me.myEventCls.onIds("#" + me.pre + "mn6_igrefTpl", "click", async function(e) { me.icn3d; //e.preventDefault();
+            me.htmlCls.dialogCls.openDlg('dl_igrefTpl', 'Choose an Ig template');
+         });
+
+        me.myEventCls.onIds("#" + me.pre + "mn6_igrefTpl_apply", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
+            if(!me.cfg.notebook) dialog.dialog( "close" );
+                  
+            let template = $("#" + me.pre + "igrefTpl").val();
+            thisClass.setLogCmd('ig template ' + template, true);
+            await ic.refnumCls.showIgRefNum(template);
+         });
+
          me.myEventCls.onIds("#" + me.pre + "mn6_igrefNo", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
             thisClass.setLogCmd('ig refnum off', true);
             await ic.refnumCls.hideIgRefNum();
@@ -8474,7 +8497,8 @@ class ClickMenu {
            //    alert("The url is more than 4000 characters and may not work.");
            //}
            //else {
-               url = url.replace("full.html", "full2.html");
+               url = url.replace("icn3d/full.html?", "icn3d/full2.html?");
+               url = url.replace("icn3d/?", "icn3d/full2.html?");
                url += '&closepopup=1';
                let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
                window.open(url, urlTarget);
@@ -8803,6 +8827,14 @@ class ClickMenu {
       let pos = str.indexOf('|||');
       if(pos !== -1) str = str.substr(0, pos);
       let transformation = {};
+
+      if(!ic.quaternion) {
+         // reset parameters
+         ic._zoomFactor = 1.0;
+         ic.mouseChange = new THREE.Vector2(0,0);
+         ic.quaternion = new THREE.Quaternion(0,0,0,1);
+      }
+
       transformation.factor = ic._zoomFactor;
       transformation.mouseChange = ic.mouseChange;
       transformation.quaternion = {};
@@ -9518,21 +9550,23 @@ class SetMenu {
 
         html += this.getLink('mn1_exportPdbRes', 'PDB', 1, 2);
         html += this.getLink('profixpdb', 'PDB with Missing Atoms', undefined, 2);
-        html += this.getLink('profixpdbh', 'PDB with Hydrogens', undefined, 2);
+        
+        // the quality is not good to add hydrogen
+        //html += this.getLink('profixpdbh', 'PDB with Hydrogens', undefined, 2);
 
         if(me.cfg.cid === undefined) {
             html += this.getLink('mn1_exportSecondary', 'Secondary Structure', undefined, 2);
         }
 
         //!!!
-        /*
+/*
         html += this.getMenuText('m1_exportrefnum', 'Reference Numbers', undefined, undefined, 2);
         html += "<ul>";
         html += this.getLink('mn1_exportIgstrand', 'Ig Strand', undefined, 3);
         html += this.getLink('mn1_exportKabat', 'Kabat', undefined, 3);
         html += this.getLink('mn1_exportImgt', 'IMGT', undefined, 3);
         html += "</ul>";
-        */
+*/
 
         html += "<li><br/></li>";
 
@@ -10369,7 +10403,7 @@ class SetMenu {
 
             //if(me.cfg.afid) html += this.getRadio('mn4_clr', 'mn4_clrConfidence', 'AF Confidence');
             //if(!me.cfg.mmtfid && !me.cfg.pdbid && !me.cfg.opmid && !me.cfg.mmdbid && !me.cfg.gi && !me.cfg.uniprotid && !me.cfg.blast_rep_id && !me.cfg.cid && !me.cfg.mmcifid && !me.cfg.align && !me.cfg.chainalign) {
-                html += this.getRadio('mn4_clr', 'mn4_clrConfidence', 'AlphaFold<br><span style="padding-left:1.5em;">Confidence</span>', undefined, 1, 1);
+                html += this.getRadio('mn4_clr', 'mn4_clrConfidence', 'pLDDT', undefined, 1, 1);
             //}
 
             //!!!
@@ -10599,10 +10633,11 @@ class SetMenu {
 //!!!
 /*
             html += this.getLink('mn6_igrefYes', 'Show Ig Ref. Number', undefined, 2);
+            html += this.getLink('mn6_igrefTpl', 'Ig w/ Specified Template', undefined, 2);
             html += this.getLink('mn6_igrefNo', 'Hide Ig Ref. Number', undefined, 2);
-
-            html += this.getMenuSep();
 */
+            html += this.getMenuSep();
+
             html += this.getLink('mn6_customref', 'Custom Ref. Number', undefined, 2);
             html += "</ul>";
             html += "</li>";
@@ -12689,10 +12724,10 @@ class SetDialog {
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_propbybfactor' class='" + dialogClass + "'>";
-        html += this.addNotebookTitle('dl_propbybfactor', 'Select residues basen on B-factor');
-        html += "<div style='width:400px'>Select residue based on B-factor. The values are in the range of 0-100.</div><br>";
-        html += "<b>Min B-factor</b>: " + me.htmlCls.inputTextStr + "id='" + me.pre + "minbfactor' value='0' size='10'>% <br>";
-        html += "<b>Max B-factor</b>: " + me.htmlCls.inputTextStr + "id='" + me.pre + "maxbfactor' value='100' size='10'>% <br>";
+        html += this.addNotebookTitle('dl_propbybfactor', 'Select residues basen on B-factor/pLDDT');
+        html += "<div style='width:400px'>Select residue based on B-factor/pLDDT. The values are in the range of 0-100.</div><br>";
+        html += "<b>Min B-factor/pLDDT</b>: " + me.htmlCls.inputTextStr + "id='" + me.pre + "minbfactor' value='0' size='10'>% <br>";
+        html += "<b>Max B-factor/pLDDT</b>: " + me.htmlCls.inputTextStr + "id='" + me.pre + "maxbfactor' value='100' size='10'>% <br>";
         html += "<button style='white-space:nowrap;' id='" + me.pre + "applypropbybfactor'>Apply</button><br/><br/>";
         html += "</div>";
 
@@ -12704,6 +12739,31 @@ class SetDialog {
         html += this.addNotebookTitle('dl_disttable', 'Distance Table', true);
         html += "</div>";
 
+        html += me.htmlCls.divStr + "dl_igrefTpl' class='" + dialogClass + "'>";
+        html += this.addNotebookTitle('dl_igrefTpl', 'Choose an Ig template');
+        html += "<span style='white-space:nowrap;font-weight:bold;'>Choose an Ig template for selected residues:</span> <br><br><select id='" + me.pre + "igrefTpl'>";
+
+        //html += me.htmlCls.setHtmlCls.getOptionHtml(['0', '10', '20', '30', '40', '50', '60', '70', '80', '90', '100'], 3);
+        let group2tpl = {};
+        group2tpl['V'] = ['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', 'ICOS_6x4gA_human_V', 'CD28_1yjdC_human_V', 'PDL1_4z18B_human_V-n1', 'CD2_1hnfA_human_V-n1', 'LAG3_7tzgD_human_V-n1'];
+        group2tpl['C1'] = ['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', 'TCRa_6jxrm_human_C1-n2'];
+        group2tpl['C2'] = ['CD2_1hnfA_human_C2-n2', 'Siglec3_5j0bB_human_C2-n2', 'LAG3_7tzgD_human_C2-n2', 'Contactin1_3s97C_human_C2-n2'];
+        group2tpl['Iset'] = ['BTLA_2aw2A_human_Iset', 'Palladin_2dm3A_human_Iset-n1', 'Titin_4uowM_human_Unk-n152', 'JAM1_1nbqA_human_VorIset-n2', 'CD19_6al5A_human_C2orV-n1'];
+        group2tpl['FN3'] = ['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'];
+        group2tpl['Other'] = ['Endo-1,4-BetaXylanase10A_1i8aA_bacteria_n4', 'CoAtomerGamma1_1r4xA_human', 'TP34_2o6cA_bacteria', 'RBPJ_6py8C_human_Unk-n2', 'TP47_1o75A_bacteria', 'C3_2qkiD_human_n1', 'BArrestin1_4jqiA_rat_n1', 'RBPJ_6py8C_human_Unk-n1', 'CuZnSuperoxideDismutase_1hl5C_human', 'TEAD1_3kysC_human', 'ASF1A_2iijA_human', 'MPT63_1lmiA_bacteria', 'NaCaExchanger_2fwuA_dog_n2', 'ORF7a_1xakA_virus', 'ECadherin_4zt1A_human_n2', 'NaKATPaseTransporterBeta_2zxeB_spurdogshark', 'LaminAC_1ifrA_human', 'IsdA_2iteA_bacteria'];  
+
+        for(let group in group2tpl) {
+            html += "<optgroup label='" + group + "'>";
+            for(let i = 0, il = group2tpl[group].length; i < il; ++i) {
+                let template = group2tpl[group][i];
+                html += me.htmlCls.optionStr + "'" + template + "'>" + template + "</option>";
+            }
+            html += "</optgroup>";
+        }
+
+        html += "</select><br><br><span style='white-space:nowrap;'>" + me.htmlCls.buttonStr + "mn6_igrefTpl_apply'>Show Ig Ref. Number</button></span>";
+        html += "</div>";
+
         html += "</div>";
         html += "<!--/form-->";
 
@@ -16308,10 +16368,11 @@ class SetHtml {
 
             let pdbstr = '';
 
-            pdbstr += ic.saveFileCls.getAtomPDB(atomHash);
+            let bMergeIntoOne = true;
+            pdbstr += ic.saveFileCls.getAtomPDB(atomHash, undefined, undefined, undefined, undefined, undefined, bMergeIntoOne);
             pdbstr += ic.saveFileCls.getAtomPDB(ionHash, true, undefined, true);
 
-            let url = "https://www.ncbi.nlm.nih.gov/Structure/delphi/delphi.fcgi";
+            let url = me.htmlCls.baseUrl + "delphi/delphi.cgi";
 
             let pdbid =(me.cfg.cid) ? me.cfg.cid : Object.keys(ic.structures).toString();
 
@@ -18750,7 +18811,8 @@ function createDefaultMaterial( cache ) {
             roughness: 1,
             transparent: false,
             depthTest: true,
-            side: FrontSide
+            side: FrontSide,
+            //needsUpdate: true 
         } );
 
     }
@@ -21677,7 +21739,7 @@ function findNodes( motionController, scene ) {
 
                 // Attach a touch dot to the touchpad.
                 const sphereGeometry = new SphereGeometry( 0.001 );
-                const material = new MeshBasicMaterial( { color: 0x0000FF } );
+                const material = new MeshBasicMaterial( {color: 0x0000FF } );
                 const sphere = new Mesh( sphereGeometry, material );
                 component.touchPointNode.add( sphere );
 
@@ -22299,7 +22361,7 @@ class CanvasUI{
         if ( this.scene ){
             const radius = 0.015;
             const geometry = new THREE.IcosahedronBufferGeometry( radius );
-            const material = new THREE.MeshBasicMaterial( { color: 0x0000aa } );
+            const material = new THREE.MeshBasicMaterial( {color: 0x0000aa } );
 
             const mesh1 = new THREE.Mesh( geometry, material );
             mesh1.visible = false;
@@ -24106,7 +24168,7 @@ class Box {
               specular: ic.frac, shininess: ic.shininess, emissive: ic.emissive, color: color }));
         // }
         // else {
-        //   mesh = new THREE.Mesh(ic.boxGeometry, new THREE.MeshPhongMaterial({
+        //   mesh = new THREE.Mesh(ic.boxGeometry, new THREE.MeshPhongMaterial({needsUpdate: true,
         //       specular: ic.frac, shininess: ic.shininess, emissive: ic.emissive, color: color }));
         // }
 
@@ -24567,18 +24629,18 @@ class Cylinder {
         else {
             if(bHighlight === 2) {
               mesh = new THREE.Mesh(ic.cylinderGeometry, new THREE.MeshPhongMaterial(
-                  { transparent: true, opacity: opacity, specular: ic.frac, shininess: ic.shininess, emissive: ic.emissive, color: color }));
+                  {transparent: true, opacity: opacity, specular: ic.frac, shininess: ic.shininess, emissive: ic.emissive, color: color }));
 
               radius *= 1.5;
             }
             //else if(bGlycan) {
             else {
               mesh = new THREE.Mesh(ic.cylinderGeometry, new THREE.MeshPhongMaterial(
-                  { transparent: true, opacity: opacity, specular: ic.frac, shininess: ic.shininess, emissive: ic.emissive, color: color }));
+                  {transparent: true, opacity: opacity, specular: ic.frac, shininess: ic.shininess, emissive: ic.emissive, color: color }));
             }
             // else {
             //   mesh = new THREE.Mesh(ic.cylinderGeometry, new THREE.MeshPhongMaterial(
-            //       { specular: ic.frac, shininess: ic.shininess, emissive: ic.emissive, color: color }));
+            //       {specular: ic.frac, shininess: ic.shininess, emissive: ic.emissive, color: color }));
             // }
 
             mesh.position.copy(p0).add(p1).multiplyScalar(0.5);
@@ -24645,7 +24707,7 @@ class Cylinder {
         if(me.bNode) return;
 
         let mesh = new THREE.Mesh(ic.cylinderGeometry, new THREE.MeshPhongMaterial(
-            { specular: ic.frac, shininess: ic.shininess, emissive: ic.emissive, color: color }));
+            {specular: ic.frac, shininess: ic.shininess, emissive: ic.emissive, color: color }));
 
         mesh.position.copy(p0).add(p1).multiplyScalar(0.5);
         mesh.matrixAutoUpdate = false;
@@ -24876,7 +24938,7 @@ class Line$1 {
             if(bHighlight === 1) ;
             else {
                 line = new THREE.LineSegments(geo, new THREE.LineBasicMaterial(
-                    { linewidth: ic.linewidth, vertexColors: true }));
+                    {linewidth: ic.linewidth, vertexColors: true }));
                 ic.mdl.add(line);
             }
 
@@ -25009,7 +25071,7 @@ class Line$1 {
                let p2 = line.position2;
 
                let dashed = (line.dashed) ? line.dashed : false;
-               let dashSize = 0.3;
+               let dashSize = (name == 'missingres') ? 0.8 : 0.3;
 
                let radius = (line.radius) ? line.radius : ic.lineRadius;
                let opacity = (line.opacity) ? line.opacity : 1.0;
@@ -27080,7 +27142,8 @@ class TextSprite {
             map: texture,
             //useScreenCoordinates: false,
             depthTest: !frontOfTarget,
-            depthWrite: !frontOfTarget
+            depthWrite: !frontOfTarget,
+            //needsUpdate: true
         } );
 
         //https://stackoverflow.com/questions/29421702/threejs-texture
@@ -28379,19 +28442,25 @@ ProteinSurface.prototype.initparm = function(extent, btype, in_bCalcArea, atomli
 
     // 2. If size > 90, change scale
     //var threshbox = 180; // maximum possible boxsize
-    if(this.bCalcArea || this.defaultScaleFactor * maxLen > this.threshbox) {
+    //if(this.bCalcArea || this.defaultScaleFactor * maxLen > this.threshbox) {
+    if(this.defaultScaleFactor * maxLen > this.threshbox) {
         boxLength = Math.floor(this.threshbox);
         this.scaleFactor =(this.threshbox - 1.0) / maxLen;
     }
+
+    // 3. use a fixed scaleFactor for surface area calculation
+    if(this.bCalcArea) {
+        this.scaleFactor = this.defaultScaleFactor;
+    }
     // end of surface.js part
 
     this.pLength = Math.ceil(this.scaleFactor *(this.pmaxx - this.pminx)) + 1;
     this.pWidth = Math.ceil(this.scaleFactor *(this.pmaxy - this.pminy)) + 1;
     this.pHeight = Math.ceil(this.scaleFactor *(this.pmaxz - this.pminz)) + 1;
 
-    this.finalScaleFactor.x =(this.pLength - 1.0) /(this.pmaxx - this.pminx);
-    this.finalScaleFactor.y =(this.pWidth - 1.0) /(this.pmaxy - this.pminy);
-    this.finalScaleFactor.z =(this.pHeight - 1.0) /(this.pmaxz - this.pminz);
+    // this.finalScaleFactor.x =(this.pLength - 1.0) /(this.pmaxx - this.pminx);
+    // this.finalScaleFactor.y =(this.pWidth - 1.0) /(this.pmaxy - this.pminy);
+    // this.finalScaleFactor.z =(this.pHeight - 1.0) /(this.pmaxz - this.pminz);
 
     this.boundingatom(btype);
     this.cutRadius = this.probeRadius * this.scaleFactor;
@@ -28505,9 +28574,13 @@ ProteinSurface.prototype.fillvoxels = function(atoms, atomlist) { //(int seqinit
         for(i = 0; i < this.pLength; ++i) {
             for(j = 0; j < this.pWidth; ++j) {
                 for(k = 0; k < this.pHeight; ++k) {
-                    let x = i / this.finalScaleFactor.x - this.ptranx;
-                    let y = j / this.finalScaleFactor.y - this.ptrany;
-                    let z = k / this.finalScaleFactor.z - this.ptranz;
+                    // let x = i / this.finalScaleFactor.x - this.ptranx;
+                    // let y = j / this.finalScaleFactor.y - this.ptrany;
+                    // let z = k / this.finalScaleFactor.z - this.ptranz;
+
+                    let x = i / this.scaleFactor - this.ptranx;
+                    let y = j / this.scaleFactor - this.ptrany;
+                    let z = k / this.scaleFactor - this.ptranz;
 
                     let r = new THREE.Vector3(x, y, z);
 
@@ -29137,7 +29210,7 @@ ProteinSurface.prototype.marchingcube = function(stype) {
     }
 
     // calculate surface area
-    let serial2area, maxScaleFactor, area = 0;
+    let serial2area, area = 0;
     if(this.bCalcArea) {
         let faceHash = {};
         serial2area = {};
@@ -29207,14 +29280,15 @@ ProteinSurface.prototype.marchingcube = function(stype) {
             //}
         } // for loop
 
-        maxScaleFactor = Math.max(this.finalScaleFactor.x, this.finalScaleFactor.y, this.finalScaleFactor.z);
-        area = area / maxScaleFactor / maxScaleFactor;
-        //area = area / this.scaleFactor / this.scaleFactor;
+        //maxScaleFactor = Math.max(this.finalScaleFactor.x, this.finalScaleFactor.y, this.finalScaleFactor.z);
+        //area = area / maxScaleFactor / maxScaleFactor;
+        area = area / this.scaleFactor / this.scaleFactor;
     }
 
     if(!this.bCalcArea) this.marchingCube.laplacianSmooth(1, this.verts, this.faces);
 
-    return {"area": area, "serial2area": serial2area, "scaleFactor": maxScaleFactor};
+    //return {"area": area, "serial2area": serial2area, "scaleFactor": maxScaleFactor};
+    return {"area": area, "serial2area": serial2area, "scaleFactor": this.scaleFactor};
 };
 
 /* ProteinSurface4.js
@@ -30194,7 +30268,8 @@ class Surface {
                 wireframe: wireframe,
                 opacity: opacity,
                 transparent: true,
-                side: THREE.DoubleSide
+                side: THREE.DoubleSide,
+                //needsUpdate: true
             }));
 
             //http://www.html5gamedevs.com/topic/7288-threejs-transparency-bug-or-limitation-or-what/
@@ -30263,7 +30338,8 @@ class Surface {
                 opacity: opacity,
                 transparent: true,
                 depthWrite: (parseInt(10*opacity) != 10) ? false : true, // important to make the transparency work
-                side: THREE.DoubleSide
+                side: THREE.DoubleSide,
+                //needsUpdate: true 
                 //depthTest: (ic.ic.transparentRenderOrder) ? false : true
             }));
 
@@ -32447,7 +32523,7 @@ class Impostor {
           fragmentShader: this.getShader(shaderName + ".frag"),
           depthTest: true,
           depthWrite: true,
-          //needsUpdate: true,
+          //needsUpdate: true, 
           lights: true
       });
 
@@ -33214,7 +33290,7 @@ class Instancing {
           fragmentShader: ic.impostorCls.getShader(name + ".frag"),
           depthTest: true,
           depthWrite: true,
-          //needsUpdate: true,
+          //needsUpdate: true, 
           lights: true
        });
 
@@ -33337,7 +33413,7 @@ class Alternate {
     // change the display atom when alternating
     //Show structures one by one.
     alternateStructures() { let ic = this.icn3d, me = ic.icn3dui;
-        ic.bAlernate = true;
+        ic.bAlternate = true;
 
         //ic.transformCls.zoominSelection();
         
@@ -33434,14 +33510,14 @@ class Alternate {
         ic.applyMapCls.removeEmmaps();
         ic.applyMapCls.applyEmmapOptions();
 
-    // disallow the alternation of DelPhi map
+    // allow the alternation of DelPhi map
         ic.applyMapCls.removePhimaps();
-    //    ic.applyMapCls.applyPhimapOptions();
+        ic.applyMapCls.applyPhimapOptions();
         // should recalculate the potential
         //ic.loadDelphiFileBase('delphi');
 
-    //    ic.applyMapCls.removeSurfaces();
-    //    ic.applyMapCls.applyphisurfaceOptions();
+        ic.applyMapCls.removeSurfaces();
+        ic.applyMapCls.applyphisurfaceOptions();
         // should recalculate the potential
         //ic.loadDelphiFileBase('delphi2');
 
@@ -33720,6 +33796,7 @@ class Alternate {
         if(ic.scene) {
             // https://github.com/gkjohnson/three-gpu-pathtracer/blob/main/example/basic.js
             ic.renderer.outputEncoding = THREE.sRGBEncoding;
+            //ic.renderer.outputEncoding = THREE.LinearEncoding
 
             ic.renderer.render(ic.scene, cam);
         }
@@ -36570,7 +36647,7 @@ class SetOption {
 
         let colorLabel = colorType.substr(0, 1).toUpperCase() + colorType.substr(1);
         if(colorType == 'confidence') {
-            colorLabel = 'AlphaFold Confidence (pLDDT)';
+            colorLabel = 'pLDDT';
         }
         else if(colorType == 'normalized hydrophobic') {
             colorLabel = 'Normalized Hydrophobicity';
@@ -36857,15 +36934,15 @@ class SetOption {
 
         const name2color = {
             //"A- Strand": "FF00FF", 
-            "A Strand": "663399",
-            //"A+ Strand": "663399", //"FFC0CB",
-            "A' Strand": "663399", //"9370db",
+            "A Strand": "9400D3", //"663399",
+            //"A+ Strand": "9400D3", //"663399",
+            "A' Strand": "9400D3", //"663399",
             "B Strand": "ba55d3",
             "C Strand": "0000FF",
             "C' Strand": "6495ED",
             "C'' Strand": "006400",
             "D Strand": "00FF00",
-            "E Strand": "FFFF00", //"F0E68C",
+            "E Strand": "F7DC6F", //"FFFF00", //"F0E68C",
             "F Strand": "FFA500",
             "G Strand": "FF0000",
             //"G+ Strand": "8B0000",
@@ -36893,14 +36970,14 @@ class SetOption {
             "<b>Protodomain 1</b>": "",
             "A Strand": "0000FF",
             "B Strand": "006400",
-            "C Strand": "FFFF00", //"F0E68C",
+            "C Strand": "F7DC6F", //"FFFF00", //"F0E68C",
             "C' Strand": "FFA500",
             "<br><b>Linker</b>": "",
             "C'' Strand": "FF0000",
             "<br><b>Protodomain 2</b>": "",
             "D Strand": "0000FF",
             "E Strand": "006400",
-            "F Strand": "FFFF00", //"F0E68C",
+            "F Strand": "F7DC6F", //"FFFF00", //"F0E68C",
             "G Strand": "FFA500",
             "": "",
             "Loop": "CCCCCC"
@@ -43060,7 +43137,7 @@ class ShowAnno {
             let proteinName = fullProteinName;
             //if(proteinName.length > 40) proteinName = proteinName.substr(0, 40) + "...";
             let categoryStr =(index == 0) ? "<span class='icn3d-annoLargeTitle'><b>Proteins</b>: </span><br><br>" : "";
-            let geneLink =(ic.chainsGene[chnid] && ic.chainsGene[chnid].geneId) ? "(Gene: <a href='https://www.ncbi.nlm.nih.gov/gene/" + ic.chainsGene[chnid].geneId + "?report=gene_table' target='_blank' title='" + ic.chainsGene[chnid].geneDesc + "'>" + ic.chainsGene[chnid].geneSymbol + "</a>)" : '';
+            let geneLink =(ic.chainsGene[chnid] && ic.chainsGene[chnid].geneId && ic.chainsGene[chnid].geneDesc) ? "(Gene: <a href='https://www.ncbi.nlm.nih.gov/gene/" + ic.chainsGene[chnid].geneId + "?report=gene_table' target='_blank' title='" + ic.chainsGene[chnid].geneDesc + "'>" + ic.chainsGene[chnid].geneSymbol + "</a>)" : '';
             let structure = chnid.substr(0, chnid.indexOf('_'));
             let chainLink = (structure.length > 5) ? '<a href="https://alphafold.ebi.ac.uk/entry/' + structure + '" target="_blank">' + chnid + '</a>' : chnid;
             let chainHtml = "<div id='" + ic.pre + "anno_" + chnid + "' class='icn3d-annotation'>" + categoryStr
@@ -43737,7 +43814,7 @@ class ShowSeq {
             html += '<span>-</span>'; //'<span>-</span>';
           }
         }
-
+        
         if(ic.seqStartLen && ic.seqStartLen[chnid]) html += this.insertMulGap(ic.seqEndLen[chnid], '-');
 
         html += '<span class="icn3d-residueNum"></span>';
@@ -43956,7 +44033,7 @@ class ShowSeq {
         html += '</div>';
         html2 += '</div>';
         html3 += '</div>';
-
+        
         //if(Object.keys(ic.chains[chnid]).length > 10) {
         if(ic.giSeq[chnid].length > 10) {
             let atom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.chains[chnid]);
@@ -44004,27 +44081,31 @@ class ShowSeq {
                 html += '</div>';
                 html3 += '</div></div>';
             }         
-            else if(ic.bShowRefnum && ic.chainid2refpdbname.hasOwnProperty(chnid) && ic.chainid2refpdbname[chnid].length > 0) {                          
+            
+            if(ic.bShowRefnum && ic.chainid2refpdbname.hasOwnProperty(chnid) && ic.chainid2refpdbname[chnid].length > 0) {                                       
                 let result = this.showAllRefNum(giSeq, chnid);
+                
                 html += result.html;
                 html3 += result.html3;
             }
-            else if(ic.bShowCustomRefnum && ic.chainsMapping.hasOwnProperty(chnid)) {              
+            
+            if(ic.bShowCustomRefnum && ic.chainsMapping.hasOwnProperty(chnid)) {              
                 let bCustom = true;
                 let result = this.showRefNum(giSeq, chnid, undefined, bCustom);
                 html += result.html;
                 html3 += result.html3;
             }
         }
-
+        
         // highlight reference numbers
         if(ic.bShowRefnum) {
-            ic.hAtoms = ic.hAtomsRefnum;
+            // comment out so that this process didn't change the selection
+            //ic.hAtoms = ic.hAtomsRefnum;
             
             // commented out because it produced too many commands
             // let name = 'refnum_anchors';
             // ic.selectionCls.saveSelection(name, name);
-            
+
             ic.hlUpdateCls.updateHlAll();
         }
 
@@ -44055,9 +44136,10 @@ class ShowSeq {
             //ic.setColorCls.setColorByOptions(ic.opts, ic.atoms);
             ic.setColorCls.setColorByOptions(ic.opts, ic.dAtoms);
 
-            ic.selectionCls.selectAll_base();
+            //ic.selectionCls.selectAll_base();
             ic.hlUpdateCls.updateHlAll();
             //ic.drawCls.draw();
+            ic.drawCls.draw();
         }
 
         return {'html': html, 'html3': html3};
@@ -44133,7 +44215,10 @@ class ShowSeq {
 
         if(!bCustom && !kabat_or_imgt && !me.bNode) { // do not overwrite loops in node  
             // reset ic.residIgLoop for the current selection, which could be the second round of ref num assignment
-            let residHash = ic.firstAtomObjCls.getResiduesFromAtoms(ic.hAtoms);
+            // just current chain
+            let atomHash = me.hashUtilsCls.intHash(ic.chains[chnid], ic.hAtoms);
+            let residHash = ic.firstAtomObjCls.getResiduesFromAtoms(atomHash);
+            
             for(let resid in residHash) {
                 // not in loop any more if you assign ref numbers multiple times
                 delete ic.residIgLoop[resid];
@@ -44171,8 +44256,10 @@ class ShowSeq {
 
                     postfix = strandPostfix + '_' + index;
 
+                    let firstTwo = parseInt(refnum.toString().substr(0, 2)); // A- strand
+
                     if(currStrand && currStrand != ' ') {
-                        if(refnum3c.substr(0,1) != '9') {
+                        if(refnum3c.substr(0,1) != '9' || firstTwo == 10) {
                             let lastTwo = parseInt(refnum.toString().substr(refnum.toString().length - 2, 2));
                             
                             if(currStrand != prevStrand) { // reset currCnt
@@ -44199,6 +44286,10 @@ class ShowSeq {
                                     resCntAtAnchor = 0;
                                 }
 
+                                if(firstTwo == 10) {
+                                    strandArray[strandCnt].anchorRefnum = 0;
+                                }
+
                                 strandArray[strandCnt].strandPostfix = strandPostfix; // a in A1250a
                                 strandArray[strandCnt].strand = currStrand; // A in A1250a
 
@@ -44221,6 +44312,10 @@ class ShowSeq {
                                         resCntAtAnchor = 0;
                                     }
 
+                                    if(firstTwo == 10) {
+                                        strandArray[strandCnt - 1].anchorRefnum = 0;
+                                    }
+
                                     strandArray[strandCnt - 1].endResi = currResi;
                                     strandArray[strandCnt - 1].endRefnum = refnum; // 1250a
                                     strandArray[strandCnt - 1].resCntAtAnchor = resCntAtAnchor;
@@ -44555,13 +44650,13 @@ class ShowSeq {
 
         let html = '';
 
-        if(refnumLabel && lastTwo == 50 && !bLoop) {
+        if(refnumLabel && (lastTwo == 50 || refnum == 1094) && !bLoop) {
             // highlight the anchor residues
             ic.hAtomsRefnum = me.hashUtilsCls.unionHash(ic.hAtomsRefnum, ic.residues[residueid]);
 
             html += '<span ' + colorStr + ' title="' + refnumLabel + '"><b>' + refnumLabel.substr(0, 1) + '</b>' + refnumLabel.substr(1) + '</span>';
         }
-        else if(refnumLabel && lastTwo % 2 == 0 && lastTwo != 52 && !bHidelabel) { // don't show label for the first, middle, and last loop residues
+        else if(refnumLabel && lastTwo % 2 == 0 && lastTwo != 52 && refnum != 1096 && !bHidelabel) { // don't show label for the first, middle, and last loop residues
             // e.g., 2152a
             lastTwoStr = isNaN(refnumStr) ? lastTwoStr + refnumStr.substr(refnumStr.length - 1, 1) : lastTwoStr;
             html += '<span ' + colorStr + ' title="' + refnumLabel + '">' + lastTwoStr + '</span>';
@@ -44575,17 +44670,17 @@ class ShowSeq {
 
     getRefnumColor(currStrand, bText) {  let ic = this.icn3d, me = ic.icn3dui;
         if(currStrand == "A-") { 
-            return '#663399'; 
+            return '#9400D3'; //'#663399'; 
         }
         else if(currStrand == "A") { 
-            return '#663399'; 
+            return '#9400D3'; //'#663399'; 
         }
         //else if(currStrand == "A*") { 
         else if(currStrand == "A+") { 
-            return '#663399'; //'#FFC0CB'; 
+            return '#9400D3'; //'#663399'; 
         }
         else if(currStrand == "A'") { 
-            return '#663399'; 
+            return '#9400D3'; //'#663399'; 
         }
         else if(currStrand == "B") { 
             return '#ba55d3'; 
@@ -44603,7 +44698,8 @@ class ShowSeq {
             return '#00FF00'; 
         }
         else if(currStrand == "E") { 
-            return (bText) ? "#F7DC6F" : "#FFFF00"; 
+            //return (bText) ? "#F7DC6F" : "#FFFF00"; 
+            return "#F7DC6F"; 
         }
         else if(currStrand == "F") { 
             return '#FFA500'; 
@@ -44627,7 +44723,7 @@ class ShowSeq {
             return '#006400';
         }
         else if(currStrand == "C" || currStrand == "F") {
-            return "#FFFF00"; //'#F0E68C'; 
+            return "#F7DC6F"; //"#FFFF00"; //'#F0E68C'; 
         }
         else if(currStrand == "C'" || (currStrand && currStrand.substr(0, 1) == "G")) {
             return '#FFA500'; 
@@ -46326,31 +46422,31 @@ class LineGraph {
         ic.hlUpdateCls.updateHlAll();
     }
  
-    async showIgRefNum() { let ic = this.icn3d, me = ic.icn3dui;
+    async showIgRefNum(template) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
         // 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', '1CD28_1yjdC_human_V'];
+        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', '1NaKATPaseTransporterBeta_2zxeB_spurdogshark', '1FAB-HEAVY_5esv_V-n1', '1PDL1_4z18B_human_V-n1', '1BTLA_2aw2A_human_Iset', '1LaminAC_1ifrA_human', '1CD3g_6jxrg_human_Iset', '1CD28_1yjdC_human_V', '1CD19_6al5A_human_C2orV-n1'];
 
         // round 2
         ic.refpdbHash = {};
         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['1CoAtomerGamma1_1r4xA_human'] = ['CoAtomerGamma1_1r4xA_human', 'TP34_2o6cA_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['1ASF1A_2iijA_human'] = ['ASF1A_2iijA_human', 'MPT63_1lmiA_bacteria'];
+        ic.refpdbHash['1ASF1A_2iijA_human'] = ['ASF1A_2iijA_human', 'RBPJ_6py8C_human_Unk-n2', 'TP47_1o75A_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['1NaCaExchanger_2fwuA_dog_n2'] = ['NaCaExchanger_2fwuA_dog_n2', 'ORF7a_1xakA_virus', 'ECadherin_4zt1A_human_n2'];
+        ic.refpdbHash['1NaKATPaseTransporterBeta_2zxeB_spurdogshark'] = ['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['1TCRa_6jxrm_human_C1-n2'] = ['TCRa_6jxrm_human_C1-n2'];
-        ic.refpdbHash['1CD19_6al5A_human_C2orV-n1'] = ['CD19_6al5A_human_C2orV-n1'];  
-        ic.refpdbHash['1CD28_1yjdC_human_V'] = ['CD28_1yjdC_human_V']; 
+        ic.refpdbHash['1LaminAC_1ifrA_human'] = ['LaminAC_1ifrA_human', 'CD3d_6jxrd_human_Iset'];
+        ic.refpdbHash['1CD3g_6jxrg_human_Iset'] = ['CD3g_6jxrg_human_Iset', 'TCRa_6jxrm_human_C1-n2', 'IsdA_2iteA_bacteria'];
+        ic.refpdbHash['1CD28_1yjdC_human_V'] = ['CD28_1yjdC_human_V', 'MPT63_1lmiA_bacteria', 'CD3e_6jxrf_human_Iset'];
+        ic.refpdbHash['1CD19_6al5A_human_C2orV-n1'] = ['CD19_6al5A_human_C2orV-n1']; 
 
         // use known ref structure
         ic.refpdbHash['5ESV_C'] = ['FAB-HEAVY_5esv_V-n1', 'FAB-HEAVY_5esv_C1-n2'];
@@ -46398,11 +46494,14 @@ class LineGraph {
         ic.refpdbHash['6A15_A'] = ['CD19_6al5A_human_C2orV-n1'];
         ic.refpdbHash['2QKI_D'] = ['C3_2qkiD_human_n1'];
         ic.refpdbHash['1YJD_C'] = ['CD28_1yjdC_human_V'];
+        ic.refpdbHash['6JXR_d'] = ['CD3d_6jxrd_human_Iset'];
+        ic.refpdbHash['6JXR_f'] = ['CD3e_6jxrf_human_Iset'];
+        ic.refpdbHash['6JXR_g'] = ['CD3g_6jxrg_human_Iset'];
 
         let pdbAjaxArray = [];
         for(let k = 0, kl = ic.refpdbArray.length; k < kl; ++k) {
-            //let urlpdb = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi?refpdbid=" + ic.refpdbArray[k];
-            let urlpdb = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi?refjsonid=" + ic.refpdbArray[k];
+            let urlpdb = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi?refpdbid=" + ic.refpdbArray[k];
+            //let urlpdb = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi?refjsonid=" + ic.refpdbArray[k];
 
             let pdbAjax = me.getAjaxPromise(urlpdb, 'text');
 
@@ -46410,9 +46509,14 @@ class LineGraph {
         }
 
         // try {
-            let allPromise = Promise.allSettled(pdbAjaxArray);
-            ic.pdbDataArray = await allPromise;
-            await thisClass.parseRefPdbData(ic.pdbDataArray);
+            if(!template) {
+                let allPromise = Promise.allSettled(pdbAjaxArray);
+                ic.pdbDataArray = await allPromise;
+                await thisClass.parseRefPdbData(ic.pdbDataArray, template);
+            }
+            else {
+                await thisClass.parseRefPdbData(undefined, template);
+            }
         // }
         // catch(err) {
         //     if(!me.bNode) alert("Error in retrieveing reference PDB data...");
@@ -46420,7 +46524,7 @@ class LineGraph {
         // }
     }
 
-    async parseRefPdbData(dataArray) { let ic = this.icn3d, me = ic.icn3dui;
+    async parseRefPdbData(dataArray, template) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
         let struArray = Object.keys(ic.structures);
@@ -46428,8 +46532,8 @@ class LineGraph {
         let ajaxArray = [];
         let domainidpairArray = [];
 
-        me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
-        let urlalign = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi";
+        let urltmalign = me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
+        me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi";
 
         if(!ic.resid2domainid) ic.resid2domainid = {};
         //ic.resid2domainid = {};
@@ -46467,11 +46571,16 @@ class LineGraph {
 
                     let atomFirst = ic.firstAtomObjCls.getFirstAtomObj(currAtoms);
                     let atomLast = ic.firstAtomObjCls.getLastAtomObj(currAtoms);
-                    let resiSum = parseInt(atomFirst.resi) + parseInt(atomLast.resi);
+                    let resiSum = atomFirst.resi + ':' + atomLast.resi;
 
                     for(let n = 0, nl = residueArray.length; n < nl; ++n) {
                         let resid = residueArray[n];
                         ic.resid2domainid[resid] = chainid + '-0' + '_' + resiSum; 
+
+                        // clear previous refnum assignment if any
+                        if(ic.resid2refnum && ic.resid2refnum[resid]) {
+                            delete ic.resid2refnum[resid];
+                        }
                     }
                 }
                 else {                 
@@ -46486,6 +46595,11 @@ class LineGraph {
                                 let resid = chainid + '_' + pos2resi[n];
                                 domainAtoms = me.hashUtilsCls.unionHash(domainAtoms, ic.residues[resid]);
                                 //ic.resid2domainid[resid] = chainid + '-' + k;
+
+                                // clear previous refnum assignment if any
+                                if(ic.resid2refnum && ic.resid2refnum[resid]) {
+                                    delete ic.resid2refnum[resid];
+                                }
                             }
                         }
 
@@ -46493,7 +46607,7 @@ class LineGraph {
 
                         let atomFirst = ic.firstAtomObjCls.getFirstAtomObj(domainAtoms);
                         let atomLast = ic.firstAtomObjCls.getLastAtomObj(domainAtoms);
-                        let resiSum = parseInt(atomFirst.resi) + parseInt(atomLast.resi);
+                        let resiSum = atomFirst.resi + ':' + atomLast.resi;
 
                         for(let m = 0, ml = segArray.length; m < ml; m += 2) {
                             let startResi = segArray[m];
@@ -46507,69 +46621,121 @@ class LineGraph {
                     }
                 }
 
+                if(!ic.domainid2refpdbname) ic.domainid2refpdbname = {};
+
                 for(let k = 0, kl = domainAtomsArray.length; k < kl; ++k) {
                     let pdb_target = ic.saveFileCls.getAtomPDB(domainAtomsArray[k], undefined, undefined, undefined, undefined, struct);
-                    let bForceOneDomain = true;
-                    let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(domainAtomsArray[k], bForceOneDomain);
+                    //let bForceOneDomain = true;
+                    //let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(domainAtomsArray[k], bForceOneDomain);
 
                     // ig strand for any subset will have the same k, use the number of residue to separate them
                     let atomFirst = ic.firstAtomObjCls.getFirstAtomObj(domainAtomsArray[k]);
                     let atomLast = ic.firstAtomObjCls.getLastAtomObj(domainAtomsArray[k]);
-                    let resiSum = parseInt(atomFirst.resi) + parseInt(atomLast.resi);
+                    let resiSum = atomFirst.resi + ':' + atomLast.resi;
                     //let domainid = chainid + '-' + k + '_' + Object.keys(domainAtomsArray[k]).length; 
                     let domainid = chainid + '-' + k + '_' + resiSum; 
                     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 header = 'HEADER                                                        ' + struct2 + '\n';
-                        // pdb_query = header + pdb_query;
-                        let jsonStr_q = dataArray[index].value; //[0];
+                    if(!template) {
+                        for(let index = 0, indexl = dataArray.length; index < indexl; ++index) {
+                            let struct2 = ic.defaultPdbId + index;
+                            let pdb_query = dataArray[index].value; //[0];
+                            let header = 'HEADER                                                        ' + struct2 + '\n';
+                            pdb_query = header + pdb_query;
+                            //let jsonStr_q = dataArray[index].value; //[0];
 
-                        // TM-align is not good when you align a full structure with the strand-only structure. VAST is better in this case.
-                        // let dataObj = {'pdb_query': pdb_query, 'pdb_target': pdb_target, "queryid": ic.refpdbArray[index]};
-                        // let alignAjax = me.getAjaxPostPromise(urltmalign, dataObj);
+                            let dataObj = {'pdb_query': pdb_query, 'pdb_target': pdb_target, "queryid": ic.refpdbArray[index]};
+                            let alignAjax = me.getAjaxPostPromise(urltmalign, dataObj);
 
-                        let dataObj = {'domains1': jsonStr_q, 'domains2': jsonStr_t};
-                        let alignAjax = me.getAjaxPostPromise(urlalign, dataObj);
+                            // let dataObj = {'domains1': jsonStr_q, 'domains2': jsonStr_t};
+                            // let alignAjax = me.getAjaxPostPromise(urlalign, dataObj);
 
-                        ajaxArray.push(alignAjax);
-                        
-                        domainidpairArray.push(domainid + "|" + ic.refpdbArray[index]);
+                            ajaxArray.push(alignAjax);
+                            
+                            domainidpairArray.push(domainid + "|" + ic.refpdbArray[index]);
+                        }
+                    }
+                    else {
+                        ic.domainid2refpdbname[domainid] = template;
+                        domainidpairArray.push(domainid + "|1" + template); // "1" was added for the first round strand-only template
                     }
                 }
             }
         }
 
         try {
-            let dataArray2 = [];
+            if(!template) {
+                let dataArray2 = [];
 
-            // let allPromise = Promise.allSettled(ajaxArray);
-            // dataArray2 = await allPromise;
+                // let allPromise = Promise.allSettled(ajaxArray);
+                // dataArray2 = await allPromise;
 
-            //split arrays into chunks of 96 jobs or me.cfg.maxajax jobs
-            let n = (me.cfg.maxajax) ? me.cfg.maxajax : 96;
+                //split arrays into chunks of 48 jobs or me.cfg.maxajax jobs
+                let n = (me.cfg.maxajax) ? me.cfg.maxajax : ic.refpdbArray.length * 6;
 
-            for(let i = 0, il = parseInt((ajaxArray.length - 1) / n + 1); i < il; ++i) {
-                let currAjaxArray = [];
-                if(i == il - 1) { // last one 
-                    currAjaxArray = ajaxArray.slice(i * n, ajaxArray.length);
-                }
-                else {
-                    currAjaxArray = ajaxArray.slice(i * n, (i + 1) * n);
-                }
+                for(let i = 0, il = parseInt((ajaxArray.length - 1) / n + 1); i < il; ++i) {
+                    let currAjaxArray = [];
+                    if(i == il - 1) { // last one 
+                        currAjaxArray = ajaxArray.slice(i * n, ajaxArray.length);
+                    }
+                    else {
+                        currAjaxArray = ajaxArray.slice(i * n, (i + 1) * n);
+                    }
 
-                let currPromise = Promise.allSettled(currAjaxArray);
-                let currDataArray = await currPromise;
+                    let currPromise = Promise.allSettled(currAjaxArray);
+                    let currDataArray = await currPromise;
 
-                dataArray2 = dataArray2.concat(currDataArray);
+                    dataArray2 = dataArray2.concat(currDataArray);
+                }
+            
+                let bRound1 = true;
+                await thisClass.parseAlignData(dataArray2, domainidpairArray, bRound1);
+
+                /// if(ic.deferredRefnum !== undefined) ic.deferredRefnum.resolve();
             }
-        
-            let bRound1 = true;
-            await thisClass.parseAlignData(dataArray2, domainidpairArray, bRound1);
+            else {
+                if(!me.bNode) console.log("Start alignment with the reference culsters " + JSON.stringify(ic.domainid2refpdbname));   
+
+                // start round2
+                let ajaxArray = [];
+                let domainidpairArray3 = [];
+                let urltmalign = me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
+
+                let urlpdb = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi?refpdbid=" + template;
+                let pdbAjax = me.getAjaxPromise(urlpdb, 'text');
+                let pdbAjaxArray = [];
+                pdbAjaxArray.push(pdbAjax);
 
-            /// if(ic.deferredRefnum !== undefined) ic.deferredRefnum.resolve();
+                let allPromise2 = Promise.allSettled(pdbAjaxArray);
+                ic.pdbDataArray = await allPromise2;
+
+                for(let domainid in ic.domainid2refpdbname) {
+                    let refpdbname = ic.domainid2refpdbname[domainid];
+                    let chainid = domainid.substr(0, domainid.indexOf('-'));
+
+                    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 header = 'HEADER                                                        ' + struct2 + '\n';
+                        pdb_query = header + pdb_query;
+    
+                        let dataObj = {'pdb_query': pdb_query, 'pdb_target': pdb_target, "queryid": template};
+                        let alignAjax = me.getAjaxPostPromise(urltmalign, dataObj);
+                        ajaxArray.push(alignAjax);
+                        
+                        //domainidpairArray3.push(domainid + "," + refpdbname);
+                        domainidpairArray3.push(domainid + "|" + template);
+                    }
+                }
+    
+                let dataArray3 = [];
+                let allPromise = Promise.allSettled(ajaxArray);
+                dataArray3 = await allPromise;
+    
+                await thisClass.parseAlignData(dataArray3, domainidpairArray3);
+            }
         }
         catch(err) {
             let mess = "Some of " + ajaxArray.length + " TM-align alignments failed. Please select a chain or a subset to assing reference numbers to avoid overloading the server...";
@@ -46581,7 +46747,7 @@ class LineGraph {
             }
             //console.log("Error in aligning with TM-align...");
             return;
-        }                       
+        }                   
     }
 
     getTemplateList(chainid) { let ic = this.icn3d; ic.icn3dui;
@@ -46612,7 +46778,6 @@ class LineGraph {
         let thisClass = this;
 
         let tmscoreThreshold = 0.4; // 0.4; //0.5;
-        let rmsdThreshold = 10;
 
         // find the best alignment for each chain
         let domainid2score = {}, domainid2segs = {}, chainid2segs = {};
@@ -46646,7 +46811,10 @@ class LineGraph {
                 }
             }
             else {
-                if(queryData[0].super_rmsd > rmsdThreshold || queryData[0].num_res < minResidues) {
+                // if(queryData[0].super_rmsd > rmsdThreshold || queryData[0].num_res < minResidues) {
+                //     continue;
+                // }
+                if(queryData[0].score < tmscoreThreshold || queryData[0].num_res < minResidues) {
                     continue;
                 }
             }
@@ -46661,7 +46829,8 @@ class LineGraph {
                 if(!me.bNode) console.log("refpdbname " + refpdbname + " TM-score: " + queryData[0].score);
             }
             else {
-                if(!me.bNode) console.log("domainid: " + domainid + " refpdbname " + refpdbname + " RMSD: " + queryData[0].super_rmsd + ", num_res: " + queryData[0].num_res + ",  10/RMSD + num_res/5: " + (10 / queryData[0].super_rmsd + queryData[0].num_seg / 5).toFixed(1));
+                // if(!me.bNode) console.log("domainid: " + domainid + " refpdbname " + refpdbname + " RMSD: " + queryData[0].super_rmsd + ", num_seg: " + queryData[0].num_seg + ",  10/RMSD + num_seg/5: " + (10 / queryData[0].super_rmsd + queryData[0].num_seg / 5).toFixed(1));
+                if(!me.bNode) console.log("domainid: " + domainid + " refpdbname " + refpdbname + " TM-score: " + queryData[0].score);
             }
 
             // Ig-like domains: B (2150, 2150a, 2150b), C (3150, 3250), E (7150, 7250), F (8150, 8250) strands
@@ -46691,7 +46860,7 @@ class LineGraph {
                 //if(!(bBstrand && bCstrand && bEstrand && bFstrand && bGstrand)) continue;
                 if(!(bBstrand && bCstrand && bEstrand && bFstrand)) {
                     if(!me.bNode) console.log("Some of the Ig strands B, C, E, F are missing in the domain " + domainid + "...");
-                    if(ic.domainid2refpdbname[domainid]) delete ic.domainid2refpdbname[domainid];
+                    if(ic.domainid2refpdbname[domainid] == refpdbname) delete ic.domainid2refpdbname[domainid];
                     continue;
                 }
             }
@@ -46709,7 +46878,8 @@ class LineGraph {
                 }
             }
             else {
-                let mixScore = 10 / queryData[0].super_rmsd + queryData[0].num_seg / 5; 
+                //let mixScore = 10 / queryData[0].super_rmsd + queryData[0].num_seg / 5; 
+                let mixScore = queryData[0].score; 
 
                 if(!domainid2score.hasOwnProperty(domainid) || mixScore > domainid2score[domainid]) {
                     domainid2score[domainid] = mixScore;  
@@ -46777,10 +46947,28 @@ class LineGraph {
             }
 
             let dataArray3 = [];
-            let allPromise = Promise.allSettled(ajaxArray);
-            dataArray3 = await allPromise;
+            //let allPromise = Promise.allSettled(ajaxArray);
+            //dataArray3 = await allPromise;
+
+            //split arrays into chunks of 48 jobs or me.cfg.maxajax jobs
+            let n = (me.cfg.maxajax) ? me.cfg.maxajax : ic.refpdbArray.length * 6;
+
+            for(let i = 0, il = parseInt((ajaxArray.length - 1) / n + 1); i < il; ++i) {
+                let currAjaxArray = [];
+                if(i == il - 1) { // last one 
+                    currAjaxArray = ajaxArray.slice(i * n, ajaxArray.length);
+                }
+                else {
+                    currAjaxArray = ajaxArray.slice(i * n, (i + 1) * n);
+                }
+
+                let currPromise = Promise.allSettled(currAjaxArray);
+                let currDataArray = await currPromise;
 
-            await thisClass.parseAlignData(dataArray3, domainidpairArray3);
+                dataArray3 = dataArray3.concat(currDataArray);
+            }
+
+            await thisClass.parseAlignData(dataArray3, domainidpairArray3, false);
             
             // end of round 2
             return;
@@ -46811,6 +46999,7 @@ class LineGraph {
         if(!ic.chainsMapping) ic.chainsMapping = {};
 
         if(!ic.refPdbList) ic.refPdbList = [];
+
         for(let chainid in chainid2segs) {
             let segArray = chainid2segs[chainid];
 
@@ -46879,7 +47068,7 @@ class LineGraph {
             else {
                 await ic.showAnnoCls.showAnnotations();
             }
-
+            
             ic.annotationCls.setAnnoViewAndDisplay('detailed view');
         }
         else {
@@ -50291,7 +50480,7 @@ class ChainalignParser {
             //hAtoms = me.hashUtilsCls.unionHash(hAtoms, ic.chains[chainidArray[0]]);
             //hAtoms = me.hashUtilsCls.unionHash(hAtoms, ic.chains[chainidArray[1]]);
         }
-        
+
         // set up the view of sequence alignment for each pair
         for(let mmdbidpair in mmdbidpairFinalHash) {                 
             if(ic.q_rotation !== undefined) {
@@ -50722,7 +50911,11 @@ class ChainalignParser {
                 if(me.cfg.aligntool == 'tmalign') logStr += "; TM-score: " + align[0].score.toPrecision(4);
                 me.htmlCls.clickMenuCls.setLogCmd(logStr, false);
                 let html = "<br><b>Alignment RMSD</b>: " + rmsd.toPrecision(4) + " &#8491;<br>";
-                if(me.cfg.aligntool == 'tmalign') html += "<b>TM-score</b>: " + align[0].score.toPrecision(4) + "<br><br>";
+                if(me.cfg.aligntool == 'tmalign') {
+                    html += "<b>TM-score</b>: " + align[0].score.toPrecision(4) + "<br><br>";
+                    ic.tmscore = align[0].score.toPrecision(4);
+                }
+
                 $("#" + ic.pre + "dl_rmsd_html").html(html);
                 if(!me.cfg.bSidebyside) me.htmlCls.dialogCls.openDlg('dl_rmsd', 'RMSD of alignment');
 
@@ -50977,15 +51170,15 @@ class Dsn6Parser {
         this.icn3d = icn3d;
     }
 
-    dsn6Parser(pdbid, type, sigma) { let ic = this.icn3d; ic.icn3dui;
+    async dsn6Parser(pdbid, type, sigma) { let ic = this.icn3d; ic.icn3dui;
         // https://edmaps.rcsb.org/maps/1kq2_2fofc.dsn6
         // https://edmaps.rcsb.org/maps/1kq2_fofc.dsn6
 
         let url = "https://edmaps.rcsb.org/maps/" + pdbid.toLowerCase() + "_" + type + ".dsn6";
-        this.dsn6ParserBase(url, type, sigma);
+        await this.dsn6ParserBase(url, type, sigma);
     }
 
-    dsn6ParserBase(url, type, sigma) { let ic = this.icn3d; ic.icn3dui;
+    async dsn6ParserBase(url, type, sigma) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
         //https://stackoverflow.com/questions/33902299/using-jquery-ajax-to-download-a-binary-file
@@ -50998,37 +51191,17 @@ class Dsn6Parser {
             ic.setOptionCls.setOption('map', type);
         }
         else {
-            let oReq = new XMLHttpRequest();
-            oReq.open("GET", url, true);
-            oReq.responseType = "arraybuffer";
-
-            oReq.onreadystatechange = function() {
-                if(this.readyState == 4) {
-                   if(this.status == 200) {
-                       let arrayBuffer = oReq.response;
-                       thisClass.loadDsn6Data(arrayBuffer, type, sigma);
-
-                       if(type == '2fofc') {
-                           ic.bAjax2fofc = true;
-                       }
-                       else if(type == 'fofc') {
-                           ic.bAjaxfofc = true;
-                       }
+            let arrayBuffer = await me.getXMLHttpRqstPromise(url, 'GET', 'arraybuffer', 'rcsbEdmaps');
+            thisClass.loadDsn6Data(arrayBuffer, type, sigma);
 
-                       ic.setOptionCls.setOption('map', type);
-                    }
-                    else {
-                        alert("RCSB server has no corresponding eletron density map for this structure.");
-                    }
-
-                    /// if(ic.deferredMap !== undefined) ic.deferredMap.resolve();
-                }
-                else {
-                    ic.ParserUtilsCls.showLoading();
-                }
-            };
+            if(type == '2fofc') {
+                ic.bAjax2fofc = true;
+            }
+            else if(type == 'fofc') {
+                ic.bAjaxfofc = true;
+            }
 
-            oReq.send();
+            ic.setOptionCls.setOption('map', type);
         }
     }
 
@@ -51766,6 +51939,11 @@ class MmdbParser {
 
           let color =(molid2rescount[i].color === undefined) ? '#CCCCCC' : '#' +( '000000' + molid2rescount[i].color.toString( 16 ) ).slice( - 6 );
           let chainName =(molid2rescount[i].chain === undefined) ? '' : molid2rescount[i].chain.trim();
+          // remove "_" in chain name
+          if(parseInt(me.cfg.date) >= 20231001 || (!me.cfg.date && parseInt(me.utilsCls.getDateDigitStr()) >= 20231001)) {
+            chainName = chainName.replace(/_/g, '');
+          }
+
           if(chainNameHash[chainName] === undefined) {
               chainNameHash[chainName] = 1;
           }
@@ -52800,7 +52978,7 @@ class PdbParser {
 
         if(me.cfg.rotate !== undefined) ic.resizeCanvasCls.rotStruc(me.cfg.rotate, true);
 
-        if(bAppend) {
+        if(bAppend && !me.bNode) {
             // show all
             ic.definedSetsCls.setModeAndDisplay('all');
         }
@@ -54022,7 +54200,7 @@ class DensityCifParser {
         this.icn3d = icn3d;
     }
 
-    densityCifParser(pdbid, type, sigma, emd) { let ic = this.icn3d, me = ic.icn3dui;
+    async densityCifParser(pdbid, type, sigma, emd) { let ic = this.icn3d, me = ic.icn3dui;
        let thisClass = this;
 
        let url;
@@ -54052,46 +54230,21 @@ class DensityCifParser {
             ic.setOptionCls.setOption('emmap', type);
         }
         else {
-            let oReq = new XMLHttpRequest();
-            oReq.open("GET", url, true);
-            oReq.responseType = "arraybuffer";
-
-            oReq.onreadystatechange = function() {
-                if (this.readyState == 4) {
-                   if(this.status == 200) {
-                       let arrayBuffer = oReq.response;
-
-                       thisClass.parseChannels(arrayBuffer, type, sigma);
-
-                       if(type == '2fofc' || type == 'fofc') {
-                           ic.bAjax2fofc = true;
-                           ic.bAjaxfofc = true;
+            let arrayBuffer = await me.getXMLHttpRqstPromise(url, 'GET', 'arraybuffer', type);
 
-                           ic.setOptionCls.setOption('map', type);
-                       }
-                       else if(type == 'em') {
-                           ic.bAjaxEm = true;
+            thisClass.parseChannels(arrayBuffer, type, sigma);
 
-                           ic.setOptionCls.setOption('emmap', type);
-                       }
-                    }
-                    else {
-                       if(type == '2fofc' || type == 'fofc') {
-                           alert("Density server at EBI has no corresponding electron density map for this structure.");
-                       }
-                       else if(type == 'em') {
-                           alert("Density server at EBI has no corresponding EM density map for this structure.");
-                       }
-                    }
+            if(type == '2fofc' || type == 'fofc') {
+                ic.bAjax2fofc = true;
+                ic.bAjaxfofc = true;
 
-                    /// if(ic.deferredEmmap !== undefined) ic.deferredEmmap.resolve();
-                }
-                else {
-                    ic.ParserUtilsCls.showLoading();
-                }
-            };
+                ic.setOptionCls.setOption('map', type);
+            }
+            else if(type == 'em') {
+                ic.bAjaxEm = true;
 
-            oReq.send();
+                ic.setOptionCls.setOption('emmap', type);
+            }
         }
     }
 
@@ -55143,16 +55296,20 @@ class ParserUtils {
 
     getMissingResidues(seqArray, type, chainid) { let ic = this.icn3d, me = ic.icn3dui;
         ic.chainsSeq[chainid] = [];
+
+        // find the offset of MMDB sequence
+        let offset = 0;
         if(type === 'mmdbid' || type === 'align') {
             for(let i = 0, il = seqArray.length; i < il; ++i) {
                 if(seqArray[i][0] != 0) {
-                    seqArray[i][0] - (i + 1);
+                    offset = seqArray[i][0] - (i + 1);
                     break;
                 }
             }
         }
 
-        let prevResi = 0;
+        //let prevResi = 0;
+        let prevResi = offset;
         for(let i = 0, il = seqArray.length; i < il; ++i) {
             let seqName, resiPos;
             // mmdbid: ["0","R","ARG"],["502","V","VAL"]; mmcifid: [1, "ARG"]; align: ["0","R","ARG"] //align: [1, "0","R","ARG"]
@@ -55971,6 +56128,12 @@ class LoadAtomData {
                   if(Object.keys(data.moleculeInfor[molid]).length === 0) continue;
 
                   let chain = data.moleculeInfor[molid].chain.trim();
+
+                  // remove "_" in chain name
+                  if(parseInt(me.cfg.date) >= 20231001 || (!me.cfg.date && parseInt(me.utilsCls.getDateDigitStr()) >= 20231001)) {
+                    chain = chain.replace(/_/g, '');
+                  }
+
                   let chainid = pdbidTmp + '_' + chain;
 
                   if(chainHash.hasOwnProperty(chain)) {
@@ -56035,6 +56198,7 @@ class LoadAtomData {
         let CSerial, prevCSerial, OSerial, prevOSerial;
 
         let biopolymerChainsHash = {};
+
         for(let i in atoms) {
             ++serial;
 
@@ -56064,21 +56228,21 @@ class LoadAtomData {
                       atm.chain = ic.molid2chain[molid].substr(pos + 1);
                   }
                   else {
-                      let miscName = 'Misc';
+                        let miscName = 'Misc';
 
-                      //if(atm.resn != prevResn || chainid2kind[chainNum] === 'solvent' || atm.resn === 'HOH' || atm.name == atm.elem) {
-                      if((chainid2kind[chainNum] === 'protein' && chainid2kind[chainNum] === 'nucleotide' && atm.resi != prevResiOri)
-                        ||(chainid2kind[chainNum] !== 'protein' && chainid2kind[chainNum] !== 'nucleotide'
-                        &&(atm.resn.substr(0,3) != prevResn.substr(0,3) || atm.resi != prevResiOri || chainid2kind[chainNum] === 'solvent' || atm.resn === 'HOH')) ) {
-                          ++miscCnt;
-                      }
+                        //if(atm.resn != prevResn || chainid2kind[chainNum] === 'solvent' || atm.resn === 'HOH' || atm.name == atm.elem) {
+                        if((chainid2kind[chainNum] === 'protein' && chainid2kind[chainNum] === 'nucleotide' && atm.resi != prevResiOri)
+                            ||(chainid2kind[chainNum] !== 'protein' && chainid2kind[chainNum] !== 'nucleotide'
+                            &&(atm.resn.substr(0,3) != prevResn.substr(0,3) || atm.resi != prevResiOri || chainid2kind[chainNum] === 'solvent' || atm.resn === 'HOH')) ) {
+                            ++miscCnt;
+                        }
 
-                          atm.resi_ori = atm.resi;
-                          atm.resi = miscCnt;
-                          bSetResi = true;
+                        atm.resi_ori = atm.resi;
+                        atm.resi = miscCnt;
+                        bSetResi = true;
 
-                      //if all are defined in the chain section, no "Misc" should appear
-                      atm.chain = miscName;
+                        //if all are defined in the chain section, no "Misc" should appear
+                        atm.chain = miscName;
                   }
 
                   //if(ic.mmdbid_q !== undefined && ic.mmdbid_q === ic.mmdbid_t && alignType === 'query') {
@@ -56116,6 +56280,11 @@ class LoadAtomData {
 
             atm.chain = atm.chain.trim(); //.replace(/_/g, '');
 
+            // remove "_" in chain name
+            if(parseInt(me.cfg.date) >= 20231001 || (!me.cfg.date && parseInt(me.utilsCls.getDateDigitStr()) >= 20231001)) {
+                atm.chain = atm.chain.replace(/_/g, '');
+            }
+
             // mmcif has pre-assigned structure in mmcifparser.cgi output
             if(type === 'mmdbid' || type === 'align') {
                 atm.structure = mmdbId;
@@ -58524,10 +58693,7 @@ class LoadPDB {
 
                     if(ic.atoms[oriSerial2NewSerial[from]] !== undefined) ic.atoms[oriSerial2NewSerial[from]].bonds.push(oriSerial2NewSerial[to]);
                 }
-            } else if (record.substr(0,3) === 'TER') {
-                // Concatenation of two pdbs will have several atoms for the same serial
-                ++serial;
-            }
+            } else if (record.substr(0,3) === 'TER') ;
         }
 
         // add the last residue set
@@ -60101,24 +60267,28 @@ class ApplyCommand {
       else if(command == 'rotate left') {
          ic.bStopRotate = false;
          ic.ROT_DIR = 'left';
+         ic.transformCls.rotateCountMax = 6000;
 
          ic.resizeCanvasCls.rotStruc('left');
       }
       else if(command == 'rotate right') {
          ic.bStopRotate = false;
          ic.ROT_DIR = 'right';
+         ic.transformCls.rotateCountMax = 6000;
 
          ic.resizeCanvasCls.rotStruc('right');
       }
       else if(command == 'rotate up') {
          ic.bStopRotate = false;
          ic.ROT_DIR = 'up';
+         ic.transformCls.rotateCountMax = 6000;
 
          ic.resizeCanvasCls.rotStruc('up');
       }
       else if(command == 'rotate down') {
          ic.bStopRotate = false;
          ic.ROT_DIR = 'down';
+         ic.transformCls.rotateCountMax = 6000;
 
          ic.resizeCanvasCls.rotStruc('down');
       }
@@ -62244,10 +62414,14 @@ class LoadScript {
           let bFinalStep =(i === steps - 1) ? true : false;
 
           if(!ic.commands[i].trim()) continue;
-          if(!ic.atoms && ic.commands[i].indexOf('load') == -1) continue;
+          let nAtoms = Object.keys(ic.atoms).length;
+
+          if(nAtoms == 0 && ic.commands[i].indexOf('load') == -1) continue;
 
           let strArray = ic.commands[i].split("|||");
           let command = strArray[0].trim();
+
+          if(ic.inputid) ic.bNotLoadStructure = true;
   
           if(command.indexOf('load') !== -1) {
               if(end === 0 && start === end) {
@@ -62336,6 +62510,10 @@ class LoadScript {
           else if(command.indexOf('ig refnum on') == 0 ) { 
             await ic.refnumCls.showIgRefNum();
           }
+          else if(command.indexOf('ig template') == 0 ) { 
+            let template = command.substr(command.lastIndexOf(' ') + 1);
+            await ic.refnumCls.showIgRefNum(template);
+          }
           else if(command.indexOf('set annotation 3ddomain') == 0) { // the command may have "|||{"factor"...
               if(Object.keys(ic.proteins).length > 0) {
                   thisClass.applyCommand3ddomain(strArray[0].trim());   
@@ -62509,10 +62687,10 @@ class LoadScript {
                         await thisClass.applyCommandLoad(lastCommand);
                     }
                     else if(lastCommand.indexOf('set map') !== -1 && lastCommand.indexOf('set map wireframe') === -1) {
-                        thisClass.applyCommandMap(lastCommand);
+                        await thisClass.applyCommandMap(lastCommand);
                     }
                     else if(lastCommand.indexOf('set emmap') !== -1 && lastCommand.indexOf('set emmap wireframe') === -1) {
-                        thisClass.applyCommandEmmap(lastCommand);
+                        await thisClass.applyCommandEmmap(lastCommand);
                     }
                     else if(lastCommand.indexOf('set phi') !== -1) {
                         await ic.delphiCls.applyCommandPhi(lastCommand);
@@ -62782,7 +62960,7 @@ class LoadScript {
     }
 
     //Apply the command to show electron density map.
-    applyCommandMap(command) { let ic = this.icn3d; ic.icn3dui;
+    async applyCommandMap(command) { let ic = this.icn3d; ic.icn3dui;
 
       // chain functions together
     //   ic.deferredMap = $.Deferred(function() { let ic = thisClass.icn3d;
@@ -62798,10 +62976,10 @@ class LoadScript {
               let type = paraArray[0];
 
               if(urlArray.length == 2) {
-                  ic.dsn6ParserCls.dsn6ParserBase(urlArray[1], type, sigma);
+                await ic.dsn6ParserCls.dsn6ParserBase(urlArray[1], type, sigma);
               }
               else {
-                  ic.dsn6ParserCls.dsn6Parser(ic.inputid, type, sigma);
+                await ic.dsn6ParserCls.dsn6Parser(ic.inputid, type, sigma);
               }
           }
     //   }); // end of me.deferred = $.Deferred(function() {
@@ -62810,7 +62988,7 @@ class LoadScript {
     }
 
     //Apply the command to show EM density map.
-    applyCommandEmmap(command) { let ic = this.icn3d; ic.icn3dui;
+    async applyCommandEmmap(command) { let ic = this.icn3d; ic.icn3dui;
 
       // chain functions together
     //   ic.deferredEmmap = $.Deferred(function() { let ic = thisClass.icn3d;
@@ -62821,7 +62999,7 @@ class LoadScript {
               let percentage = paraArray[1];
               let type = 'em';
 
-              ic.densityCifParserCls.densityCifParser(ic.inputid, type, percentage, ic.emd);
+              await ic.densityCifParserCls.densityCifParser(ic.inputid, type, percentage, ic.emd);
           }
     //   }); // end of me.deferred = $.Deferred(function() {
 
@@ -63153,7 +63331,7 @@ class SelectByCommand {
            // $1,2,3: Structure
            // .A,B,C: chain
            // :5-10,K,chemicals: residues, could be 'proteins', 'nucleotides', 'chemicals', 'ions', and 'water'
-           // :ref_1250,anchors,strands,loops: reference numbers 1250, anchor residues (e.g., 2250), residues in strands, residues in loops
+           // :ref_1250,ref_anchors,ref_strands,ref_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 = {}
@@ -64758,31 +64936,12 @@ class Delphi {
         this.icn3d = icn3d;
     }
 
-    CalcPhiUrl(gsize, salt, contour, bSurface, url) { let ic = this.icn3d; ic.icn3dui;
+    async CalcPhiUrl(gsize, salt, contour, bSurface, url) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
-        let oReq = new XMLHttpRequest();
-        oReq.open("GET", url, true);
-
-        oReq.responseType = "text";
+        let data = await me.getXMLHttpRqstPromise(url, 'GET', 'text', 'PQR');
 
-        oReq.onreadystatechange = async function() {
-            if(this.readyState == 4) {
-               if(this.status == 200) {
-                   let data = oReq.response;
-
-                   await thisClass.CalcPhi(gsize, salt, contour, bSurface, data);
-                }
-                else {
-                    alert("The PQR file is unavailable...");
-                }
-            }
-            else {
-                ic.ParserUtilsCls.showLoading();
-            }
-        };
-
-        oReq.send();
+        await thisClass.CalcPhi(gsize, salt, contour, bSurface, data);
     }
 
     getPdbStr(bNode) { let ic = this.icn3d, me = ic.icn3dui;
@@ -64828,7 +64987,8 @@ class Delphi {
        let pdbstr = '';
 ///       pdbstr += ic.saveFileCls.getPDBHeader();
 
-       pdbstr +=(me.cfg.cid) ? ic.saveFileCls.getAtomPDB(atomHash, true) : ic.saveFileCls.getAtomPDB(atomHash);
+       let bMergeIntoOne = true;
+       pdbstr +=(me.cfg.cid) ? ic.saveFileCls.getAtomPDB(atomHash, true, undefined, undefined, undefined, undefined, bMergeIntoOne) : ic.saveFileCls.getAtomPDB(atomHash, undefined, undefined, undefined, undefined, undefined, bMergeIntoOne);
        pdbstr += ic.saveFileCls.getAtomPDB(ionHash, true, undefined, true);
 
        return pdbstr;
@@ -64869,7 +65029,7 @@ class Delphi {
         }
 
         return new Promise(function(resolve, reject) {
-            // see full_ui.js for ajaxTransport
+            // see icn3dui.js for ajaxTransport
             $.ajax({
                 url: url,
                 type: 'POST',
@@ -64893,7 +65053,7 @@ class Delphi {
         });
     }
 
-    PhiParser(url, type, contour, bSurface) { let ic = this.icn3d; ic.icn3dui;
+    async PhiParser(url, type, contour, bSurface) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
         //var dataType;
 
@@ -64911,49 +65071,32 @@ class Delphi {
         }
         else {
     */
-            let oReq = new XMLHttpRequest();
-            oReq.open("GET", url, true);
 
+            let responseType;
             if(type == 'phiurl' || type == 'phiurl2') {
-                oReq.responseType = "arraybuffer";
+                responseType = "arraybuffer";
             }
             else {
-                oReq.responseType = "text";
+                responseType = "text";
             }
 
-            oReq.onreadystatechange = function() {
-                if(this.readyState == 4) {
-                   if(this.status == 200) {
-                       let data = oReq.response;
+            let data = await me.getXMLHttpRqstPromise(url, 'GET', responseType, 'potential');
 
-                       if(type == 'phiurl' || type == 'phiurl2') {
-                           thisClass.loadPhiData(data, contour, bSurface);
-                       }
-                       else {
-                           thisClass.loadCubeData(data, contour, bSurface);
-                       }
-
-                       ic.bAjaxPhi = true;
-
-                       if(bSurface) {
-                         ic.setOptionCls.setOption('phisurface', 'phi');
-                       }
-                       else {
-                         ic.setOptionCls.setOption('phimap', 'phi');
-                       }
-                    }
-                    else {
-                        alert("The potential file is unavailable...");
-                    }
+            if(type == 'phiurl' || type == 'phiurl2') {
+                thisClass.loadPhiData(data, contour, bSurface);
+            }
+            else {
+                thisClass.loadCubeData(data, contour, bSurface);
+            }
 
-                    /// if(ic.deferredPhi !== undefined) ic.deferredPhi.resolve();
-                }
-                else {
-                    ic.ParserUtilsCls.showLoading();
-                }
-            };
+            ic.bAjaxPhi = true;
 
-            oReq.send();
+            if(bSurface) {
+              ic.setOptionCls.setOption('phisurface', 'phi');
+            }
+            else {
+              ic.setOptionCls.setOption('phimap', 'phi');
+            }
     //    }
     }
 
@@ -65131,7 +65274,7 @@ class Delphi {
               await thisClass.CalcPhiUrl(gsize, salt, contour, bSurface, url);
           }
           else {
-              thisClass.PhiParser(url, type, contour, bSurface);
+              await thisClass.PhiParser(url, type, contour, bSurface);
           }
     //   }); // end of me.deferred = $.Deferred(function() {
 
@@ -65310,7 +65453,7 @@ class Delphi {
                await this.CalcPhiUrl(gsize, salt, contour, bSurface, url);
            }
            else {
-               this.PhiParser(url, type, contour, bSurface);
+               await this.PhiParser(url, type, contour, bSurface);
            }
 
            if(bSurface) {
@@ -65818,7 +65961,8 @@ console.log("free energy: " + energy + " kcal/mol");
       }
       else {
         let atoms = me.hashUtilsCls.intHash(ic.dAtoms, ic.hAtoms);
-        pdbStr = ic.saveFileCls.getAtomPDB(atoms);
+        let bMergeIntoOne = true;
+        pdbStr = ic.saveFileCls.getAtomPDB(atoms, undefined, undefined, undefined, undefined, undefined, bMergeIntoOne);
       }
 
       let url = me.htmlCls.baseUrl + "scap/scap.cgi";
@@ -69739,7 +69883,7 @@ class SaveFile {
     }
 
     //getAtomPDB: function(atomHash, bPqr, bPdb, bNoChem) { let ic = this.icn3d, me = ic.icn3dui;
-    getAtomPDB(atomHash, bPqr, bNoChem, bNoHeader, chainResi2pdb, pdbid) { let ic = this.icn3d, me = ic.icn3dui;
+    getAtomPDB(atomHash, bPqr, bNoChem, bNoHeader, chainResi2pdb, pdbid, bMergeIntoOne) { let ic = this.icn3d, me = ic.icn3dui;
         let pdbStr = '';
 
         // get all phosphate groups in lipids
@@ -69892,6 +70036,7 @@ class SaveFile {
         let bMulStruc =(struArray.length > 1) ? true : false;
 
         let molNum = 1, prevStru = '', prevChain = '';
+        let chainIndex = 0, fakeChain = '', chainNameArray = 'abcdefghijklmnopqrstuvwxyz0123456789';
 
         let addedChainResiHash = {};
         for(let i in atomHash) {
@@ -69902,20 +70047,22 @@ class SaveFile {
 
             //if(bMulStruc && atom.structure != prevStru) {
             if(atom.structure != prevStru) {
-                pdbStr += connStr;
-                connStr = '';
+                if(!bMergeIntoOne || !bMulStruc) {
+                    pdbStr += connStr;
+                    connStr = '';
 
-                if(molNum > 1)  pdbStr += '\nENDMDL\n';
+                    if(molNum > 1)  pdbStr += '\nENDMDL\n';
 
-                if(bMulStruc) pdbStr += 'MODEL        ' + molNum + '\n';
+                    if(bMulStruc) pdbStr += 'MODEL        ' + molNum + '\n';
+                }
 
                 // add header            
                 let mutantInfo = (chainResi2pdb) ? "Mutated chain_residue " + Object.keys(chainResi2pdb) + '; ' : '';
                 if(!bNoHeader) {
                     //pdbStr += this.getPDBHeader(molNum - 1, stru2header, mutantInfo, pdbid);
 
-                    // make sur ethe PDB ID is correct
-                    pdbStr += this.getPDBHeader(molNum - 1, stru2header, mutantInfo, atom.structure);
+                    // make sure the PDB ID is correct
+                    if(!bMergeIntoOne || !bMulStruc) pdbStr += this.getPDBHeader(molNum - 1, stru2header, mutantInfo, atom.structure);
 
                     //pdbStr += '\n'; // separate from incomplete secondary structures 
                 }
@@ -69923,6 +70070,7 @@ class SaveFile {
                 //prevStru = atom.structure;
                 ++molNum;
             }
+
             //else {
                 //if(atom.chain != prevChain) {
                 if(atom.chain != prevChain && atom.structure == prevStru) {
@@ -69996,17 +70144,28 @@ class SaveFile {
     */
 
             line +=(resn.length <= 3) ? resn.padStart(3, ' ') : resn.substr(0, 3);
-            //line += ' ';
-            //line +=(atom.chain.length <= 1) ? atom.chain.padStart(1, ' ') : atom.chain.substr(0, 1);
-            if(atom.chain.length >= 2) {
-                let chainTmp = atom.chain.replace(/_/gi, '').substr(0, 2);
-                line += chainTmp;
-            }
-            else if(atom.chain.length == 1) {
-                line += ' ' + atom.chain.substr(0, 1);
+
+            if(bMergeIntoOne && molNum > 2 && (ic.proteins.hasOwnProperty(atom.serial) || ic.nucleotides.hasOwnProperty(atom.serial))) {
+                if(atom.structure != prevStru || atom.chain != prevChain) {
+                    fakeChain = (chainIndex < 36) ? chainNameArray[chainIndex] : '?';
+                    ++chainIndex;
+                }
+
+                line += ' ' + fakeChain;
             }
-            else if(atom.chain.length == 0) {
-                line += ' A';
+            else {
+                //line += ' ';
+                //line +=(atom.chain.length <= 1) ? atom.chain.padStart(1, ' ') : atom.chain.substr(0, 1);
+                if(atom.chain.length >= 2) {
+                    let chainTmp = atom.chain.replace(/_/gi, '').substr(0, 2);
+                    line += chainTmp;
+                }
+                else if(atom.chain.length == 1) {
+                    line += ' ' + atom.chain.substr(0, 1);
+                }
+                else if(atom.chain.length == 0) {
+                    line += ' A';
+                }
             }
 
             let resi = atom.resi;
@@ -70102,9 +70261,11 @@ class SaveFile {
             prevChain = atom.chain;
         }
 
-        pdbStr += connStr;
-        
-        if(bMulStruc) pdbStr += '\nENDMDL\n';
+        if(!bMergeIntoOne || !bMulStruc) {
+            pdbStr += connStr;
+            
+            if(bMulStruc) pdbStr += '\nENDMDL\n';
+        }
 
         return pdbStr;
     }
@@ -70624,14 +70785,7 @@ class ShareLink {
            }
 
            // add time stamp
-           let date = new Date();
-           let monthStr =(date.getMonth() + 1).toString();
-           if(date.getMonth() + 1 < 10) monthStr = '0' + monthStr;
-
-           let dateStr = date.getDate().toString();
-           if(date.getDate() < 10) dateStr = '0' + dateStr;
-
-           let dateAllStr = date.getFullYear().toString() + monthStr + dateStr;
+           let dateAllStr = me.utilsCls.getDateDigitStr();
            if(!bPrevDate) url += 'date=' + dateAllStr + '&';
            url += 'v=' + me.REVISION + '&';
 
@@ -73596,7 +73750,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.28.2';
+    this.REVISION = '3.28.4';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -73803,16 +73957,17 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
                 }
             }
             
-            // realign
-            ic.chainidArray = [chain_t].concat(chainidArray);
-            ic.chainidArray = ic.chainalignParserCls.addPostfixForChainids(ic.chainidArray);
-
+            // get the matched structures, do not include the template
             let mmdbafid = '';
-            for(let i = 0, il = ic.chainidArray.length; i < il; ++i) {
+            for(let i = 0, il = chainidArray.length; i < il; ++i) {
                 if(i > 0) mmdbafid += ',';
-                mmdbafid += ic.chainidArray[i].substr(0, ic.chainidArray[i].indexOf('_'));
+                mmdbafid += chainidArray[i].substr(0, chainidArray[i].indexOf('_'));
             }
 
+            // realign, include the template
+            ic.chainidArray = [chain_t].concat(chainidArray);
+            ic.chainidArray = ic.chainalignParserCls.addPostfixForChainids(ic.chainidArray);
+            
             me.htmlCls.clickMenuCls.setLogCmd('resdef ' + me.cfg.resdef, true);
 
             ic.loadCmd = 'vast_search_chainid ' + ic.chainidArray;
@@ -74028,7 +74183,7 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
         // ic.bNCBI = true;
 
         // remove space
-        me.cfg.mmdbafid = me.cfg.mmdbafid.replace(/\s+/g, '');
+        me.cfg.mmdbafid = me.cfg.mmdbafid.replace(/\s+/g, '').toUpperCase();
 
         ic.bMmdbafid = true;
         ic.inputid = me.cfg.mmdbafid;
@@ -74117,6 +74272,44 @@ iCn3DUI.prototype.getMmtfReducedPromise = function(mmtfid) {    return new Promi
     });
 };
 
+iCn3DUI.prototype.getXMLHttpRqstPromise = function(url, dataType, responseType, mapType) { let me = this;
+    return new Promise(function(resolve, reject) {
+        let oReq = new XMLHttpRequest();
+        oReq.open(dataType, url, true);
+        oReq.responseType = responseType;
+        
+        oReq.onreadystatechange = function() {
+            if (this.readyState == 4) {
+               if(this.status == 200) {
+                   let arrayBuffer = oReq.response;
+                   resolve(arrayBuffer);
+                }
+                else {
+                   if(mapType == '2fofc' || mapType == 'fofc') {
+                       alert("Density server at EBI has no corresponding electron density map for this structure.");
+                   }
+                   else if(mapType == 'em') {
+                       alert("Density server at EBI has no corresponding EM density map for this structure.");
+                   }
+                   else if(mapType == 'rcsbEdmaps') {
+                       alert("RCSB server has no corresponding eletron density map for this structure.");
+                   }
+                   else {
+                       alert("The " + mapType + " file is unavailable...");
+                   }
+
+                   reject('error');
+                }
+            }
+            else {
+                me.icn3d.ParserUtilsCls.showLoading();
+            }
+        };
+
+        oReq.send();
+    });
+};
+
 iCn3DUI.prototype.getAjaxPromise = function(url, dataType, beforeSend, alertMess, logMess, complete, bNode) { let me = this;
     // if(!bNode || dataType != 'json') {
         return new Promise(function(resolve, reject) {