icn3d 3.28.8 → 3.28.10

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;
+    }
 }
 
 /**
@@ -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();
@@ -9525,14 +9548,14 @@ class SetMenu {
         }
 
         //!!!
-        /*
+/*
         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>";
 
@@ -10599,10 +10622,11 @@ 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>";
@@ -12704,6 +12728,31 @@ 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-->";
 
@@ -16523,7 +16572,7 @@ class SetHtml {
         if(postfix == 'style') {
             if(bReset) {
                 $("#" + me.pre + "shininess").val('40');
-                $("#" + me.pre + "light1").val('0.6');
+                $("#" + me.pre + "light1").val('0.8');
                 $("#" + me.pre + "light2").val('0.4');
                 $("#" + me.pre + "light3").val('0.2');
                 $("#" + me.pre + "glycan").val('0');
@@ -18750,7 +18799,8 @@ function createDefaultMaterial( cache ) {
             roughness: 1,
             transparent: false,
             depthTest: true,
-            side: FrontSide
+            side: FrontSide,
+            //needsUpdate: true 
         } );
 
     }
@@ -21677,7 +21727,7 @@ 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 +22349,7 @@ 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 +24156,7 @@ 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 +24617,18 @@ 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 +24695,7 @@ 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 +24926,7 @@ 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 +25059,7 @@ 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 +27130,8 @@ class TextSprite {
             map: texture,
             //useScreenCoordinates: false,
             depthTest: !frontOfTarget,
-            depthWrite: !frontOfTarget
+            depthWrite: !frontOfTarget,
+            //needsUpdate: true
         } );
 
         //https://stackoverflow.com/questions/29421702/threejs-texture
@@ -28379,19 +28430,25 @@ 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 +28562,13 @@ 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 +29198,7 @@ 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 +29268,15 @@ 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 +30256,8 @@ 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 +30326,8 @@ 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 +32511,7 @@ class Impostor {
           fragmentShader: this.getShader(shaderName + ".frag"),
           depthTest: true,
           depthWrite: true,
-          //needsUpdate: true,
+          //needsUpdate: true, 
           lights: true
       });
 
@@ -33214,7 +33278,7 @@ class Instancing {
           fragmentShader: ic.impostorCls.getShader(name + ".frag"),
           depthTest: true,
           depthWrite: true,
-          //needsUpdate: true,
+          //needsUpdate: true, 
           lights: true
        });
 
@@ -33720,6 +33784,7 @@ 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);
         }
@@ -36857,9 +36922,9 @@ 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",
@@ -44004,12 +44069,14 @@ 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;
@@ -44019,7 +44086,8 @@ class ShowSeq {
 
         // 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';
@@ -44058,6 +44126,7 @@ class ShowSeq {
             ic.selectionCls.selectAll_base();
             ic.hlUpdateCls.updateHlAll();
             //ic.drawCls.draw();
+            ic.drawCls.draw();
         }
 
         return {'html': html, 'html3': html3};
@@ -44133,7 +44202,10 @@ 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];
@@ -44575,17 +44647,17 @@ 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'; 
@@ -46326,7 +46398,7 @@ 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
@@ -46410,9 +46482,14 @@ 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 +46497,7 @@ 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);
@@ -46472,6 +46549,11 @@ class LineGraph {
                     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 +46568,11 @@ 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];
+                                }
                             }
                         }
 
@@ -46507,6 +46594,8 @@ 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;
@@ -46520,56 +46609,107 @@ class LineGraph {
                     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);
+                            // 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 = {'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 96 jobs or me.cfg.maxajax jobs
+                let n = (me.cfg.maxajax) ? me.cfg.maxajax : 96;
 
-            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 +46721,7 @@ class LineGraph {
             }
             //console.log("Error in aligning with TM-align...");
             return;
-        }                       
+        }                   
     }
 
     getTemplateList(chainid) { let ic = this.icn3d; ic.icn3dui;
@@ -46691,7 +46831,7 @@ 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;
                 }
             }
@@ -46777,10 +46917,28 @@ 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 96 jobs or me.cfg.maxajax jobs
+            let n = (me.cfg.maxajax) ? me.cfg.maxajax : 96;
+
+            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;
+
+                dataArray3 = dataArray3.concat(currDataArray);
+            }
 
-            await thisClass.parseAlignData(dataArray3, domainidpairArray3);
+            await thisClass.parseAlignData(dataArray3, domainidpairArray3, false);
             
             // end of round 2
             return;
@@ -46811,6 +46969,7 @@ class LineGraph {
         if(!ic.chainsMapping) ic.chainsMapping = {};
 
         if(!ic.refPdbList) ic.refPdbList = [];
+
         for(let chainid in chainid2segs) {
             let segArray = chainid2segs[chainid];
 
@@ -50977,15 +51136,15 @@ 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 +51157,17 @@ 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;
-                       }
-
-                       ic.setOptionCls.setOption('map', type);
-                    }
-                    else {
-                        alert("RCSB server has no corresponding eletron density map for this structure.");
-                    }
+            let arrayBuffer = await me.getXMLHttpRqstPromise(url, 'GET', 'arraybuffer', 'rcsbEdmaps');
+            thisClass.loadDsn6Data(arrayBuffer, type, sigma);
 
-                    /// 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 +51905,11 @@ 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;
           }
@@ -54022,7 +54166,7 @@ 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 +54196,21 @@ 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;
+            let arrayBuffer = await me.getXMLHttpRqstPromise(url, 'GET', 'arraybuffer', type);
 
-                       thisClass.parseChannels(arrayBuffer, type, sigma);
-
-                       if(type == '2fofc' || type == 'fofc') {
-                           ic.bAjax2fofc = true;
-                           ic.bAjaxfofc = true;
-
-                           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);
+            }
         }
     }
 
@@ -55143,13 +55262,10 @@ 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) {
-                    offset = seqArray[i][0] - (i + 1);
+                    seqArray[i][0] - (i + 1);
                     break;
                 }
             }
@@ -55184,14 +55300,12 @@ class ParserUtils {
                 resObject.resi = i + 1;
             }
             else {
-                //let offset =(ic.chainid2offset[chainid]) ? ic.chainid2offset[chainid] : 0;
-                
-                if(type === 'mmdbid' || type === 'align') {
-                    resObject.resi =(seqArray[i][resiPos] == '0') ? i + 1 + offset : seqArray[i][resiPos];
-                }
-                else {
+                //if(type === 'mmdbid' || type === 'align') {
+                //    resObject.resi =(seqArray[i][resiPos] == '0') ? i + 1 + offset : seqArray[i][resiPos];
+                //}
+                //else {
                     resObject.resi =(seqArray[i][resiPos] == '0') ? parseInt(prevResi) + 1 : seqArray[i][resiPos];
-                }
+                //}
             }
 
             //resObject.resi =(seqArray[i][resiPos] == '0') ? i + 1 + offset : seqArray[i][resiPos];
@@ -55976,6 +56090,12 @@ 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)) {
@@ -56121,6 +56241,11 @@ 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;
@@ -62249,10 +62374,14 @@ 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) {
@@ -62341,6 +62470,10 @@ 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());   
@@ -62514,10 +62647,10 @@ 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);
@@ -62787,7 +62920,7 @@ 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;
@@ -62803,10 +62936,10 @@ 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() {
@@ -62815,7 +62948,7 @@ 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;
@@ -62826,7 +62959,7 @@ 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() {
 
@@ -63158,7 +63291,7 @@ 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 = {}
@@ -64763,31 +64896,12 @@ 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";
-
-        oReq.onreadystatechange = async function() {
-            if(this.readyState == 4) {
-               if(this.status == 200) {
-                   let data = oReq.response;
+        let data = await me.getXMLHttpRqstPromise(url, 'GET', 'text', 'PQR');
 
-                   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;
@@ -64874,7 +64988,7 @@ class Delphi {
         }
 
         return new Promise(function(resolve, reject) {
-            // see full_ui.js for ajaxTransport
+            // see icn3dui.js for ajaxTransport
             $.ajax({
                 url: url,
                 type: 'POST',
@@ -64898,7 +65012,7 @@ 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;
 
@@ -64916,49 +65030,32 @@ 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');
+            }
     //    }
     }
 
@@ -65136,7 +65233,7 @@ 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() {
 
@@ -65315,7 +65412,7 @@ 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) {
@@ -70629,14 +70726,7 @@ 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 + '&';
 
@@ -73601,7 +73691,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.28.2';
+    this.REVISION = '3.28.3';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -74122,6 +74212,44 @@ 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) {