icn3d 3.4.11 → 3.7.0

package/icn3d.js

@@ -3952,7 +3952,7 @@ class ParasCls {
             black: this.thr(0x000000),
              grey: this.thr(0xCCCCCC),
             white: this.thr(0xFFFFFF),
-            transparent: this.thr(0x000000)
+            transparent: this.thr(0xFFFFFF) //this.thr(0x000000)
         };
 
         this.residueColors = {
@@ -4113,6 +4113,7 @@ class ParasCls {
     }
 
     thr(color) { this.icn3dui;
+        if(color == '#0') color = '#000';
         return new THREE.Color(color);
     }
 }
@@ -4483,6 +4484,16 @@ class UtilsCls {
         if(viewer_width && me.htmlCls.WIDTH > viewer_width) me.htmlCls.WIDTH = viewer_width;
         if(viewer_height && me.htmlCls.HEIGHT > viewer_height) me.htmlCls.HEIGHT = viewer_height;
     }
+
+    sumArray(numArray) {
+      let sum = 0;
+
+      for(let i = 0, il = numArray.length; i < il; ++i) {
+        sum += numArray[i];
+      }
+
+      return sum;
+    }
 }
 
 /**
@@ -7258,7 +7269,8 @@ class Strand {
         let atomsAdjust = {};
 
         //if( (bHighlight === 1 || bHighlight === 2) && !ic.bAllAtoms) {
-        if( !ic.bAllAtoms) {
+        //if( !ic.bAllAtoms) {
+        if( Object.keys(atoms).length < Object.keys(ic.atoms).length) {
             atomsAdjust = this.getSSExpandedAtoms(atoms);
         }
         else {
@@ -11885,7 +11897,8 @@ class ShareLink {
 
            if(ic.commands.length > start) {
                let command_tf = ic.commands[start].split('|||');
-               prevCommandStr = command_tf[0].trim();
+               let command_tf2 = command_tf[0].split('&command=');
+               prevCommandStr = command_tf2[0].trim();
 
                //statefile += ic.commands[start] + "\n";
 
@@ -11896,7 +11909,8 @@ class ShareLink {
            let tmpUrl = '';
            for(let il = ic.commands.length; i < il; ++i) {
                let command_tf = ic.commands[i].split('|||');
-               let commandStr = command_tf[0].trim();
+               let command_tf2 = command_tf[0].split('&command=');
+               let commandStr = command_tf2[0].trim();
 
                //statefile += ic.commands[i] + "\n";
 
@@ -11947,7 +11961,7 @@ class ShareLink {
            }
 
            statefile = statefile.replace(/!/g, Object.keys(ic.structures)[0] + '_');
-           if((ic.bInputfile && !ic.bInputUrlfile) || url.length > 4000) url = statefile;
+           if((ic.bInputfile && !ic.bInputUrlfile) || (ic.bInputUrlfile && ic.bAppend) || url.length > 4000) url = statefile;
            let id;
            if(ic.structures !== undefined && Object.keys(ic.structures).length == 1 && ic.inputid !== undefined) {
                id = Object.keys(ic.structures)[0];
@@ -11967,22 +11981,27 @@ class ShareLink {
 
         let text = "";
         if(ic.bInputfile) {
-            url = this.shareLinkUrl(bAllCommands); // output state file if ic.bInputfile is true or the URL is mor than 4000 chars
+            url = this.shareLinkUrl(bAllCommands); // output state file if ic.bInputfile is true or the URL is more than 4000 chars
 
-            text += "\nStart of type file======\n";
-            text += ic.InputfileType + "\n";
-            text += "End of type file======\n";
+            if(url.substr(0,4) == 'http') {
+                text += "\nShare Link: " + url;
+            }
+            else {
+                text += "\nStart of type file======\n";
+                text += ic.InputfileType + "\n";
+                text += "End of type file======\n";
 
-            text += "Start of data file======\n";
-            //text += ic.InputfileData;
-///            text += ic.saveFileCls.getPDBHeader();
-            text += ic.saveFileCls.getAtomPDB(ic.atoms);
+                text += "Start of data file======\n";
+                //text += ic.InputfileData;
+    ///            text += ic.saveFileCls.getPDBHeader();
+                text += ic.saveFileCls.getAtomPDB(ic.atoms);
 
-            text += "End of data file======\n";
+                text += "End of data file======\n";
 
-            text += "Start of state file======\n";
-            text += url;
-            text += "End of state file======\n";
+                text += "Start of state file======\n";
+                text += url + "\n";
+                text += "End of state file======\n";
+            }
         }
         else {
             url = this.shareLinkUrl();
@@ -11992,7 +12011,7 @@ class ShareLink {
 
                 text += "\nStart of state file======\n";
 
-                text += url;
+                text += url + "\n";
                 text += "End of state file======\n";
             }
             else {
@@ -12018,11 +12037,14 @@ class HlObjects {
     //Show the highlight for the selected atoms: hAtoms.
     addHlObjects(color, bRender, atomsHash) { let ic = this.icn3d, me = ic.icn3dui;
        if(color === undefined) color = ic.hColor;
-       if(atomsHash === undefined) atomsHash = ic.hAtoms;
+       //if(atomsHash === undefined) atomsHash = ic.hAtoms;
+       let atomsHashDisplay = (atomsHash) ? me.hashUtilsCls.intHash(atomsHash, ic.dAtoms) : me.hashUtilsCls.intHash(ic.hAtoms, ic.dAtoms);
 
-       ic.applyDisplayCls.applyDisplayOptions(ic.opts, me.hashUtilsCls.intHash(atomsHash, ic.dAtoms), ic.bHighlight);
+       ic.applyDisplayCls.applyDisplayOptions(ic.opts, atomsHashDisplay, ic.bHighlight);
 
-       if( (bRender) || (ic.bRender) ) ic.drawCls.render();
+       if( (bRender) || (ic.bRender) ) {
+           ic.drawCls.render();
+       }
     };
 
     //Remove the highlight. The atom selection does not change.
@@ -14311,6 +14333,9 @@ class HBond {
                             break;
                         }
                     }
+
+                    if(!C_atom) continue;
+
                     let inAcceptorC = C_atom.coord;
                     let inAcceptorO = inAcceptor.coord;
 
@@ -14585,9 +14610,10 @@ class PiHalogen {
               // available in 1a and 1b
               // only parallel or perpendicular
               if(interactionType == 'pi-stacking' && atom1.normal !== undefined && atom2.normal !== undefined) {
-                  let dotResult = Math.abs(atom1.normal.dot(atom2.normal));
+                  Math.abs(atom1.normal.dot(atom2.normal));
                   // perpendicular 30 degree || parellel, 30 degree
-                  if(dotResult > 0.5 && dotResult < 0.866) continue;
+                  // remove this condition on Nov 19, 2021
+                  //if(dotResult > 0.5 && dotResult < 0.866) continue;
               }
 
               let bResult = this.getHalogenPiInteractions(atom1, atom2, type, interactionType, threshold, maxlengthSq, oriResidName, bInternal);
@@ -15467,7 +15493,7 @@ class GetGraph {
         let  strokecolor = '#000';
         let  strokewidth = '1';
         let  textcolor = '#000';
-        let  fontsize = '6';
+        let  fontsize = '6px'; // '6';
         let  html = "<g class='icn3d-node' resid='" + resid + "' >";
         html += "<title>" + node.id + "</title>";
         if(bVertical) {
@@ -15481,23 +15507,31 @@ class GetGraph {
         html += "</g>";
         return html;
     }
-    getNodeTopBottom(nameHash, name2node, bReverseNode) { let ic = this.icn3d; ic.icn3dui;
+    getNodeTopBottom(nameHash, name2node, bReverseNode, bCommon, nameHashCommon) { let  ic = this.icn3d, me = ic.icn3dui;
         let  thisClass = this;
-        let  nodeArray1 = [], nodeArray2 = [];
+        let  nodeArray1 = [], nodeArray2 = [], name2nodeCommon = {};
         for(let name in nameHash) {
             let  node = name2node[name];
             if(!node) continue;
 
+            if(bCommon) {
+                node = me.hashUtilsCls.cloneHash(node);
+
+                let mapping = (nameHashCommon[name]) ? nameHashCommon[name] : '-';
+                node.id += ">" + mapping;
+                name2nodeCommon[node.id] = node;
+            }
+
             if(node.s == 'a') {
                 nodeArray1.push(node);
             }
             else if(node.s == 'b') {
                 nodeArray2.push(node);
             }
-            else if(node.s == 'ab') {
-                nodeArray1.push(node);
-                nodeArray2.push(node);
-            }
+            //else if(node.s == 'ab') {
+            //    nodeArray1.push(node);
+            //    nodeArray2.push(node);
+            //}
         }
         // sort array
         nodeArray1.sort(function(a,b) {
@@ -15506,7 +15540,7 @@ class GetGraph {
         nodeArray2.sort(function(a,b) {
           return thisClass.compNode(a, b, bReverseNode);
         });
-        return {"nodeArray1": nodeArray1, "nodeArray2": nodeArray2}
+        return {"nodeArray1": nodeArray1, "nodeArray2": nodeArray2, "name2node": name2nodeCommon};
     }
     updateGraphJson(struc, index, nodeArray1, nodeArray2, linkArray) { let  ic = this.icn3d, me = ic.icn3dui;
         let  lineGraphStr = '';
@@ -15829,22 +15863,31 @@ class LineGraph {
         let structureArray = ic.resid2specCls.atoms2structureArray(ic.hAtoms);
         //if(Object.keys(ic.structures).length > 1) {
         if(structureArray.length > 1) {
-            let  nodeArray1a = [],
-                nodeArray1b = [],
-                nodeArray2a = [],
-                nodeArray2b = [],
-                nodeArray3a = [],
-                nodeArray3b = [];
-            //let  struc1 = Object.keys(ic.structures)[0],
-            //    struc2 = Object.keys(ic.structures)[1];
-            let  struc1 = structureArray[0],
-                struc2 = structureArray[1];
-            let  linkArrayA = [],
-                linkArrayB = [],
-                linkArrayAB = [];
-            let  nameHashA = {},
-                nameHashB = {},
-                nameHashAB = {};
+
+            let struc2index= {};
+            let nodeArray1Split = [], nodeArray2Split = [], linkArraySplit = [], nameHashSplit = [];
+
+            // show common interactions: nodes will be the same. The links/interactins are different.
+            // The mapped residue name and number are attached to "id".
+            // Original node: {id : "Q24.A.2AJF", r : "1_1_2AJF_A_24", s: "a", ...}
+            // Node for common interaction: {id : "Q24.A.2AJF|Q24", r : "1_1_2AJF_A_24", s: "a", ...}
+            let nodeArray1SplitCommon = [], nodeArray2SplitCommon = [], linkArraySplitCommon = [], nameHashSplitCommon = [];
+            let linkedNodeCnt = {};
+
+            for(let i = 0, il = structureArray.length; i < il; ++i) {   
+                nodeArray1Split[i] = [];
+                nodeArray2Split[i] = [];
+                linkArraySplit[i] = [];
+                nameHashSplit[i] = {};
+
+                nodeArray1SplitCommon[i] = [];
+                nodeArray2SplitCommon[i] = [];
+                linkArraySplitCommon[i] = [];
+                nameHashSplitCommon[i] = {};
+
+                struc2index[structureArray[i]] = i;
+            }
+
             for(let i = 0, il = linkArray.length; i < il; ++i) {
                 let  link = linkArray[i];
                 let  nodeA = name2node[link.source];
@@ -15854,70 +15897,131 @@ class LineGraph {
                     continue;
                 }
 
-                //var idArrayA = nodeA.r.split('_'); // 1_1_1KQ2_A_1
-                let  idArrayA = [];
-                idArrayA.push('');
-                idArrayA.push('');
+                let  idArrayA = this.getIdArrayFromNode(nodeA);
+                let  idArrayB = this.getIdArrayFromNode(nodeB);
 
-                let  tmpStr = nodeA.r.substr(4);
-                idArrayA = idArrayA.concat(me.utilsCls.getIdArray(tmpStr));
+                let index = struc2index[idArrayA[2]];
 
-                //var idArrayB = nodeB.r.split('_'); // 1_1_1KQ2_A_1
-                let  idArrayB = [];
-                idArrayB.push('');
-                idArrayB.push('');
+                if(idArrayA[2] == structureArray[index] && idArrayB[2] == structureArray[index]) {
+                    linkArraySplit[index].push(link);
+                    nameHashSplit[index][link.source] = 1;
+                    nameHashSplit[index][link.target] = 1;
 
-                tmpStr = nodeB.r.substr(4);
-                idArrayB = idArrayB.concat(me.utilsCls.getIdArray(tmpStr));
+                    let chainid1 = idArrayA[2] + '_' + idArrayA[3];
+                    let chainid2 = idArrayB[2] + '_' + idArrayB[3];
+                    let resid1 = chainid1 + '_' + idArrayA[4];
+                    let resid2 = chainid2 + '_' + idArrayB[4];
 
-                if(idArrayA[2] == struc1 && idArrayB[2] == struc1) {
-                    linkArrayA.push(link);
-                    nameHashA[link.source] = 1;
-                    nameHashA[link.target] = 1;
-                } else if(idArrayA[2] == struc2 && idArrayB[2] == struc2) {
-                    linkArrayB.push(link);
-                    nameHashB[link.source] = 1;
-                    nameHashB[link.target] = 1;
-                } else {
-                    linkArrayAB.push(link);
-                    nameHashAB[link.source] = 1;
-                    nameHashAB[link.target] = 1;
-                }
-            }
-            let  nodeArraysA = ic.getGraphCls.getNodeTopBottom(nameHashA, name2node);
-            nodeArray1a = nodeArraysA.nodeArray1;
-            nodeArray1b = nodeArraysA.nodeArray2;
-            let  nodeArraysB = ic.getGraphCls.getNodeTopBottom(nameHashB, name2node);
-            nodeArray2a = nodeArraysB.nodeArray1;
-            nodeArray2b = nodeArraysB.nodeArray2;
-            let  nodeArraysAB = ic.getGraphCls.getNodeTopBottom(nameHashAB, name2node, true);
-            nodeArray3a = nodeArraysAB.nodeArray1;
-            nodeArray3b = nodeArraysAB.nodeArray2;
-            let  len1a = nodeArray1a.length,
-                len1b = nodeArray1b.length;
-            let  len2a = nodeArray2a.length,
-                len2b = nodeArray2b.length;
-            let  len3a = nodeArray3a.length,
-                len3b = nodeArray3b.length;
-            let  maxLen = Math.max(len1a, len1b, len2a, len2b, len3a, len3b);
+                    let mapping1, mapping2;
+                    
+                    if(ic.chainsMapping[chainid1] && ic.chainsMapping[chainid1][resid1]
+                      && ic.chainsMapping[chainid2] && ic.chainsMapping[chainid2][resid2]) { 
+                        mapping1 = (nodeA.s == "a") ? ic.chainsMapping[chainid1][resid1] : ic.chainsMapping[chainid2][resid2];
+                        mapping2 = (nodeA.s == "a") ? ic.chainsMapping[chainid2][resid2] : ic.chainsMapping[chainid1][resid1];
+
+                        let mappingid = mapping1 + '_' + mapping2 + '_' + link.c; // link.c determines the interaction type
+                        if(!linkedNodeCnt.hasOwnProperty(mappingid)) {
+                            linkedNodeCnt[mappingid] = 1;
+                        }
+                        else {
+                            ++linkedNodeCnt[mappingid];
+                        }
+                    }
+                } 
+            }
+            
+            // set linkArraySplitCommon and nameHashSplitCommon
+            for(let i = 0, il = linkArray.length; i < il; ++i) {
+                let  link = linkArray[i];
+                let  nodeA = name2node[link.source];
+                let  nodeB = name2node[link.target];
+
+                if(!nodeA || !nodeB || !nodeA.r || !nodeB.r) {
+                    continue;
+                }
+
+                let  idArrayA = this.getIdArrayFromNode(nodeA);
+                let  idArrayB = this.getIdArrayFromNode(nodeB);
+
+                let index = struc2index[idArrayA[2]];
+
+                if(idArrayA[2] == structureArray[index] && idArrayB[2] == structureArray[index]) {
+                    let chainid1 = idArrayA[2] + '_' + idArrayA[3];
+                    let chainid2 = idArrayB[2] + '_' + idArrayB[3];
+                    let resid1 = chainid1 + '_' + idArrayA[4];
+                    let resid2 = chainid2 + '_' + idArrayB[4];
+
+                    let mapping1, mapping2;
+                    
+                    if(ic.chainsMapping[chainid1] && ic.chainsMapping[chainid1][resid1]
+                      && ic.chainsMapping[chainid2] && ic.chainsMapping[chainid2][resid2]) { 
+                        mapping1 = (nodeA.s == "a") ? ic.chainsMapping[chainid1][resid1] : ic.chainsMapping[chainid2][resid2];
+                        mapping2 = (nodeA.s == "a") ? ic.chainsMapping[chainid2][resid2] : ic.chainsMapping[chainid1][resid1];
+
+                        let mappingid = mapping1 + '_' + mapping2 + '_' + link.c; // link.c determines the interaction type
+
+                        if(linkedNodeCnt[mappingid] == structureArray.length) {
+                            let linkCommon = me.hashUtilsCls.cloneHash(link);
+                            linkCommon.source += '>' + ic.chainsMapping[chainid1][resid1];
+                            linkCommon.target += '>' + ic.chainsMapping[chainid2][resid2];
+
+                            linkArraySplitCommon[index].push(linkCommon);
+                        }  
+
+                        nameHashSplitCommon[index][link.source] = ic.chainsMapping[chainid1][resid1];
+                        nameHashSplitCommon[index][link.target] = ic.chainsMapping[chainid2][resid2];
+                    }
+                } 
+            }
+
+            let len1Split = [], len2Split = [], maxWidth = 0;
             let  strucArray = [];
-            if(linkArrayA.length > 0) strucArray.push(struc1);
-            if(linkArrayB.length > 0) strucArray.push(struc2);
-            if(linkArrayAB.length > 0) strucArray.push(struc1 + '_' + struc2);
+            for(let i = 0, il = structureArray.length; i < il; ++i) {  
+                let  nodeArraysTmp = ic.getGraphCls.getNodeTopBottom(nameHashSplit[i], name2node);
+                nodeArray1Split[i] = nodeArraysTmp.nodeArray1;
+                nodeArray2Split[i] = nodeArraysTmp.nodeArray2;
+
+                let bCommon = true;
+                nodeArraysTmp = ic.getGraphCls.getNodeTopBottom(nameHashSplit[i], name2node, undefined, bCommon, nameHashSplitCommon[i]);
+                nodeArray1SplitCommon[i] = nodeArraysTmp.nodeArray1;
+                nodeArray2SplitCommon[i] = nodeArraysTmp.nodeArray2;
+                name2node = me.hashUtilsCls.unionHash(name2node, nodeArraysTmp.name2node);
+
+                len1Split[i] = nodeArray1Split[i].length;
+                len2Split[i] = nodeArray2Split[i].length;
+                
+                maxWidth = Math.max(maxWidth, len2Split[i]);
+
+                //if(linkArraySplit[i].length > 0) strucArray.push(structureArray[i]);
+                strucArray.push(structureArray[i]);
+            }
+
             let  factor = 1;
             let  r = 3 * factor;
             let  gap = 7 * factor;
             let  height, width, heightAll;
             let  marginX = 10,
                 marginY = 10,
-                legendWidth = 30;
+                legendWidth = 30,
+                textHeight = 20;
+            
             if(bScatterplot) {
-                heightAll =(len1a + 2 + len2a + 2) *(r + gap) + 4 * marginY + 2 * legendWidth;
-                width =(Math.max(len1b, len2b) + 2) *(r + gap) + 2 * marginX + legendWidth;
+                //heightAll =(len1a + 2 + len2a + 2) *(r + gap) + 4 * marginY + 2 * legendWidth;
+                //width =(Math.max(len1b, len2b) + 2) *(r + gap) + 2 * marginX + legendWidth;
+                heightAll =(me.utilsCls.sumArray(len1Split) + 2*strucArray.length) *(r + gap) + 4 * marginY 
+                  + 2 * legendWidth + textHeight*strucArray.length;
+                // show common interaction as well
+                heightAll *= 2;
+
+                width = (maxWidth + 2) * (r + gap) + 2 * marginX + legendWidth;
+                  
             } else {
-                height = 110;
+                height = 110 + textHeight;
                 heightAll = height * strucArray.length;
-                width = maxLen *(r + gap) + 2 * marginX;
+                // show common interaction as well
+                heightAll *= 2;
+
+                width = (maxWidth + 2) * (r + gap) + 2 * marginX;
             }
             let  id, graphWidth;
             if(bScatterplot) {
@@ -15930,43 +16034,42 @@ class LineGraph {
                 id = me.linegraphid;
             }
             html =(strucArray.length == 0) ? "No interactions found for each structure<br><br>" :
-                "2D integration graph for structure(s) <b>" + strucArray + "</b><br><br>";
+                "2D integration graph for " + strucArray.length + " structure(s) <b>" + strucArray + "</b>. Common interactions are shown in the last " + strucArray.length + " graphs.<br><br>";
             html += "<svg id='" + id + "' viewBox='0,0," + width + "," + heightAll + "' width='" + graphWidth + "px'>";
-            let  heightFinal = 0;
-            if(linkArrayA.length > 0) {
+
+            let  heightFinal = 0;            
+            for(let i = 0, il = structureArray.length; i < il; ++i) {  
                 if(bScatterplot) {
-                    heightFinal -= 15;
-                    html += this.drawScatterplot_base(nodeArray1a, nodeArray1b, linkArrayA, name2node, heightFinal);
-                    heightFinal = 15;
-                    height =(len1a + 1) *(r + gap) + 2 * marginY;
+                    //heightFinal -= 15;
+                    html += this.drawScatterplot_base(nodeArray1Split[i], nodeArray2Split[i], linkArraySplit[i], name2node, heightFinal, undefined, "Interactions in structure " + strucArray[i], textHeight);
+                    //heightFinal = 15;
+                    height =(len1Split[i] + 1) *(r + gap) + 2 * marginY + textHeight;
                 } else {
-                    html += this.drawLineGraph_base(nodeArray1a, nodeArray1b, linkArrayA, name2node, heightFinal);
+                    html += this.drawLineGraph_base(nodeArray1Split[i], nodeArray2Split[i], linkArraySplit[i], name2node, heightFinal, "Interactions in structure " + strucArray[i], textHeight);
                 }
                 heightFinal += height;
-                ic.lineGraphStr += ic.getGraphCls.updateGraphJson(struc1, 1, nodeArray1a, nodeArray1b, linkArrayA);
+
+                if(i > 0) ic.lineGraphStr += ', \n';
+                ic.lineGraphStr += ic.getGraphCls.updateGraphJson(strucArray[i], i, nodeArray1Split[i], nodeArray2Split[i], linkArraySplit[i]);
             }
-            if(linkArrayB.length > 0) {
+
+            // draw common interaction
+            for(let i = 0, il = structureArray.length; i < il; ++i) {  
                 if(bScatterplot) {
-                    html += this.drawScatterplot_base(nodeArray2a, nodeArray2b, linkArrayB, name2node, heightFinal);
-                    height =(len2a + 1) *(r + gap) + 2 * marginY;
+                    //heightFinal -= 15;
+                    html += this.drawScatterplot_base(nodeArray1SplitCommon[i], nodeArray2SplitCommon[i], linkArraySplitCommon[i], name2node, heightFinal, undefined, "Common interactions in structure " + strucArray[i], textHeight);
+                    //heightFinal = 15;
+                    height =(len1Split[i] + 1) *(r + gap) + 2 * marginY + textHeight;
                 } else {
-                    html += this.drawLineGraph_base(nodeArray2a, nodeArray2b, linkArrayB, name2node, heightFinal);
+                    html += this.drawLineGraph_base(nodeArray1SplitCommon[i], nodeArray2SplitCommon[i], linkArraySplitCommon[i], name2node, heightFinal, "Common interactions in structure " + strucArray[i], textHeight);
                 }
                 heightFinal += height;
-                if(linkArrayA.length > 0) ic.lineGraphStr += ', \n';
-                ic.lineGraphStr += ic.getGraphCls.updateGraphJson(struc2, 2, nodeArray2a, nodeArray2b, linkArrayB);
-            }
-            if(linkArrayAB.length > 0 && !bScatterplot) {
-                html += this.drawLineGraph_base(nodeArray3a, nodeArray3b, linkArrayAB, name2node, heightFinal);
-                if(linkArrayA.length > 0 || linkArrayB.length > 0) ic.lineGraphStr += ', \n';
-                ic.lineGraphStr += '"structure1_2": {"id1": "' + struc1 + '", "id2": "' + struc2 + '", "nodes1":[';
-                ic.lineGraphStr += me.utilsCls.getJSONFromArray(nodeArray3a);
-                ic.lineGraphStr += '], \n"nodes2":[';
-                ic.lineGraphStr += me.utilsCls.getJSONFromArray(nodeArray3b);
-                ic.lineGraphStr += '], \n"links":[';
-                ic.lineGraphStr += me.utilsCls.getJSONFromArray(linkArrayAB);
-                ic.lineGraphStr += ']}';
+
+                //if(i > 0) ic.lineGraphStr += ', \n';
+                ic.lineGraphStr += ', \n';
+                ic.lineGraphStr += ic.getGraphCls.updateGraphJson(strucArray[i], i + '_common', nodeArray1SplitCommon[i], nodeArray2SplitCommon[i], linkArraySplitCommon[i]);
             }
+
             html += "</svg>";
         } else {
             if(!bScatterplot) {
@@ -16024,7 +16127,18 @@ class LineGraph {
         return html;
     }
 
-    drawLineGraph_base(nodeArray1, nodeArray2, linkArray, name2node, height) { let  ic = this.icn3d, me = ic.icn3dui;
+    getIdArrayFromNode(node) { let  ic = this.icn3d, me = ic.icn3dui;
+        let  idArray = []; // 1_1_1KQ2_A_1
+        idArray.push('');
+        idArray.push('');
+
+        let  tmpStr = node.r.substr(4); 
+        idArray = idArray.concat(me.utilsCls.getIdArray(tmpStr));
+
+        return idArray;
+    }
+
+    drawLineGraph_base(nodeArray1, nodeArray2, linkArray, name2node, height, label, textHeight) { let  ic = this.icn3d, me = ic.icn3dui;
         let  html = '';
         let  len1 = nodeArray1.length,
             len2 = nodeArray2.length;
@@ -16041,6 +16155,11 @@ class LineGraph {
             margin2 = margin;
             margin1 = Math.abs(len1 - len2) *(r + gap) * 0.5 + margin;
         }
+
+        // draw label
+        height += textHeight;
+        html += "<text x='" + margin1 + "' y='" + height + "' style='font-size:8px; font-weight:bold'>" + label + "</text>";
+
         let  h1 = 30 + height,
             h2 = 80 + height;
         let  nodeHtml = '';
@@ -16096,7 +16215,7 @@ class LineGraph {
         return html;
     }
 
-    drawScatterplot_base(nodeArray1, nodeArray2, linkArray, name2node, height, bContactMap) { let ic = this.icn3d; ic.icn3dui;
+    drawScatterplot_base(nodeArray1, nodeArray2, linkArray, name2node, height, bContactMap, label, textHeight) { let ic = this.icn3d; ic.icn3dui;
         let  html = '';
         let  len1 = nodeArray1.length,
             len2 = nodeArray2.length;
@@ -16107,12 +16226,19 @@ class LineGraph {
         let  marginX = 10,
             marginY = 20;
         let  heightTotal =(len1 + 1) *(r + gap) + legendWidth + 2 * marginY;
+
+        // draw label
+        height += textHeight;
+
+        html += "<text x='" + marginX + "' y='" + (height + 15).toString() + "' style='font-size:8px; font-weight:bold'>" + label + "</text>";
+ 
         let  margin1 = height + heightTotal -(legendWidth + marginY +(r + gap)); // y-axis
         let  margin2 = legendWidth + marginX +(r + gap); // x-axis
-        let  x = legendWidth + marginX;
+
         let  nodeHtml = '';
         let  node2posSet1 = {},
             node2posSet2 = {};
+        let  x = legendWidth + marginX;
         for(let i = 0; i < len1; ++i) {
             nodeHtml += ic.getGraphCls.drawResNode(nodeArray1[i], i, r, gap, margin1, x, 'a', true);
             node2posSet1[nodeArray1[i].id] = { x: x, y: margin1 - i *(r + gap) };
@@ -16484,8 +16610,9 @@ class ViewInterPairs {
                tmpText = 'Set 2';
            }
            html += '<div style="text-align:center"><br><b>Interactions Sorted on ' + tmpText + '</b>: <button class="' + ic.pre + 'showintercntonly" style="margin-left:20px">Show Count Only</button><button class="' + ic.pre + 'showinterdetails" style="margin-left:20px">Show Details</button></div>';
-           html += this.getAllInteractionTable(type).html;
-           bondCnt = this.getAllInteractionTable(type).bondCnt;
+           let result = this.getAllInteractionTable(type);
+           html += result.html;
+           bondCnt = result.bondCnt;
 
            $("#" + ic.pre + "dl_interactionsorted").html(html);
            me.htmlCls.dialogCls.openDlg('dl_interactionsorted', 'Show sorted interactions');
@@ -18358,7 +18485,7 @@ class ResidueLabels {
         if(me.bNode) return;
 
         let size = 18;
-        let background = "#CCCCCC";
+        let background = "#FFFFFF"; //"#CCCCCC";
 
         let atomsHash = me.hashUtilsCls.intHash(ic.hAtoms, atoms);
 
@@ -18398,7 +18525,15 @@ class ResidueLabels {
                 label.factor = 0.3;
 
                 let atomColorStr = atom.color.getHexString().toUpperCase();
-                label.color = (atomColorStr === "CCCCCC" || atomColorStr === "C8C8C8") ? "#888888" : "#" + atomColorStr;
+                //label.color = (ic.opts.background != 'black') ? ic.colorWhitebkgd : ic.colorBlackbkgd; //(atomColorStr === "CCCCCC" || atomColorStr === "C8C8C8") ? "#888888" : "#" + atomColorStr;
+                //if(bSchematic) label.color = (atomColorStr === "CCCCCC" || atomColorStr === "C8C8C8") ? "#888888" : "#" + atomColorStr;
+                // don't change residue labels
+                if(bNumber) {
+                    label.color = (ic.opts.background != 'black') ? ic.colorWhitebkgd : ic.colorBlackbkgd;
+                }
+                else {
+                    label.color = (atomColorStr === "CCCCCC" || atomColorStr === "C8C8C8") ? "#888888" : "#" + atomColorStr;
+                }
                 label.background = background;
                 //label.alpha = alpha; // ic.labelCls.hideLabels() didn't work. Remove this line for now
 
@@ -18442,7 +18577,7 @@ class ResidueLabels {
             label.text = atom.elem;
             label.size = size;
 
-            label.color = "#" + atom.color.getHexString();
+            label.color = (ic.opts.background != 'black') ? ic.colorWhitebkgd : atom.color.getHexString();
             label.background = background;
 
             ic.labels['schematic'].push(label);
@@ -18480,7 +18615,8 @@ class ResidueLabels {
             }
 
             let atomColorStr = atom.color.getHexString().toUpperCase();
-            label.color = (atomColorStr === "CCCCCC" || atomColorStr === "C8C8C8") ? "#888888" : "#" + atomColorStr;
+            label.color = (ic.opts.background != 'black') ? ic.colorWhitebkgd : ic.colorBlackbkgd; //(atomColorStr === "CCCCCC" || atomColorStr === "C8C8C8") ? "#888888" : "#" + atomColorStr; 
+            if(bElement) label.color = (atomColorStr === "CCCCCC" || atomColorStr === "C8C8C8") ? "#888888" : "#" + atomColorStr;
             label.background = background;
 
             ic.labels['residue'].push(label);
@@ -19259,7 +19395,8 @@ class Scap {
                   if(!ic.alertAlt) {
                     ic.alertAlt = true;
 
-                    if(ic.bRender) var aaa = 1; //alert('Please press the letter "a" to alternate between wild type and mutant.');
+                    //if(ic.bRender) var aaa = 1; //alert('Please press the letter "a" to alternate between wild type and mutant.');
+                    var aaa = 1; //alert('Please press the letter "a" to alternate between wild type and mutant.');
                   }
               }
 
@@ -19907,8 +20044,7 @@ class LoadPDB {
     // modified from iview (http://istar.cse.cuhk.edu.hk/iview/)
     //This PDB parser feeds the viewer with the content of a PDB file, pdbData.
     loadPDB(src, pdbid, bOpm, bVector, bMutation, bAppend) { let  ic = this.icn3d, me = ic.icn3dui;
-        let  helices = [], sheets = [];
-        //ic.atoms = {}
+        let bNMR = false;
         let  lines = src.split('\n');
 
         let  chainsTmp = {}; // serial -> atom
@@ -19947,20 +20083,23 @@ class LoadPDB {
             serial = (ic.atoms) ? Object.keys(ic.atoms).length : 0;
         }
 
-        let  sheetArray = [], sheetStart = [], sheetEnd = [], helixArray = [], helixStart = [], helixEnd = [];
+        //let helices = [], sheets = [];
+        let sheetArray = [], sheetStart = [], sheetEnd = [], helixArray = [], helixStart = [], helixEnd = [];
 
         let  chainNum, residueNum, oriResidueNum;
         let prevChainNum = '', prevResidueNum = '', prevOriResidueNum = '';
 
         let  oriSerial2NewSerial = {};
 
-        let  chainMissingResidueArray = {};
+        //let  chainMissingResidueArray = {}
 
         let  id = (pdbid) ? pdbid : 'stru';
 
-        let  maxMissingResi = 0, prevMissingChain = '';
+        let prevMissingChain = '';
         let  CSerial, prevCSerial, OSerial, prevOSerial;
 
+        let  structure = "stru";
+
         for (let i in lines) {
             let  line = lines[i];
             let  record = line.substr(0, 6);
@@ -19981,6 +20120,12 @@ class LoadPDB {
                     }
                 }
 
+                structure = id;
+
+                if(id == 'stru' || bMutation || (bAppend && id.length != 4)) { // bMutation: side chain prediction
+                    structure = (moleculeNum === 1) ? id : id + moleculeNum.toString();
+                }
+
                 ic.molTitle = '';
 
             } else if (record === 'TITLE ') {
@@ -19995,22 +20140,23 @@ class LoadPDB {
                 let  startResi = parseInt(line.substr(21, 4));
                 let  endResi = parseInt(line.substr(33, 4));
 
-                let  chain_resi;
                 for(let j = startResi; j <= endResi; ++j) {
-                  chain_resi = startChain + "_" + j;
-                  helixArray.push(chain_resi);
+                  let resid = structure + "_" + startChain + "_" + j;
+                  helixArray.push(resid);
 
-                  if(j === startResi) helixStart.push(chain_resi);
-                  if(j === endResi) helixEnd.push(chain_resi);
+                  if(j === startResi) helixStart.push(resid);
+                  if(j === endResi) helixEnd.push(resid);
                 }
-
+/*
                 helices.push({
+                    structure: structure,
                     chain: startChain,
                     initialResidue: startResi,
                     initialInscode: line.substr(25, 1),
                     terminalResidue: endResi,
                     terminalInscode: line.substr(37, 1),
                 });
+*/                
             } else if (record === 'SHEET ') {
                 //ic.bSecondaryStructure = true;
                 if(bOpm === undefined || !bOpm) ic.bSecondaryStructure = true;
@@ -20021,20 +20167,22 @@ class LoadPDB {
                 let  endResi = parseInt(line.substr(33, 4));
 
                 for(let j = startResi; j <= endResi; ++j) {
-                  let  chain_resi = startChain + "_" + j;
-                  sheetArray.push(chain_resi);
+                  let  resid = structure + "_" + startChain + "_" + j;
+                  sheetArray.push(resid);
 
-                  if(j === startResi) sheetStart.push(chain_resi);
-                  if(j === endResi) sheetEnd.push(chain_resi);
+                  if(j === startResi) sheetStart.push(resid);
+                  if(j === endResi) sheetEnd.push(resid);
                 }
-
+/*
                 sheets.push({
+                    structure: structure,
                     chain: startChain,
                     initialResidue: startResi,
                     initialInscode: line.substr(26, 1),
                     terminalResidue: endResi,
                     terminalInscode: line.substr(37, 1),
                 });
+*/                
             } else if (record === 'HBOND ') {
                 if(bOpm === undefined || !bOpm) ic.bSecondaryStructure = true;
     /*
@@ -20081,6 +20229,11 @@ class LoadPDB {
                  if(line.indexOf('1/2 of bilayer thickness:') !== -1) { // OPM transmembrane protein
                     ic.halfBilayerSize = parseFloat(line.substr(line.indexOf(':') + 1).trim());
                  }
+                 else if (type == 210) {
+                     if((line.substr(11, 32).trim() == 'EXPERIMENT TYPE') && line.substr(45).trim() == 'NMR') {
+                        bNMR = true;
+                     }
+                 }
                  else if (type == 350 && line.substr(13, 5) == 'BIOMT') {
                     let  n = parseInt(line[18]) - 1;
                     //var m = parseInt(line.substr(21, 2));
@@ -20097,7 +20250,8 @@ class LoadPDB {
                     let  resn = line.substr(15, 3);
                     //let  chain = line.substr(19, 1);
                     let  chain = line.substr(18, 2).trim();
-                    let  resi = parseInt(line.substr(21, 5));
+                    //let  resi = parseInt(line.substr(21, 5));
+                    let  resi = line.substr(21, 5);
 
                     //var structure = parseInt(line.substr(13, 1));
                     //if(line.substr(13, 1) == ' ') structure = 1;
@@ -20105,20 +20259,15 @@ class LoadPDB {
                     //var chainNum = structure + '_' + chain;
                     let  chainNum = id + '_' + chain;
 
-                    if(chainMissingResidueArray[chainNum] === undefined) chainMissingResidueArray[chainNum] = [];
+                    if(ic.chainMissingResidueArray[chainNum] === undefined) ic.chainMissingResidueArray[chainNum] = [];
                     let  resObject = {};
                     resObject.resi = resi;
                     resObject.name = me.utilsCls.residueName2Abbr(resn).toLowerCase();
 
-                    if(chain != prevMissingChain) {
-                        maxMissingResi = 0;
-                    }
-
                     // not all listed residues are considered missing, e.g., PDB ID 4OR2, only the firts four residues are considered missing
-                    if(!isNaN(resi) && (prevMissingChain == '' || (chain != prevMissingChain) || (chain == prevMissingChain && resi > maxMissingResi)) ) {
-                        chainMissingResidueArray[chainNum].push(resObject);
-
-                        maxMissingResi = resi;
+                    //if(!isNaN(resi) && (prevMissingChain == '' || (chain != prevMissingChain) || (chain == prevMissingChain && resi > maxMissingResi)) ) {
+                    if(prevMissingChain == '' || (chain != prevMissingChain) || (chain == prevMissingChain) ) {
+                        ic.chainMissingResidueArray[chainNum].push(resObject);
                         prevMissingChain = chain;
                     }
 
@@ -20134,21 +20283,27 @@ class LoadPDB {
             } else if (record === 'ENDMDL') {
                 ++moleculeNum;
                 id = 'stru';
+
+                structure = id;
+                if(id == 'stru' || bMutation || (bAppend && id.length != 4)) { // bMutation: side chain prediction
+                    structure = (moleculeNum === 1) ? id : id + moleculeNum.toString();
+                }
+
+                //helices = [];
+                //sheets = [];
+                if(!bNMR) {
+                    sheetArray = [];
+                    sheetStart = [];
+                    sheetEnd = [];
+                    helixArray = [];
+                    helixStart = [];
+                    helixEnd = [];
+                }
             } else if (record === 'JRNL  ') {
                 if(line.substr(12, 4) === 'PMID') {
                     ic.pmid = line.substr(19).trim();
                 }
             } else if (record === 'ATOM  ' || record === 'HETATM') {
-                //if(id == 'stru' && bOpm) {
-                //    id = pdbid;
-                //}
-
-                let  structure = id;
-                //if(id == 'stru' || bMutation || (bAppend && id == 'stru')) { // bMutation: side chain prediction
-                if(id == 'stru' || bMutation || (bAppend)) { // bMutation: side chain prediction
-                    structure = (moleculeNum === 1) ? id : id + moleculeNum.toString();
-                }
-
                 let  alt = line.substr(16, 1);
                 //if (alt !== " " && alt !== "A") continue;
 
@@ -20190,7 +20345,7 @@ class LoadPDB {
 
                 residueNum = chainNum + "_" + resi;
 
-                let  chain_resi = chain + "_" + resi;
+                //let  chain_resi = chain + "_" + resi;
 
                 let  x = parseFloat(line.substr(30, 8));
                 let  y = parseFloat(line.substr(38, 8));
@@ -20241,27 +20396,26 @@ class LoadPDB {
 
                 // Assign secondary structures from the input
                 // if a residue is assigned both sheet and helix, it is assigned as sheet
-                if($.inArray(chain_resi, sheetArray) !== -1) {
+                if(this.isSecondary(residueNum, sheetArray, bNMR)) {
                   ic.atoms[serial].ss = 'sheet';
-
-                  if($.inArray(chain_resi, sheetStart) !== -1) {
+                  if(this.isSecondary(residueNum, sheetStart, bNMR)) {
                     ic.atoms[serial].ssbegin = true;
                   }
 
                   // do not use else if. Some residues are both start and end of secondary structure
-                  if($.inArray(chain_resi, sheetEnd) !== -1) {
+                  if(this.isSecondary(residueNum, sheetEnd, bNMR)) {
                     ic.atoms[serial].ssend = true;
                   }
                 }
-                else if($.inArray(chain_resi, helixArray) !== -1) {
+                else if(this.isSecondary(residueNum, helixArray, bNMR)) {
                   ic.atoms[serial].ss = 'helix';
 
-                  if($.inArray(chain_resi, helixStart) !== -1) {
+                  if(this.isSecondary(residueNum, helixStart, bNMR)) {
                     ic.atoms[serial].ssbegin = true;
                   }
 
                   // do not use else if. Some residues are both start and end of secondary structure
-                  if($.inArray(chain_resi, helixEnd) !== -1) {
+                  if(this.isSecondary(residueNum, helixEnd, bNMR)) {
                     ic.atoms[serial].ssend = true;
                   }
                 }
@@ -20359,7 +20513,7 @@ class LoadPDB {
         if(ic.chains[chainNum] === undefined) ic.chains[chainNum] = {};
         ic.chains[chainNum] = me.hashUtilsCls.unionHash2Atoms(ic.chains[chainNum], chainsTmp, ic.atoms);
 
-        if(!bMutation) this.adjustSeq(chainMissingResidueArray);
+        if(!bMutation) this.adjustSeq(ic.chainMissingResidueArray);
 
     //    ic.missingResidues = [];
     //    for(let chainid in chainMissingResidueArray) {
@@ -20544,10 +20698,11 @@ class LoadPDB {
         for(let chainNum in ic.chainsSeq) {
             if(chainMissingResidueArray[chainNum] === undefined) continue;
 
-            let  A = ic.chainsSeq[chainNum];
-            //var A2 = ic.chainsAn[chainNum][0];
-            //var A3 = ic.chainsAn[chainNum][1];
-            let  B = chainMissingResidueArray[chainNum];
+            //let  A = ic.chainsSeq[chainNum];
+            //let  B = chainMissingResidueArray[chainNum];
+
+            let  A = chainMissingResidueArray[chainNum];
+            let  B = ic.chainsSeq[chainNum];
 
             let  m = A.length;
             let  n = B.length;
@@ -20565,7 +20720,7 @@ class LoadPDB {
               j = 0;
               k = 0;
               while (i < m && j < n) {
-                    if (A[i].resi <= B[j].resi) {
+                    if (parseInt(A[i].resi) <= parseInt(B[j].resi)) {
                           C[k] = A[i];
                           //C2[k] = A2[i];
                           //C3[k] = A3[i];
@@ -20701,6 +20856,24 @@ class LoadPDB {
         return {'chainresiCalphaHash': chainCalphaHash, 'center': ic.center.clone()}
     }
 
+    isSecondary(resid, residArray, bNMR) { let ic = this.icn3d; ic.icn3dui;
+        if(!bNMR) {
+            return $.inArray(resid, residArray) != -1;
+        }
+        else {
+            let chain_resi = resid.substr(resid.indexOf('_') + 1);
+
+            let bFound = false;
+            for(let i = 0, il = residArray.length; i < il; ++i) {
+                if(chain_resi == residArray[i].substr(residArray[i].indexOf('_') + 1)) {
+                    bFound = true;
+                    break;
+                }
+            }
+
+            return bFound;
+        }
+    }
 }
 
 /**
@@ -20748,6 +20921,7 @@ class LoadAtomData {
           let  refinedStr =(me.cfg.inpara && me.cfg.inpara.indexOf('atype=1') !== -1) ? 'Invariant Core ' : '';
           ic.molTitle = refinedStr + 'Structure Alignment of ';
 
+          let bTitle = false;
           for(let i = 0, il = data.alignedStructures[0].length; i < il; ++i) {
               let  structure = data.alignedStructures[0][i];
 
@@ -20785,10 +20959,13 @@ class LoadAtomData {
                   ic.molTitle += " and ";
                   if(structure.descr !== undefined) ic.pmid += "_";
               }
+
+              bTitle = true;
           }
 
           ic.molTitle += ' from VAST+';
 
+          if(!bTitle) ic.molTitle = '';
         }
         else { // mmdbid or mmcifid
             if(data.descr !== undefined) ic.molTitle += data.descr.name;
@@ -22288,7 +22465,7 @@ class PdbParser {
        let  url, dataType;
 
        if(bAf) {
-           url = "https://alphafold.ebi.ac.uk/files/AF-" + pdbid + "-F1-model_v1.pdb";
+           url = "https://alphafold.ebi.ac.uk/files/AF-" + pdbid + "-F1-model_v2.pdb";
            ic.ParserUtilsCls.setYourNote(pdbid.toUpperCase() + '(AlphaFold) in iCn3D');
        }
        else {
@@ -22340,7 +22517,7 @@ class PdbParser {
 
     //Load structures from a "URL". Due to the same domain policy of Ajax call, the URL should be in the same
     //domain. "type" could be "pdb", "mol2", "sdf", or "xyz" for pdb file, mol2file, sdf file, and xyz file, respectively.
-    downloadUrl(url, type) { let  ic = this.icn3d, me = ic.icn3dui;
+    downloadUrl(url, type, command) { let  ic = this.icn3d, me = ic.icn3dui;
        let  thisClass = this;
 
        let pos = url.lastIndexOf('/');
@@ -22377,6 +22554,7 @@ class PdbParser {
 
             if(type === 'pdb') {
                 thisClass.loadPdbData(data);
+                ic.loadScriptCls.loadScript(command);
             }
             else if(type === 'mol2') {
                 ic.mol2ParserCls.loadMol2Data(data);
@@ -22392,7 +22570,7 @@ class PdbParser {
             }
             else if(type === 'icn3dpng') {
                 ic.mmcifParserCls.loadMmcifData(data);
-                me.htmlCls.setHtmlCls.loadPng(data);
+                me.htmlCls.setHtmlCls.loadPng(data, command);
             }
           },
           error : function(xhr, textStatus, errorThrown ) {
@@ -23003,13 +23181,13 @@ class AlignParser {
 
         request
         .fail(function() {
-            var aaa = 1; //alert("These two MMDB IDs " + alignArray + " do not have 3D alignment data.");
+            var aaa = 1; //alert("These two MMDB IDs " + alignArray + " do not have 3D alignment data in the VAST+ database. You can try the VAST alignment by visiting the VAST+ page https://www.ncbi.nlm.nih.gov/Structure/vastplus/vastplus.cgi?uid=[PDB ID] (e.g., uid=1KQ2), and clicking \"Original VAST\"");
             return false;
         })
         .then(function( data ) {
             seqalign = data.seqalign;
             if(seqalign === undefined) {
-                var aaa = 1; //alert("These two MMDB IDs " + alignArray + " do not have 3D alignment data.");
+                var aaa = 1; //alert("These two MMDB IDs " + alignArray + " do not have 3D alignment data in the VAST+ database. You can try the VAST alignment by visiting the VAST+ page https://www.ncbi.nlm.nih.gov/Structure/vastplus/vastplus.cgi?uid=[PDB ID] (e.g., uid=1KQ2), and clicking \"Original VAST\"");
                 return false;
             }
 
@@ -23092,11 +23270,11 @@ class AlignParser {
                 ic.alignmolid2color.push(tmpHash);
             }
 
-            //var url3 = me.htmlCls.baseUrl + 'mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&atomonly=1&uid=' + ic.mmdbidArray[0];
-            //var url4 = me.htmlCls.baseUrl + 'mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&atomonly=1&uid=' + ic.mmdbidArray[1];
+            //var url3 = me.htmlCls.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&buidx=" + me.cfg.buidx + "&atomonly=1&uid=" + ic.mmdbidArray[0];
+            //var url4 = me.htmlCls.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&buidx=" + me.cfg.buidx + "&atomonly=1&uid=" + ic.mmdbidArray[1];
             // need the parameter moleculeInfor
-            let  url3 = me.htmlCls.baseUrl + 'mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&uid=' + ic.mmdbidArray[0];
-            let  url4 = me.htmlCls.baseUrl + 'mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&uid=' + ic.mmdbidArray[1];
+            let  url3 = me.htmlCls.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&buidx=" + me.cfg.buidx + "&uid=" + ic.mmdbidArray[0];
+            let  url4 = me.htmlCls.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&buidx=" + me.cfg.buidx + "&uid=" + ic.mmdbidArray[1];
 
             let  d3 = $.ajax({
               url: url3,
@@ -23631,10 +23809,10 @@ class MmdbParser {
        // b: b-factor, s: water, ft: pdbsite
        //&ft=1
        if(bGi) {
-           url = me.htmlCls.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&simple=1&gi=" + mmdbid;
+           url = me.htmlCls.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&buidx=" + me.cfg.buidx + "&simple=1&gi=" + mmdbid;
        }
        else {
-           url = me.htmlCls.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&simple=1&uid=" + mmdbid;
+           url = me.htmlCls.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&buidx=" + me.cfg.buidx + "&simple=1&uid=" + mmdbid;
        }
 
        // use asymmetric unit for BLAST search, e.g., https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?from=blast&blast_rep_id=5XZC_B&query_id=1TUP_A&command=view+annotations;set+annotation+cdd;set+annotation+site;set+view+detailed+view;select+chain+5XZC_B;show+selection&log$=align&blast_rank=1&RID=EPUCYNVV014&buidx=0
@@ -24520,7 +24698,7 @@ class ChainalignParser {
         let  pos1 = alignArray[0].indexOf('_');
         ic.mmdbid_t = alignArray[0].substr(0, pos1).toUpperCase();
         ic.chain_t = alignArray[0].substr(pos1+1);
-        let  url_t = me.htmlCls.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&uid=" + ic.mmdbid_t;
+        let  url_t = me.htmlCls.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&buidx=" + me.cfg.buidx + "&uid=" + ic.mmdbid_t;
         if(me.cfg.inpara !== undefined) url_t += me.cfg.inpara;
 
         let  ajaxArray = [];
@@ -24546,7 +24724,7 @@ class ChainalignParser {
             let  chainalignFinal = ic.mmdbid_q + "_" + ic.chain_q + "," + ic.mmdbid_t + "_" + ic.chain_t;
 
             let  urlalign = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi?chainpairs=" + chainalignFinal;
-            let  url_q = me.htmlCls.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&uid=" + ic.mmdbid_q;
+            let  url_q = me.htmlCls.baseUrl + "mmdb/mmdb_strview.cgi?v=2&program=icn3d&b=1&s=1&ft=1&buidx=" + me.cfg.buidx + "&uid=" + ic.mmdbid_q;
 
             if(me.cfg.inpara !== undefined) url_q += me.cfg.inpara;
 
@@ -26615,18 +26793,30 @@ class LoadScript {
           me.cfg.mmcifid = id;
           ic.mmcifParserCls.downloadMmcif(id);
         }
-        else if(command.indexOf('load mmdb') !== -1) {
+        else if(command.indexOf('load mmdb') !== -1 || command.indexOf('load mmdb1') !== -1) {
           me.cfg.mmdbid = id;
+          me.cfg.buidx = 1;
 
           ic.mmdbParserCls.downloadMmdb(id);
         }
+        else if(command.indexOf('load mmdb0') !== -1) {
+            me.cfg.mmdbid = id;
+            me.cfg.buidx = 0;
+  
+            ic.mmdbParserCls.downloadMmdb(id);
+        }
         else if(command.indexOf('load gi') !== -1) {
           me.cfg.gi = id;
           ic.mmdbParserCls.downloadGi(id);
         }
-        else if(command.indexOf('load seq_struct_ids') !== -1) {
+        else if(command.indexOf('load seq_struct_ids ') !== -1) {
+          ic.bSmithwm = false;
           ic.mmdbParserCls.downloadBlast_rep_id(id);
         }
+        else if(command.indexOf('load seq_struct_ids_smithwm ') !== -1) {
+            ic.bSmithwm = true;
+            ic.mmdbParserCls.downloadBlast_rep_id(id);
+        }
         else if(command.indexOf('load cid') !== -1) {
           me.cfg.cid = id;
           ic.sdfParserCls.downloadCid(id);
@@ -27248,7 +27438,9 @@ class ShowSeq {
             }
         }
         giSeq = giSeqTmp;
-        let divLength = me.htmlCls.RESIDUE_WIDTH * ic.giSeq[chnid].length + 200;
+        //let divLength = me.htmlCls.RESIDUE_WIDTH * ic.giSeq[chnid].length + 200;
+        let divLength = me.htmlCls.RESIDUE_WIDTH * (ic.giSeq[chnid].length + ic.nTotalGap) + 200;
+
         let seqLength = ic.giSeq[chnid].length;
         if(seqLength > ic.maxAnnoLength) {
             ic.maxAnnoLength = seqLength;
@@ -27401,7 +27593,7 @@ class ShowSeq {
         html += '</div>'; // corresponds to above: html += '<div class="icn3d-dl_sequence">';
         html3 += '</div></div>';
         if(me.cfg.blast_rep_id === chnid) {
-            htmlTmp = '<div id="' + ic.pre + 'giseq_sequence" class="icn3d-dl_sequence" style="border: solid 1px #000;">';
+            htmlTmp = '<div id="' + ic.pre + 'giseq_sequence" class="icn3d-dl_sequence" style="border: solid 1px #000">';
         }
         else {
             htmlTmp = '<div id="' + ic.pre + 'giseq_sequence" class="icn3d-dl_sequence">';
@@ -28875,7 +29067,7 @@ class Analysis {
     //Display chain name in the 3D structure display for the chains intersecting with the atoms in "atomHash".
     addChainLabels(atoms) {var ic = this.icn3d, me = ic.icn3dui;
         let size = 18;
-        let background = "#CCCCCC";
+        let background = "#FFFFFF"; //"#CCCCCC";
         let atomsHash = me.hashUtilsCls.intHash(ic.hAtoms, atoms);
         if(ic.labels['chain'] === undefined) ic.labels['chain'] = [];
         let chainHash = ic.firstAtomObjCls.getChainsFromAtoms(atomsHash);
@@ -28888,8 +29080,8 @@ class Analysis {
             if(proteinName.length > 20) proteinName = proteinName.substr(0, 20) + '...';
             label.text = 'Chain ' + chainName + ': ' + proteinName;
             label.size = size;
-            let atomColorStr = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.chains[chainid]).color.getHexString().toUpperCase();
-            label.color =(atomColorStr === "CCCCCC" || atomColorStr === "C8C8C8") ? "#888888" : "#" + atomColorStr;
+            ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.chains[chainid]).color.getHexString().toUpperCase();
+            label.color = (ic.opts.background != 'black') ? ic.colorWhitebkgd : ic.colorBlackbkgd; //(atomColorStr === "CCCCCC" || atomColorStr === "C8C8C8") ? "#888888" : "#" + atomColorStr;
             label.background = background;
             ic.labels['chain'].push(label);
         }
@@ -28899,7 +29091,7 @@ class Analysis {
     //as "N-" and "C-". The termini of nucleotides are labeled as "5'" and "3'".
     addTerminiLabels(atoms) {var ic = this.icn3d, me = ic.icn3dui;
         let size = 18;
-        let background = "#CCCCCC";
+        let background = "#FFFFFF"; //"#CCCCCC";
         let protNucl;
         protNucl = me.hashUtilsCls.unionHash(protNucl, ic.proteins);
         protNucl = me.hashUtilsCls.unionHash(protNucl, ic.nucleotides);
@@ -28923,10 +29115,10 @@ class Analysis {
             }
             labelN.size = size;
             labelC.size = size;
-            let atomNColorStr = firstAtom.color.getHexString().toUpperCase();
-            let atomCColorStr = lastAtom.color.getHexString().toUpperCase();
-            labelN.color =(atomNColorStr === "CCCCCC" || atomNColorStr === "C8C8C8") ? "#888888" : "#" + atomNColorStr;
-            labelC.color =(atomCColorStr === "CCCCCC" || atomCColorStr === "C8C8C8") ? "#888888" : "#" + atomCColorStr;
+            firstAtom.color.getHexString().toUpperCase();
+            lastAtom.color.getHexString().toUpperCase();
+            labelN.color = (ic.opts.background != 'black') ? ic.colorWhitebkgd : ic.colorBlackbkgd; //(atomNColorStr === "CCCCCC" || atomNColorStr === "C8C8C8") ? "#888888" : "#" + atomNColorStr;
+            labelC.color = (ic.opts.background != 'black') ? ic.colorWhitebkgd : ic.colorBlackbkgd; //(atomCColorStr === "CCCCCC" || atomCColorStr === "C8C8C8") ? "#888888" : "#" + atomCColorStr;
             labelN.background = background;
             labelC.background = background;
             ic.labels['chain'].push(labelN);
@@ -28961,11 +29153,44 @@ class AnnoCddSite {
         // live search for AlphaFold structures
         //if(me.cfg.afid) {
 
-        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) {
+        // use precalculated CDD annotation if
+        if( (Object.keys(ic.structures).length == 1 && (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))
+            || (Object.keys(ic.structures).length == 2 && me.cfg.align) ) {
+            $.ajax({
+              url: url,
+              dataType: 'jsonp',
+              cache: true,
+              tryCount : 0,
+              retryLimit : 1,
+              success: function(data) {
+                thisClass.parseCddData([data], chnidArray);
+                if(ic.deferredAnnoCddSite !== undefined) ic.deferredAnnoCddSite.resolve();
+              },
+              error : function(xhr, textStatus, errorThrown ) {
+                this.tryCount++;
+                if(this.tryCount <= this.retryLimit) {
+                    //try again
+                    $.ajax(this);
+                    return;
+                }
+
+                thisClass.getNoCdd(chnidBaseArray);
+                if(ic.deferredAnnoCddSite !== undefined) ic.deferredAnnoCddSite.resolve();
+
+                return;
+              }
+            });
+        }
+        else {
           let ajaxArray = [];
 
           for(let i = 0, il = chnidArray.length; i < il; ++i) {
-               let seq = Array.isArray(ic.giSeq[chnidArray[i]]) ? ic.giSeq[chnidArray[i]].join('') : ic.giSeq[chnidArray[i]];
+               //let seq = Array.isArray(ic.giSeq[chnidArray[i]]) ? ic.giSeq[chnidArray[i]].join('') : ic.giSeq[chnidArray[i]];
+               let seq = Array.isArray(ic.giSeq[chnidArray[i]]) ? ic.giSeq[chnidArray[i]].join('').toUpperCase() : ic.giSeq[chnidArray[i]].toUpperCase();
+
+               // remove water molecules
+               seq = seq.replace(/O/g, '');
+
                //url = me.htmlCls.baseUrl + "cdannots/cdannots.fcgi?fmt&live=lcl&queries=" + ic.giSeq[chnidArray[0]].join('');
                url = me.htmlCls.baseUrl + "cdannots/cdannots.fcgi?fmt&live=lcl&queries=" + seq;
 
@@ -28992,32 +29217,6 @@ class AnnoCddSite {
               return;
           });
         }
-        else {
-            $.ajax({
-              url: url,
-              dataType: 'jsonp',
-              cache: true,
-              tryCount : 0,
-              retryLimit : 1,
-              success: function(data) {
-                thisClass.parseCddData([data], chnidArray);
-                if(ic.deferredAnnoCddSite !== undefined) ic.deferredAnnoCddSite.resolve();
-              },
-              error : function(xhr, textStatus, errorThrown ) {
-                this.tryCount++;
-                if(this.tryCount <= this.retryLimit) {
-                    //try again
-                    $.ajax(this);
-                    return;
-                }
-
-                thisClass.getNoCdd(chnidBaseArray);
-                if(ic.deferredAnnoCddSite !== undefined) ic.deferredAnnoCddSite.resolve();
-
-                return;
-              }
-            });
-        }
     }
 
     parseCddData(dataArray, chnidArray, bSeq) { let ic = this.icn3d, me = ic.icn3dui;
@@ -29508,7 +29707,7 @@ class Picking {
             let  text =(ic.pk == 1) ? atom.resn + atom.resi + '@' + atom.name : atom.resn + atom.resi;
             if(ic.structures !== undefined && Object.keys(ic.structures).length > 1) {
                 text = atom.structure + '_' + atom.chain + ' ' + text;
-                $("#" + ic.pre + "popup").css("width", "140px");
+                $("#" + ic.pre + "popup").css("width", "160px");
             }
             else {
                 $("#" + ic.pre + "popup").css("width", "80px");
@@ -29736,8 +29935,9 @@ class ApplyCommand {
       ic.bAddCommands = false;
 
       let  commandTransformation = commandStr.split('|||');
+      let commandTransformation2 = commandTransformation[0].split('%7C%7C%7C'); // sometimes encoded transformation is also included
 
-      let  commandOri = commandTransformation[0].replace(/\s+/g, ' ').trim();
+      let  commandOri = commandTransformation2[0].replace(/\s+/g, ' ').trim();
       let  command = commandOri.toLowerCase();
 
     // exact match =============
@@ -30333,15 +30533,18 @@ class ApplyCommand {
         let  value = command.substr(command.lastIndexOf(' ') + 1);
         ic.opts['background'] = value;
 
-        if(value == 'white' || value == 'grey') {
-            $("#" + ic.pre + "title").css("color", "black");
-            $("#" + ic.pre + "titlelink").css("color", "black");
+        if(value == 'black') {
+          $("#" + ic.pre + "title").css("color", me.htmlCls.GREYD);
+          $("#" + ic.pre + "titlelink").css("color", me.htmlCls.GREYD);
         }
         else {
-            $("#" + ic.pre + "title").css("color", me.htmlCls.GREYD);
-            $("#" + ic.pre + "titlelink").css("color", me.htmlCls.GREYD);
+          $("#" + ic.pre + "title").css("color", "black");
+          $("#" + ic.pre + "titlelink").css("color", "black");
         }
       }
+      else if(command.indexOf('set label color') == 0) {
+        ic.labelcolor = command.substr(command.lastIndexOf(' ') + 1);
+      }
       else if(commandOri.indexOf('set thickness') == 0) {
         let  paraArray = command.split(' | ');
 
@@ -30396,6 +30599,13 @@ class ApplyCommand {
 
         ic.drawCls.draw();
       }
+      else if(commandOri.indexOf('set membrane') == 0) {
+        let  pos = command.lastIndexOf(' ');
+
+        ic.bMembrane = parseInt(command.substr(pos + 1));
+
+        ic.drawCls.draw();
+      }
       else if(command.indexOf('set highlight color') == 0) {
            let  color = command.substr(20);
            if(color === 'yellow') {
@@ -32166,6 +32376,8 @@ class SetSeqAlign {
               ic.alnChainsAnTtl[chainid1][6].push("");
 
               let  alignIndex = 1;
+              if(!ic.chainsMapping[chainid1]) ic.chainsMapping[chainid1] = {};
+              if(!ic.chainsMapping[chainid2]) ic.chainsMapping[chainid2] = {};
               //for(let j = 0, jl = alignData.sseq.length; j < jl; ++j) {
               for(let j = start; j <= end; ++j) {
                   // 0: internal resi id, 1: pdb resi id, 2: resn, 3: aligned or not
@@ -32197,6 +32409,10 @@ class SetSeqAlign {
                           ic.nconsHash2[chainid2 + '_' + resi] = 1;
                       }
 
+                      // mapping, use the firstsequence as the reference structure
+                      ic.chainsMapping[chainid1][chainid1 + '_' + id2aligninfo[j].resi] = id2aligninfo[j].resn + id2aligninfo[j].resi;
+                      ic.chainsMapping[chainid2][chainid2 + '_' + resi] = id2aligninfo[j].resn + id2aligninfo[j].resi;
+
                       color2 = '#' + ic.showAnnoCls.getColorhexFromBlosum62(id2aligninfo[j].resn, resn);
 
                       // expensive and thus remove
@@ -32381,6 +32597,8 @@ class SetSeqAlign {
           if(ic.qt_start_end[chainIndex] === undefined) return;
 
           let  alignIndex = 1;
+          if(!ic.chainsMapping[chainid1]) ic.chainsMapping[chainid1] = {};
+          if(!ic.chainsMapping[chainid2]) ic.chainsMapping[chainid2] = {};
           for(let i = 0, il = ic.qt_start_end[chainIndex].length; i < il; ++i) {
               //var start1 = ic.qt_start_end[chainIndex][i].q_start - 1;
               //var start2 = ic.qt_start_end[chainIndex][i].t_start - 1;
@@ -32474,6 +32692,10 @@ class SetSeqAlign {
                       ic.nconsHash2[chainid2 + '_' + resi2] = 1;
                   }
 
+                  // mapping, use the firstsequence as the reference structure
+                  ic.chainsMapping[chainid1][chainid1 + '_' + resi1] = resn1 + resi1;
+                  ic.chainsMapping[chainid2][chainid2 + '_' + resi2] = resn1 + resi1;
+
                   color2 = '#' + ic.showAnnoCls.getColorhexFromBlosum62(resn1, resn2);
 
                   let  bFirstResi =(i === 0 && j === 0) ? true : false;
@@ -32523,6 +32745,8 @@ class SetSeqAlign {
     //      let  prevChainid1 = '', prevChainid2 = '', cnt1 = 0, cnt2 = 0;
 
           let  residuesHash = {};
+          if(!ic.chainsMapping[chainid_t]) ic.chainsMapping[chainid_t] = {};
+          if(!ic.chainsMapping[chainid]) ic.chainsMapping[chainid] = {};
 
           for(let i = 0, il = ic.realignResid[structure1].length; i < il; ++i) {
               let  resObject1 = ic.realignResid[structure1][i];
@@ -32549,6 +32773,11 @@ class SetSeqAlign {
               else {
                   color = "#0000FF";
               }
+
+              // mapping, use the firstsequence as the reference structure
+              ic.chainsMapping[chainid_t][chainid_t + '_' + resObject1.resi] = resObject1.resn + resObject1.resi;
+              ic.chainsMapping[chainid][chainid + '_' + resObject2.resi] = resObject1.resn + resObject1.resi;
+
               let  color2 = '#' + ic.showAnnoCls.getColorhexFromBlosum62(resObject1.resn, resObject2.resn);
 
               resObject1.color = color;
@@ -33433,13 +33662,16 @@ class MmcifParser {
        let  thisClass = this;
 
        let  url, dataType;
-
+/*
        if(me.utilsCls.isMac()) { // safari has a problem in getting data from https://files.rcsb.org/header/
            url = "https://files.rcsb.org/view/" + mmcifid + ".cif";
        }
        else {
            url = "https://files.rcsb.org/header/" + mmcifid + ".cif";
        }
+*/
+
+       url = "https://files.rcsb.org/header/" + mmcifid + ".cif";
 
        dataType = "text";
 
@@ -33564,7 +33796,7 @@ class MmcifParser {
                 if(type === 'mmtfid' && missingseq !== undefined) {
                     // adjust missing residues
                     let  maxMissingResi = 0, prevMissingChain = '';
-                    let  chainMissingResidueArray = {};
+                    //let  chainMissingResidueArray = {}
                     for(let i = 0, il = missingseq.length; i < il; ++i) {
 
                         let  resn = missingseq[i].resn;
@@ -33573,7 +33805,7 @@ class MmcifParser {
 
                         let  chainNum = mmcifid + '_' + chain;
 
-                        if(chainMissingResidueArray[chainNum] === undefined) chainMissingResidueArray[chainNum] = [];
+                        if(ic.chainMissingResidueArray[chainNum] === undefined) ic.chainMissingResidueArray[chainNum] = [];
                         let  resObject = {};
                         resObject.resi = resi;
                         resObject.name = me.utilsCls.residueName2Abbr(resn).toLowerCase();
@@ -33584,14 +33816,14 @@ class MmcifParser {
 
                         // not all listed residues are considered missing, e.g., PDB ID 4OR2, only the firts four residues are considered missing
                         if(!isNaN(resi) &&(prevMissingChain == '' ||(chain != prevMissingChain) ||(chain == prevMissingChain && resi > maxMissingResi)) ) {
-                            chainMissingResidueArray[chainNum].push(resObject);
+                            ic.chainMissingResidueArray[chainNum].push(resObject);
 
                             maxMissingResi = resi;
                             prevMissingChain = chain;
                         }
                     }
 
-                    ic.loadPDBCls.adjustSeq(chainMissingResidueArray);
+                    ic.loadPDBCls.adjustSeq(ic.chainMissingResidueArray);
                 }
 
                 if(ic.deferredSymmetry !== undefined) ic.deferredSymmetry.resolve();
@@ -33616,7 +33848,7 @@ class MmcifParser {
                       if(type === 'mmtfid' && data.missingseq !== undefined) {
                             // adjust missing residues
                             let  maxMissingResi = 0, prevMissingChain = '';
-                            let  chainMissingResidueArray = {};
+                            //let  chainMissingResidueArray = {}
                             for(let i = 0, il = data.missingseq.length; i < il; ++i) {
 
                                 let  resn = data.missingseq[i].resn;
@@ -33625,7 +33857,7 @@ class MmcifParser {
 
                                 let  chainNum = mmcifid + '_' + chain;
 
-                                if(chainMissingResidueArray[chainNum] === undefined) chainMissingResidueArray[chainNum] = [];
+                                if(ic.chainMissingResidueArray[chainNum] === undefined) ic.chainMissingResidueArray[chainNum] = [];
                                 let  resObject = {};
                                 resObject.resi = resi;
                                 resObject.name = me.utilsCls.residueName2Abbr(resn).toLowerCase();
@@ -33643,7 +33875,7 @@ class MmcifParser {
                                 }
                             }
 
-                            ic.loadPDBCls.adjustSeq(chainMissingResidueArray);
+                            ic.loadPDBCls.adjustSeq(ic.chainMissingResidueArray);
                       }
 
                       if(ic.deferredSymmetry !== undefined) ic.deferredSymmetry.resolve();
@@ -33839,8 +34071,16 @@ class HlSeq {
       .on('click', '.icn3d-seqTitle', function(e) { let ic = thisClass.icn3d;
           e.stopImmediatePropagation();
 
-          ic.bAlignSeq = false;
-          ic.bAnnotations = true;
+          //if($(this).attr('id') === ic.pre + "dl_sequence2") {
+          if($(this).parents('div').attr('id') === ic.pre + "dl_sequence2") {
+              ic.bAlignSeq = true;
+              ic.bAnnotations = false;
+          }
+          //else if($(this).attr('id') === ic.pre + "dl_annotations") {
+          else {
+              ic.bAlignSeq = false;
+              ic.bAnnotations = true;
+          }
 
           // select annotation title
           //$("div .ui-selected", this).each(function() {
@@ -33869,8 +34109,9 @@ class HlSeq {
 
       $("#" + ic.pre + "dl_sequence2").add("[id^=" + ic.pre + "giseq]").add("[id^=" + ic.pre + "custom]").add("[id^=" + ic.pre + "site]").add("[id^=" + ic.pre + "clinvar]").add("[id^=" + ic.pre + "snp]").add("[id^=" + ic.pre + "cdd]").add("[id^=" + ic.pre + "domain]").add("[id^=" + ic.pre + "interaction]").add("[id^=" + ic.pre + "ssbond]").add("[id^=" + ic.pre + "crosslink]").add("[id^=" + ic.pre + "transmem]").on('click', '.icn3d-residue', function(e) { let ic = thisClass.icn3d;
           e.stopImmediatePropagation();
-
-          if($(this).attr('id') === ic.pre + "dl_sequence2") {
+/*
+          //if($(this).attr('id') === ic.pre + "dl_sequence2") {
+          if($(this).parents('span').parents('div').attr('id') === ic.pre + "dl_sequence2") {
               ic.bAlignSeq = true;
               ic.bAnnotations = false;
           }
@@ -33879,7 +34120,7 @@ class HlSeq {
               ic.bAlignSeq = false;
               ic.bAnnotations = true;
           }
-
+*/
           // select residues
           //$("span.ui-selected", this).each(function() {
               let id = $(this).attr('id');
@@ -33918,7 +34159,8 @@ class HlSeq {
       $("#" + ic.pre + "dl_sequence2").add("[id^=" + ic.pre + "giseq]").add("[id^=" + ic.pre + "custom]").add("[id^=" + ic.pre + "site]").add("[id^=" + ic.pre + "feat]").add("[id^=" + ic.pre + "clinvar]").add("[id^=" + ic.pre + "snp]").add("[id^=" + ic.pre + "cdd]").add("[id^=" + ic.pre + "domain]").add("[id^=" + ic.pre + "interaction]").add("[id^=" + ic.pre + "ssbond]").add("[id^=" + ic.pre + "crosslink]").add("[id^=" + ic.pre + "transmem]").on('click', '.icn3d-seqTitle', function(e) { let ic = thisClass.icn3d;
           e.stopImmediatePropagation();
 
-          if($(this).attr('id') === ic.pre + "dl_sequence2") {
+          //if($(this).attr('id') === ic.pre + "dl_sequence2") {
+          if($(this).parents('div').attr('id') === ic.pre + "dl_sequence2") {
               ic.bAlignSeq = true;
               ic.bAnnotations = false;
           }
@@ -34115,7 +34357,7 @@ class HlSeq {
 
                         //var size = parseInt(ic.LABELSIZE * 10 / commandname.length);
                         let size = ic.LABELSIZE;
-                        let color = "FFFF00";
+                        let color = (ic.opts.background != 'black') ? ic.colorWhitebkgd : ic.colorBlackbkgd; //"FFFF00";
                         if(position !== undefined) ic.analysisCls.addLabel(commanddescr, position.center.x, position.center.y, position.center.z, size, color, undefined, 'custom');
 
                         ic.drawCls.draw();
@@ -34149,6 +34391,10 @@ class HlSeq {
     selectResidues(id, that) { let ic = this.icn3d, me = ic.icn3dui;
       if(me.bNode) return;
 
+      if(ic.bSelectResidue === false && !ic.bShift && !ic.bCtrl) {
+          ic.selectionCls.removeSelection();
+      }
+
       if(id !== undefined && id !== '') {
         // add "align_" in front of id so that full sequence and aligned sequence will not conflict
         //if(id.substr(0, 5) === 'align') id = id.substr(5);
@@ -34321,7 +34567,7 @@ class ShowAnno {
                    }
                }
             }
-            else if(me.cfg.blast_rep_id !== undefined) { // align sequence to structure
+            else if(me.cfg.blast_rep_id !== undefined && !ic.bSmithwm) { // align sequence to structure
                let url = me.htmlCls.baseUrl + 'pwaln/pwaln.fcgi?from=querytarget';
                let dataObj = {'targets': me.cfg.blast_rep_id, 'queries': me.cfg.query_id};
                if(me.cfg.query_from_to !== undefined ) {
@@ -34363,6 +34609,63 @@ class ShowAnno {
                   }
                 });
             } // align seq to structure
+            else if(me.cfg.blast_rep_id !== undefined && ic.bSmithwm) { // align sequence to structure
+                //{'targets': me.cfg.blast_rep_id, 'queries': me.cfg.query_id}
+                let idArray = [me.cfg.blast_rep_id];
+
+                let target, query;
+                if(me.cfg.query_id.indexOf('>') != -1) { //FASTA with header
+                    query = me.cfg.query_id.substr(me.cfg.query_id.indexOf('\n') + 1);
+                }
+                else if(!(/\d/.test(me.cfg.query_id)) || me.cfg.query_id.length > 50) { //FASTA
+                    query = me.cfg.query_id;
+                }
+                else { // accession
+                    idArray.push(me.cfg.query_id);
+                }
+
+                // show the sequence and 3D structure
+                //var url = "https://eme.utilsCls.ncbi.nlm.nih.gov/entrez/eUtilsCls/efetch.fcgi?db=protein&retmode=json&rettype=fasta&id=" + chnidBaseArray;
+                let url = me.htmlCls.baseUrl + "/vastdyn/vastdyn.cgi?chainlist=" + idArray;
+
+                $.ajax({
+                    url: url,
+                    dataType: 'jsonp', //'text',
+                    cache: true,
+                    tryCount : 0,
+                    retryLimit : 1,
+                    success: function(chainid_seq) {
+                        let index = 0;
+                        for(let acc in chainid_seq) {
+                            if(index == 0) {
+                                target = chainid_seq[acc];
+                            }
+                            else if(!query) {
+                                query = chainid_seq[acc];
+                            }
+
+                            ++index;
+                        }
+
+                        let match_score = 1, mismatch = -1, gap = -1, extension = -1;
+                        ic.seqStructAlignDataSmithwm = ic.alignSWCls.alignSW(target, query, match_score, mismatch, gap, extension);
+
+                        thisClass.showAnnoSeqData(nucleotide_chainid, chemical_chainid, chemical_set);
+                    },
+                    error : function(xhr, textStatus, errorThrown ) {
+                        this.tryCount++;
+                        if(this.tryCount <= this.retryLimit) {
+                            //try again
+                            $.ajax(this);
+                            return;
+                        }
+
+                        var aaa = 1; //alert("Can not retrieve the sequence of the accession(s) " + idArray.join(", "));
+
+                        return;
+                    }
+                });
+             } // align seq to structure
         }
         ic.bAnnoShown = true;
     }
@@ -34458,7 +34761,7 @@ class ShowAnno {
                     $.ajax(this);
                     return;
                 }
-                this.enableHlSeq();
+                thisClass.enableHlSeq();
                 console.log( "No data were found for the protein " + chnidBaseArray + "..." );
                 for(let chnid in ic.protein_chainid) {
                     let chnidBase = ic.protein_chainid[chnid];
@@ -34590,7 +34893,7 @@ class ShowAnno {
             if(me.cfg.blast_rep_id != chnid) {
                 ic.showSeqCls.showSeq(chnid, chnidBase);
             }
-            else if(me.cfg.blast_rep_id == chnid && ic.seqStructAlignData.data === undefined) {
+            else if(me.cfg.blast_rep_id == chnid && ic.seqStructAlignData === undefined && ic.seqStructAlignDataSmithwm === undefined) {
               let title;
               if(me.cfg.query_id.length > 14) {
                   title = 'Query: ' + me.cfg.query_id.substr(0, 6) + '...';
@@ -34606,7 +34909,7 @@ class ShowAnno {
               var aaa = 1; //alert('The sequence can NOT be aligned to the structure');
               ic.showSeqCls.showSeq(chnid, chnidBase, undefined, title, compTitle, text, compText);
             }
-            else if(me.cfg.blast_rep_id == chnid && ic.seqStructAlignData.data !== undefined) { // align sequence to structure
+            else if(me.cfg.blast_rep_id == chnid && (ic.seqStructAlignData !== undefined || ic.seqStructAlignDataSmithwm !== undefined) ) { // align sequence to structure
               //var title = 'Query: ' + me.cfg.query_id.substr(0, 6);
               let title;
               if(me.cfg.query_id.length > 14) {
@@ -34615,27 +34918,72 @@ class ShowAnno {
               else {
                   title =(isNaN(me.cfg.query_id)) ? 'Query: ' + me.cfg.query_id : 'Query: gi ' + me.cfg.query_id;
               }
-              let data = ic.seqStructAlignData;
 
-              let query, target;
-              if(data.data !== undefined) {
-                  query = data.data[0].query;
-                  //target = data.data[0].targets[chnid.replace(/_/g, '')];
-                  target = data.data[0].targets[chnid];
-                  target =(target !== undefined && target.hsps.length > 0) ? target.hsps[0] : undefined;
+              
+              let evalue, targetSeq, querySeq, segArray;
+
+              if(ic.seqStructAlignData !== undefined) {
+                let query, target;
+                let data = ic.seqStructAlignData;
+                if(data.data !== undefined) {
+                    query = data.data[0].query;
+                    //target = data.data[0].targets[chnid.replace(/_/g, '')];
+                    target = data.data[0].targets[chnid];
+                    target =(target !== undefined && target.hsps.length > 0) ? target.hsps[0] : undefined;
+                }
+
+                if(query !== undefined && target !== undefined) {
+                    evalue = target.scores.e_value.toPrecision(2);
+                    if(evalue > 1e-200) evalue = parseFloat(evalue).toExponential();
+                    target.scores.bit_score;
+                    //var targetSeq = data.targets[chnid.replace(/_/g, '')].seqdata;
+                    targetSeq = data.targets[chnid].seqdata;
+                    querySeq = query.seqdata;
+                    segArray = target.segs;
+                }               
+              }
+              else { // mimic the output of the cgi pwaln.fcgi
+                let data = ic.seqStructAlignDataSmithwm;
+                evalue = data.score;
+                targetSeq = data.target.replace(/-/g, '');
+                querySeq = data.query.replace(/-/g, '');
+                segArray = [];
+                // target, 0-based: orifrom, orito
+                // query, 0-based: from, to
+
+                let targetCnt = -1, queryCnt = -1;
+                let bAlign = false, seg = {};
+                for(let i = 0, il = data.target.length; i < il; ++i) {
+                    if(data.target[i] != '-')  ++targetCnt;
+                    if(data.query[i] != '-')  ++queryCnt;
+                    if(!bAlign && data.target[i] != '-' && data.query[i] != '-') {
+                        bAlign = true;
+                        seg.orifrom = targetCnt;
+                        seg.from = queryCnt;
+                    }
+                    else if(bAlign && (data.target[i] == '-' || data.query[i] == '-') ) {
+                        bAlign = false;
+                        seg.orito = (data.target[i] == '-') ? targetCnt : targetCnt - 1;
+                        seg.to = (data.query[i] == '-') ? queryCnt : queryCnt - 1;
+                        segArray.push(seg);
+                        seg = {};
+                    }
+                }
+
+                // end condition
+                if(data.target[data.target.length - 1] != '-' && data.query[data.target.length - 1] != '-') {
+                    seg.orito = targetCnt;
+                    seg.to = queryCnt;
+
+                    segArray.push(seg);
+                }
               }
+
               let text = '', compText = '';
               ic.queryStart = '';
               ic.queryEnd = '';
-              let evalue;
-              if(query !== undefined && target !== undefined) {
-                  evalue = target.scores.e_value.toPrecision(2);
-                  if(evalue > 1e-200) evalue = parseFloat(evalue).toExponential();
-                  target.scores.bit_score;
-                  //var targetSeq = data.targets[chnid.replace(/_/g, '')].seqdata;
-                  let targetSeq = data.targets[chnid].seqdata;
-                  let querySeq = query.seqdata;
-                  let segArray = target.segs;
+              
+              if(segArray !== undefined) {
                   let target2queryHash = {};
                   if(ic.targetGapHash === undefined) ic.targetGapHash = {};
                   ic.fullpos2ConsTargetpos = {};
@@ -34663,6 +35011,7 @@ class ShowAnno {
                       prevTargetTo = seg.orito;
                       prevQueryTo = seg.to;
                   }
+
                   // the missing residues at the end of the seq will be filled up in the API showNewTrack()
                   let nGap = 0;
                   ic.alnChainsSeq[chnid] = [];
@@ -34703,13 +35052,14 @@ class ShowAnno {
                           compText += ' ';
                       }
                   }
+
                   //title += ', E: ' + evalue;
               }
               else {
                   text += "cannot be aligned";
                   var aaa = 1; //alert('The sequence can NOT be aligned to the structure');
               }
-              let compTitle = 'BLAST, E: ' + evalue;
+              let compTitle = (ic.seqStructAlignData !== undefined) ? 'BLAST, E: ' + evalue : 'Score: ' + evalue;
               ic.showSeqCls.showSeq(chnid, chnidBase, undefined, title, compTitle, text, compText);
               let residueidHash = {};
               let residueid;
@@ -35101,7 +35451,7 @@ class AnnoDomain {
                 }
                 ic.showAnnoCls.enableHlSeq();
                 ic.bAjax3ddomain = true;
-                bAjaxDone1 = true;
+                //bAjaxDone1 = true;
                 if(ic.deferred3ddomain !== undefined) {
                     if(me.cfg.align === undefined || me.cfg.chainalign === undefined) {
                         ic.deferred3ddomain.resolve();
@@ -35314,7 +35664,7 @@ class AnnoSnpClinVar {
           ic.labels['clinvar'] = [];
           //var size = Math.round(ic.LABELSIZE * 10 / label.length);
           let size = ic.LABELSIZE;
-          let color = "#FFFF00";
+          let color = (ic.opts.background != 'black') ? ic.colorWhitebkgd : ic.colorBlackbkgd; //"#FFFF00";
           ic.analysisCls.addLabel(label, position.center.x + 1, position.center.y + 1, position.center.z + 1, size, color, undefined, 'clinvar');
           ic.hAtoms = {};
           for(let j in ic.residues[residueid]) {
@@ -37595,23 +37945,25 @@ class HlUpdate {
         $("#" + ic.pre + "atomsCustom")[0].blur();
     }
 
+    //Update the highlight of 3D structure, 2D interaction, sequences, and the menu of defined sets
+    //according to the current highlighted atoms.
     updateHlAll(commandnameArray, bSetMenu, bUnion, bForceHighlight) { let ic = this.icn3d, me = ic.icn3dui;
-           // update the previously highlisghted atoms for switching between all and selection
-           ic.prevHighlightAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
+       // update the previously highlisghted atoms for switching between all and selection
+       ic.prevHighlightAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
 
-           this.updateHlObjects(bForceHighlight);
+       this.updateHlObjects(bForceHighlight);
 
-           if(commandnameArray !== undefined) {
-               this.updateHlSeqInChain(commandnameArray, bUnion);
-           }
-           else {
-               this.updateHlSeq(undefined, undefined, bUnion);
-           }
+       if(commandnameArray !== undefined) {
+           this.updateHlSeqInChain(commandnameArray, bUnion);
+       }
+       else {
+           this.updateHlSeq(undefined, undefined, bUnion);
+       }
 
-           this.updateHl2D();
-           if(bSetMenu === undefined || bSetMenu) this.updateHlMenus(commandnameArray);
+       this.updateHl2D();
+       if(bSetMenu === undefined || bSetMenu) this.updateHlMenus(commandnameArray);
 
-           //ic.annotationCls.showAnnoSelectedChains();
+       //ic.annotationCls.showAnnoSelectedChains();
     }
 
     //Update the highlight of 3D structure display according to the current highlighted atoms.
@@ -37915,27 +38267,6 @@ class HlUpdate {
           $( this ).removeClass('icn3d-highlightSeq');
         });
     }
-
-    //Update the highlight of 3D structure, 2D interaction, sequences, and the menu of defined sets
-    //according to the current highlighted atoms.
-    updateHlAll(commandnameArray, bSetMenu, bUnion, bForceHighlight) { let ic = this.icn3d, me = ic.icn3dui;
-       // update the previously highlisghted atoms for switching between all and selection
-       ic.prevHighlightAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
-
-       this.updateHlObjects(bForceHighlight);
-
-       if(commandnameArray !== undefined) {
-           this.updateHlSeqInChain(commandnameArray, bUnion);
-       }
-       else {
-           this.updateHlSeq(undefined, undefined, bUnion);
-       }
-
-       this.updateHl2D();
-       if(bSetMenu === undefined || bSetMenu) this.updateHlMenus(commandnameArray);
-
-       //ic.annotationCls.showAnnoSelectedChains();
-    }
 }
 
 /**
@@ -38235,9 +38566,12 @@ class Selection {
           ic.graphStr = this.getGraphDataForDisplayed();
         }
 
+        // don not redraw graphs after the selection changes
+        /*
         if(ic.bGraph) ic.drawGraphCls.drawGraph(ic.graphStr, ic.pre + 'dl_graph');
         if(ic.bLinegraph) ic.lineGraphCls.drawLineGraph(ic.graphStr);
         if(ic.bScatterplot) ic.lineGraphCls.drawLineGraph(ic.graphStr, true);
+        */
     }
 
     hideSelection() { let  ic = this.icn3d, me = ic.icn3dui;
@@ -38318,6 +38652,9 @@ class Selection {
 
         ic.loadScriptCls.renderFinalStep(1);
         ic.definedSetsCls.setMode('all');
+
+        ic.selectionCls.selectAll();
+
         me.htmlCls.clickMenuCls.setLogCmd("reset", true);
 
         ic.hlUpdateCls.removeSeqChainBkgd();
@@ -38441,7 +38778,7 @@ class Selection {
         ic.drawCls.draw();
     }
 
-    toggleMembrane() {var ic = this.icn3d, me = ic.icn3dui;
+    toggleMembrane(bShowMembrane) {var ic = this.icn3d, me = ic.icn3dui;
         let  structureArray = Object.keys(ic.structures);
 
         for(let i = 0, il = structureArray.length; i < il; ++i) {
@@ -38456,6 +38793,7 @@ class Selection {
                 ic.dAtoms = me.hashUtilsCls.unionHash(ic.dAtoms, atomsHash);
                 oriStyle = 'nothing';
             }
+
             for(let j in atomsHash) {
                 let  atom = ic.atoms[j];
                 if(oriStyle !== 'nothing') {
@@ -38464,10 +38802,14 @@ class Selection {
                 else {
                     atom.style = 'stick';
                 }
+
+                if(bShowMembrane !== undefined) {
+                    atom.style = (bShowMembrane) ? 'stick' : 'nothing';
+                }
             }
         }
 
-        ic.drawCls.draw();
+        if(bShowMembrane === undefined) ic.drawCls.draw();
     }
 
     adjustMembrane(extra_mem_z, intra_mem_z) {var ic = this.icn3d; ic.icn3dui;
@@ -38758,7 +39100,8 @@ class SetStyle {
     setBackground(color) {var ic = this.icn3d, me = ic.icn3dui;
        ic.setOptionCls.setOption('background', color);
        me.htmlCls.clickMenuCls.setLogCmd('set background ' + color, true);
-       let titleColor =(color == 'black' || color == 'transparent') ? me.htmlCls.GREYD : 'black';
+       //let titleColor =(color == 'black' || color == 'transparent') ? me.htmlCls.GREYD : 'black';
+       let titleColor = (color == 'black') ? me.htmlCls.GREYD : 'black';
        $("#" + ic.pre + "title").css("color", titleColor);
        $("#" + ic.pre + "titlelink").css("color", titleColor);
     }
@@ -39281,10 +39624,11 @@ class TextSprite {
 
         let a = parameters.hasOwnProperty("alpha") ? parameters["alpha"] : 1.0;
 
-        let bBkgd = true;
+        let bBkgd = false; //true;
         let bSchematic = false;
         if(parameters.hasOwnProperty("bSchematic") &&  parameters["bSchematic"]) {
             bSchematic = true;
+            bBkgd = true;
 
             fontsize = 40;
         }
@@ -39304,9 +39648,13 @@ class TextSprite {
         }
 
         let textAlpha = 1.0;
-
-        let textColor = parameters.hasOwnProperty("textColor") &&  parameters["textColor"] !== undefined ? me.utilsCls.hexToRgb(parameters["textColor"], textAlpha) : { r:255, g:255, b:0, a:1.0 };
-        if(!textColor) textColor = { r:255, g:255, b:0, a:1.0 };
+        // default yellow
+        //let textColor = parameters.hasOwnProperty("textColor") &&  parameters["textColor"] !== undefined ? me.utilsCls.hexToRgb(parameters["textColor"], textAlpha) : { r:255, g:255, b:0, a:1.0 };
+        // default black or white
+        let defaultColor = (ic.opts.background != 'black') ? { r:0, g:0, b:0, a:1.0 } : { r:255, g:255, b:0, a:1.0 };
+        let textColor = parameters.hasOwnProperty("textColor") &&  parameters["textColor"] !== undefined ? me.utilsCls.hexToRgb(parameters["textColor"], textAlpha) 
+            : defaultColor;
+        if(!textColor) textColor = defaultColor;
 
         let canvas = document.createElement('canvas');
 
@@ -39443,6 +39791,7 @@ class Label {
 
         for(let name in labels) {
             let labelArray = (labels[name] !== undefined) ? labels[name] : [];
+            let defaultColor = (ic.opts.background != 'black') ? ic.colorWhitebkgd : ic.colorBlackbkgd;
 
             for (let i = 0, il = labelArray.length; i < il; ++i) {
                 let label = labelArray[i];
@@ -39453,7 +39802,9 @@ class Label {
                 if(label.background == 0) label.background = undefined;
 
                 let labelsize = (label.size !== undefined) ? label.size : ic.LABELSIZE;
-                let labelcolor = (label.color !== undefined) ? label.color : '#ffff00';
+                let labelcolor = (label.color !== undefined) ? label.color : defaultColor;
+                if(ic.labelcolor) labelcolor = ic.labelcolor;
+                
                 let labelbackground = (label.background !== undefined) ? label.background : '#cccccc';
                 let labelalpha = (label.alpha !== undefined) ? label.alpha : 1.0;
 
@@ -39479,7 +39830,8 @@ class Label {
                     }
                 }
 
-                bb.position.set(label.position.x, label.position.y, label.position.z);
+                let labelOffset = (name == 'schematic' || name == 'residue') ? 0 : ic.coilWidth; // 0.3
+                bb.position.set(label.position.x + labelOffset, label.position.y + labelOffset, label.position.z + labelOffset);
                 ic.mdl.add(bb);
                 // do not add labels to objects for pk
             }
@@ -39654,49 +40006,68 @@ class ApplyDisplay {
             atomsObj = {};
         } // end if(bHighlight === 1)
 
-        ic.setStyleCls.setStyle2Atoms(atoms);
+        if(ic.bInitial) {
+            if(me.htmlCls.setHtmlCls.getCookie('membrane') != '') {
+                let bMembrane = parseInt(me.htmlCls.setHtmlCls.getCookie('membrane'));
 
-        //ic.bAllAtoms = (Object.keys(atoms).length === Object.keys(ic.atoms).length);
-        ic.bAllAtoms = false;
-        if(atoms && atoms !== undefined ) {
-            ic.bAllAtoms = (Object.keys(atoms).length === Object.keys(ic.atoms).length);
+                if(ic.bMembrane != bMembrane) {
+                    me.htmlCls.clickMenuCls.setLogCmd('set membrane ' + bMembrane, true);
+                }
+
+                ic.bMembrane = (!isNaN(bMembrane)) ? parseInt(bMembrane) : 0;
+            }
+
+            // show membrane
+            if(ic.bMembrane) {
+                ic.selectionCls.toggleMembrane(true);
+            }
+            else {
+                ic.selectionCls.toggleMembrane(false);
+            }
         }
 
+        ic.setStyleCls.setStyle2Atoms(atoms);
+
+        //ic.bAllAtoms = false;
+        //if(atoms && atoms !== undefined ) {
+        //    ic.bAllAtoms = (Object.keys(atoms).length === Object.keys(ic.atoms).length);
+        //}
+
         let chemicalSchematicRadius = ic.cylinderRadius * 0.5;
 
         // remove schematic labels
         //if(ic.labels !== undefined) ic.labels['schematic'] = undefined;
         if(ic.labels !== undefined) delete ic.labels['schematic'];
-
-        let bOnlySideChains = false;
-
+/*
         if(bHighlight) {
-            let residueHashCalpha = ic.firstAtomObjCls.getResiduesFromCalphaAtoms(ic.hAtoms);
+            //let residueHashCalpha = ic.firstAtomObjCls.getResiduesFromCalphaAtoms(ic.hAtoms);
 
             let proteinAtoms = me.hashUtilsCls.intHash(ic.hAtoms, ic.proteins);
+
             let residueHash = ic.firstAtomObjCls.getResiduesFromAtoms(proteinAtoms);
+            let residueHashCalpha = ic.firstAtomObjCls.getResiduesFromCalphaAtoms(proteinAtoms);
 
-            if(Object.keys(residueHash) > Object.keys(residueHashCalpha)) { // some residues have only side chains
+            if(Object.keys(residueHash).length > Object.keys(residueHashCalpha).length) { // some residues have only side chains
                 bOnlySideChains = true;
             }
         }
-
+*/
         for(let style in ic.style2atoms) {
           // 14 styles: ribbon, strand, cylinder and plate, nucleotide cartoon, o3 trace, schematic, c alpha trace, b factor tube, lines, stick, ball and stick, sphere, dot, nothing
           let atomHash = ic.style2atoms[style];
           //var bPhosphorusOnly = me.utilsCls.isCalphaPhosOnly(me.hashUtilsCls.hash2Atoms(atomHash), "O3'", "O3*") || me.utilsCls.isCalphaPhosOnly(me.hashUtilsCls.hash2Atoms(atomHash), "P");
           let bPhosphorusOnly = me.utilsCls.isCalphaPhosOnly(me.hashUtilsCls.hash2Atoms(atomHash, ic.atoms));
 
-          //if(style === 'ribbon') {
-          if(style === 'ribbon' && (!bHighlight || (bHighlight && !bOnlySideChains))) {
+          if(style === 'ribbon') {
+          //if(style === 'ribbon' && (!bHighlight || (bHighlight && !bOnlySideChains))) {
               ic.strandCls.createStrand(me.hashUtilsCls.hash2Atoms(atomHash, ic.atoms), 2, undefined, true, undefined, undefined, false, ic.ribbonthickness, bHighlight);
           }
-          //else if(style === 'strand') {
-          else if(style === 'strand' && (!bHighlight || (bHighlight && !bOnlySideChains))) {
+          else if(style === 'strand') {
+          //else if(style === 'strand' && (!bHighlight || (bHighlight && !bOnlySideChains))) {
               ic.strandCls.createStrand(me.hashUtilsCls.hash2Atoms(atomHash, ic.atoms), null, null, null, null, null, false, undefined, bHighlight);
           }
-          //else if(style === 'cylinder and plate') {
-          else if(style === 'cylinder and plate' && (!bHighlight || (bHighlight && !bOnlySideChains))) {
+          else if(style === 'cylinder and plate') {
+          //else if(style === 'cylinder and plate' && (!bHighlight || (bHighlight && !bOnlySideChains))) {
             ic.cylinderCls.createCylinderHelix(me.hashUtilsCls.hash2Atoms(atomHash, ic.atoms), ic.cylinderHelixRadius, bHighlight);
           }
           else if(style === 'nucleotide cartoon') {
@@ -39787,11 +40158,30 @@ class ApplyDisplay {
         if(ic.labels !== undefined && Object.keys(ic.labels).length > 0) {
             ic.labelCls.hideLabels();
 
+            // change label color
+            for(let labeltype in ic.labels) {
+                if(labeltype != 'schematic') this.changeLabelColor(ic.labels[labeltype]);
+            }
+
             // labels
             ic.labelCls.createLabelRepresentation(ic.labels);
         }
     }
 
+    changeLabelColor(labelArray) { let ic = this.icn3d; ic.icn3dui;
+        if(labelArray) {
+            for(let i = 0, il = labelArray.length; i < il; ++i) {
+                let label = labelArray[i];
+                if((ic.opts.background != 'black') && label.color == ic.colorBlackbkgd) {
+                    label.color = ic.colorWhitebkgd;
+                }
+                else if((ic.opts.background == 'black') && label.color == ic.colorWhitebkgd) {
+                    label.color = ic.colorBlackbkgd;
+                }
+            }
+        }
+    }
+
     selectMainChainSubset(atoms) { let ic = this.icn3d; ic.icn3dui;
         let nuclMainArray = ["C1'", "C1*", "C2'", "C2*", "C3'", "C3*", "C4'", "C4*", "C5'", "C5*", "O3'", "O3*", "O4'", "O4*", "O5'", "O5*", "P", "OP1", "O1P", "OP2", "O2P"];
 
@@ -40259,14 +40649,16 @@ class ApplyOther {
             }
         }
 
-        if(me.htmlCls.setHtmlCls.getCookie('glycan') != '') {
-            let bGlycansCartoon = parseInt(me.htmlCls.setHtmlCls.getCookie('glycan'));
+        if(ic.bInitial) {
+            if(me.htmlCls.setHtmlCls.getCookie('glycan') != '') {
+                let bGlycansCartoon = parseInt(me.htmlCls.setHtmlCls.getCookie('glycan'));
 
-            if(ic.bGlycansCartoon != bGlycansCartoon) {
-                me.htmlCls.clickMenuCls.setLogCmd('set glycan ' + bGlycansCartoon, true);
-            }
+                if(ic.bGlycansCartoon != bGlycansCartoon) {
+                    me.htmlCls.clickMenuCls.setLogCmd('set glycan ' + bGlycansCartoon, true);
+                }
 
-            ic.bGlycansCartoon = bGlycansCartoon;
+                ic.bGlycansCartoon = bGlycansCartoon;
+            }
         }
 
         // add cartoon for glycans
@@ -41497,7 +41889,6 @@ class Instancing {
        let mdlImpostorTmp = new THREE.Object3D();
        let mdl_ghostTmp = new THREE.Object3D();
 
-console.log("no instancing, Object.keys(ic.structures).length: " + Object.keys(ic.structures).length);
 //       for (let i = 0; i < ic.biomtMatrices.length; i++) {  // skip itself
        for (let i = 0; i < ic.biomtMatrices.length && Object.keys(ic.structures).length == 1; i++) {  // skip itself
           let mat = ic.biomtMatrices[i];
@@ -41895,7 +42286,6 @@ console.log("no instancing, Object.keys(ic.structures).length: " + Object.keys(i
            let identity = new THREE.Matrix4();
            identity.identity();
 
-console.log("instancing, Object.keys(ic.structures).length: " + Object.keys(ic.structures).length);
            for (let i = 0; i < ic.biomtMatrices.length && Object.keys(ic.structures).length == 1; i++) {  // skip itself
               let mat = ic.biomtMatrices[i];
               if (mat === undefined) continue;
@@ -42055,7 +42445,9 @@ class Draw {
 //        ic.renderer.gammaOutput = true
 
         ic.renderer.setPixelRatio( window.devicePixelRatio ); // r71
-        if(ic.scene) ic.renderer.render(ic.scene, cam);
+        if(ic.scene) {
+            ic.renderer.render(ic.scene, cam);
+        }
     }
 
 }
@@ -42579,7 +42971,7 @@ class SaveFile {
         };
     }
 
-    exportCustomAtoms() {var ic = this.icn3d; ic.icn3dui;
+    exportCustomAtoms(bDetails) {var ic = this.icn3d; ic.icn3dui;
        let html = "";
        let nameArray =(ic.defNames2Residues !== undefined) ? Object.keys(ic.defNames2Residues).sort() : [];
        for(let i = 0, il = nameArray.length; i < il; ++i) {
@@ -42588,9 +42980,8 @@ class SaveFile {
          ic.defNames2Descr[name];
          let command = ic.defNames2Command[name];
          command = command.replace(/,/g, ', ');
-         html += name + "\tselect ";
-         html += ic.resid2specCls.residueids2spec(residueArray);
-         html += "\n";
+
+         html += this.exportResidues(name, residueArray, bDetails);
        } // outer for
        nameArray =(ic.defNames2Atoms !== undefined) ? Object.keys(ic.defNames2Atoms).sort() : [];
        for(let i = 0, il = nameArray.length; i < il; ++i) {
@@ -42600,15 +42991,51 @@ class SaveFile {
          let command = ic.defNames2Command[name];
          command = command.replace(/,/g, ', ');
          let residueArray = ic.resid2specCls.atoms2residues(atomArray);
-         if(residueArray.length > 0) {
-             html += name + "\tselect ";
-             html += ic.resid2specCls.residueids2spec(residueArray);
-             html += "\n";
-         }
+
+         html += this.exportResidues(name, residueArray, bDetails);
        } // outer for
        return html;
     }
 
+    exportResidues(name, residueArray, bDetails) {var ic = this.icn3d, me = ic.icn3dui;
+         let html = '';
+
+         if(residueArray.length > 0) {
+             if(bDetails) {
+                 let chainidHash = {};
+                 for(let i = 0, il = residueArray.length; i < il; ++i) {
+                     let resid = residueArray[i];
+                     let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
+                     let chainid = atom.structure + '_' + atom.chain;
+                     let resnAbbr = me.utilsCls.residueName2Abbr(atom.resn);
+                     let resName = resnAbbr + atom.resi;
+
+                     if(!chainidHash.hasOwnProperty(chainid)) {
+                         chainidHash[chainid] = [];
+                     }
+
+                     chainidHash[chainid].push(resName);
+                 }
+
+                 html += name + ":\n";
+                 for(let chainid in chainidHash) {
+                     let resStr = (chainidHash[chainid].length == 1) ? "residue" : "residues";
+                     html += chainid + " (" + chainidHash[chainid].length + " " + resStr + "): ";
+                     html += chainidHash[chainid].join(", ");
+                     html += "\n";
+                 }
+                 html += "\n";
+             }
+             else {
+                 html += name + "\tselect ";
+                 html += ic.resid2specCls.residueids2spec(residueArray);
+                 html += "\n";
+             }
+         }
+
+         return html;
+    }
+
     //getAtomPDB: function(atomHash, bPqr, bPdb, bNoChem) { let ic = this.icn3d, me = ic.icn3dui;
     getAtomPDB(atomHash, bPqr, bNoChem, bNoHeader) { let ic = this.icn3d, me = ic.icn3dui;
         let pdbStr = '';
@@ -42700,37 +43127,53 @@ class SaveFile {
             }
         }
 
+ /*
         // get missing residues
-        let chainid2missingResi = {};
+        let ic.chainMissingResidueArray = {};
         for(let chainid in ic.chainsSeq) {
             let pos = chainid.indexOf('_');
-            chainid.substr(0, pos);
+            let chain = chainid.substr(0, pos);
 
             for(let i = 0, il = ic.chainsSeq[chainid].length; i < il; ++i) {
                 let resi = ic.chainsSeq[chainid][i].resi;
                 let resid = chainid + '_' + resi;
                 if(!ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid])) { // mising coordinate
-                    if(chainid2missingResi[chainid] === undefined) chainid2missingResi[chainid] = [];
+                    if(ic.chainMissingResidueArray[chainid] === undefined) ic.chainMissingResidueArray[chainid] = [];
                     let seq = me.utilsCls.residueAbbr2Name(ic.chainsSeq[chainid][i].name);
                     let resiObj = {'resi': resi, 'seq': seq};
-                    chainid2missingResi[chainid].push(resiObj);
+                    ic.chainMissingResidueArray[chainid].push(resiObj);
                 }
             }
         }
 
         // add missing residues "REMARK 465..."
-        for(let chainid in chainid2missingResi) {
+        for(let chainid in ic.chainMissingResidueArray) {
             let pos = chainid.indexOf('_');
             let chain = chainid.substr(pos + 1, 2);
             let stru = chainid.substr(0, pos);
 
-            for(let i = 0, il = chainid2missingResi[chainid].length; i < il; ++i) {
-                let resi = chainid2missingResi[chainid][i].resi;
-                let seq = chainid2missingResi[chainid][i].seq;
+            for(let i = 0, il = ic.chainMissingResidueArray[chainid].length; i < il; ++i) {
+                let resi = ic.chainMissingResidueArray[chainid][i].resi;
+                let seq = ic.chainMissingResidueArray[chainid][i].seq;
 
                 stru2header[stru] += "REMARK 465     " + seq.padStart(3, " ") + chain.padStart(2, " ") + " " + resi.toString().padStart(5, " ") + "\n";
             }
         }
+*/
+
+        // add missing residues "REMARK 465..."
+        for(let chainid in ic.chainMissingResidueArray) {
+            let pos = chainid.indexOf('_');
+            let chain = chainid.substr(pos + 1, 2);
+            let stru = chainid.substr(0, pos);
+
+            for(let i = 0, il = ic.chainMissingResidueArray[chainid].length; i < il; ++i) {
+                let resi = ic.chainMissingResidueArray[chainid][i].resi;
+                let resn = me.utilsCls.residueAbbr2Name(ic.chainMissingResidueArray[chainid][i].name);
+
+                stru2header[stru] += "REMARK 465     " + resn.padStart(3, " ") + chain.padStart(2, " ") + " " + resi.toString().padStart(5, " ") + "\n";
+            }
+        }
 
         let connStr = '';
         let struArray = Object.keys(ic.structures);
@@ -43009,7 +43452,7 @@ class SaveFile {
         if(ic.molTitle !== undefined && ic.molTitle !== '') {
             let title = ic.molTitle;
 
-            let titlelinkColor =(ic.opts['background'] == 'white' || ic.opts['background'] == 'grey') ? 'black' : me.htmlCls.GREYD;
+            let titlelinkColor =(ic.opts['background'] == 'black') ?  me.htmlCls.GREYD : 'black';
 
             if(ic.inputid === undefined) {
                 if(ic.molTitle.length > 40) title = ic.molTitle.substr(0, 40) + "...";
@@ -43456,6 +43899,21 @@ class ClickMenu {
            let file_pref =(ic.inputid) ? ic.inputid : "custom";
            ic.saveFileCls.saveFile(file_pref + '_selections.txt', 'text', [text]);
         });
+
+        me.myEventCls.onIds("#" + me.pre + "mn1_exportSelDetails", "click", function(e) { let ic = me.icn3d;
+           thisClass.setLogCmd("export all selections with details", false);
+          if(ic.bSetChainsAdvancedMenu === undefined || !ic.bSetChainsAdvancedMenu) {
+               let prevHAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
+               ic.definedSetsCls.setPredefinedInMenu();
+               ic.bSetChainsAdvancedMenu = true;
+               ic.hAtoms = me.hashUtilsCls.cloneHash(prevHAtoms);
+          }
+           let bDetails = true;
+           let text = ic.saveFileCls.exportCustomAtoms(bDetails);
+           let file_pref =(ic.inputid) ? ic.inputid : "custom";
+           ic.saveFileCls.saveFile(file_pref + '_sel_details.txt', 'text', [text]);
+        });
+
     //    },
     //    clkMn1_sharelink: function() {
         me.myEventCls.onIds("#" + me.pre + "mn1_sharelink", "click", function(e) { let ic = me.icn3d;
@@ -44597,6 +45055,10 @@ class ClickMenu {
         me.myEventCls.onIds("#" + me.pre + "mn6_addlabelSelection", "click", function(e) { me.icn3d;
            me.htmlCls.dialogCls.openDlg('dl_addlabelselection', 'Add custom labels by the selected');
         });
+
+         me.myEventCls.onIds("#" + me.pre + "mn6_labelColor", "click", function(e) { me.icn3d;
+           me.htmlCls.dialogCls.openDlg('dl_labelColor', 'Change color for all labels');
+        });
     //    },
     //    clkMn2_saveselection: function() {
         me.myEventCls.onIds("#" + me.pre + "mn2_saveselection", "click", function(e) { me.icn3d;
@@ -44605,7 +45067,8 @@ class ClickMenu {
     //    },
     //    clkMn6_addlabelNo: function() {
         me.myEventCls.onIds(["#" + me.pre + "mn6_addlabelNo", "#" + me.pre + "removeLabels"], "click", function(e) { let ic = me.icn3d;
-           ic.pickpair = false;
+           ic.labelcolor = undefined;
+            ic.pickpair = false;
            //ic.labels['residue'] = [];
            //ic.labels['custom'] = [];
            let select = "set labels off";
@@ -45158,6 +45621,8 @@ class SetMenu {
     setTopMenusHtml(id, str1, str2) { let me = this.icn3dui;
         if(me.bNode) return '';
 
+        let titleColor =(me.htmlCls.opts['background'] == 'black') ? me.htmlCls.GREYD : 'black';
+
         let html = "";
 
         html += "<div style='position:relative;'>";
@@ -45173,15 +45638,15 @@ class SetMenu {
         let tdStr = '<td valign="top">';
         html += tdStr + this.setMenu1() + '</td>';
 
-        if(!me.cfg.simplemenu) {
+        //if(!me.cfg.simplemenu) {
             html += tdStr + this.setMenu2() + '</td>';
-        }
+        //}
 
         html += tdStr + this.setMenu2b() + '</td>';
         html += tdStr + this.setMenu3() + '</td>';
         html += tdStr + this.setMenu4() + '</td>';
 
-        if(!me.cfg.simplemenu) {
+        //if(!me.cfg.simplemenu) {
             html += tdStr + this.setMenu5() + '</td>';
             //html += tdStr + this.setMenu5b() + '</td>';
             html += tdStr + this.setMenu6() + '</td>';
@@ -45192,7 +45657,7 @@ class SetMenu {
             html += tdStr + '<div class="icn3d-commandTitle" style="white-space:nowrap; margin-top:10px; border-left:solid 1px #888888"><span id="' + me.pre +  'selection_expand" class="icn3d-expand icn3d-link" title="Expand">' + me.htmlCls.space2 + 'Toolbar <span class="ui-icon ui-icon-plus" style="width:15px"></span>' + me.htmlCls.space2 + '</span><span id="' + me.pre +  'selection_shrink" class="icn3d-shrink icn3d-link" style="display:none;" title="Shrink">' + me.htmlCls.space2 + 'Toolbar <span class="ui-icon ui-icon-minus" style="width:15px"></span>' + me.htmlCls.space2 + '</span></div></td>';
 
             html += tdStr + '<div class="icn3d-commandTitle" style="white-space:nowrap; margin-top:8px; border-left:solid 1px #888888">' + me.htmlCls.space2 + '<input type="text" id="' + me.pre + 'search_seq" size="10" placeholder="one-letter seq."> <button style="white-space:nowrap;" id="' + me.pre + 'search_seq_button">Search</button> <a style="text-decoration: none;" href="' + me.htmlCls.baseUrl + 'icn3d/icn3d.html#selectb" target="_blank" title="Specification tips">?</a></div></td>';
-        }
+        //}
 
         html += "</tr>";
         html += "</table>";
@@ -45201,7 +45666,7 @@ 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:" + me.htmlCls.GREYD + "; width:" + me.htmlCls.WIDTH + "px'></div>";
+        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 + "viewer' style='position:relative; width:100%; height:100%; background-color: " + me.htmlCls.GREYD + ";'>";
 
@@ -45218,7 +45683,7 @@ class SetMenu {
             let tmpStr = 'top:180px; font-size: 1.8em;';
             html += me.htmlCls.divStr + "wait' style='position:absolute; left:50px; " + tmpStr + " color: #444444;'>Loading data...</div>";
         }
-        html += "<canvas id='" + me.pre + "canvas' style='width:100%; height: 100%; background-color: #000;'>Your browser does not support WebGL.</canvas>";
+        html += "<canvas id='" + me.pre + "canvas' style='width:100%; height: 100%; background-color: #FFF;'>Your browser does not support WebGL.</canvas>";
 
         // separate for the log box
         if(me.cfg.showcommand === undefined || me.cfg.showcommand) {
@@ -45254,6 +45719,8 @@ class SetMenu {
     setTopMenusHtmlMobile(id, str1, str2) { let me = this.icn3dui;
         if(me.bNode) return '';
 
+        let titleColor =(me.htmlCls.opts['background'] == 'black') ? me.htmlCls.GREYD : 'black';
+
         let html = "";
 
         html += "<div style='position:relative;'>";
@@ -45323,8 +45790,6 @@ class SetMenu {
         //html += me.htmlCls.setMenuCls.setTools();
 
         // show title at the top left corner
-        let titleColor =(me.htmlCls.opts['background'] == 'white' || me.htmlCls.opts['background'] == 'grey') ? 'black' : me.htmlCls.GREYD;
-
         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 + "viewer' style='position:relative; width:100%; height:100%; background-color: " + me.htmlCls.GREYD + ";'>";
         html += me.htmlCls.divStr + "mnLogSection'>";
@@ -45336,7 +45801,7 @@ class SetMenu {
             let tmpStr = 'top:180px; font-size: 1.8em;';
             html += me.htmlCls.divStr + "wait' style='position:absolute; left:50px; " + tmpStr + " color: #444444;'>Loading data...</div>";
         }
-        html += "<canvas id='" + me.pre + "canvas' style='width:100%; height: 100%; background-color: #000;'>Your browser does not support WebGL.</canvas>";
+        html += "<canvas id='" + me.pre + "canvas' style='width:100%; height: 100%; background-color: #FFF;'>Your browser does not support WebGL.</canvas>";
 
         // separate for the log box
         if(me.cfg.showcommand === undefined || me.cfg.showcommand) {
@@ -45528,15 +45993,18 @@ class SetMenu {
         let html = "";
 
         html += "<ul class='icn3d-mn-item'>";
+        html += "<li><a href='https://www.ncbi.nlm.nih.gov/structure' target='_blank'>Search Structure " + me.htmlCls.wifiStr + "</a></li>";
         html += "<li><span>Retrieve by ID</span>";
         html += "<ul>";
         html += me.htmlCls.setHtmlCls.getLink('mn1_mmdbid', 'MMDB ID ' + me.htmlCls.wifiStr);
         html += me.htmlCls.setHtmlCls.getLink('mn1_mmtfid', 'MMTF ID ' + me.htmlCls.wifiStr);
         html += me.htmlCls.setHtmlCls.getLink('mn1_pdbid', 'PDB ID ' + me.htmlCls.wifiStr);
         html += me.htmlCls.setHtmlCls.getLink('mn1_afid', 'AlphaFold UniProt ID ' + me.htmlCls.wifiStr);
-        html += me.htmlCls.setHtmlCls.getLink('mn1_opmid', 'OPM PDB ID ' + me.htmlCls.wifiStr);
-        html += me.htmlCls.setHtmlCls.getLink('mn1_mmcifid', 'mmCIF ID ' + me.htmlCls.wifiStr);
-        html += me.htmlCls.setHtmlCls.getLink('mn1_gi', 'NCBI gi ' + me.htmlCls.wifiStr);
+        if(!me.cfg.simplemenu) {
+            html += me.htmlCls.setHtmlCls.getLink('mn1_opmid', 'OPM PDB ID ' + me.htmlCls.wifiStr);
+            html += me.htmlCls.setHtmlCls.getLink('mn1_mmcifid', 'mmCIF ID ' + me.htmlCls.wifiStr);
+            html += me.htmlCls.setHtmlCls.getLink('mn1_gi', 'NCBI gi ' + me.htmlCls.wifiStr);
+        }
         html += me.htmlCls.setHtmlCls.getLink('mn1_uniprotid', 'UniProt ID ' + me.htmlCls.wifiStr);
         html += me.htmlCls.setHtmlCls.getLink('mn1_cid', 'PubChem CID ' + me.htmlCls.wifiStr);
         html += "</ul>";
@@ -45546,29 +46014,32 @@ class SetMenu {
 //        html += me.htmlCls.setHtmlCls.getLink('mn1_pdbfile', 'PDB File');
 //        html += me.htmlCls.setHtmlCls.getLink('mn1_pdbfile_app', 'PDB File (append)');
         html += me.htmlCls.setHtmlCls.getLink('mn1_pdbfile_app', 'PDB File (appendable)');
-        html += me.htmlCls.setHtmlCls.getLink('mn1_mmciffile', 'mmCIF File');
+        if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getLink('mn1_mmciffile', 'mmCIF File');
         html += me.htmlCls.setHtmlCls.getLink('mn1_mol2file', 'Mol2 File');
         html += me.htmlCls.setHtmlCls.getLink('mn1_sdffile', 'SDF File');
         html += me.htmlCls.setHtmlCls.getLink('mn1_xyzfile', 'XYZ File');
-        html += me.htmlCls.setHtmlCls.getLink('mn1_urlfile', 'URL(Same Host) ' + me.htmlCls.wifiStr);
+        if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getLink('mn1_urlfile', 'URL(Same Host) ' + me.htmlCls.wifiStr);
         html += "<li>-</li>";
         html += me.htmlCls.setHtmlCls.getLink('mn1_pngimage', 'iCn3D PNG Image');
         html += me.htmlCls.setHtmlCls.getLink('mn1_state', 'State/Script File');
-        html += me.htmlCls.setHtmlCls.getLink('mn1_fixedversion', 'Share Link in Archived Ver. ' + me.htmlCls.wifiStr);
+        if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getLink('mn1_fixedversion', 'Share Link in Archived Ver. ' + me.htmlCls.wifiStr);
         html += me.htmlCls.setHtmlCls.getLink('mn1_selection', 'Selection File');
-        html += "<li>-</li>";
+        
+        if(!me.cfg.simplemenu) {
+            html += "<li>-</li>";
 
-        html += "<li><span>Electron Density(DSN6)</span>";
-        html += "<ul>";
-        html += me.htmlCls.setHtmlCls.getLink('mn1_dsn6', 'Local File');
-        html += me.htmlCls.setHtmlCls.getLink('mn1_dsn6url', 'URL(Same Host) ' + me.htmlCls.wifiStr);
-        html += "</ul>";
+            html += "<li><span>Electron Density(DSN6)</span>";
+            html += "<ul>";
+            html += me.htmlCls.setHtmlCls.getLink('mn1_dsn6', 'Local File');
+            html += me.htmlCls.setHtmlCls.getLink('mn1_dsn6url', 'URL(Same Host) ' + me.htmlCls.wifiStr);
+            html += "</ul>";
+        }
 
         html += "</ul>";
         html += "</li>";
         html += "<li><span>Align</span>";
         html += "<ul>";
-        html += me.htmlCls.setHtmlCls.getLink('mn1_blast_rep_id', 'Sequence to Structure ' + me.htmlCls.wifiStr);
+        html += me.htmlCls.setHtmlCls.getLink('mn1_blast_rep_id', 'Sequence to Structure');
         html += me.htmlCls.setHtmlCls.getLink('mn1_align', 'Structure to Structure ' + me.htmlCls.wifiStr);
         //html += me.htmlCls.setHtmlCls.getLink('mn1_chainalign', 'Chain to Chain');
         html += me.htmlCls.setHtmlCls.getLink('mn1_chainalign', 'Multiple Chains ' + me.htmlCls.wifiStr);
@@ -45593,15 +46064,18 @@ class SetMenu {
             html += "<li>-</li>";
             html += me.htmlCls.setHtmlCls.getLink('mn1_exportVrml', 'WRL/VRML(Color)');
             html += me.htmlCls.setHtmlCls.getLink('mn1_exportStl', 'STL');
-            html += "<li>-</li>";
-            html += me.htmlCls.setHtmlCls.getLink('mn1_stabilizerYes', 'Add All Stabilizers');
-            html += me.htmlCls.setHtmlCls.getLink('mn1_stabilizerNo', 'Remove All Stabilizers');
-            html += "<li>-</li>";
-            html += me.htmlCls.setHtmlCls.getLink('mn1_stabilizerOne', 'Add One Stabilizer');
-            html += me.htmlCls.setHtmlCls.getLink('mn1_stabilizerRmOne', 'Remove One Stabilizer');
-            html += "<li>-</li>";
-            html += me.htmlCls.setHtmlCls.getLink('mn1_thicknessSet', 'Set Thickness');
-            //html += me.htmlCls.setHtmlCls.getLink('mn1_thicknessReset', 'Reset Thickness');
+
+            if(!me.cfg.simplemenu) {
+                html += "<li>-</li>";
+                html += me.htmlCls.setHtmlCls.getLink('mn1_stabilizerYes', 'Add All Stabilizers');
+                html += me.htmlCls.setHtmlCls.getLink('mn1_stabilizerNo', 'Remove All Stabilizers');
+                html += "<li>-</li>";
+                html += me.htmlCls.setHtmlCls.getLink('mn1_stabilizerOne', 'Add One Stabilizer');
+                html += me.htmlCls.setHtmlCls.getLink('mn1_stabilizerRmOne', 'Remove One Stabilizer');
+                html += "<li>-</li>";
+                html += me.htmlCls.setHtmlCls.getLink('mn1_thicknessSet', 'Set Thickness');
+                //html += me.htmlCls.setHtmlCls.getLink('mn1_thicknessReset', 'Reset Thickness');
+            }
         }
         else {
             html += me.htmlCls.setHtmlCls.getLink('mn1_exportVrml', 'VRML(Color)');
@@ -45619,14 +46093,17 @@ class SetMenu {
         html += "<ul>";
         html += me.htmlCls.setHtmlCls.getLink('mn1_exportCanvas', 'Original Size & HTML');
         html += me.htmlCls.setHtmlCls.getLink('mn1_exportCanvas1', 'Original Size');
-        html += me.htmlCls.setHtmlCls.getLink('mn1_exportCanvas2', '2X Large');
-        html += me.htmlCls.setHtmlCls.getLink('mn1_exportCanvas4', '4X Large');
-        html += me.htmlCls.setHtmlCls.getLink('mn1_exportCanvas8', '8X Large');
+        if(!me.cfg.simplemenu) {
+            html += me.htmlCls.setHtmlCls.getLink('mn1_exportCanvas2', '2X Large');
+            html += me.htmlCls.setHtmlCls.getLink('mn1_exportCanvas4', '4X Large');
+            html += me.htmlCls.setHtmlCls.getLink('mn1_exportCanvas8', '8X Large');
+        }
         html += "</ul>";
         html += "</li>";
 
         html += me.htmlCls.setHtmlCls.getLink('mn1_exportState', 'State File');
         html += me.htmlCls.setHtmlCls.getLink('mn1_exportSelections', 'Selection File');
+        html += me.htmlCls.setHtmlCls.getLink('mn1_exportSelDetails', 'Selection Details');
         html += me.htmlCls.setHtmlCls.getLink('mn1_exportCounts', 'Residue Counts');
 
     /*
@@ -45688,9 +46165,9 @@ class SetMenu {
 
         html += "<ul class='icn3d-mn-item'>";
 
-        html += me.htmlCls.setHtmlCls.getLink('mn2_definedsets', 'Defined Sets');
+        if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getLink('mn2_definedsets', 'Defined Sets');
         html += me.htmlCls.setHtmlCls.getLink('mn2_selectall', 'All');
-        html += me.htmlCls.setHtmlCls.getLink('mn2_selectdisplayed', 'Displayed Set');
+        if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getLink('mn2_selectdisplayed', 'Displayed Set');
         html += me.htmlCls.setHtmlCls.getLink('mn2_aroundsphere', 'by Distance');
 
         html += "<li><span>by Property</span>";
@@ -45704,11 +46181,13 @@ class SetMenu {
         html += "</ul>";
         html += "</li>";
 
-        html += me.htmlCls.setHtmlCls.getLink('mn2_selectcomplement', 'Inverse');
-        html += me.htmlCls.setHtmlCls.getLink('mn2_selectmainchains', 'Main Chains');
-        html += me.htmlCls.setHtmlCls.getLink('mn2_selectsidechains', 'Side Chains');
-        html += me.htmlCls.setHtmlCls.getLink('mn2_selectmainsidechains', 'Main & Side Chains');
-        html += me.htmlCls.setHtmlCls.getLink('mn2_command', 'Advanced');
+        if(!me.cfg.simplemenu) {
+            html += me.htmlCls.setHtmlCls.getLink('mn2_selectcomplement', 'Inverse');
+            html += me.htmlCls.setHtmlCls.getLink('mn2_selectmainchains', 'Main Chains');
+            html += me.htmlCls.setHtmlCls.getLink('mn2_selectsidechains', 'Side Chains');
+            html += me.htmlCls.setHtmlCls.getLink('mn2_selectmainsidechains', 'Main & Side Chains');
+            html += me.htmlCls.setHtmlCls.getLink('mn2_command', 'Advanced');
+        }
 
         if(me.cfg.cid === undefined) {
             html += "<li><span>Select on 3D</span>";
@@ -45745,22 +46224,24 @@ class SetMenu {
 
         html += "<li>-</li>";
 
-        html += "<li><span>Highlight Color</span>";
-        html += "<ul>";
-        html += me.htmlCls.setHtmlCls.getRadio('mn2_hl_clr', 'mn2_hl_clrYellow', 'Yellow', true);
-        html += me.htmlCls.setHtmlCls.getRadio('mn2_hl_clr', 'mn2_hl_clrGreen', 'Green');
-        html += me.htmlCls.setHtmlCls.getRadio('mn2_hl_clr', 'mn2_hl_clrRed', 'Red');
-        html += "</ul>";
-        html += "</li>";
-        html += "<li><span>Highlight Style</span>";
-        html += "<ul>";
+        if(!me.cfg.simplemenu) {
+            html += "<li><span>Highlight Color</span>";
+            html += "<ul>";
+            html += me.htmlCls.setHtmlCls.getRadio('mn2_hl_clr', 'mn2_hl_clrYellow', 'Yellow', true);
+            html += me.htmlCls.setHtmlCls.getRadio('mn2_hl_clr', 'mn2_hl_clrGreen', 'Green');
+            html += me.htmlCls.setHtmlCls.getRadio('mn2_hl_clr', 'mn2_hl_clrRed', 'Red');
+            html += "</ul>";
+            html += "</li>";
+            html += "<li><span>Highlight Style</span>";
+            html += "<ul>";
 
-        html += me.htmlCls.setHtmlCls.getRadio('mn2_hl_style', 'mn2_hl_styleOutline', 'Outline', true);
-        html += me.htmlCls.setHtmlCls.getRadio('mn2_hl_style', 'mn2_hl_styleObject', '3D Objects');
-        //html += me.htmlCls.setHtmlCls.getRadio('mn2_hl_style', 'mn2_hl_styleNone', 'No Highlight');
+            html += me.htmlCls.setHtmlCls.getRadio('mn2_hl_style', 'mn2_hl_styleOutline', 'Outline', true);
+            html += me.htmlCls.setHtmlCls.getRadio('mn2_hl_style', 'mn2_hl_styleObject', '3D Objects');
+            //html += me.htmlCls.setHtmlCls.getRadio('mn2_hl_style', 'mn2_hl_styleNone', 'No Highlight');
 
-        html += "</ul>";
-        html += "</li>";
+            html += "</ul>";
+            html += "</li>";
+        }
 
         //html += me.htmlCls.setHtmlCls.getLink('mn2_hl_styleNone', 'Clear Highlight');
 
@@ -45799,7 +46280,7 @@ class SetMenu {
         html += "<ul class='icn3d-mn-item'>";
 
         html += me.htmlCls.setHtmlCls.getLink('mn2_show_selected', 'View Selection');
-        html += me.htmlCls.setHtmlCls.getLink('mn2_hide_selected', 'Hide Selection');
+        if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getLink('mn2_hide_selected', 'Hide Selection');
         html += me.htmlCls.setHtmlCls.getLink('mn2_selectedcenter', 'Zoom in Selection');
         html += me.htmlCls.setHtmlCls.getLink('mn6_center', 'Center Selection');
         html += me.htmlCls.setHtmlCls.getLink('mn2_fullstru', 'View Full Structure');
@@ -45877,8 +46358,10 @@ class SetMenu {
         html += "</ul>";
         html += "</li>";
 
-        html += me.htmlCls.setHtmlCls.getLink('mn6_back', 'Undo');
-        html += me.htmlCls.setHtmlCls.getLink('mn6_forward', 'Redo');
+        if(!me.cfg.simplemenu) {
+            html += me.htmlCls.setHtmlCls.getLink('mn6_back', 'Undo');
+            html += me.htmlCls.setHtmlCls.getLink('mn6_forward', 'Redo');
+        }
 
         html += me.htmlCls.setHtmlCls.getLink('mn6_fullscreen', 'Full Screen');
     //    html += me.htmlCls.setHtmlCls.getLink('mn6_exitfullscreen', 'Exit Full Screen');
@@ -46026,21 +46509,22 @@ class SetMenu {
 
         html += me.htmlCls.setHtmlCls.getLink('mn3_setThickness', 'Preferences');
 
-        html += "<li>-</li>";
-
-        html += me.htmlCls.setHtmlCls.getLink('mn3_styleSave', 'Save Style');
-        html += me.htmlCls.setHtmlCls.getLink('mn3_styleApplySave', 'Apply Saved Style');
+        if(!me.cfg.simplemenu) {
+            html += "<li>-</li>";
+            html += me.htmlCls.setHtmlCls.getLink('mn3_styleSave', 'Save Style');
+            html += me.htmlCls.setHtmlCls.getLink('mn3_styleApplySave', 'Apply Saved Style');
+        }
 
         html += "<li>-</li>";
 
         html += "<li><span>Surface Type</span>";
         html += "<ul>";
         html += me.htmlCls.setHtmlCls.getRadio('mn5_surface', 'mn5_surfaceVDW', 'Van der Waals');
-        html += me.htmlCls.setHtmlCls.getRadio('mn5_surface', 'mn5_surfaceVDWContext', 'VDW with Context');
+        if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getRadio('mn5_surface', 'mn5_surfaceVDWContext', 'VDW with Context');
         html += me.htmlCls.setHtmlCls.getRadio('mn5_surface', 'mn5_surfaceMolecular', 'Molecular Surface');
-        html += me.htmlCls.setHtmlCls.getRadio('mn5_surface', 'mn5_surfaceMolecularContext', 'MS with Context');
+        if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getRadio('mn5_surface', 'mn5_surfaceMolecularContext', 'MS with Context');
         html += me.htmlCls.setHtmlCls.getRadio('mn5_surface', 'mn5_surfaceSAS', 'Solvent Accessible');
-        html += me.htmlCls.setHtmlCls.getRadio('mn5_surface', 'mn5_surfaceSASContext', 'SA with Context');
+        if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getRadio('mn5_surface', 'mn5_surfaceSASContext', 'SA with Context');
         html += "</ul>";
         html += "</li>";
 
@@ -46063,36 +46547,38 @@ class SetMenu {
         html += "</li>";
 
         if(me.cfg.cid === undefined && me.cfg.align === undefined && me.cfg.chainalign === undefined) {
-            html += "<li>-</li>";
-
-            html += "<li id='" + me.pre + "mapWrapper1'><span>Electron Density</span>";
-            html += "<ul>";
-            html += me.htmlCls.setHtmlCls.getRadio('mn5_elecmap', 'mn5_elecmap2fofc', '2Fo-Fc Map');
-            html += me.htmlCls.setHtmlCls.getRadio('mn5_elecmap', 'mn5_elecmapfofc', 'Fo-Fc Map');
-            html += "</ul>";
-            html += "</li>";
-
-            html += me.htmlCls.setHtmlCls.getLinkWrapper('mn5_elecmapNo', 'Remove Map', 'mapWrapper2');
+            if(!me.cfg.simplemenu) {
+                html += "<li>-</li>";
 
-            html += "<li id='" + me.pre + "mapWrapper3'><span>Map Wireframe</span>";
-            html += "<ul>";
-            html += me.htmlCls.setHtmlCls.getRadio('mn5_mapwireframe', 'mn5_mapwireframeYes', 'Yes', true);
-            html += me.htmlCls.setHtmlCls.getRadio('mn5_mapwireframe', 'mn5_mapwireframeNo', 'No');
-            html += "</ul>";
-            html += "</li>";
-
-            if(me.cfg.mmtfid === undefined) {
-                //html += "<li>-</li>";
+                html += "<li id='" + me.pre + "mapWrapper1'><span>Electron Density</span>";
+                html += "<ul>";
+                html += me.htmlCls.setHtmlCls.getRadio('mn5_elecmap', 'mn5_elecmap2fofc', '2Fo-Fc Map');
+                html += me.htmlCls.setHtmlCls.getRadio('mn5_elecmap', 'mn5_elecmapfofc', 'Fo-Fc Map');
+                html += "</ul>";
+                html += "</li>";
 
-                html += me.htmlCls.setHtmlCls.getLinkWrapper('mn5_emmap', 'EM Density Map', 'emmapWrapper1');
-                html += me.htmlCls.setHtmlCls.getLinkWrapper('mn5_emmapNo', 'Remove EM Map', 'emmapWrapper2');
+                html += me.htmlCls.setHtmlCls.getLinkWrapper('mn5_elecmapNo', 'Remove Map', 'mapWrapper2');
 
-                html += "<li id='" + me.pre + "emmapWrapper3'><span>EM Map Wireframe</span>";
+                html += "<li id='" + me.pre + "mapWrapper3'><span>Map Wireframe</span>";
                 html += "<ul>";
-                html += me.htmlCls.setHtmlCls.getRadio('mn5_emmapwireframe', 'mn5_emmapwireframeYes', 'Yes', true);
-                html += me.htmlCls.setHtmlCls.getRadio('mn5_emmapwireframe', 'mn5_emmapwireframeNo', 'No');
+                html += me.htmlCls.setHtmlCls.getRadio('mn5_mapwireframe', 'mn5_mapwireframeYes', 'Yes', true);
+                html += me.htmlCls.setHtmlCls.getRadio('mn5_mapwireframe', 'mn5_mapwireframeNo', 'No');
                 html += "</ul>";
                 html += "</li>";
+
+                if(me.cfg.mmtfid === undefined) {
+                    //html += "<li>-</li>";
+
+                    html += me.htmlCls.setHtmlCls.getLinkWrapper('mn5_emmap', 'EM Density Map', 'emmapWrapper1');
+                    html += me.htmlCls.setHtmlCls.getLinkWrapper('mn5_emmapNo', 'Remove EM Map', 'emmapWrapper2');
+
+                    html += "<li id='" + me.pre + "emmapWrapper3'><span>EM Map Wireframe</span>";
+                    html += "<ul>";
+                    html += me.htmlCls.setHtmlCls.getRadio('mn5_emmapwireframe', 'mn5_emmapwireframeYes', 'Yes', true);
+                    html += me.htmlCls.setHtmlCls.getRadio('mn5_emmapwireframe', 'mn5_emmapwireframeNo', 'No');
+                    html += "</ul>";
+                    html += "</li>";
+                }
             }
         }
 
@@ -46100,20 +46586,22 @@ class SetMenu {
 
         html += "<li><span>Background</span>";
         html += "<ul>";
-        html += me.htmlCls.setHtmlCls.getRadio('mn6_bkgd', 'mn6_bkgdTransparent', 'Transparent', true);
-        html += me.htmlCls.setHtmlCls.getRadio('mn6_bkgd', 'mn6_bkgdBlack', 'Black');
+        html += me.htmlCls.setHtmlCls.getRadio('mn6_bkgd', 'mn6_bkgdTransparent', 'Transparent');
+        html += me.htmlCls.setHtmlCls.getRadio('mn6_bkgd', 'mn6_bkgdBlack', 'Black', true);
         html += me.htmlCls.setHtmlCls.getRadio('mn6_bkgd', 'mn6_bkgdGrey', 'Gray');
         html += me.htmlCls.setHtmlCls.getRadio('mn6_bkgd', 'mn6_bkgdWhite', 'White');
         html += "</ul>";
         html += "</li>";
 
-        html += "<li><span>Dialog Color</span>";
-        html += "<ul>";
-        html += me.htmlCls.setHtmlCls.getRadio('mn6_theme', 'mn6_themeBlue', 'Blue', true);
-        html += me.htmlCls.setHtmlCls.getRadio('mn6_theme', 'mn6_themeOrange', 'Orange');
-        html += me.htmlCls.setHtmlCls.getRadio('mn6_theme', 'mn6_themeBlack', 'Black');
-        html += "</ul>";
-        html += "</li>";
+        if(!me.cfg.simplemenu) {
+            html += "<li><span>Dialog Color</span>";
+            html += "<ul>";
+            html += me.htmlCls.setHtmlCls.getRadio('mn6_theme', 'mn6_themeBlue', 'Blue', true);
+            html += me.htmlCls.setHtmlCls.getRadio('mn6_theme', 'mn6_themeOrange', 'Orange');
+            html += me.htmlCls.setHtmlCls.getRadio('mn6_theme', 'mn6_themeBlack', 'Black');
+            html += "</ul>";
+            html += "</li>";
+        }
 
 //        html += "<li><span>Two-color Helix</span>";
 //        html += "<ul>";
@@ -46357,8 +46845,10 @@ class SetMenu {
 
         html += "</ul>";
 
-        html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrCustom', 'Color Picker');
-        html += "<li>-</li>";
+        if(!me.cfg.simplemenu) {
+            html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrCustom', 'Color Picker');
+            html += "<li>-</li>";
+        }
 
         if(me.cfg.cid === undefined) {
             //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrRainbow', 'Rainbow (R-V)');
@@ -46368,12 +46858,14 @@ class SetMenu {
             html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrRainbowChain', 'for Chains');
             html += "</ul>";
 
-            //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSpectrum', 'Spectrum (V-R)');
-            html += "<li><span style='padding-left:1.5em;'>Spectrum (V-R)</span>";
-            html += "<ul>";
-            html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSpectrum', 'for Selection');
-            html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSpectrumChain', 'for Chains');
-            html += "</ul>";
+            if(!me.cfg.simplemenu) {
+                //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSpectrum', 'Spectrum (V-R)');
+                html += "<li><span style='padding-left:1.5em;'>Spectrum (V-R)</span>";
+                html += "<ul>";
+                html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSpectrum', 'for Selection');
+                html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrSpectrumChain', 'for Chains');
+                html += "</ul>";
+            }
 
             html += "<li><span style='padding-left:1.5em;'>Secondary</span>";
             html += "<ul>";
@@ -46402,7 +46894,7 @@ class SetMenu {
             html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrBfactorNorm', 'Percentile');
             html += "</ul>";
 
-            html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrArea', 'Solvent<br><span style="padding-left:1.5em;">Accessibility</span>');
+            if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrArea', 'Solvent<br><span style="padding-left:1.5em;">Accessibility</span>');
 
             if(me.cfg.align !== undefined || me.cfg.chainalign !== undefined || me.cfg.blast_rep_id !== undefined) {
               html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrChain', 'Chain');
@@ -46416,10 +46908,12 @@ class SetMenu {
             }
 
             if(me.cfg.cid === undefined) {
-                html += "<li><span style='padding-left:1.5em;'>Defined Sets</span>";
-                html += "<ul>";
-                html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrsets', 'Rainbow for Selected Sets<br>in "Analysis > Defined Sets"');
-                html += "</ul>";
+                if(!me.cfg.simplemenu) {
+                    html += "<li><span style='padding-left:1.5em;'>Defined Sets</span>";
+                    html += "<ul>";
+                    html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrsets', 'Rainbow for Selected Sets<br>in "Analysis > Defined Sets"');
+                    html += "</ul>";
+                }
             }
 
             //html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrResidue', 'Residue');
@@ -46442,17 +46936,21 @@ class SetMenu {
             }
 
             //if(me.cfg.afid) html += me.htmlCls.setHtmlCls.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 += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrConfidence', 'AlphaFold<br><span style="padding-left:1.5em;">Confidence</span>');
+            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 += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrConfidence', 'AlphaFold<br><span style="padding-left:1.5em;">Confidence</span>');
+            }
         }
         else {
             //if(!me.cfg.hidelicense) html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn1_delphi2', 'DelPhi<br><span style="padding-left:1.5em;">Potential ' + me.htmlCls.licenseStr + '</span>');
             html += me.htmlCls.setHtmlCls.getRadio('mn4_clr', 'mn4_clrAtom', 'Atom', true);
         }
 
-        html += "<li>-</li>";
+        if(!me.cfg.simplemenu) {
+            html += "<li>-</li>";
 
-        html += me.htmlCls.setHtmlCls.getLink('mn4_clrSave', 'Save Color');
-        html += me.htmlCls.setHtmlCls.getLink('mn4_clrApplySave', 'Apply Saved Color');
+            html += me.htmlCls.setHtmlCls.getLink('mn4_clrSave', 'Save Color');
+            html += me.htmlCls.setHtmlCls.getLink('mn4_clrApplySave', 'Apply Saved Color');
+        }
 
         html += "<li><br/></li>";
         html += "</ul>";
@@ -46513,8 +47011,8 @@ class SetMenu {
             html += me.htmlCls.setHtmlCls.getLink('mn6_hbondsYes', 'Interactions');
             //html += me.htmlCls.setHtmlCls.getLink('mn6_hbondsNo', 'Remove H-Bonds <br>& Interactions');
 
-            html += me.htmlCls.setHtmlCls.getLink('mn6_contactmap', 'Contact Map');
-
+            if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getLink('mn6_contactmap', 'Contact Map');
+/*
             html += "<li><span>Bring to Front</span>";
             html += "<ul>";
             html += me.htmlCls.setHtmlCls.getLink('mn1_window_table', 'Interaction Table');
@@ -46523,22 +47021,26 @@ class SetMenu {
             html += me.htmlCls.setHtmlCls.getLink('mn1_window_graph', '2D Graph(Force-Directed)');
             html += "</ul>";
             html += "</li>";
+*/
 
             if(!me.cfg.notebook) {
                 html += me.htmlCls.setHtmlCls.getLink('mn1_mutation', 'Mutation ' + me.htmlCls.wifiStr);
             }
 
-            html += "<li>-</li>";
+            if(!me.cfg.simplemenu) html += "<li>-</li>";
         }
 
         if(!me.cfg.notebook && !me.cfg.hidelicense) {
             html += me.htmlCls.setHtmlCls.getLink('mn1_delphi', 'DelPhi Potential ' + me.htmlCls.licenseStr);
-            html += "<li><span>Load PQR/Phi</span>";
-            html += "<ul>";
-            html += me.htmlCls.setHtmlCls.getLink('mn1_phi', 'Local PQR/Phi/Cube File');
-            html += me.htmlCls.setHtmlCls.getLink('mn1_phiurl', 'URL PQR/Phi/Cube File');
-            html += "</ul>";
-            html += me.htmlCls.setHtmlCls.getLink('delphipqr', 'Download PQR');
+            
+            if(!me.cfg.simplemenu) {
+                html += "<li><span>Load PQR/Phi</span>";
+                html += "<ul>";
+                html += me.htmlCls.setHtmlCls.getLink('mn1_phi', 'Local PQR/Phi/Cube File');
+                html += me.htmlCls.setHtmlCls.getLink('mn1_phiurl', 'URL PQR/Phi/Cube File');
+                html += "</ul>";
+                html += me.htmlCls.setHtmlCls.getLink('delphipqr', 'Download PQR');
+            }
 
             html += "<li>-</li>";
         }
@@ -46566,6 +47068,8 @@ class SetMenu {
             html += me.htmlCls.setHtmlCls.getRadio('mn6_addlabel', 'mn6_addlabelTermini', 'N- & C-Termini');
         }
 
+        html += "<li>-</li>";
+        html += me.htmlCls.setHtmlCls.getRadio('mn6_addlabel', 'mn6_labelColor', 'Change Label Color', true);
         html += me.htmlCls.setHtmlCls.getRadio('mn6_addlabel', 'mn6_addlabelNo', 'Remove', true);
         html += "</ul>";
         html += "</li>";
@@ -46593,12 +47097,14 @@ class SetMenu {
         html += "<li>-</li>";
 
         if(me.cfg.cid === undefined) {
-            html += "<li><span>Chem. Binding</span>";
-            html += "<ul>";
-            html += me.htmlCls.setHtmlCls.getRadio('mn6_chemicalbinding', 'mn6_chemicalbindingshow', 'Show');
-            html += me.htmlCls.setHtmlCls.getRadio('mn6_chemicalbinding', 'mn6_chemicalbindinghide', 'Hide', true);
-            html += "</ul>";
-            html += "</li>";
+            if(!me.cfg.simplemenu) {
+                html += "<li><span>Chem. Binding</span>";
+                html += "<ul>";
+                html += me.htmlCls.setHtmlCls.getRadio('mn6_chemicalbinding', 'mn6_chemicalbindingshow', 'Show');
+                html += me.htmlCls.setHtmlCls.getRadio('mn6_chemicalbinding', 'mn6_chemicalbindinghide', 'Hide', true);
+                html += "</ul>";
+                html += "</li>";
+            }
 
             html += "<li><span>Disulfide Bonds</span>";
             html += "<ul>";
@@ -46608,15 +47114,19 @@ class SetMenu {
             html += "</ul>";
             html += "</li>";
 
-            html += "<li><span>Cross-Linkages</span>";
-            html += "<ul>";
-            html += me.htmlCls.setHtmlCls.getRadio('mn6_clbonds', 'mn6_clbondsYes', 'Show', true);
-            html += me.htmlCls.setHtmlCls.getRadio('mn6_clbonds', 'mn6_clbondsExport', 'Export Pairs');
-            html += me.htmlCls.setHtmlCls.getRadio('mn6_clbonds', 'mn6_clbondsNo', 'Hide');
-            html += "</ul>";
-            html += "</li>";
+            if(!me.cfg.simplemenu) {
+                html += "<li><span>Cross-Linkages</span>";
+                html += "<ul>";
+                html += me.htmlCls.setHtmlCls.getRadio('mn6_clbonds', 'mn6_clbondsYes', 'Show', true);
+                html += me.htmlCls.setHtmlCls.getRadio('mn6_clbonds', 'mn6_clbondsExport', 'Export Pairs');
+                html += me.htmlCls.setHtmlCls.getRadio('mn6_clbonds', 'mn6_clbondsNo', 'Hide');
+                html += "</ul>";
+                html += "</li>";
+            }
 
             let bOnePdb = me.cfg.mmtfid !== undefined || me.cfg.pdbid !== undefined || me.cfg.opmid !== undefined || me.cfg.mmcifid !== undefined || me.cfg.mmdbid !== undefined || me.cfg.gi !== undefined || me.cfg.blast_rep_id !== undefined;
+console.log("me.cfg.mmdbid: " + me.cfg.mmdbid + " bOnePdb: " + bOnePdb);
+
             if(bOnePdb) {
               html += "<li id='" + me.pre + "assemblyWrapper'><span>Assembly</span>";
               html += "<ul>";
@@ -46632,16 +47142,18 @@ class SetMenu {
             html += "<li><span>Symmetry</span>";
             html += "<ul>";
             if(bOnePdb) html += me.htmlCls.setHtmlCls.getLink('mn6_symmetry', 'from PDB(precalculated) ' + me.htmlCls.wifiStr);
-            html += me.htmlCls.setHtmlCls.getLink('mn6_symd', 'from SymD(Dynamic) ' + me.htmlCls.wifiStr);
-            html += me.htmlCls.setHtmlCls.getLink('mn6_clear_sym', 'Clear SymD Symmetry');
-            html += me.htmlCls.setHtmlCls.getLink('mn6_axes_only', 'Show Axes Only');
+            if(!me.cfg.simplemenu) {
+                html += me.htmlCls.setHtmlCls.getLink('mn6_symd', 'from SymD(Dynamic) ' + me.htmlCls.wifiStr);
+                html += me.htmlCls.setHtmlCls.getLink('mn6_clear_sym', 'Clear SymD Symmetry');
+                html += me.htmlCls.setHtmlCls.getLink('mn6_axes_only', 'Show Axes Only');
+            }
             html += "</ul>";
             html += "</li>";
 
             html += "<li>-</li>";
         }
 
-        html += me.htmlCls.setHtmlCls.getLink('mn6_yournote', 'Window Title');
+        if(!me.cfg.simplemenu) html += me.htmlCls.setHtmlCls.getLink('mn6_yournote', 'Window Title');
 
         if(me.cfg.cid !== undefined) {
             html += "<li><span>Links</span>";
@@ -46725,16 +47237,18 @@ class SetMenu {
         html += "</ul>";
         html += "</li>";
 
-        html += "<li><span>Develop</span>";
-        html += "<ul>";
-        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#HowToUse' target='_blank'>How to Embed</a></li>";
-        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#datastructure' target='_blank'>Data Structure</a></li>";
-        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#classstructure' target='_blank'>Class Structure</a></li>";
-        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#addclass' target='_blank'>Add New Classes</a></li>";
-        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#modifyfunction' target='_blank'>Modify Functions</a></li>";
-        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#restfulapi' target='_blank'>RESTful APIs</a></li>";
-        html += "</ul>";
-        html += "</li>";
+        if(!me.cfg.simplemenu) {
+            html += "<li><span>Develop</span>";
+            html += "<ul>";
+            html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#HowToUse' target='_blank'>How to Embed</a></li>";
+            html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#datastructure' target='_blank'>Data Structure</a></li>";
+            html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#classstructure' target='_blank'>Class Structure</a></li>";
+            html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#addclass' target='_blank'>Add New Classes</a></li>";
+            html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#modifyfunction' target='_blank'>Modify Functions</a></li>";
+            html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#restfulapi' target='_blank'>RESTful APIs</a></li>";
+            html += "</ul>";
+            html += "</li>";
+        }
 
         html += liStr + me.htmlCls.baseUrl + "icn3d/docs/icn3d_help.html' target='_blank'>Help Doc " + me.htmlCls.wifiStr + "</a></li>";
 
@@ -46744,7 +47258,7 @@ class SetMenu {
         html += "<ul>";
         html += "<li><span>Rotate</span>";
         html += "<ul>";
-        html += "<li>Left Mouse</li>";
+        html += "<li>Left Mouse (Click & Drag)</li>";
         html += "<li>Key l: Left</li>";
         html += "<li>Key j: Right</li>";
         html += "<li>Key i: Up</li>";
@@ -46757,20 +47271,20 @@ class SetMenu {
         html += "</li>";
         html += "<li><span>Zoom</span>";
         html += "<ul>";
-        html += "<li>Middle Mouse</li>";
+        html += "<li>Middle Mouse <br>(Pinch & Spread)</li>";
         html += "<li>Key z: Zoom in</li>";
         html += "<li>Key x: Zoom out</li>";
         html += "</ul>";
         html += "</li>";
         html += "<li><span>Translate</span>";
         html += "<ul>";
-        html += "<li>Right Mouse</li>";
+        html += "<li>Right Mouse <br>(Two Finger Click & Drag)</li>";
         html += "</ul>";
         html += "</li>";
         html += "</ul>";
         html += "</li>";
 
-        html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#HowToUseStep5' target='_blank'>Selection Hints</a></li>";
+        if(!me.cfg.simplemenu) html += liStr + me.htmlCls.baseUrl + "icn3d/icn3d.html#HowToUseStep5' target='_blank'>Selection Hints</a></li>";
 
         html += "<li><br/></li>";
         html += "</ul>";
@@ -47371,6 +47885,8 @@ class SetDialog {
 
         let html = "";
 
+        let defaultColor = "#ffff00"; //ic.colorBlackbkgd; 
+ 
         me.htmlCls.optionStr = "<option value=";
 
         html += "<!-- dialog will not be part of the form -->";
@@ -47526,7 +48042,7 @@ class SetDialog {
         html += "<b>Optional 1</b>, full chains are used for structure alignment<br/><br/>";
         html += "<b>Optional 2</b>, sequence alignment (followed by structure alignemnt) based on residue numbers in the First/Master chain: <br>" + me.htmlCls.inputTextStr + "id='" + me.pre + "resalignids' placeholder='1,5,10-50' size=50><br/><br/>";
         html += "<b>Optional 3</b>, predefined alignment with residue numbers in each chain specified (one chain per line): <br><textarea id='" + me.pre + "predefinedres' rows='5' style='width: 100%; height: " +(me.htmlCls.LOG_HEIGHT) + "px; padding: 0px; border: 0px;' placeholder='1,5,10-50\n1,5,10-50\n1,5,10-50'></textarea><br/><br/>";
-        html += me.htmlCls.buttonStr + "reload_chainalign'>Align Biological Unit</button>" + me.htmlCls.buttonStr + "reload_chainalign_asym' style='margin-left:30px'>Align Asymmetric Unit</button><br/><br/>";
+        html += me.htmlCls.buttonStr + "reload_chainalign_asym'>Align Asymmetric Unit</button>" + me.htmlCls.buttonStr + "reload_chainalign' style='margin-left:30px'>Align Biological Unit</button><br/><br/>";
         html += "(Note: To align chains in custom PDB files, you could concatenate PDB files in a single PDB file with the separation line \"ENDMDL\". Then load it in \"Open File > PDB File\" in the \"File\" menu and click \"View Sequences & Annotations\" in the \"Window\" menu. Finally select multiple chains in the sequence window and click \"Realign Selection\" in the \"File\" menu.)<br><br>";
         html += "</div></div>";
 
@@ -47575,16 +48091,18 @@ class SetDialog {
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_mmdbid' class='" + dialogClass + "'>";
-        html += "MMDB or PDB ID: " + me.htmlCls.inputTextStr + "id='" + me.pre + "mmdbid' value='1TUP' size=8> ";
-        html += me.htmlCls.buttonStr + "reload_mmdb'>Load</button>";
+        html += "MMDB or PDB ID: " + me.htmlCls.inputTextStr + "id='" + me.pre + "mmdbid' value='1TUP' size=8> <br><br>";
+        html += me.htmlCls.buttonStr + "reload_mmdb_asym'>Load Asymmetric Unit (All Chains)</button>" + me.htmlCls.buttonStr + "reload_mmdb' style='margin-left:30px'>Load Biological Unit</button><br/><br/>";
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_blast_rep_id' style='max-width:500px;' class='" + dialogClass + "'>";
-        html += "Enter a Sequence ID(or FASTA sequence) and the aligned Structure ID, which can be found using the <a href='https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&DATABASE=pdb' target='_blank'>BLAST</a> search against the pdb database with the Sequence ID or FASTA sequence as input.<br><br> ";
+        html += "Enter a Sequence ID (or FASTA sequence) and the aligned Structure ID, which can be found using the <a href='https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&DATABASE=pdb' target='_blank'>BLAST</a> search against the pdb database with the Sequence ID or FASTA sequence as input.<br><br> ";
         html += "<b>Sequence ID</b>(NCBI protein accession of a sequence): " + me.htmlCls.inputTextStr + "id='" + me.pre + "query_id' value='NP_001108451.1' size=8><br> ";
         html += "or FASTA sequence: <br><textarea id='" + me.pre + "query_fasta' rows='5' style='width: 100%; height: " +(me.htmlCls.LOG_HEIGHT) + "px; padding: 0px; border: 0px;'></textarea><br><br>";
         html += "<b>Structure ID</b>(NCBI protein accession of a chain of a 3D structure): " + me.htmlCls.inputTextStr + "id='" + me.pre + "blast_rep_id' value='1TSR_A' size=8><br> ";
-        html += me.htmlCls.buttonStr + "reload_blast_rep_id'>Load</button>";
+        //html += me.htmlCls.buttonStr + "reload_blast_rep_id'>Load</button>";
+        html += me.htmlCls.buttonStr + "reload_blast_rep_id'>Align with BLAST</button> " + me.htmlCls.wifiStr
+            + me.htmlCls.buttonStr + "reload_alignsw' style='margin-left:30px'>Align with Smith-Waterman</button>";
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_yournote' class='" + dialogClass + "'>";
@@ -47965,23 +48483,28 @@ class SetDialog {
         html += me.htmlCls.divStr + "dl_addlabel' class='" + dialogClass + "'>";
         html += "1. Text: " + me.htmlCls.inputTextStr + "id='" + me.pre + "labeltext' value='Text' size=4><br/>";
         html += "2. Size: " + me.htmlCls.inputTextStr + "id='" + me.pre + "labelsize' value='18' size=4 maxlength=2><br/>";
-        html += "3. Color: " + me.htmlCls.inputTextStr + "id='" + me.pre + "labelcolor' value='ffff00' size=4><br/>";
-        html += "4. Background: " + me.htmlCls.inputTextStr + "id='" + me.pre + "labelbkgd' value='cccccc' size=4><br/>";
+        html += "3. Color: " + me.htmlCls.inputTextStr + "id='" + me.pre + "labelcolor' value='" + defaultColor + "' size=4><br/>";
+        //html += "4. Background: " + me.htmlCls.inputTextStr + "id='" + me.pre + "labelbkgd' value='' size=4><br/>";
         if(me.utilsCls.isMobile()) {
-            html += me.htmlCls.spanNowrapStr + "5. Touch TWO atoms</span><br/>";
+            html += me.htmlCls.spanNowrapStr + "4. Touch TWO atoms</span><br/>";
         }
         else {
-            html += me.htmlCls.spanNowrapStr + "5. Pick TWO atoms while holding \"Alt\" key</span><br/>";
+            html += me.htmlCls.spanNowrapStr + "4. Pick TWO atoms while holding \"Alt\" key</span><br/>";
         }
-        html += me.htmlCls.spanNowrapStr + "6. " + me.htmlCls.buttonStr + "applypick_labels'>Display</button></span>";
+        html += me.htmlCls.spanNowrapStr + "5. " + me.htmlCls.buttonStr + "applypick_labels'>Display</button></span>";
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_addlabelselection' class='" + dialogClass + "'>";
         html += "1. Text: " + me.htmlCls.inputTextStr + "id='" + me.pre + "labeltext2' value='Text' size=4><br/>";
         html += "2. Size: " + me.htmlCls.inputTextStr + "id='" + me.pre + "labelsize2' value='18' size=4 maxlength=2><br/>";
-        html += "3. Color: " + me.htmlCls.inputTextStr + "id='" + me.pre + "labelcolor2' value='ffff00' size=4><br/>";
-        html += "4. Background: " + me.htmlCls.inputTextStr + "id='" + me.pre + "labelbkgd2' value='cccccc' size=4><br/>";
-        html += me.htmlCls.spanNowrapStr + "5. " + me.htmlCls.buttonStr + "applyselection_labels'>Display</button></span>";
+        html += "3. Color: " + me.htmlCls.inputTextStr + "id='" + me.pre + "labelcolor2' value='" + defaultColor + "' size=4><br/>";
+        //html += "4. Background: " + me.htmlCls.inputTextStr + "id='" + me.pre + "labelbkgd2' value='' size=4><br/>";
+        html += me.htmlCls.spanNowrapStr + "4. " + me.htmlCls.buttonStr + "applyselection_labels'>Display</button></span>";
+        html += "</div>";
+
+        html += me.htmlCls.divStr + "dl_labelColor' class='" + dialogClass + "'>";
+        html += "Color for all labels: " + me.htmlCls.inputTextStr + "id='" + me.pre + "labelcolorall' value='" + defaultColor + "' size=4><br/><br/>";
+        html += me.htmlCls.spanNowrapStr + me.htmlCls.buttonStr + "applylabelcolor'>Display</button></span>";
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_distance' class='" + dialogClass + "'>";
@@ -47991,7 +48514,7 @@ class SetDialog {
         else {
             html += me.htmlCls.spanNowrapStr + "1. Pick TWO atoms while holding \"Alt\" key</span><br/>";
         }
-        html += me.htmlCls.spanNowrapStr + "2. Color: " + me.htmlCls.inputTextStr + "id='" + me.pre + "distancecolor' value='ffff00' size=4><br/>";
+        html += me.htmlCls.spanNowrapStr + "2. Line Color: " + me.htmlCls.inputTextStr + "id='" + me.pre + "distancecolor' value='" + defaultColor + "' size=4><br/>";
         html += me.htmlCls.spanNowrapStr + "3. " + me.htmlCls.buttonStr + "applypick_measuredistance'>Display</button></span>";
         html += "</div>";
 
@@ -48022,7 +48545,7 @@ class SetDialog {
 
         html += "</td></tr></table>";
 
-        html += me.htmlCls.spanNowrapStr + "2. Color: " + me.htmlCls.inputTextStr + "id='" + me.pre + "distancecolor2' value='ffff00' size=4><br/><br/>";
+        html += me.htmlCls.spanNowrapStr + "2. Color: " + me.htmlCls.inputTextStr + "id='" + me.pre + "distancecolor2' value='" + defaultColor + "' size=4><br/><br/>";
         html += me.htmlCls.spanNowrapStr + "3. " + me.htmlCls.buttonStr + "applydist2'>Display</button></span>";
         html += "</div>";
 
@@ -48799,20 +49322,24 @@ class Events {
         me.myEventCls.onIds("#" + me.pre + "reload_mmdb", "click", function(e) { me.icn3d;
            e.preventDefault();
            if(!me.cfg.notebook) dialog.dialog( "close" );
-           me.htmlCls.clickMenuCls.setLogCmd("load mmdb " + $("#" + me.pre + "mmdbid").val(), false);
-           //ic.mmdbParserCls.downloadMmdb($("#" + me.pre + "mmdbid").val());
-           //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmdbid=' + $("#" + me.pre + "mmdbid").val(), '_blank');
-           window.open(hostUrl + '?mmdbid=' + $("#" + me.pre + "mmdbid").val(), '_blank');
+           me.htmlCls.clickMenuCls.setLogCmd("load mmdb1 " + $("#" + me.pre + "mmdbid").val(), false);
+           window.open(hostUrl + '?mmdbid=' + $("#" + me.pre + "mmdbid").val() + '&buidx=1', '_blank');
         });
 
+        me.myEventCls.onIds("#" + me.pre + "reload_mmdb_asym", "click", function(e) { me.icn3d;
+            e.preventDefault();
+            if(!me.cfg.notebook) dialog.dialog( "close" );
+            me.htmlCls.clickMenuCls.setLogCmd("load mmdb0 " + $("#" + me.pre + "mmdbid").val(), false);
+            window.open(hostUrl + '?mmdbid=' + $("#" + me.pre + "mmdbid").val() + '&buidx=0', '_blank');
+         });
+
         me.myEventCls.onIds("#" + me.pre + "mmdbid", "keyup", function(e) { me.icn3d;
            if (e.keyCode === 13) {
                e.preventDefault();
                if(!me.cfg.notebook) dialog.dialog( "close" );
-               me.htmlCls.clickMenuCls.setLogCmd("load mmdb " + $("#" + me.pre + "mmdbid").val(), false);
-               //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?mmdbid=' + $("#" + me.pre + "mmdbid").val(), '_blank');
-               window.open(hostUrl + '?mmdbid=' + $("#" + me.pre + "mmdbid").val(), '_blank');
-           }
+               me.htmlCls.clickMenuCls.setLogCmd("load mmdb0 " + $("#" + me.pre + "mmdbid").val(), false);
+               window.open(hostUrl + '?mmdbid=' + $("#" + me.pre + "mmdbid").val() + '&buidx=0', '_blank');
+              }
         });
 
     //    },
@@ -48826,12 +49353,27 @@ class Events {
            me.htmlCls.clickMenuCls.setLogCmd("load seq_struct_ids " + query_id + "," + blast_rep_id, false);
            query_id =(query_id !== '' && query_id !== undefined) ? query_id : query_fasta;
            //window.open(me.htmlCls.baseUrl + 'icn3d/full.html?from=icn3d&blast_rep_id=' + blast_rep_id
-           window.open(hostUrl + '?from=icn3d&blast_rep_id=' + blast_rep_id
+           window.open(hostUrl + '?from=icn3d&alg=blast&blast_rep_id=' + blast_rep_id
              + '&query_id=' + query_id
              + '&command=view annotations; set annotation cdd; set annotation site; set view detailed view; select chain '
              + blast_rep_id + '; show selection', '_blank');
         });
 
+        me.myEventCls.onIds("#" + me.pre + "reload_alignsw", "click", function(e) { me.icn3d;
+            e.preventDefault();
+            if(!me.cfg.notebook) dialog.dialog( "close" );
+            let query_id = $("#" + me.pre + "query_id").val();
+            let query_fasta = encodeURIComponent($("#" + me.pre + "query_fasta").val());
+            let blast_rep_id = $("#" + me.pre + "blast_rep_id").val();
+            me.htmlCls.clickMenuCls.setLogCmd("load seq_struct_ids_smithwm " + query_id + "," + blast_rep_id, false);
+            query_id =(query_id !== '' && query_id !== undefined) ? query_id : query_fasta;
+            
+            window.open(hostUrl + '?from=icn3d&alg=smithwm&blast_rep_id=' + blast_rep_id
+              + '&query_id=' + query_id
+              + '&command=view annotations; set annotation cdd; set annotation site; set view detailed view; select chain '
+              + blast_rep_id + '; show selection', '_blank');
+         });
+
     //    },
     //    clickReload_gi: function() {
         me.myEventCls.onIds("#" + me.pre + "reload_gi", "click", function(e) { me.icn3d;
@@ -49070,11 +49612,11 @@ class Events {
            thisClass.loadPdbFile(bAppend);
         });
 
-        me.myEventCls.onIds("#" + me.pre + "reload_pdbfile_app", "click", function(e) { me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_pdbfile_app", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
 
-           var bAppend = true;
-           thisClass.loadPdbFile(bAppend);
+           ic.bAppend = true;
+           thisClass.loadPdbFile(ic.bAppend);
         });
 
     //    },
@@ -49658,6 +50200,15 @@ class Events {
              me.htmlCls.clickMenuCls.setLogCmd('add label ' + text + ' | x ' + x.toPrecision(4)  + ' y ' + y.toPrecision(4) + ' z ' + z.toPrecision(4) + sizeStr + colorStr + backgroundStr + ' | type custom', true);
              ic.drawCls.draw();
         });
+
+        me.myEventCls.onIds("#" + me.pre + "applylabelcolor", "click", function(e) { let ic = me.icn3d;
+            e.preventDefault();
+            if(!me.cfg.notebook) dialog.dialog( "close" );
+            ic.labelcolor = $("#" + me.pre + "labelcolorall" ).val();
+
+            me.htmlCls.clickMenuCls.setLogCmd('set label color ' + ic.labelcolor, true);
+            ic.drawCls.draw();
+        });
     //    },
     //    clickApplypick_stabilizer: function() {
         me.myEventCls.onIds("#" + me.pre + "applypick_stabilizer", "click", function(e) { let ic = me.icn3d;
@@ -50517,6 +51068,7 @@ class SetHtml {
         let light2 = 0.4;
         let light3 = 0.2;
         let bGlycansCartoon = 0;
+        let bMembrane = 1;
 
         // retrieve from cache
         if(type == 'style') {
@@ -50545,6 +51097,10 @@ class SetHtml {
                 bGlycansCartoon = parseFloat(this.getCookie('glycan'));
             }
 
+            if(this.getCookie('membrane') != '') {
+                bMembrane = parseFloat(this.getCookie('membrane'));
+            }
+
             html += "<b>Note</b>: The following parameters will be saved in cache. You just need to set them once. <br><br>";
 
             html += "<b>1. Shininess</b>: " + me.htmlCls.inputTextStr + "id='" + me.pre + "shininess' value='" + shininess + "' size=4>" + me.htmlCls.space3 + "(for the shininess of the 3D objects, default 40)<br/><br/>";
@@ -50567,7 +51123,9 @@ class SetHtml {
         html += "<b>Ball Scale</b>: " + me.htmlCls.inputTextStr + "id='" + me.pre + "ballscale_" + type + "' value='" + ballscale + "' size=4>" + me.htmlCls.space3 + "(for styles 'Ball and Stick' and 'Dot', default 0.3)<br/>";
 
         if(type == 'style') {
-            html += "<br><b>4. Show Glycan Cartoon</b>: " + me.htmlCls.inputTextStr + "id='" + me.pre + "glycan' value='" + bGlycansCartoon + "' size=4>" + me.htmlCls.space3 + "(0: hide, 1: show, default 0)<br/><br/>";
+            html += "<br><b>4. Show Glycan Cartoon</b>: " + me.htmlCls.inputTextStr + "id='" + me.pre + "glycan' value='" + bGlycansCartoon + "' size=4>" + me.htmlCls.space3 + "(0: hide, 1: show, default 0)<br/>";
+
+            html += "<br><b>5. Show Membrane</b>: " + me.htmlCls.inputTextStr + "id='" + me.pre + "membrane' value='" + bMembrane + "' size=4>" + me.htmlCls.space3 + "(0: hide, 1: show, default 1)<br/><br/>";
         }
 
         html += me.htmlCls.spanNowrapStr + "" + me.htmlCls.buttonStr + "apply_thickness_" + type + "'>Apply</button></span>&nbsp;&nbsp;&nbsp;";
@@ -50760,8 +51318,8 @@ class SetHtml {
 
         html += "<span style='white-space:nowrap;font-weight:bold;'>Potential contour at: <select id='" + me.pre + name1 + "contour'>";
 
-        let optArray1b = ['0.5', '1', '2', '4', '6', '8', '10'];
-        html += this.getOptionHtml(optArray1b, 1);
+        let optArray1b = ['0.5', '1', '2', '3', '4', '5', '6', '7', '8', '9', '10'];
+        html += this.getOptionHtml(optArray1b, 2);
 
         html += "</select> kT/e(25.6mV at 298K)</span><br/><br/>";
 
@@ -50825,7 +51383,7 @@ class SetHtml {
 
         html += "<span style='white-space:nowrap;font-weight:bold;'>Surface with max potential at: <select id='" + me.pre + name1 + "contour2'>";
 
-        let optArray1c = ['1', '2', '3', '4', '5', '6', '7', '8', '9', '10'];
+        let optArray1c = ['0.5', '1', '2', '3', '4', '5', '6', '7', '8', '9', '10'];
         html += this.getOptionHtml(optArray1c, 2);
 
         html += "</select> kT/e(25.6mV at 298K)</span><br/><br/>";
@@ -51038,7 +51596,7 @@ class SetHtml {
         });
     }
 
-    loadPng(imageStr) { let me = this.icn3dui, ic = me.icn3d;
+    loadPng(imageStr, command) { let me = this.icn3dui, ic = me.icn3d;
        let matchedStr = 'Share Link: ';
        let pos = imageStr.indexOf(matchedStr);
        let matchedStrState = "Start of state file======\n";
@@ -51055,6 +51613,8 @@ class SetHtml {
            let matchedStrData = "Start of data file======\n";
            let posData = imageStr.indexOf(matchedStrData);
            ic.bInputfile =(posData == -1) ? false : true;
+           let commandStr = (command) ? command.replace(/;/g, "\n") : '';
+
            if(ic.bInputfile) {
                let posDataEnd = imageStr.indexOf("End of data file======\n");
                let data = imageStr.substr(posData + matchedStrData.length, posDataEnd - posData - matchedStrData.length);
@@ -51070,7 +51630,9 @@ class SetHtml {
                //var posState = imageStr.indexOf(matchedStrState);
                let posStateEnd = imageStr.indexOf("End of state file======\n");
                let statefile = imageStr.substr(posState + matchedStrState.length, posStateEnd - posState- matchedStrState.length);
-               statefile = decodeURIComponent(statefile);
+               //statefile = decodeURIComponent(statefile);
+               statefile = decodeURIComponent(statefile + "\n" + commandStr);
+
                 if(type === 'pdb') {
                     $.when( ic.pdbParserCls.loadPdbData(data))
                      .then(function() {
@@ -51102,7 +51664,9 @@ class SetHtml {
                //var posState = imageStr.indexOf(matchedStrState);
                let posStateEnd = imageStr.indexOf("End of state file======\n");
                let statefile = imageStr.substr(posState + matchedStrState.length, posStateEnd - posState- matchedStrState.length);
-               statefile = decodeURIComponent(statefile);
+               //statefile = decodeURIComponent(statefile);
+               statefile = decodeURIComponent(statefile + "\n" + commandStr);
+
                ic.commands = [];
                ic.optsHistory = [];
                ic.loadScriptCls.loadScript(statefile, true);
@@ -51165,6 +51729,7 @@ class SetHtml {
                 $("#" + me.pre + "light2").val('0.4');
                 $("#" + me.pre + "light3").val('0.2');
                 $("#" + me.pre + "glycan").val('0');
+                $("#" + me.pre + "membrane").val('1');
             }
 
             ic.shininess = parseFloat($("#" + me.pre + "shininess").val()); //40;
@@ -51172,6 +51737,7 @@ class SetHtml {
             ic.light2 = parseFloat($("#" + me.pre + "light2").val()); //0.4;
             ic.light3 = parseFloat($("#" + me.pre + "light3").val()); //0.2;
             ic.bGlycansCartoon = parseInt($("#" + me.pre + "glycan").val()); //0;
+            ic.bMembrane = parseInt($("#" + me.pre + "membrane").val()); //1;
         }
 
         if(bReset) {
@@ -51202,6 +51768,7 @@ class SetHtml {
             this.setCookie('light2', ic.light2, exdays);
             this.setCookie('light3', ic.light3, exdays);
             this.setCookie('glycan', ic.bGlycansCartoon, exdays);
+            this.setCookie('membrane', ic.bMembrane, exdays);
         }
 
         this.setCookieForThickness();
@@ -51214,6 +51781,9 @@ class SetHtml {
         }
         else {
             me.htmlCls.clickMenuCls.setLogCmd('set thickness | linerad ' + ic.lineRadius + ' | coilrad ' + ic.coilWidth + ' | stickrad ' + ic.cylinderRadius + ' | tracerad ' + ic.traceRadius + ' | ribbonthick ' + ic.ribbonthickness + ' | proteinwidth ' + ic.helixSheetWidth + ' | nucleotidewidth ' + ic.nucleicAcidWidth  + ' | ballscale ' + ic.dotSphereScale, true);
+
+            me.htmlCls.clickMenuCls.setLogCmd('set glycan ' + ic.bGlycansCartoon, true);
+            me.htmlCls.clickMenuCls.setLogCmd('set membrane ' + ic.bMembrane, true);
         }
 
         ic.drawCls.draw();
@@ -51263,7 +51833,7 @@ class Html {
     this.cfg = this.icn3dui.cfg;
 
     this.opts = {};
-    this.opts['background']         = 'transparent';        //transparent, black, grey, white
+    this.opts['background']         = 'black';        //transparent, black, grey, white
 
     this.WIDTH = 400; // total width of view area
     this.HEIGHT = 400; // total height of view area
@@ -53019,6 +53589,398 @@ class DensityCifParser {
     }
 }
 
+/**
+ * @author Jack Lin, modified from https://github.com/lh3/bioseq-js/blob/master/bioseq.js
+ */
+
+//import { HashUtilsCls } from '../../utils/hashUtilsCls.js';
+
+//import { Html } from '../../html/html.js';
+
+//import { SaveFile } from '../export/saveFile.js';
+//import { PdbParser } from '../parsers/pdbParser.js';
+
+class AlignSW {
+    constructor(icn3d) {
+        this.icn3d = icn3d;
+    }
+
+    alignSW(target, query, match_score, mismatch, gap, extension, is_local = false) { let ic = this.icn3d; ic.icn3dui;
+        //let time_start = new Date().getTime();
+
+        let rst = this.bsa_align(is_local, target, query, [match_score, mismatch], [gap, extension]);
+        let str = 'score: ' + rst[0] + '\n';
+        str += 'start: ' + rst[1] + '\n';
+        str += 'cigar: ' + this.bsa_cigar2str(rst[2]) + '\n\n';
+        str += 'alignment:\n\n';
+        let fmt = this.bsa_cigar2gaps(target, query, rst[1], rst[2]);
+
+/*
+        //let anno_seq = document.getElementById("div0_dl_annotations")
+        let algn = "<div id=waterman_alignment><span>" + 'score: ' + rst[0] + '<br>' + 'start: ' + rst[1] + '<br>' + 'cigar: ' + this.bsa_cigar2str(rst[2]) + '<br><br>' + 'alignment:' + '<br>'
+
+        let linelen = 100,
+            n_lines = 10;
+        for (let l = 0; l < fmt[0].length; l += linelen) {
+            str += fmt[0].substr(l, linelen) + '\n';
+            str += fmt[2].substr(l, linelen) + '\n';
+            str += fmt[1].substr(l, linelen) + '\n\n';
+            n_lines += 4;
+        }
+
+        algn += '<pre>'
+        algn += fmt[0] + '<br>';
+        algn += fmt[2] + '<br>';
+        algn += fmt[1] + '<br><br>';
+        algn += '</pre><br>' + "</span></div>"
+
+        //anno_seq.innerHTML += algn
+
+        //let elapse = (new Date().getTime() - time_start) / 1000.0;
+        //console.log("in " + elapse.toFixed(3) + "s");
+*/
+        let algn = {};
+        algn.score = rst[0];
+        algn.start = rst[1];
+        algn.cigar = this.bsa_cigar2str(rst[2]);
+        algn.target = fmt[0];
+        algn.query = fmt[1];
+
+        return algn;
+    }
+
+    /**
+     * Encode a sequence string with table
+     *
+     * @param seq    sequence
+     * @param table  encoding table; must be of size 256
+     *
+     * @return an integer array
+     */
+
+    bsg_enc_seq(seq, table) { let ic = this.icn3d; ic.icn3dui;
+        if (table == null) return null;
+        let s = [];
+        s.length = seq.length;
+        for (let i = 0; i < seq.length; ++i)
+            s[i] = table[seq.charCodeAt(i)];
+        return s;
+    }
+
+    /*
+        ks_revcomp(s) { let ic = this.icn3d, me = ic.icn3dui;
+            let ks_comp = {'A':'T','C':'G','G':'C','T':'A','M':'K','K':'M','Y':'R','R':'Y','V':'B','B':'V','H':'D','D':'H',
+                        'a':'t','c':'g','g':'c','t':'a','m':'k','k':'m','y':'r','r':'y','v':'b','b':'v','h':'d','d':'h'};
+
+            let i, t = '';
+            for (i = 0; i < s.length; ++i) {
+                let c = s.charAt(s.length - 1 - i);
+                let d = ks_comp[c];
+                t += d? d : c;
+            }
+            return t;
+        }
+    */
+
+    /**************************
+     *** Pairwise alignment ***
+        **************************/
+
+    /*
+        * The following implements local and global pairwise alignment with affine gap
+        * penalties. There are two formulations: the Durbin formulation as is
+        * described in his book and the Green formulation as is implemented in phrap.
+        * The Durbin formulation is easier to understand, while the Green formulation
+        * is simpler to code and probably faster in practice.
+        *
+        * The Durbin formulation is:
+        *
+        *   M(i,j) = max{M(i-1,j-1)+S(i,j), E(i-1,j-1), F(i-1,j-1)}
+        *   E(i,j) = max{M(i-1,j)-q-r, F(i-1,j)-q-r, E(i-1,j)-r}
+        *   F(i,j) = max{M(i,j-1)-q-r, F(i,j-1)-r, E(i,j-1)-q-r}
+        *
+        * where q is the gap open penalty, r the gap extension penalty and S(i,j) is
+        * the score between the i-th residue in the row sequence and the j-th residue
+        * in the column sequence. Note that the original Durbin formulation disallows
+        * transitions between between E and F states, but we allow them here.
+        *
+        * In the Green formulation, we introduce:
+        *
+        *   H(i,j) = max{M(i,j), E(i,j), F(i,j)}
+        *
+        * The recursion becomes:
+        *
+        *   H(i,j) = max{H(i-1,j-1)+S(i,j), E(i,j), F(i,j)}
+        *   E(i,j) = max{H(i-1,j)-q, E(i-1,j)} - r
+        *   F(i,j) = max{H(i,j-1)-q, F(i,j-1)} - r
+        *
+        * It is in fact equivalent to the Durbin formulation. In implementation, we
+        * calculate the scores in a different order:
+        *
+        *   H(i,j)   = max{H(i-1,j-1)+S(i,j), E(i,j), F(i,j)}
+        *   E(i+1,j) = max{H(i,j)-q, E(i,j)} - r
+        *   F(i,j+1) = max{H(i,j)-q, F(i,j)} - r
+        *
+        * i.e. at cell (i,j), we compute E for the next row and F for the next column.
+        * Please see inline comments below for details.
+        *
+        *
+        * The following implementation is ported from klib/ksw.c. The original C
+        * implementation has a few bugs which have been fixed here. Like the C
+        * version, this implementation should be very efficient. It could be made more
+        * efficient if we use typed integer arrays such as Uint8Array. In addition,
+        * I mixed the local and global alignments together. For performance,
+        * it would be preferred to separate them out.
+        */
+
+    /**
+     * Generate scoring matrix from match/mismatch score
+     *
+     * @param n     size of the alphabet
+     * @param a     match score, positive
+     * @param b     mismatch score, negative
+     *
+     * @return sqaure scoring matrix. The last row and column are zero, for
+     * matching an ambiguous residue.
+     */
+    bsa_gen_score_matrix(n, a, b) { let ic = this.icn3d; ic.icn3dui;
+        let m = [];
+        if (b > 0) b = -b; // mismatch score b should be non-positive
+        let i, j;
+        for (i = 0; i < n - 1; ++i) {
+            m[i] = [];
+            for (j = 0; j < n - 1; ++j)
+                m[i][j] = i == j ? a : b;
+            m[i][j] = 0;
+        }
+        m[n - 1] = [];
+        for (let j = 0; j < n; ++j) m[n - 1][j] = 0;
+        return m;
+    }
+
+    /**
+     * Generate query profile (a preprocessing step)
+     *
+     * @param _s      sequence in string or post bsg_enc_seq()
+     * @param _m      score matrix or [match,mismatch] array
+     * @param table   encoding table; must be consistent with _s and _m
+     *
+     * @return query profile. It is a two-dimensional integer matrix.
+     */
+    bsa_gen_query_profile(_s, _m, table) { let ic = this.icn3d; ic.icn3dui;
+        let s = typeof _s == 'string' ? this.bsg_enc_seq(_s, table) : _s;
+        let qp = [],
+            matrix;
+        if (_m.length >= 2 && typeof _m[0] == 'number' && typeof _m[1] == 'number') { // match/mismatch score
+            if (table == null) return null;
+            let n = typeof table == 'number' ? table : table[table.length - 1] + 1;
+            matrix = this.bsa_gen_score_matrix(n, _m[0], _m[1]);
+        } else matrix = _m; // _m is already a matrix; FIXME: check if it is really a square matrix!
+        for (let j = 0; j < matrix.length; ++j) {
+            let qpj, mj = matrix[j];
+            qpj = qp[j] = [];
+            for (let i = 0; i < s.length; ++i)
+                qpj[i] = mj[s[i]];
+        }
+        return qp;
+    }
+
+    /**
+     * Local or global pairwise alignemnt
+     *
+     * @param is_local  perform local alignment
+     * @param target    target string
+     * @param query     query string or query profile
+     * @param matrix    square score matrix or [match,mismatch] array
+     * @param gapsc     [gap_open,gap_ext] array; k-length gap costs gap_open+gap_ext*k
+     * @param w         bandwidth, disabled by default
+     * @param table     encoding table. It defaults to bst_nt5.
+     *
+     * @return [score,target_start,cigar]. cigar is encoded in the BAM way, where
+     * higher 28 bits keeps the length and lower 4 bits the operation in order of
+     * "MIDNSH". See bsa_cigar2str() for converting cigar to string.
+     */
+    bsa_align(is_local, target, query, matrix, gapsc, w, table) { let ic = this.icn3d; ic.icn3dui;
+        let bst_nt5 = [
+            4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+            4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+            4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+            4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+            4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
+            4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+            4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
+            4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+
+            4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+            4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+            4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+            4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+            4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+            4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+            4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+            4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
+        ];
+
+        // convert bases to integers
+        if (table == null) table = bst_nt5;
+        let t = this.bsg_enc_seq(target, table);
+        let qp = this.bsa_gen_query_profile(query, matrix, table);
+        let qlen = qp[0].length;
+
+        // adjust band width
+        let max_len = qlen > t.length ? qlen : t.length;
+        w = w == null || w < 0 ? max_len : w;
+        let len_diff = t.target > qlen ? t.target - qlen : qlen - t.target;
+        w = w > len_diff ? w : len_diff;
+
+        // set gap score
+        let gapo, gape; // these are penalties which should be non-negative
+        if (typeof gapsc == 'number') gapo = 0, gape = gapsc > 0 ? gapsc : -gapsc;
+        else gapo = gapsc[0] > 0 ? gapsc[0] : -gapsc[0], gape = gapsc[1] > 0 ? gapsc[1] : -gapsc[1];
+        let gapoe = gapo + gape; // penalty for opening the first gap
+
+        // initial values
+        let NEG_INF = -0x40000000;
+        let H = [],
+            E = [],
+            z = [],
+            score, max = 0,
+            end_i = -1,
+            end_j = -1;
+        if (is_local) {
+            for (let j = 0; j <= qlen; ++j) H[j] = E[j] = 0;
+        } else {
+            H[0] = 0;
+            E[0] = -gapoe - gapoe;
+            for (let j = 1; j <= qlen; ++j) {
+                if (j >= w) H[j] = E[j] = NEG_INF; // everything is -inf outside the band
+                else H[j] = -(gapoe + gape * (j - 1)), E[j] = -(gapoe + gapoe + gape * j);
+            }
+        }
+
+        // the DP loop
+        for (let i = 0; i < t.length; ++i) {
+            let h1 = 0,
+                f = 0,
+                m = 0,
+                mj = -1;
+            let zi, qpi = qp[t[i]];
+            zi = z[i] = [];
+            let beg = i > w ? i - w : 0;
+            let end = i + w + 1 < qlen ? i + w + 1 : qlen; // only loop through [beg,end) of the query sequence
+            if (!is_local) {
+                h1 = beg > 0 ? NEG_INF : -(gapoe + gape * i);
+                f = beg > 0 ? NEG_INF : -(gapoe + gapoe + gape * i);
+            }
+            for (let j = beg; j < end; ++j) {
+                // At the beginning of the loop: h=H[j]=H(i-1,j-1), e=E[j]=E(i,j), f=F(i,j) and h1=H(i,j-1)
+                // If we only want to compute the max score, delete all lines involving direction "d".
+                let e = E[j],
+                    h = H[j],
+                    d;
+                H[j] = h1; // set H(i,j-1) for the next row
+                h += qpi[j]; // h = H(i-1,j-1) + S(i,j)
+                d = h >= e ? 0 : 1;
+                h = h >= e ? h : e;
+                d = h >= f ? d : 2;
+                h = h >= f ? h : f; // h = H(i,j) = max{H(i-1,j-1)+S(i,j), E(i,j), F(i,j)}
+                d = !is_local || h > 0 ? d : 1 << 6;
+                h1 = h; // save H(i,j) to h1 for the next column
+                mj = m > h ? mj : j;
+                m = m > h ? m : h; // update the max score in this row
+                h -= gapoe;
+                h = !is_local || h > 0 ? h : 0;
+                e -= gape;
+                d |= e > h ? 1 << 2 : 0;
+                e = e > h ? e : h; // e = E(i+1,j)
+                E[j] = e; // save E(i+1,j) for the next row
+                f -= gape;
+                d |= f > h ? 2 << 4 : 0;
+                f = f > h ? f : h; // f = F(i,j+1)
+                zi[j] = d; // z[i,j] keeps h for the current cell and e/f for the next cell
+            }
+            H[end] = h1, E[end] = is_local ? 0 : NEG_INF;
+            if (m > max) max = m, end_i = i, end_j = mj;
+        }
+        if (is_local && max == 0) return null;
+        score = is_local ? max : H[qlen];
+
+        let cigar = [],
+            tmp, which = 0,
+            i, k, start_i = 0;
+        if (is_local) {
+            i = end_i, k = end_j;
+            if (end_j != qlen - 1) // then add soft cliping
+                this.push_cigar(cigar, 4, qlen - 1 - end_j);
+        } else i = t.length - 1, k = (i + w + 1 < qlen ? i + w + 1 : qlen) - 1; // (i,k) points to the last cell
+        while (i >= 0 && k >= 0) {
+            tmp = z[i][k - (i > w ? i - w : 0)];
+            which = tmp >> (which << 1) & 3;
+            if (which == 0 && tmp >> 6) break;
+            if (which == 0) which = tmp & 3;
+            if (which == 0) { this.push_cigar(cigar, 0, 1);--i, --k; } // match
+            else if (which == 1) { this.push_cigar(cigar, 2, 1);--i; } // deletion
+            else { this.push_cigar(cigar, 1, 1), --k; } // insertion
+        }
+        if (is_local) {
+            if (k >= 0) this.push_cigar(cigar, 4, k + 1); // add soft clipping
+            start_i = i + 1;
+        } else { // add the first insertion or deletion
+            if (i >= 0) this.push_cigar(cigar, 2, i + 1);
+            if (k >= 0) this.push_cigar(cigar, 1, k + 1);
+        }
+        for (let i = 0; i < cigar.length >> 1; ++i) // reverse CIGAR
+            tmp = cigar[i], cigar[i] = cigar[cigar.length - 1 - i], cigar[cigar.length - 1 - i] = tmp;
+        return [score, start_i, cigar];
+    }
+
+    // backtrack to recover the alignment/cigar
+    push_cigar(ci, op, len) { let ic = this.icn3d; ic.icn3dui;
+        if (ci.length == 0 || op != (ci[ci.length - 1] & 0xf))
+            ci.push(len << 4 | op);
+        else ci[ci.length - 1] += len << 4;
+    }
+
+    bsa_cigar2gaps(target, query, start, cigar) { let ic = this.icn3d; ic.icn3dui;
+        let oq = '',
+            ot = '',
+            mid = '',
+            lq = 0,
+            lt = start;
+        for (let k = 0; k < cigar.length; ++k) {
+            let op = cigar[k] & 0xf,
+                len = cigar[k] >> 4;
+            if (op == 0) { // match
+                oq += query.substr(lq, len);
+                ot += target.substr(lt, len);
+                lq += len, lt += len;
+            } else if (op == 1) { // insertion
+                oq += query.substr(lq, len);
+                ot += Array(len + 1).join("-");
+                lq += len;
+            } else if (op == 2) { // deletion
+                oq += Array(len + 1).join("-");
+                ot += target.substr(lt, len);
+                lt += len;
+            } else if (op == 4) { // soft clip
+                lq += len;
+            }
+        }
+        let ut = ot.toUpperCase();
+        let uq = oq.toUpperCase();
+        for (let k = 0; k < ut.length; ++k)
+            mid += ut.charAt(k) == uq.charAt(k) ? '|' : ' ';
+        return [ot, oq, mid];
+    }
+
+    bsa_cigar2str(cigar) { let ic = this.icn3d; ic.icn3dui;
+        let s = [];
+        for (let k = 0; k < cigar.length; ++k)
+            s.push((cigar[k] >> 4).toString() + "MIDNSHP=XB".charAt(cigar[k] & 0xf));
+        return s.join("");
+    }
+}
+
 /**
  * @author Jiyao Wang <wangjiy@ncbi.nlm.nih.gov> / https://github.com/ncbi/icn3d
  */
@@ -53114,7 +54076,7 @@ class Ray {
             // the intersections are sorted so that the closest point is the first one.
             intersects[ 0 ].point.sub(position); // mdl.position was moved to the original (0,0,0) after reading the molecule coordinates. The raycasting was done based on the original. The position of the original should be substracted.
 
-            let  threshold = 0.5;
+            let  threshold = ic.rayThreshold; //0.5;
             let  atom = this.getAtomsFromPosition(intersects[ 0 ].point, threshold); // the second parameter is the distance threshold. The first matched atom will be returned. Use 1 angstrom, not 2 angstrom. If it's 2 angstrom, other atom will be returned.
 
             while(!atom && threshold < 10) {
@@ -53643,6 +54605,8 @@ class iCn3D {
     this.bImpo = true;
     this.bInstanced = true;
 
+    this.chainMissingResidueArray = {};
+
     if(!this.icn3dui.bNode) {
         this.bExtFragDepth = this.renderer.extensions.get( "EXT_frag_depth" );
         if(!this.bExtFragDepth) {
@@ -53702,7 +54666,7 @@ class iCn3D {
     this.bCalphaOnly = false; // by default the input has both Calpha and O, used for drawing strands. If atoms have Calpha only, the orientation of the strands is random
 //    this.bSSOnly = false; // a flag to turn on when only helix and bricks are available to draw 3D dgm
 
-    this.bAllAtoms = true; // no need to adjust atom for strand style
+//    this.bAllAtoms = true; // no need to adjust atom for strand style
 
     this.bConsiderNeighbors = false; // a flag to show surface considering the neighboring atoms or not
 
@@ -53763,10 +54727,14 @@ class iCn3D {
 
     this.LABELSIZE = 30;
 
+    this.rayThreshold = 0.5; // threadshold for raycast
+    this.colorBlackbkgd = '#ffff00';
+    this.colorWhitebkgd = '#000000';
+
     //The default display options
     this.optsOri = {};
     this.optsOri['camera']             = 'perspective';        //perspective, orthographic
-    this.optsOri['background']         = 'transparent';        //transparent, black, grey, white
+    this.optsOri['background']         = 'black';              //transparent, black, grey, white
     this.optsOri['color']              = 'chain';              //spectrum, secondary structure, charge, hydrophobic, conserved, chain, residue, atom, b factor, red, green, blue, magenta, yellow, cyan, white, grey, custom
     this.optsOri['proteins']           = 'ribbon';             //ribbon, strand, cylinder and plate, schematic, c alpha trace, backbone, b factor tube, lines, stick, ball and stick, sphere, nothing
     this.optsOri['sidec']              = 'nothing';            //lines, stick, ball and stick, sphere, nothing
@@ -53958,6 +54926,7 @@ class iCn3D {
     this.dsspCls = new Dssp(this);
     this.scapCls = new Scap(this);
     this.symdCls = new Symd(this);
+    this.alignSWCls = new AlignSW(this);
 
     this.analysisCls = new Analysis(this);
     this.resizeCanvasCls = new ResizeCanvas(this);
@@ -54014,6 +54983,8 @@ iCn3D.prototype.init_base = function (bKeepCmd) {
     this.chainsAn = {}; // structure_chain name -> array of annotations, such as residue number
     this.chainsAnTitle = {}; // structure_chain name -> array of annotation title
 
+    this.chainsMapping = {}; // structure_chain name -> residue id hash such as {'structure_chain_resi1': 'reference residue such as K10', ...}
+
     this.alnChainsSeq = {}; // structure_chain name -> array of residue object: {mmdbid, chain, resi, resn, aligned}
     this.alnChainsAnno = {}; // structure_chain name -> array of annotations, such as residue number
     this.alnChainsAnTtl = {}; // structure_chain name -> array of annotation title
@@ -54090,9 +55061,13 @@ iCn3D.prototype.init_base = function (bKeepCmd) {
 
     this.axes = [];
 
-    this.bGlycansCartoon = false;
+    this.bGlycansCartoon = 0;
+    this.bMembrane = 1;
 
     this.chainid2offset = {};
+
+    this.chainMissingResidueArray = {};
+    this.nTotalGap = 0;
 };
 
 //Reset parameters for displaying the loaded structure.
@@ -54159,7 +55134,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.4.11';
+    this.REVISION = '3.7.0';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -54205,7 +55180,7 @@ class iCn3DUI {
 iCn3DUI.prototype.show3DStructure = function() { let me = this;
   let thisClass = this;
   me.deferred = $.Deferred(function() {
-    if(me.cfg.menumode == 1) {
+    if(me.cfg.menuicon) {
         me.htmlCls.wifiStr = '<i class="icn3d-wifi" title="requires internet">&nbsp;</i>';
         me.htmlCls.licenseStr = '<i class="icn3d-license" title="requires license">&nbsp;</i>';
     }
@@ -54336,7 +55311,7 @@ iCn3DUI.prototype.show3DStructure = function() { let me = this;
 
         ic.loadCmd = 'load url ' + url + ' | type ' + type;
         me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
-        ic.pdbParserCls.downloadUrl(url, type);
+        ic.pdbParserCls.downloadUrl(url, type, me.cfg.command);
     }
     else if(me.cfg.mmtfid !== undefined) {
        ic.inputid = me.cfg.mmtfid;
@@ -54387,7 +55362,16 @@ iCn3DUI.prototype.show3DStructure = function() { let me = this;
        // custom seqeunce has query_id such as "Query_78989" in BLAST
        if(me.cfg.query_id.substr(0,5) !== 'Query' && me.cfg.rid === undefined) {
            ic.inputid = me.cfg.query_id + '_' + me.cfg.blast_rep_id;
-           ic.loadCmd = 'load seq_struct_ids ' + me.cfg.query_id + ',' + me.cfg.blast_rep_id;
+
+           if(me.cfg.alg == 'smithwm') {
+            ic.loadCmd = 'load seq_struct_ids_smithwm ' + me.cfg.query_id + ',' + me.cfg.blast_rep_id;
+            ic.bSmithwm = true;
+           }
+           else {
+            ic.loadCmd = 'load seq_struct_ids ' + me.cfg.query_id + ',' + me.cfg.blast_rep_id;
+            ic.bSmithwm = false;
+           }
+           
            me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
            ic.mmdbParserCls.downloadBlast_rep_id(me.cfg.query_id + ',' + me.cfg.blast_rep_id);
        }
@@ -54627,6 +55611,7 @@ class printMsg {
 
 exports.AddTrack = AddTrack;
 exports.AlignParser = AlignParser;
+exports.AlignSW = AlignSW;
 exports.AlignSeq = AlignSeq;
 exports.Alternate = Alternate;
 exports.Analysis = Analysis;