icn3d 3.45.1 → 3.45.3

package/css/icn3d.css

@@ -1,31 +1,64 @@
+.ui-dialog { font-size: 12px;}
+.ui-dialog .ui-dialog-title { font-size: 16px; height: 18px; }
+.ui-dialog .ui-button { width: 12px; height:12px; margin: -5px 0px 0px 0px;}
+.ui-dialog .ui-dialog-titlebar { padding: 0px 1em 2px 1em; }
+
+.ui-dialog .ui-resizable-se {
+    width: 14px;
+    height: 14px;
+    right: 3px;
+    bottom: 3px;
+    background-position: -80px -224px;
+}
+
 /* theme: orange */
 /*
-.ui-widget-header{border:1px solid #e78f08;background:#f6a828 url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-bg_gloss-wave_35_f6a828_500x100.png") 50% 50% repeat-x;color:#fff;font-weight:bold}
-.ui-button .ui-icon {background-image: url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-icons_ef8c08_256x240.png");}
-.ui-state-active a, .ui-state-active a:link, .ui-state-active a:visited {color: #eb8f00;text-decoration: none;}
+.icn3d-menu .ui-widget-header{border:1px solid #e78f08;background:#f6a828 url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-bg_gloss-wave_35_f6a828_500x100.png") 50% 50% repeat-x;color:#fff;font-weight:bold}
+.icn3d-menu .ui-button .ui-icon {background-image: url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-icons_ef8c08_256x240.png");}
+.icn3d-menu .ui-state-active a, .ui-state-active a:link, .ui-state-active a:visited {color: #eb8f00;text-decoration: none;}
 */
 
 /* theme: black */
 /*
-.ui-widget-header{border:1px solid #333333;background:#333333 url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-bg_gloss-wave_25_333333_500x100.png") 50% 50% repeat-x;color:#fff;font-weight:bold}
-.ui-button .ui-icon {background-image: url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-icons_222222_256x240.png");}
-.ui-state-active a, .ui-state-active a:link, .ui-state-active a:visited {color: #222222;text-decoration: none;}
+.icn3d-menu .ui-widget-header{border:1px solid #333333;background:#333333 url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-bg_gloss-wave_25_333333_500x100.png") 50% 50% repeat-x;color:#fff;font-weight:bold}
+.icn3d-menu .ui-button .ui-icon {background-image: url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-icons_222222_256x240.png");}
+.icn3d-menu .ui-state-active a, .ui-state-active a:link, .ui-state-active a:visited {color: #222222;text-decoration: none;}
 */
 
 /* theme: blue */
-.ui-widget-header {border:1px solid #4297d7;background:#5c9ccc url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-bg_gloss-wave_55_5c9ccc_500x100.png") 50% 50% repeat-x;color:#fff;font-weight:bold}
+.icn3d-menu .ui-widget-header {border:1px solid #4297d7;background:#5c9ccc url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-bg_gloss-wave_55_5c9ccc_500x100.png") 50% 50% repeat-x;color:#fff;font-weight:bold}
 /*.ui-button .ui-icon {background-image: url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-icons_228ef1_256x240.png");}*/
-.ui-icon {background-image: url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-icons_228ef1_256x240.png")!important;}
-.ui-state-active a, .ui-state-active a:link, .ui-state-active a:visited {color: #444;text-decoration: none;}
+.icn3d-menu .ui-icon {background-image: url("https://www.ncbi.nlm.nih.gov/Structure/icn3d/lib/images/ui-icons_228ef1_256x240.png")!important;}
+.icn3d-menu .ui-state-active a, .ui-state-active a:link, .ui-state-active a:visited {color: #444;text-decoration: none;}
 
-.icn3d-text {font-family: Verdana, Arial, Helvetica, sans-serif; font-size:12px!important;}
+.icn3d-menu .ui-accordion .ui-accordion-icons { padding-left: 0; text-align: center; }
 
-.ui-dialog { font-size: 12px;}
-.ui-dialog .ui-dialog-title { font-size: 16px; height: 18px; }
-.ui-dialog .ui-button { width: 12px; height:12px; margin: -5px 0px 0px 0px;}
-.ui-dialog .ui-dialog-titlebar { padding: 0px 1em 2px 1em; }
+.icn3d-menu .ui-menu-icon {
+    float: right;
+}
+
+.icn3d-menu .ui-widget {
+  font-family: Arial,Helvetica,sans-serif;
+  font-size: 12px!important; /* 0.9em is a little too large */
+}
+.icn3d-menu .ui-menu-item {
+  position: relative;
+  padding: 3px 1em 3px .4em;
+}
+
+/* remove the extra bar in the menu */
+    /* background: #eee url(images/ui-bg_highlight-soft_100_eeeeee_1x100.png) 50% top repeat-x; */
+.icn3d-menu .ui-widget-content {
+    border: 1px solid #ddd;
+    background: #eee;
+    color: #333;
+}
 
-.ui-accordion .ui-accordion-icons { padding-left: 0; text-align: center; }
+.icn3d-menu .ui-menu-icons .ui-menu-item-wrapper, .ui-menu-icons .ui-menu-item {
+    padding-left: 0.4em!important;
+}
+
+.icn3d-text {font-family: Verdana, Arial, Helvetica, sans-serif; font-size:12px!important;}
 
 .icn3d-menu {float:left; width:110px;}
 .icn3d-menu-color {color:#369; font-weight:bold; font-size: 14px!important;}
@@ -70,6 +103,7 @@ button, select, input { font-size: 10px; }
 
 .icn3d-dialog {font-family: Verdana, Arial, Helvetica, sans-serif; color: #666666;}
 .icn3d-commandTitle  {font-size: 12px; font-weight:bold; font-family: Verdana, Arial, Helvetica, sans-serif; color: #666666;}
+.icn3d-title  {font-size:1.2em; font-weight:normal; position:absolute; z-index:1; float:left; }
 .icn3d-modeselection  {color: #f8b84e!important;}
 /*.icn3d-viewselection  {color: #800000!important;}*/
 .icn3d-viewselection  {color: #f8b84e!important;}
@@ -98,18 +132,6 @@ button, select, input { font-size: 10px; }
 .icn3d-node-text24 {font-size: 24px; font-weight: bold}
 .icn3d-node-text32 {font-size: 32px; font-weight: bold}
 
-.ui-dialog .ui-resizable-se {
-    width: 14px;
-    height: 14px;
-    right: 3px;
-    bottom: 3px;
-    background-position: -80px -224px;
-}
-
-.ui-menu-icon {
-    float: right;
-}
-
 /* toggle button: http://www.w3schools.com/howto/howto_css_switch.asp */
 .icn3d-switch {
   position: relative;
@@ -178,15 +200,6 @@ input:checked + .icn3d-slider:before {
   overflow:auto;
 }
 
-.ui-widget {
-  font-family: Arial,Helvetica,sans-serif;
-  font-size: 12px!important; /* 0.9em is a little too large */
-}
-.ui-menu-item {
-  position: relative;
-  padding: 3px 1em 3px .4em;
-}
-
 .icn3d-clinvar {color:green; font-size:12px; font-weight:bold;}
 .icn3d-clinvar-path {color:red; font-size:12px; font-weight:bold;}
 
@@ -213,14 +226,6 @@ input:checked + .icn3d-slider:before {
 
 .icn3d-bkgd {background-color:#eee;}
 
-/* remove the extra bar in the menu */
-    /* background: #eee url(images/ui-bg_highlight-soft_100_eeeeee_1x100.png) 50% top repeat-x; */
-.ui-widget-content {
-    border: 1px solid #ddd;
-    background: #eee;
-    color: #333;
-}
-
 .icn3d-rad > input{ /* HIDE RADIO */
   visibility: hidden; /* Makes input not-clickable */
   position: absolute; /* Remove input from document flow */
@@ -240,10 +245,6 @@ input:checked + .icn3d-slider:before {
   background-position: -160px 0px; /*empty */
 }
 
-.ui-menu-icons .ui-menu-item-wrapper, .ui-menu-icons .ui-menu-item {
-    padding-left: 0.4em!important;
-}
-
 .icn3d-rad-text, .icn3d-color-rad-text {
     padding-left: 1.2em;
 }
@@ -288,7 +289,6 @@ input:checked + .icn3d-slider:before {
 
 .ncbi-page-header {
   background-color: #369;
-  color: #fff;
   overflow: auto;
 }
 

package/icn3d.js

@@ -58909,7 +58909,7 @@ class SetMenu {
         html += this.setTools();
 
         // show title at the top left corner
-        html += me.htmlCls.divStr + "title' class='icn3d-commandTitle' style='font-size:1.2em; font-weight:normal; position:absolute; z-index:1; float:left; display:table-row; margin: 85px 0px 0px 5px; color:" + titleColor + "; width:" + me.htmlCls.WIDTH + "px'></div>";
+        html += me.htmlCls.divStr + "title' class='icn3d-commandTitle icn3d-title' style='display:table-row; margin: 85px 0px 0px 5px; color:" + titleColor + "; width:" + me.htmlCls.WIDTH + "px'></div>";
 
         html += me.htmlCls.divStr + "viewer' style='position:relative; width:100%; height:100%; background-color: " + me.htmlCls.GREYD + ";'>";
 
@@ -59043,7 +59043,7 @@ class SetMenu {
         //html += me.htmlCls.setMenuCls.setTools();
 
         // show title at the top left corner
-        html += me.htmlCls.divStr + "title' class='icn3d-commandTitle' style='font-size:1.2em; font-weight:normal; position:absolute; z-index:1; float:left; display:block; margin: 12px 0px 0px 40px; color:" + titleColor + "; width:" +(me.htmlCls.WIDTH - 40).toString() + "px'></div>";
+        html += me.htmlCls.divStr + "title' class='icn3d-commandTitle icn3d-title' style='display:block; margin: 12px 0px 0px 40px; color:" + titleColor + "; width:" +(me.htmlCls.WIDTH - 40).toString() + "px'></div>";
         html += me.htmlCls.divStr + "viewer' style='position:relative; width:100%; height:100%; background-color: " + me.htmlCls.GREYD + ";'>";
         // don't show legend in mobile
         //html += me.htmlCls.divStr + "legend' class='icn3d-text icn3d-legend'></div>";
@@ -74243,7 +74243,7 @@ class Scene {
             ic.shininess = shininess;
         }
 
-        if(!me.bNode && me.htmlCls.setHtmlCls.getCookie('light1') != '') {
+        if(!me.bNode && me.htmlCls.setHtmlCls.getCookie('light1') != '' && !me.bNode && me.htmlCls.setHtmlCls.getCookie('light2') != '' && !me.bNode && me.htmlCls.setHtmlCls.getCookie('light3') != '') {
             let light1 = parseFloat(me.htmlCls.setHtmlCls.getCookie('light1'));
             let light2 = parseFloat(me.htmlCls.setHtmlCls.getCookie('light2'));
             let light3 = parseFloat(me.htmlCls.setHtmlCls.getCookie('light3'));
@@ -78993,19 +78993,25 @@ class Tube {
           //mesh = new THREE.Mesh(geo, new THREE.MeshPhongMaterial({ transparent: true, opacity: 0.5, specular: ic.frac, shininess: ic.shininess, emissive: ic.emissive, vertexColors: THREE.FaceColors, side: THREE.DoubleSide }));
           mesh = new Mesh$1(geo, new MeshPhongMaterial({ transparent: true, opacity: 0.5, specular: ic.frac, shininess: ic.shininess, emissive: ic.emissive, vertexColors: true, side: DoubleSide$1 }));
 
-          if(ic.mdl) ic.mdl.add(mesh);
+          if(ic.mdl) {
+            ic.mdl.add(mesh);
+          }
         }
         else if(bHighlight === 1) {
           mesh = new Mesh$1(geo, ic.matShader);
           mesh.renderOrder = ic.renderOrderPicking;
           //ic.mdlPicking.add(mesh);
-          if(ic.mdl) ic.mdl.add(mesh);
+          if(ic.mdl) {
+            ic.mdl.add(mesh);
+          }
         }
         else {
           //mesh = new THREE.Mesh(geo, new THREE.MeshPhongMaterial({ specular: ic.frac, shininess: ic.shininess, emissive: ic.emissive, vertexColors: THREE.FaceColors, side: THREE.DoubleSide }));
           mesh = new Mesh$1(geo, new MeshPhongMaterial({ specular: ic.frac, shininess: ic.shininess, emissive: ic.emissive, vertexColors: true, side: DoubleSide$1 }));
 
-          if(ic.mdl) ic.mdl.add(mesh);
+          if(ic.mdl) {
+            ic.mdl.add(mesh);
+          }
         }
 
         if(bHighlight === 1 || bHighlight === 2) {
@@ -83403,7 +83409,11 @@ class ApplyClbonds {
     applyClbondsOptions(options) { let ic = this.icn3d, me = ic.icn3dui;
        if(options === undefined) options = ic.opts;
 
-       if(!ic.bCalcCrossLink) {
+       ic.lines['clbond'] = [];
+
+       if(options.chemicals == 'nothing') return {};
+       
+    //    if(!ic.bCalcCrossLink) {
          // find all bonds to chemicals
          ic.clbondpnts = {};
          ic.clbondResid2serial = {};
@@ -83414,10 +83424,11 @@ class ApplyClbonds {
          // chemical to protein/nucleotide
          this.applyClbondsOptions_base('all');
 
-         ic.bCalcCrossLink = true;
-       }
+        //  ic.bCalcCrossLink = true;
+    //    }
 
-       if (options.clbonds.toLowerCase() === 'yes' && options.chemicals !== 'nothing') {
+    //    if (options.clbonds.toLowerCase() === 'yes' && options.chemicals !== 'nothing') {
+       if (options.clbonds.toLowerCase() === 'yes') {
          let color = '#006400';
          me.parasCls.thr(0x006400);
 
@@ -83443,7 +83454,8 @@ class ApplyClbonds {
                     line.serial1 = ic.clbondResid2serial[resid0 + ',' + resid1];
                     line.serial2 = ic.clbondResid2serial[resid1 + ',' + resid0];
 
-                    if(!ic.dAtoms.hasOwnProperty(line.serial1) || !ic.dAtoms.hasOwnProperty(line.serial2)) continue;
+                    // only apply to displayed atoms
+                    // if(!ic.dAtoms.hasOwnProperty(line.serial1) || !ic.dAtoms.hasOwnProperty(line.serial2)) continue;
 
                     line.position1 = ic.atoms[line.serial1].coord;
                     line.position2 = ic.atoms[line.serial2].coord;
@@ -83475,9 +83487,14 @@ class ApplyClbonds {
       return ic.residuesHashClbonds;
     }
 
-    applyClbondsOptions_base(type) { let ic = this.icn3d; ic.icn3dui;
+    applyClbondsOptions_base(type) { let ic = this.icn3d, me = ic.icn3dui;
+         // only apply to displayed atoms
+         let atomHash = me.hashUtilsCls.cloneHash(ic.chemicals);
+         atomHash = me.hashUtilsCls.intHash(atomHash, ic.dAtoms);
+
          // chemical to chemical first
-         for (let i in ic.chemicals) {
+        //   for (let i in ic.chemicals) {
+         for (let i in atomHash) {
             let atom0 = ic.atoms[i];
 
             let chain0 = atom0.structure + '_' + atom0.chain;
@@ -86072,24 +86089,27 @@ class Instancing {
            let normalArray2 = (baseGeometry.attributes.normal) ? me.hashUtilsCls.hashvalue2array(baseGeometry.attributes.normal.array) : [];
            let colorArray2 = (baseGeometry.attributes.color) ? me.hashUtilsCls.hashvalue2array(baseGeometry.attributes.color.array) : [];
            let indexArray2 = (baseGeometry.index) ? me.hashUtilsCls.hashvalue2array(baseGeometry.index.array) : [];
+          
+           if(colorArray2.length > 0) { // avoid an black object in the center of of assembly, e.g., https://www.ncbi.nlm.nih.gov/Structure/icn3d/?pdbid=1qqp
+                positionArray = positionArray.concat(positionArray2);
+                normalArray = normalArray.concat(normalArray2);
+                colorArray = colorArray.concat(colorArray2);
+                indexArray = indexArray.concat(indexArray2);
 
-           positionArray = positionArray.concat(positionArray2);
-           normalArray = normalArray.concat(normalArray2);
-           colorArray = colorArray.concat(colorArray2);
-           indexArray = indexArray.concat(indexArray2);
-
-           let bCylinderArray = [];
-           let bCylinder = (baseGeometry.type == 'CylinderGeometry') ? 1.0 : 0.0;
-           for(let i = 0, il = positionArray.length / 3; i < il; ++i) {
-               bCylinderArray.push(bCylinder);
-           }
+                let bCylinderArray = [];
+                let bCylinder = (baseGeometry.type == 'CylinderGeometry') ? 1.0 : 0.0;
+                //    let bCylinder = (baseGeometry.geometry.type == 'CylinderGeometry') ? 1.0 : 0.0;
+                for(let i = 0, il = positionArray.length / 3; i < il; ++i) {
+                    bCylinderArray.push(bCylinder);
+                }
 
-           geometry.setAttribute('position', new BufferAttribute$1(new Float32Array(positionArray), 3));
-           geometry.setAttribute('normal', new BufferAttribute$1(new Float32Array(normalArray), 3) );
-           geometry.setAttribute('color', new BufferAttribute$1(new Float32Array(colorArray), 3) );
+                geometry.setAttribute('position', new BufferAttribute$1(new Float32Array(positionArray), 3));
+                geometry.setAttribute('normal', new BufferAttribute$1(new Float32Array(normalArray), 3) );
+                geometry.setAttribute('color', new BufferAttribute$1(new Float32Array(colorArray), 3) );
 
-           geometry.setAttribute('cylinder', new BufferAttribute$1(new Float32Array(bCylinderArray), 1) );
-           geometry.setIndex(new BufferAttribute$1(new Uint32Array(indexArray), 1));
+                geometry.setAttribute('cylinder', new BufferAttribute$1(new Float32Array(bCylinderArray), 1) );
+                geometry.setIndex(new BufferAttribute$1(new Uint32Array(indexArray), 1));
+           }
 
            positionArray2 = null;
            normalArray2 = null;
@@ -86151,7 +86171,7 @@ class Instancing {
 
            let mesh2 = new Mesh$1(geometry, ic.instancedMaterial);
 
-           mesh2.onBeforeRender = ic.impostorCls.onBeforeRender;
+           if(ic.bImpo) mesh2.onBeforeRender = ic.impostorCls.onBeforeRender;
            //mesh2.onBeforeRender = this.onBeforeRender;
 
            // important: https://stackoverflow.com/questions/21184061/mesh-suddenly-disappears-in-three-js-clipping
@@ -86377,7 +86397,7 @@ class Alternate {
 
         //ic.glycanCls.showGlycans();
 
-        ic.opts['rotationcenter'] = 'highlight center';
+        // ic.opts['rotationcenter'] = 'highlight center';
         
         ic.drawCls.draw();
 
@@ -91510,6 +91530,7 @@ class AnnoIg {
             html2 += htmlCnt + '<span class="icn3d-seqLine">';
 
             if(ic.seqStartLen && ic.seqStartLen[chnid]) html2 += ic.showSeqCls.insertMulGapOverview(chnid, ic.seqStartLen[chnid]);
+            // if(ic.seqStartLen && ic.seqStartLen[chnid]) html += ic.showSeqCls.insertMulGap(ic.seqStartLen[chnid], '-');
 
             let prevDomainindex, color;
             for(let i = 0, il = fromArray.length; i < il; ++i) {
@@ -96049,7 +96070,7 @@ class AddTrack {
 
         // adjust the total length
         if(ic.maxAnnoLength < ic.maxAnnoLengthOri + ic.seqStartLen[chainid] + ic.seqEndLen[chainid]) {
-                ic.maxAnnoLength = ic.maxAnnoLengthOri + ic.seqStartLen[chainid] + ic.seqEndLen[chainid];
+            ic.maxAnnoLength = ic.maxAnnoLengthOri + ic.seqStartLen[chainid] + ic.seqEndLen[chainid];
         }
 
         // do not remove other tracks
@@ -96350,6 +96371,9 @@ class AddTrack {
 
         me.htmlCls.clickMenuCls.setLogCmd("add exon track | chainid " + chainid + " | geneid " + geneid + " | startpos " + startpos + " | type " + type, true);
         me.htmlCls.clickMenuCls.setLogCmd("set annotation custom", true);
+        
+        // reset annotation tracks since exons may add extra space to the N-terminal
+        ic.annotationCls.resetAnnoTabAll();
     }
 
     async addMsaTracks(chainid, startpos, type, fastaList) { let ic = this.icn3d, me = ic.icn3dui;
@@ -96628,9 +96652,14 @@ class Annotation {
         $("[id^=" + ic.pre + "transmem]").hide();
         if($("#" + ic.pre + "anno_transmem").length) $("#" + ic.pre + "anno_transmem")[0].checked = false;
     }
-    async setAnnoTabIg(bSelection, template) {  let ic = this.icn3d; ic.icn3dui;
+    async setAnnoTabIg(bSelection, template) {  let ic = this.icn3d, me = ic.icn3dui;
+        let selAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
+
         await this.updateIg(bSelection, template);
 
+        // preserve previous selection
+        ic.hAtoms = me.hashUtilsCls.cloneHash(selAtoms);
+
         $("[id^=" + ic.pre + "ig]").show();
         if($("#" + ic.pre + "anno_ig").length) $("#" + ic.pre + "anno_ig")[0].checked = true;
     }
@@ -105629,7 +105658,7 @@ class MmcifParser {
         ///// if(ic.deferredSymmetry !== undefined) ic.deferredSymmetry.resolve();
       }
       catch (err) {
-        if(!me.bNode) console.log("mmcifparser.cgi issues: " + err);
+        if(!me.bNode) console.log("downloadMmcifSymmetry issues: " + err);
         return;
       }
     }
@@ -105704,7 +105733,7 @@ class MmdbParser {
             this.getNoData(mmdbid, bGi);
             return;
         }
-        
+
         if(Object.keys(data.atoms).length == 0) { // for large structures such as 3J3Q
             // use mmtfid
             let pdbid = data.pdbId;
@@ -110996,7 +111025,7 @@ class ParserUtils {
     getResiNCBI(chainid, resi) { let ic = this.icn3d; ic.icn3dui;
         let residNCBI = ic.resid2ncbi[chainid + '_' + resi];
         let resiNCBI = (residNCBI) ? parseInt(residNCBI.substr(residNCBI.lastIndexOf('_') + 1)) : 0;
-            
+
         return resiNCBI;
     }
 }
@@ -112417,7 +112446,7 @@ class SetSeqAlign {
         // start and end of MSA
         let start_t = 9999, end_t = -1;
 
-        let baseResi = ic.chainsSeq[chainid1][0].resi - 1;
+        ic.chainsSeq[chainid1][0].resi - 1;
 
         for(let index = 1, indexl = chainidArray.length; index < indexl; ++index) { 
             let chainIndex = index - 1;
@@ -112427,34 +112456,25 @@ class SetSeqAlign {
             for(let i = 0, il = ic.qt_start_end[chainIndex].length; i < il; ++i) {
                 let start1, end1;
                 
-                // if(bRealign) { // real residue numbers are stored
-                //     start1 = ic.qt_start_end[chainIndex][i].t_start;
-                //     end1 = ic.qt_start_end[chainIndex][i].t_end;
-                // }
-                // else {
-                    //ic.qt_start_end is zero-based
-                    start1 = parseInt(ic.qt_start_end[chainIndex][i].t_start) - 1;
-                    end1 = parseInt(ic.qt_start_end[chainIndex][i].t_end) - 1;
-                // }
+                // start1 = parseInt(ic.qt_start_end[chainIndex][i].t_start) - 1;
+                // end1 = parseInt(ic.qt_start_end[chainIndex][i].t_end) - 1;
+
+                start1 = ic.ParserUtilsCls.getResiNCBI(chainid1, ic.qt_start_end[chainIndex][i].t_start) - 1;
+                end1 = ic.ParserUtilsCls.getResiNCBI(chainid1, ic.qt_start_end[chainIndex][i].t_end) - 1;
+
                 for(let j = start1; j <= end1; ++j) {
                     let resi, resid;
 
-                    // if(me.cfg.aligntool == 'tmalign') { // tmalign: just one residue in this for loop
-                    //     resi = ic.qt_start_end[chainIndex][i].t_start;
+                    // let resiPos;
+                    // if(me.cfg.aligntool == 'tmalign') {
+                    //     resiPos = j - baseResi;
                     // }
                     // else {
-                        // let resiPos = (bRealign || me.cfg.aligntool != 'tmalign') ? j : j - baseResi;
-                        let resiPos;
-                        if(me.cfg.aligntool == 'tmalign') {
-                            resiPos = j - baseResi;
-                        }
-                        else {
-                            // resiPos = (bRealign) ? j : j - baseResi;
-                            resiPos = j;
-                        }
-                        resi = ic.ParserUtilsCls.getResi(chainidArray[0], resiPos);
-                        resid = chainidArray[0] + '_' + resi;
+                    //     resiPos = j;
                     // }
+                    let resiPos = j;
+                    resi = ic.ParserUtilsCls.getResi(chainidArray[0], resiPos);
+                    resid = chainidArray[0] + '_' + resi;
 
                     resid2range_t[resid] = 1;
                     if(j < start_t) start_t = j;
@@ -112514,7 +112534,8 @@ class SetSeqAlign {
             let resi = ic.chainsSeq[chainid1][j].resi;
             let resid = chainid1 + '_' + resi;
 
-            let jAdjusted = (me.cfg.aligntool != 'tmalign') ? j : j + baseResi;
+            // let jAdjusted = (me.cfg.aligntool != 'tmalign') ? j : j + baseResi;
+            let jAdjusted = ic.ParserUtilsCls.getResiNCBI(chainid1, resi) - 1;
 
             //if(j + baseResi < start_t || j + baseResi > end_t) {
             if(jAdjusted < start_t || jAdjusted > end_t) {    
@@ -112703,8 +112724,10 @@ class SetSeqAlign {
     insertNotAlignRes(chainid, start, len, bRealign) { let ic = this.icn3d; ic.icn3dui;
         // insert non-aligned residues in query seq
         for(let j = 0, jl = len; j < jl; ++j) {
-            let resi2 = ic.ParserUtilsCls.getResi(chainid, start + j);
-            let resn2 = this.getResn(chainid, start + j);
+            // let resi2 = ic.ParserUtilsCls.getResi(chainid, start + j);
+            // let resn2 = this.getResn(chainid, start + j);
+            let resi2 = start + j;
+            let resn2 = this.getResnFromResi(chainid, resi2);
             let resn1 = '-';
             let bAlign = false;
             let resObject = this.getResObject(chainid, false, bAlign, resi2, resn2, resn1);
@@ -112712,13 +112735,15 @@ class SetSeqAlign {
         }
     }
 
-    getTemplatePosFromOriPos(chainid1, start, end, bRealign) { let ic = this.icn3d; ic.icn3dui;
-        let startResi = ic.ParserUtilsCls.getResi(chainid1, start);
-        let endResi = ic.ParserUtilsCls.getResi(chainid1, end);
-            
+    getTemplatePosFromOriResi(chainid1, start, end, bRealign) { let ic = this.icn3d; ic.icn3dui;
+        // let startResi = ic.ParserUtilsCls.getResi(chainid1, start);
+        // let endResi = ic.ParserUtilsCls.getResi(chainid1, end);
+        let startResi = start;
+        let endResi = end;
+
         let result1 = this.getResiPosInTemplate(chainid1, startResi);
         let result2 = this.getResiPosInTemplate(chainid1, endResi);
-        
+ 
         return {"pos1": result1.pos, "pos2": result2.pos};
     }
 
@@ -112783,7 +112808,8 @@ class SetSeqAlign {
         let result;
 
         for(let i = 0, il = ic.qt_start_end[chainIndex].length; i < il; ++i) {
-            let start1, start2, end1, end2, resiStart1, start1Pos, end1Pos;
+            let start1, start2, end1, end2, resiStart1, start1Pos;
+            
             if(bRealign && me.cfg.aligntool == 'tmalign') { // real residue numbers are stored
                 start1 = parseInt(ic.qt_start_end[chainIndex][i].t_start);
                 start2 = parseInt(ic.qt_start_end[chainIndex][i].q_start);
@@ -112798,7 +112824,7 @@ class SetSeqAlign {
                 // 1. before the mapped residues
                 resiStart1 = start1;
                 start1Pos = this.getPosFromResi(chainid1, ic.qt_start_end[chainIndex][i].t_start);
-                end1Pos = this.getPosFromResi(chainid1, ic.qt_start_end[chainIndex][i].t_end);
+                this.getPosFromResi(chainid1, ic.qt_start_end[chainIndex][i].t_end);
             }
             else {
                 start1 = parseInt(ic.qt_start_end[chainIndex][i].t_start - 1);
@@ -112809,17 +112835,16 @@ class SetSeqAlign {
                 // 1. before the mapped residues
                 resiStart1 = ic.ParserUtilsCls.getResi(chainid1, start1);
                 start1Pos = start1;
-                end1Pos = end1;
             }
             //let range = resid2range_t[chainid1 + '_' + resiStart1];
-  
+
             // if the mapping does not start from start_t, add gaps to the query seq
             if(i == 0) {
-                //result = this.getTemplatePosFromOriPos(chainid1, start_t, start1, bRealign);
-                result = this.getTemplatePosFromOriPos(chainid1, start_t, start1Pos, bRealign);
+                //result = this.getTemplatePosFromOriResi(chainid1, start_t, start1, bRealign);
+                result = this.getTemplatePosFromOriResi(chainid1, start_t, start1Pos, bRealign);
                 pos1 = result.pos1;
                 pos2 = result.pos2;
-                
+
                 //if(start1 > start_t) {
                 if(start1Pos > start_t) {
                     for(let j = 0, jl = pos2 - pos1; j < jl; ++j) {
@@ -112829,7 +112854,7 @@ class SetSeqAlign {
             }
             else {
                 //let notAlnLen1 = start1 - (prevIndex1 + 1);
-                result = this.getTemplatePosFromOriPos(chainid1, prevIndex1, start1, bRealign);
+                result = this.getTemplatePosFromOriResi(chainid1, prevIndex1, start1, bRealign);
                 pos1 = result.pos1;
                 pos2 = result.pos2;
                 let notAlnLen1 = pos2 - (pos1 + 1);
@@ -112842,7 +112867,7 @@ class SetSeqAlign {
                     // add gaps before the query sequence
                     for(let j = 0, jl = notAlnLen1 - notAlnLen2; j < jl; ++j) {
                         ic.alnChainsSeq[chainid2].push(gapResObject2);
-                    }                       
+                    }
                 }
                 else {
                     // check the number of gaps before resiStart1 (n), and insert 'notAlnLen2 - notAlnLen1 - n' gaps
@@ -112851,8 +112876,8 @@ class SetSeqAlign {
             }
 
             // 2. In the mapped residues
-            //result = this.getTemplatePosFromOriPos(chainid1, start1, end1, bRealign);
-            result = this.getTemplatePosFromOriPos(chainid1, start1Pos, end1Pos, bRealign);
+            result = this.getTemplatePosFromOriResi(chainid1, start1, end1, bRealign);
+            //result = this.getTemplatePosFromOriResi(chainid1, start1Pos, end1Pos, bRealign);
             pos1 = result.pos1;
             pos2 = result.pos2;
             
@@ -112869,7 +112894,7 @@ class SetSeqAlign {
                     let resi2 = (bRealign) ? start2 + k : ic.ParserUtilsCls.getResi(chainid2, start2 + k);
                     let resn1 = this.getResnFromResi(chainid1, resi1); //this.getResn(chainid1, start1 + k);
                     let resn2 = this.getResnFromResi(chainid2, resi2); //this.getResn(chainid2, start2 + k);
-                    
+
                     let bAlign = true;
                     let resObject = this.getResObject(chainid2, false, bAlign, resi2, resn2, resn1);
                     ic.alnChainsSeq[chainid2].push(resObject);
@@ -112892,7 +112917,7 @@ class SetSeqAlign {
         } 
 
         // add gaps at the end
-        result = this.getTemplatePosFromOriPos(chainid1, prevIndex1, end_t, bRealign);
+        result = this.getTemplatePosFromOriResi(chainid1, prevIndex1, end_t, bRealign);
         pos1 = result.pos1;
         pos2 = result.pos2;
         for(let i = pos1; i < pos2; ++i) {
@@ -115204,7 +115229,7 @@ class Vastplus {
         }
 
         let allPromise = Promise.allSettled(ajaxArray);
-        try {
+        // try {
             let dataArray = await allPromise;
 
             // 2. cluster pairs
@@ -115216,10 +115241,10 @@ class Vastplus {
             await ic.pdbParserCls.loadPdbDataRender(true);
 
             /// if(ic.deferredRealignByVastplus !== undefined) ic.deferredRealignByVastplus.resolve();
-        }
-        catch(err) {
-            var aaa = 1; //alert("There are some problems in aligning the chains...");
-        }          
+        // }
+        // catch(err) {
+        //     var aaa = 1; //alert("There are some problems in aligning the chains...");
+        // }          
     }
 
     setAlignment(struct1, struct2, chainid1, chainid2, bRealign) { let ic = this.icn3d, me = ic.icn3dui;
@@ -122270,15 +122295,16 @@ class Dssp {
         let pdbAjaxArray = this.getPdbAjaxArray();
 
         // try {
+            let numRound = 0;
+            
             if(!template) {
                 //let allPromise = Promise.allSettled(pdbAjaxArray);
                 //ic.pdbDataArray = await allPromise;
 
                 ic.pdbDataArray = await this.promiseWithFixedJobs(pdbAjaxArray);
 
-                let numRound = 0;
                 let bNoMoreIg = await thisClass.parseRefPdbData(ic.pdbDataArray, template, undefined, numRound);
-                 ++numRound;
+                ++numRound;
 
                 //while(!bNoMoreIg) {
                 while(!bNoMoreIg && numRound < 15) {
@@ -132767,7 +132793,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.45.0';
+    this.REVISION = '3.45.1';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}", and added window = {navigator: {}, "__THREE__":"177"}
     this.bNode = (Object.keys(window).length < 3) ? true : false;
@@ -133347,7 +133373,7 @@ iCn3DUI.prototype.getXMLHttpRqstPromise = function(url, dataType, responseType,
                        var aaa = 1; //alert("RCSB server has no corresponding electron density map for this structure.");
                    }
                    else {
-                       var aaa = 1; //alert("The " + mapType + " file is unavailable...");
+                       console.log("The " + mapType + " file is unavailable...");
                    }
 
                    reject('error');