icn3d 3.23.2 → 3.23.4

package/icn3d.js

@@ -10602,7 +10602,7 @@ class SetDialog {
 
         html += me.htmlCls.divStr + "dl_mutation' class='" + dialogClass + "'>";
         html += "<div style='width:500px'>";
-        html += 'Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[<b>uppercase</b> PDB ID or AlphaFold UniProt ID]_[Chain ID]_[Residue Number]_[One Letter Mutant Residue]". E.g., the mutation of N501Y in the E chain of PDB 6M0J can be specified as "6M0J_E_501_Y". For AlphaFold structures, the "Chain ID" is "A".<br/><br/>';
+        html += 'Please specify the mutations with a comma separated mutation list. Each mutation can be specified as "[<b>uppercase</b> PDB ID or AlphaFold UniProt ID]_[Chain Name]_[Residue Number]_[One Letter Mutant Residue]". E.g., the mutation of N501Y in the E chain of PDB 6M0J can be specified as "6M0J_E_501_Y". For AlphaFold structures, the "Chain ID" is "A".<br/>If you load a custom structure without PDB or UniProt ID, you can open "Seq. & Annotations" window and find the chain ID such as "stru_A". The part before the underscore is the structure ID, which can be used to specify the mutation such as "stru_A_...". Remember to choose "Show Mutation in: Current Page".<br/><br/>';
         html += "<div style='display:inline-block; width:110px'>Mutations: </div>" + me.htmlCls.inputTextStr + "id='" + me.pre + "mutationids' value='6M0J_E_484_K,6M0J_E_501_Y,6M0J_E_417_N' size=50><br/><br/>";
  
         html += '<b>ID Type</b>: ';
@@ -10675,8 +10675,9 @@ class SetDialog {
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_mmdbafid' class='" + dialogClass + "' style='max-width:600px'>";
-        html += "Append a list of PDB, MMDB, or AlphaFold UniProt structures: " + me.htmlCls.inputTextStr + "id='" + me.pre + "mmdbafid' placeholder='e.g., 1HHO,4N7N,P69905,P01942' size=30> <br><br>";
-        html += me.htmlCls.buttonStr + "reload_mmdbaf'>Append Biological Unit</button>" + me.htmlCls.buttonStr + "reload_mmdbaf_asym' style='margin-left:30px'>Append Asymmetric Unit (All Chains)</button>" + "<br/><br/>";
+        html += "List of PDB, MMDB, or AlphaFold UniProt structures: " + me.htmlCls.inputTextStr + "id='" + me.pre + "mmdbafid' placeholder='e.g., 1HHO,4N7N,P69905,P01942' size=30> <br><br>";
+        html += "<div style='display:inline-block; width:20px'></div>" + me.htmlCls.buttonStr + "reload_mmdbaf' style='width:150px'>Load Biological Unit</button>" + me.htmlCls.buttonStr + "reload_mmdbaf_asym' style='margin-left:30px; width:250px'>Load Asymmetric Unit (All Chains)</button>" + "<br/><br/>";
+        html += "<div style='display:inline-block; width:20px'>or</div>" + me.htmlCls.buttonStr + "reload_mmdbaf_append' style='width:150px'>Append Biological Unit</button>" + me.htmlCls.buttonStr + "reload_mmdbaf_asym_append' style='margin-left:30px; width:250px'>Append Asymmetric ; Unit (All Chains)</button>" + "<br/><br/>";
 
         html += '<b>Note</b>: The "<b>biological unit</b>" is the <b>biochemically active form of a biomolecule</b>, <div style="width:20px; margin:6px 0 0 20px; display:inline-block;"><span id="'
         + me.pre + 'asu_bu2_expand" class="ui-icon ui-icon-plus icn3d-expand icn3d-link" style="width:15px;" title="Expand"></span><span id="'
@@ -11764,7 +11765,7 @@ class Events {
         $("#" + me.pre + id).resizable();
     }
 
-    async launchMmdb(ids, bBiounit, hostUrl) { let me = this.icn3dui, ic = me.icn3d, thisClass = this;
+    async launchMmdb(ids, bBiounit, hostUrl, bAppend) { let me = this.icn3dui, ic = me.icn3d, thisClass = this;
         if(!me.cfg.notebook) dialog.dialog( "close" );
         
         let flag = bBiounit ? 1 : 0;
@@ -11779,40 +11780,41 @@ class Events {
 
         let idArray = ids.split(',');
 
-        /*
-        if(idArray.length == 1 && (idArray[0].length == 4 || !isNaN(idArray[0])) ) {
-            thisClass.setLogCmd("load mmdb" + flag + " " + ids, false);
-            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
-            window.open(hostUrl + '?mmdbid=' + ids + '&bu=' + flag, urlTarget);
-        }
-        else {
-            thisClass.setLogCmd("load mmdbaf" + flag + " " + ids, false);
-            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
-            window.open(hostUrl + '?mmdbafid=' + ids + '&bu=' + flag, urlTarget);
-        }
-        */
-
-        // single MMDB ID could show memebranes
-        if(!ic.structures && idArray.length == 1 && (idArray[0].length == 4 || !isNaN(idArray[0])) ) {
-            thisClass.setLogCmd("load mmdb" + flag + " " + ids, false);
-            let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
-            window.open(hostUrl + '?mmdbid=' + ids + '&bu=' + flag, urlTarget);
+        if(!bAppend) {
+            if(idArray.length == 1 && (idArray[0].length == 4 || !isNaN(idArray[0])) ) {
+                thisClass.setLogCmd("load mmdb" + flag + " " + ids, false);
+                let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+                window.open(hostUrl + '?mmdbid=' + ids + '&bu=' + flag, urlTarget);
+            }
+            else {
+                thisClass.setLogCmd("load mmdbaf" + flag + " " + ids, false);
+                let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+                window.open(hostUrl + '?mmdbafid=' + ids + '&bu=' + flag, urlTarget);
+            }
         }
         else {
-            me.cfg.mmdbafid = ids;
-            me.cfg.bu = flag;
-
-            ic.bMmdbafid = true;
-            ic.inputid = (ic.inputid) ? ic.inputid + me.cfg.mmdbafid : me.cfg.mmdbafid;
-            if(me.cfg.bu == 1) {
-                ic.loadCmd = 'load mmdbaf1 ' + me.cfg.mmdbafid;
+            // single MMDB ID could show memebranes
+            if(!ic.structures && idArray.length == 1 && (idArray[0].length == 4 || !isNaN(idArray[0])) ) {
+                thisClass.setLogCmd("load mmdb" + flag + " " + ids, false);
+                let urlTarget = (ic.structures && Object.keys(ic.structures).length > 0) ? '_blank' : '_self';
+                window.open(hostUrl + '?mmdbid=' + ids + '&bu=' + flag, urlTarget);
             }
             else {
-                ic.loadCmd = 'load mmdbaf0 ' + me.cfg.mmdbafid;
-            }
-            me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
+                me.cfg.mmdbafid = ids;
+                me.cfg.bu = flag;
 
-            await ic.chainalignParserCls.downloadMmdbAf(me.cfg.mmdbafid);   
+                ic.bMmdbafid = true;
+                ic.inputid = (ic.inputid) ? ic.inputid + me.cfg.mmdbafid : me.cfg.mmdbafid;
+                if(me.cfg.bu == 1) {
+                    ic.loadCmd = 'load mmdbaf1 ' + me.cfg.mmdbafid;
+                }
+                else {
+                    ic.loadCmd = 'load mmdbaf0 ' + me.cfg.mmdbafid;
+                }
+                me.htmlCls.clickMenuCls.setLogCmd(ic.loadCmd, true);
+
+                await ic.chainalignParserCls.downloadMmdbAf(me.cfg.mmdbafid);   
+            }
         }
     }
 
@@ -12554,21 +12556,28 @@ class Events {
 
          me.myEventCls.onIds("#" + me.pre + "reload_mmdbaf", "click", function(e) { me.icn3d;
             e.preventDefault();
-            
-            // remove space
             let ids = $("#" + me.pre + "mmdbafid").val();
-
             thisClass.launchMmdb(ids, 1, hostUrl);
         });
  
          me.myEventCls.onIds("#" + me.pre + "reload_mmdbaf_asym", "click", function(e) { me.icn3d;
             e.preventDefault();
-
-            // remove space
             let ids = $("#" + me.pre + "mmdbafid").val();
             thisClass.launchMmdb(ids, 0, hostUrl);
         });
 
+        me.myEventCls.onIds("#" + me.pre + "reload_mmdbaf_append", "click", function(e) { me.icn3d;
+            e.preventDefault();
+            let ids = $("#" + me.pre + "mmdbafid").val();
+            thisClass.launchMmdb(ids, 1, hostUrl, true);
+        });
+ 
+         me.myEventCls.onIds("#" + me.pre + "reload_mmdbaf_asym_append", "click", function(e) { me.icn3d;
+            e.preventDefault();
+            let ids = $("#" + me.pre + "mmdbafid").val();
+            thisClass.launchMmdb(ids, 0, hostUrl, true);
+        });
+
         me.myEventCls.onIds("#" + me.pre + "mmdbid", "keyup", function(e) { let ic = me.icn3d;
            if (e.keyCode === 13) {
                e.preventDefault();
@@ -41440,14 +41449,14 @@ class ShowSeq {
 
         // set hash for the loops
         let strand2len_start_stop = {};
-        let prevRefnumStr, prevPostfix;
+        let prevRefnumStr, prevPostfix, prevRefnum;
 
         // sometimes one chain may have several Ig domains,set a index for each IgDomain
-        let index = 1;
+        let index = 1, prevStrandPostfix = '', bStart = false;
         for(let i = 0, il = giSeq.length; i < il; ++i) {
             let currResi = ic.ParserUtilsCls.getResi(chnid, i);
             let residueid = chnid + '_' + currResi;
-            if(ic.residues.hasOwnProperty(residueid)) {
+            //if(ic.residues.hasOwnProperty(residueid)) {
                 refnumLabel = ic.resid2refnum[residueid];
                 if(refnumLabel) {                        
                     refnumStr_ori = refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').substr(1); // C', C''
@@ -41465,27 +41474,37 @@ class ShowSeq {
                                 strand2len_start_stop[prevStrand + prevPostfix].len = currCnt - 1;
                                 strand2len_start_stop[prevStrand + prevPostfix].end = refnumStr;
                                 strand2len_start_stop[prevStrand + prevPostfix].nextStrand = currStrand;
-
-                                console.log("end: " + residueid);
                             }
 
+                            bStart = false;
+
+                            currCnt = 1;
+                        }
+
+                        // sometimes insertions may happen inside a strand. Reset currCnt
+                        if(currStrand == prevStrand && refnum > 1000 && refnumStr.substr(1,1) != '9') { // strand region
                             currCnt = 1;
+                            
+                            if(bStart && prevStrandPostfix) {
+                                delete strand2len_start_stop[prevStrandPostfix];
+                                prevStrandPostfix = '';
+                            }
                         }
 
                         // #9##
-                        if(prevStrand && refnum > 1000 && refnumStr.substr(1,1) == '9') { // loop region
+                        if(prevStrand && currStrand != ' ' && refnum > 1000 && refnumStr.substr(1,1) == '9') { // loop region
                             if(currCnt == 1) { // start of a loop
                                 if(strand2len_start_stop.hasOwnProperty(currStrand + postfix)) { // the strand appeared in 2nd Id domain
                                     ++index;
                                 }
-
-                                console.log("start: " + residueid + " refnumStr: " + refnumStr);
                                 
                                 postfix = refnumStr.replace(refnum.toString(), '') + '_' + index;
                                 strand2len_start_stop[currStrand + postfix] = {};
 
                                 strand2len_start_stop[currStrand + postfix].start = prevRefnumStr;
                                 strand2len_start_stop[currStrand + postfix].chainid = chnid;
+
+                                //prevStrandPostfix = currStrand + postfix;
                             }
                             refnumStr = (parseInt(currFirstDigit) * 1000 + 900 + currCnt).toString();
                             refnumLabel = currStrand + refnumStr;
@@ -41495,7 +41514,7 @@ class ShowSeq {
                     }
                 }
                 else {
-                    if(prevStrand && !bCustom && !kabat_or_imgt) {
+                    if(prevStrand && currStrand != ' ' && !bCustom && !kabat_or_imgt) {
                         if(currCnt == 1) { // start of a loop
                             if(strand2len_start_stop.hasOwnProperty(currStrand + postfix)) { // the strand appeared in 2nd Id domain
                                 ++index;
@@ -41508,8 +41527,11 @@ class ShowSeq {
 
                             strand2len_start_stop[currStrand + postfix].start = prevRefnumStr;
                             strand2len_start_stop[currStrand + postfix].chainid = chnid;
-                        }
 
+                            prevStrandPostfix = currStrand + postfix;
+                            bStart = true;
+                        }
+                        
                         // no ref num
                         refnumStr = (parseInt(currFirstDigit) * 1000 + 900 + currCnt).toString();
                         refnumLabel = currStrand + refnumStr;
@@ -41518,8 +41540,9 @@ class ShowSeq {
                 }
 
                 prevRefnumStr = refnumStr;
+                prevRefnum = refnum;
                 prevPostfix = postfix;
-            }
+            //}
 
             prevStrand = currStrand;
         }
@@ -41528,11 +41551,13 @@ class ShowSeq {
             strand2len_start_stop[prevStrand + prevPostfix].end = prevRefnumStr;
             //strand2len_start_stop[prevStrand].nextStrand = undefined;
         }
-
+        
         let refnumLabelNoPostfix;
         // sometimes one chain may have several Ig domains,set a index for each IgDomain
         index = 1;
-        let appearedStrands = {}, currStrand_ori;
+        prevStrandPostfix = '';
+        bStart = false;
+        let appearedStrands = {}, currStrand_ori, bShowRefnum = true;
         for(let i = 0, il = giSeq.length; i < il; ++i) {
             bLoop = false;
 
@@ -41541,12 +41566,12 @@ class ShowSeq {
             let currResi = ic.ParserUtilsCls.getResi(chnid, i);
             let residueid = chnid + '_' + currResi;
             let domainid = (bCustom) ? 0 : ic.resid2domainid[residueid];
-            if(!ic.residues.hasOwnProperty(residueid)) {
-                html += '<span></span>';
-            }
-            else {
+            //if(!ic.residues.hasOwnProperty(residueid)) {
+            //    html += '<span></span>';
+            //}
+            //else {
                 refnumLabel = ic.resid2refnum[residueid];
-                let bNotShow = false;
+                let bHidelabel = false;
 
                 if(refnumLabel) {                        
                     refnumStr_ori = refnumLabel.replace(/'/g, '').replace(/\*/g, '').replace(/\^/g, '').substr(1); // C', C''
@@ -41557,7 +41582,8 @@ class ShowSeq {
 
                     refnumLabelNoPostfix = currStrand + parseInt(refnumStr_ori);
 
-                    if(currStrand != prevStrand) { // reset currCnt
+                    if(currStrand_ori != prevStrand) { // reset currCnt
+                        bStart = false;
                         currCnt = 1;
                     }
 
@@ -41575,30 +41601,44 @@ class ShowSeq {
                         refnum = parseInt(refnumStr);
                         postfix = refnumStr.replace(refnum.toString(), '') + '_' + index;
 
+                        // sometimes insertions may happen inside a strand. Reset currCnt
+                        if(currStrand_ori == prevStrand && refnum > 1000 && refnumStr.substr(1,1) != '9') { // strand region
+                            currCnt = 1;
+                            
+                            if(bStart && prevStrandPostfix) {
+                                --index;
+                                prevStrandPostfix = '';
+                            }
+                        }
+
                         // #9##
                         if(prevStrand && refnum > 1000 && refnumStr.substr(1,1) == '9') { // loop region
                             bLoop = true;
 
                             if(currCnt == 1) { // start of a loop
-                                if(appearedStrands.hasOwnProperty(currStrand + postfix)) { // the strand appeared in 2nd Id domain
+                                if(appearedStrands.hasOwnProperty(currStrand_ori + postfix)) { // the strand appeared in 2nd Id domain
                                     ++index;
                                     postfix = refnumStr.replace(refnum.toString(), '') + '_' + index;
                                 }
 
-                                appearedStrands[currStrand + postfix] = 1;
+                                appearedStrands[currStrand_ori + postfix] = 1;
                             }
 
-                            let result = this.getAdjustedRefnum(strand2len_start_stop, currStrand, currCnt, currFirstDigit, postfix);
-                            
+                            let result = this.getAdjustedRefnum(strand2len_start_stop, currStrand_ori, currCnt, currFirstDigit, postfix, prevRefnum);
+
+                            refnum = result.refnum;
+                            bShowRefnum = result.bShowRefnum;
                             refnumStr = result.refnumStr;
                             refnumLabel = result.refnumLabel;
                             refnumLabelNoPostfix = result.refnumLabelNoPostfix;
 
-                            bNotShow = result.bNotShow;
+                            bHidelabel = result.bHidelabel;
                             currStrand = refnumLabel.replace(new RegExp(refnumStr,'g'), '');
 
                             ++currCnt;
                         }
+
+                        prevRefnum = refnum;
                     }
                 
                     if(bCustom) {
@@ -41636,40 +41676,59 @@ class ShowSeq {
                         }
                     }
                     else {
-                        html += this.getRefnumHtml(residueid, refnumStr, refnumStr_ori, refnumLabel, currStrand, bLoop, bNotShow);
+                        if(bShowRefnum && currStrand != ' ') {
+                            html += this.getRefnumHtml(residueid, refnumStr, refnumStr_ori, refnumLabel, currStrand, bLoop, bHidelabel);
+                        }
+                        else {
+                            html += '<span></span>';
+                        }
                     }
                 }
                 else {
                     let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[residueid]);
 
                     // skip non-protein residues
-                    if(ic.proteins.hasOwnProperty(atom.serial) && prevStrand && !bCustom && !kabat_or_imgt) {
+                    // after G strand and before A strand, just use the mapped reference number
+                    if((!atom || ic.proteins.hasOwnProperty(atom.serial)) && prevStrand && !bCustom && !kabat_or_imgt
+                      && (!currStrand_ori || currStrand_ori.substr(0,1) != 'G')) {
                         // no ref num
                         bLoop = true;
 
                         if(currCnt == 1) { // start of a loop
-                            if(appearedStrands.hasOwnProperty(currStrand + postfix)) { // the strand appeared in 2nd Id domain
+                            if(appearedStrands.hasOwnProperty(currStrand_ori + postfix)) { // the strand appeared in 2nd Id domain
                                 ++index;
                             }
                             
                             postfix = refnumStr.replace(refnum.toString(), '') + '_' + index;
 
-                            appearedStrands[currStrand + postfix] = 1;
+                            appearedStrands[currStrand_ori + postfix] = 1;
+
+                            bStart = true;
+                            prevStrandPostfix = currStrand_ori + postfix;
                         }
 
                         // use previous postfix
-                        let result = this.getAdjustedRefnum(strand2len_start_stop, currStrand, currCnt, currFirstDigit, postfix);
-                            
+                        let result = this.getAdjustedRefnum(strand2len_start_stop, currStrand_ori, currCnt, currFirstDigit, postfix, prevRefnum);
+
+                        refnum = result.refnum;
+                        bShowRefnum = result.bShowRefnum;                        
                         refnumStr = result.refnumStr;
                         refnumLabel = result.refnumLabel;
                         refnumLabelNoPostfix = result.refnumLabelNoPostfix;
 
-                        bNotShow = result.bNotShow;
+                        prevRefnum = refnum;
+
+                        bHidelabel = result.bHidelabel;
                         currStrand = refnumLabel.replace(new RegExp(refnumStr,'g'), '');
                   
                         ++currCnt;
 
-                        html += this.getRefnumHtml(residueid, refnumStr, refnumStr_ori, refnumLabel, currStrand, bLoop, bNotShow);
+                        if(bShowRefnum && currStrand != ' ') {
+                            html += this.getRefnumHtml(residueid, refnumStr, refnumStr_ori, refnumLabel, currStrand, bLoop, bHidelabel);
+                        }
+                        else {
+                            html += '<span></span>';
+                        }
                     }
                     else {
                         html += '<span></span>';
@@ -41693,7 +41752,7 @@ class ShowSeq {
                 // remove the postfix when comparing interactions
                 //ic.chainsMapping[chnid][residueid] = refnumLabel;
                 ic.chainsMapping[chnid][residueid] = refnumLabelNoPostfix;
-            }
+            //}
 
             prevStrand = currStrand_ori; //currStrand;
         }
@@ -41708,10 +41767,11 @@ class ShowSeq {
         return {html: html, html3: html3}
     }
 
-    getAdjustedRefnum(strand2len_start_stop, currStrand, currCnt, currFirstDigit, postfix) { let ic = this.icn3d; ic.icn3dui;
-        let refnumStr, refnumLabel, refnumLabelNoPostfix;
+    getAdjustedRefnum(strand2len_start_stop, currStrand, currCnt, currFirstDigit, postfix, prevRefnum) { let ic = this.icn3d; ic.icn3dui;
+        let refnum, refnumStr, refnumLabel, refnumLabelNoPostfix;
 
-        let bNotShow = false; // do not show the label
+        let bHidelabel = false; // do not show the label
+        let bShowRefnum = true;
 
         if(strand2len_start_stop[currStrand + postfix]) {
             let start = parseInt(strand2len_start_stop[currStrand + postfix].start);
@@ -41723,7 +41783,6 @@ class ShowSeq {
             let len = strand2len_start_stop[currStrand + postfix].len;
             let halfLen = (strand2len_start_stop[currStrand + postfix].nextStrand) ? parseInt(len / 2.0 + 0.5) : len;
 
-            let refnum;
             if(currCnt <= halfLen) {
                 refnum = start + currCnt;
                 refnumStr = refnum + postfixStart;
@@ -41738,28 +41797,42 @@ class ShowSeq {
 
             refnumLabelNoPostfix = currStrand + refnum;
 
-            if(currCnt == 0 || currCnt == halfLen || currCnt == halfLen + 1 || currCnt == end - 1) {
-                bNotShow = true;
+            //if(currCnt == 0 || currCnt == halfLen || currCnt == halfLen + 1 || currCnt == end - 1) {
+            // if(currCnt == 1 || currCnt == halfLen || currCnt == halfLen + 1 || currCnt == end - 1) {
+            //     bHidelabel = true;
+            // }
+            if(currCnt == 1 || currCnt == end - 1) {
+                bHidelabel = true;
+            }
+
+            if(currCnt == 1 && start != prevRefnum) { // skip insertions
+                bShowRefnum = false;
+                
+                refnum = 0;
+                refnumStr = '';
+                refnumLabel = '';
+                refnumLabelNoPostfix = '';
             }
         }
         else {
             // refnumStr = (parseInt(currFirstDigit) * 1000 + 900 + currCnt).toString();
             // refnumLabel = currStrand + refnumStr;
 
+            refnum = 0;
             refnumStr = '';
             refnumLabel = '';
             refnumLabelNoPostfix = '';
 
-            bNotShow = true;
+            bHidelabel = true;
         }
 
-        return {refnumStr: refnumStr, refnumLabel: refnumLabel, refnumLabelNoPostfix: refnumLabelNoPostfix, bNotShow: bNotShow};
+        return {refnum: refnum, refnumStr: refnumStr, refnumLabel: refnumLabel, refnumLabelNoPostfix: refnumLabelNoPostfix, bHidelabel: bHidelabel, bShowRefnum: bShowRefnum};
     }
 
-    getRefnumHtml(residueid, refnumStr, refnumStr_ori, refnumLabel, currStrand, bLoop, bNotShow) { let ic = this.icn3d, me = ic.icn3dui;
+    getRefnumHtml(residueid, refnumStr, refnumStr_ori, refnumLabel, currStrand, bLoop, bHidelabel) { let ic = this.icn3d, me = ic.icn3dui;
         let refnum = parseInt(refnumStr).toString();
         let color = this.getRefnumColor(currStrand);
-        let colorStr = 'style="color:' + color + '"';
+        let colorStr = (!bLoop) ? 'style="color:' + color + '; text-decoration: underline overline;"' : 'style="color:' + color + '"';
 
         let lastTwo = parseInt(refnum.substr(refnum.length - 2, 2));
         parseInt(refnum.substr(refnum.length - 3, 3));
@@ -41772,7 +41845,7 @@ class ShowSeq {
 
             html += '<span ' + colorStr + ' title="' + refnumLabel + '"><b>' + refnumLabel.substr(0, 1) + '</b>' + refnumLabel.substr(1) + '</span>';
         }
-        else if(lastTwo % 2 == 0 && lastTwo != 52 && !bNotShow) { // don't show label for the first, middle, and last loop residues
+        else if(lastTwo % 2 == 0 && lastTwo != 52 && !bHidelabel) { // don't show label for the first, middle, and last loop residues
             // e.g., 2152a
             let lastTwoStr = isNaN(refnumStr) ? lastTwo + refnumStr.substr(refnumStr.length - 1, 1) : lastTwo;
             html += '<span ' + colorStr + ' title="' + refnumLabel + '">' + lastTwoStr + '</span>';
@@ -41786,43 +41859,43 @@ class ShowSeq {
 
     getRefnumColor(currStrand) {  let ic = this.icn3d; ic.icn3dui;
         if(currStrand == "A^") { // deep sky blue
-            return '#00BFFF';
+            return '#9900ff'; //'#00BFFF';
         }
         else if(currStrand == "A") { // blue
-            return '#0000FF';
+            return '#9900ff'; //'#0000FF';
         }
         else if(currStrand == "A*") { // sky blue
-            return '#87CEEB';
+            return '#9900ff'; //'#87CEEB';
         }
         else if(currStrand == "A'") { // steel blue
-            return '#4682B4';
+            return '#9900ff'; //'#4682B4';
         }
         else if(currStrand == "B") { // cyan
-            return '#00FFFF';
+            return '#4a86e8'; //'#00FFFF';
         }
         else if(currStrand == "C") { // green
-            return '#00FF00';
+            return '#76d6ff'; //'#00FF00';
         }
         else if(currStrand == "C'") { // yellow
-            return '#FFFF00';
+            return '#00b050'; //'#FFFF00';
         }
         else if(currStrand == "C''") { // orange
-            return '#FFA500';
+            return '#00ff00'; //'#FFA500';
         }
         else if(currStrand == "D") { // brown
-            return '#A52A2A';
+            return '#fffb00'; //'#A52A2A';
         }
         else if(currStrand == "E") { // pink
-            return '#FFC0CB';
+            return '#ffd966'; //'#FFC0CB';
         }
         else if(currStrand == "F") { // magenta
-            return '#FF00FF';
+            return '#ff9900'; //'#FF00FF';
         }
         else if(currStrand == "G") { // red
-            return '#FF0000';
+            return '#ff2600'; //'#FF0000';
         }
         else if(currStrand == "G*") { // salmon
-            return '#FA8072';
+            return '#ff2600'; //'#FA8072';
         }
         else {
             return '#000';
@@ -43187,6 +43260,8 @@ class LineGraph {
     drawGraphPerType(bCommonDiff, structureArray, bScatterplot, nodeArray1, nodeArray2, linkArray, name2node, heightFinal, height, textHeight, len1Split, r, gap, marginY) { let ic = this.icn3d; ic.icn3dui;
         let html = "";
 
+        let bMutation = structureArray.length == 2 && structureArray[1].replace(structureArray[0], '') == '2';
+
         // draw common interaction
         let label, postfix;
         if(bCommonDiff == 0) {
@@ -43203,11 +43278,21 @@ class LineGraph {
         }
 
         for(let i = 0, il = structureArray.length; i < il; ++i) {  
+            let labelFinal = label;
+            if(bMutation) {
+                if(i == 0) {
+                    labelFinal += "Wild Type ";
+                }
+                else if(i == 1) {
+                    labelFinal += "Mutant ";
+                }
+            }
+
             if(bScatterplot) {
-                html += this.drawScatterplot_base(nodeArray1[i], nodeArray2[i], linkArray[i], name2node, heightFinal, undefined, label + structureArray[i], textHeight);
+                html += this.drawScatterplot_base(nodeArray1[i], nodeArray2[i], linkArray[i], name2node, heightFinal, undefined, labelFinal + structureArray[i], textHeight);
                 height =(len1Split[i] + 1) *(r + gap) + 2 * marginY + textHeight;
             } else {
-                html += this.drawLineGraph_base(nodeArray1[i], nodeArray2[i], linkArray[i], name2node, heightFinal, label + structureArray[i], textHeight);
+                html += this.drawLineGraph_base(nodeArray1[i], nodeArray2[i], linkArray[i], name2node, heightFinal, labelFinal + structureArray[i], textHeight);
             }
             heightFinal += height;
 
@@ -54055,6 +54140,16 @@ class LoadPDB {
         this.icn3d = icn3d;
     }
 
+    getStructureId(id, moleculeNum, bMutation) { let ic = this.icn3d; ic.icn3dui;
+        let structure = id;
+    
+        if(id == ic.defaultPdbId || bMutation) { // bMutation: side chain prediction
+            structure = (moleculeNum === 1) ? id : id + moleculeNum.toString();
+        }
+
+        return structure;
+    }
+
     // 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, type, bLastQuery) { let ic = this.icn3d, me = ic.icn3dui;
@@ -54137,12 +54232,7 @@ class LoadPDB {
                     }
                 }
 
-                structure = id;
-
-                if(id == ic.defaultPdbId || bMutation) { // bMutation: side chain prediction
-                //if(id == ic.defaultPdbId) {
-                        structure = (moleculeNum === 1) ? id : id + moleculeNum.toString();
-                }
+                structure = this.getStructureId(id, moleculeNum, bMutation);
 
                 ic.molTitle = '';
 
@@ -54257,12 +54347,7 @@ class LoadPDB {
                 ++moleculeNum;
                 id = ic.defaultPdbId;
 
-                structure = id;
-                
-                if(id == ic.defaultPdbId || bMutation) { // bMutation: side chain prediction
-                //if(id == ic.defaultPdbId) {
-                        structure = (moleculeNum === 1) ? id : id + moleculeNum.toString();
-                }
+                structure = this.getStructureId(id, moleculeNum, bMutation);
 
                 //helices = [];
                 //sheets = [];
@@ -54281,12 +54366,7 @@ class LoadPDB {
                     ic.pmid = line.substr(19).trim();
                 }
             } else if (record === 'ATOM  ' || record === 'HETATM') {
-                structure = id;
-                
-                if(id == ic.defaultPdbId || bMutation) { // bMutation: side chain prediction
-                //if(id == ic.defaultPdbId) {
-                        structure = (moleculeNum === 1) ? id : id + moleculeNum.toString();
-                }
+                structure = this.getStructureId(id, moleculeNum, bMutation);
 
                 let alt = line.substr(16, 1);
                 //if (alt !== " " && alt !== "A") continue;
@@ -59180,7 +59260,7 @@ class SelectByCommand {
                      let residArray = [];
 
                      if(bRefnum) {
-                      let residArrayTmp = ic.refnum2residArray[k];
+                      let residArrayTmp = (ic.refnum2residArray[k]) ? ic.refnum2residArray[k] : [];
                       for(let m = 0, ml = residArrayTmp.length; m < ml; ++m) {
                         let residueId = residArrayTmp[m];
                         if(residueId.substr(0, residueId.lastIndexOf('_')) == molecule_chain) {
@@ -61620,12 +61700,12 @@ if(!me.bNode) {
 }
 
             let prevStrand;
+            let bCd19 = ic.chainid2index[chainid].length == 1 && ic.refpdbArray[ic.chainid2index[chainid][0]] == '6al5_cd19';
             for(let i = 0, il = segArray.length; i < il; ++i) {
                 let seg = segArray[i];
                 let qStart = seg.q_start;
                 parseInt(seg.q_start);
-                let postfix = '';
-                if(isNaN(seg.q_start)) postfix = seg.q_start.substr(seg.q_start.length - 1, 1);
+                if(isNaN(seg.q_start)) seg.q_start.substr(seg.q_start.length - 1, 1);
 
                 // one item in "seq"
                 // q_start and q_end are numbers, but saved in string
@@ -61636,9 +61716,10 @@ if(!me.bNode) {
 
                     let resid = chainid + '_' + seg.t_start;
                     //let refnum = qStartInt.toString() + postfix;
-                    let refnum = qStart + postfix;
+                    //let refnum = qStart + postfix;
+                    let refnum = qStart;
 
-                    let refnumLabel = thisClass.getLabelFromRefnum(refnum, prevStrand);
+                    let refnumLabel = thisClass.getLabelFromRefnum(refnum, prevStrand, bCd19);
                     prevStrand = refnumLabel.replace(new RegExp(refnum,'g'), '');
 
                     ic.resid2refnum[resid] = refnumLabel;
@@ -61673,7 +61754,7 @@ if(!me.bNode) {
         }
     }
 
-    getLabelFromRefnum(oriRefnum, prevStrand) { let ic = this.icn3d; ic.icn3dui;
+    getLabelFromRefnum(oriRefnum, prevStrand, bCd19) { let ic = this.icn3d; ic.icn3dui;
         let refnum = parseInt(oriRefnum);
 
         // A^: 1xx or 2xx
@@ -61691,7 +61772,10 @@ if(!me.bNode) {
         // G*: 94xx
 
         if(refnum < 100) return " " + oriRefnum;
-        else if(refnum >= 100 && refnum < 1000) return "A^" + oriRefnum;
+        else if(refnum >= 100 && refnum < 1000) {
+            if(bCd19) return " " + oriRefnum;
+            else return "A^" + oriRefnum;
+        }
         else if(refnum >= 1000 && refnum < 1200) return "A" + oriRefnum;
         else if(refnum >= 1200 && refnum < 1300) return "A'" + oriRefnum;
         else if(refnum >= 1300 && refnum < 1400) return "A*" + oriRefnum;
@@ -61873,7 +61957,7 @@ class Scap {
 
         let data;
          
-        try {
+        // try {
           data = await me.getAjaxPostPromise(url, dataObj, true, undefined, undefined, undefined, 'text');
 
           let pos = data.indexOf('\n');
@@ -61963,8 +62047,10 @@ console.log("free energy: " + energy + " kcal/mol");
 
                   let atomWT = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
 
-                  ic.atoms[serial].color = atomWT.color;
-                  ic.atomPrevColors[serial] = atomWT.color;
+                  if(atomWT) {
+                    ic.atoms[serial].color = atomWT.color;
+                    ic.atomPrevColors[serial] = atomWT.color;
+                  }
               }
 
               let chainid = atom.structure + '_' + atom.chain;
@@ -62030,6 +62116,7 @@ console.log("free energy: " + energy + " kcal/mol");
           // expand the toolbar
           let id = ic.pre + 'selection';
           $("#" + id).show();
+/*
         }
         catch(err) {
             var aaa = 1; //alert("There are some problems in predicting the side chain of the mutant...");
@@ -62039,6 +62126,7 @@ console.log("free energy: " + energy + " kcal/mol");
             /// if(ic.deferredScap !== undefined) ic.deferredScap.resolve();
             return;
         }
+        */
     }
 
     async exportPdbProfix(bHydrogen, pdb, snpStr) { let ic = this.icn3d, me = ic.icn3dui;