icn3d 3.54.7 → 3.54.8

package/icn3d.js

@@ -60702,7 +60702,7 @@ class SetMenu {
         //html += this.getMenuText('mn1_fold', 'AlphaFold/ESM', undefined, undefined, 1);
         html += this.getMenuText('mn1_fold', 'Predict by Seq.', undefined, undefined, 1);
         html += "<ul>";
-        html += this.getLink('mn1_esmfold', 'ESMFold', undefined, 2);
+        //html += this.getLink('mn1_esmfold', 'ESMFold', undefined, 2);
         //html += this.getMenuUrl('mn1_esmfold_link', "https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/ESMFold.ipynb", "ESMFold via ColabFold" + me.htmlCls.wifiStr, undefined, 2);
         html += this.getLink('mn1_alphafold', 'AlphaFold2 via ColabFold' + me.htmlCls.wifiStr, undefined, 2);
         html += "</ul>";
@@ -62307,7 +62307,6 @@ class Dialog {
                       if(status.bSetsInit2) thisClass.openDlg2Ddgm(me.pre + 'dl_definedsets');
                   }
                   else {
-                      //ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH - me.htmlCls.LESSWIDTH, me.htmlCls.HEIGHT - me.htmlCls.LESSHEIGHT - me.htmlCls.EXTRAHEIGHT, true);
                       ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH, me.htmlCls.HEIGHT, true);
                   }
               }
@@ -62396,7 +62395,6 @@ class Dialog {
               let status = thisClass.getDialogStatus().status;
 
               if((!status.bSelectannotationsInit2) &&(!status.bGraph2) &&(!status.bLineGraph2) &&(!status.bScatterplot2) &&(!status.bHbondplot2) &&(!status.bLigplot2) &&(!status.bTable2) &&(!status.bAlignmentInit2) ) {
-                    //ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH - me.htmlCls.LESSWIDTH, me.htmlCls.HEIGHT - me.htmlCls.LESSHEIGHT - me.htmlCls.EXTRAHEIGHT, true);
                     ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH, me.htmlCls.HEIGHT, true);
               }
           },
@@ -62441,8 +62439,7 @@ class Dialog {
                 }
             }
             else {
-                //ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH - me.htmlCls.LESSWIDTH,(me.htmlCls.HEIGHT - me.htmlCls.LESSHEIGHT - me.htmlCls.EXTRAHEIGHT) * 0.5, true);
-                ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH,(me.htmlCls.HEIGHT) * 0.5, true);
+                //ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH,(me.htmlCls.HEIGHT) * 0.5, true);
 
                 //height =(me.htmlCls.HEIGHT - me.htmlCls.LESSHEIGHT - me.htmlCls.EXTRAHEIGHT) * 0.5;
                 height =(me.htmlCls.HEIGHT) * 0.5;
@@ -62482,7 +62479,6 @@ class Dialog {
                               if(status.bSetsInit2) thisClass.openDlg2Ddgm(me.pre + 'dl_definedsets');
                           }
                           else {
-                              //ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH - me.htmlCls.LESSWIDTH, me.htmlCls.HEIGHT - me.htmlCls.LESSHEIGHT - me.htmlCls.EXTRAHEIGHT, true);
                               ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH, me.htmlCls.HEIGHT, true);
                           }
                       }
@@ -64615,7 +64611,20 @@ class Events {
         let nameArray = $("#" + me.pre + "atomsCustomRealignByStruct").val();
 
         if(nameArray.length == 0) {
-            nameArray = $("#" + me.pre + "atomsCustom").val();
+            // nameArray = $("#" + me.pre + "atomsCustom").val();
+            
+            // choose the first chain for each structure
+            nameArray = [];
+            let structureHash = {};
+            let chains = ic.resid2specCls.atoms2chains(ic.hAtoms);
+
+            for(let chainid in chains) {
+                let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.chains[chainid]);
+                if(!structureHash.hasOwnProperty(atom.structure) && (ic.proteins.hasOwnProperty(atom.serial) || ic.nucleotides.hasOwnProperty(atom.serial))) {
+                    nameArray.push(chainid);
+                    structureHash[atom.structure] = 1;
+                }
+            }
         }
 
         if(nameArray.length > 0) {
@@ -64635,20 +64644,6 @@ class Events {
         }
 
         if(bMsa) {
-            // choose the first chain for each structure
-            if(nameArray.length == 0) {
-                nameArray = [];
-                let structureHash = {};
-                
-                for(let chainid in ic.chains) {
-                    let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.chains[chainid]);
-                    if(!structureHash.hasOwnProperty(atom.structure) && (ic.proteins.hasOwnProperty(atom.serial) || ic.nucleotides.hasOwnProperty(atom.serial))) {
-                        nameArray.push(chainid);
-                        structureHash[atom.structure] = 1;
-                    }
-                }
-            }
-
             await ic.realignParserCls.realignOnStructAlignMsa(nameArray);
         }
         else {
@@ -125139,8 +125134,8 @@ class MmdbParser {
 
         if(type === undefined || type === 'target') {
             // if a command contains "load...", the commands should not be cleared with init()
-            let bKeepCmd = (ic.bCommandLoad) ? true : false;
-            if(!ic.bStatefile) ic.init(bKeepCmd);
+            let bClearCmd = (ic.bCommandLoad) ? false : true;
+            if(!ic.bStatefile) ic.init(bClearCmd);
 
             ic.chainsColor = {};
             ic.chainsGene = {};
@@ -126608,8 +126603,8 @@ class PdbParser {
     async loadPdbData(data, pdbid, bOpm, bAppend, type, bLastQuery, bNoDssp, bEsmfold) { let ic = this.icn3d, me = ic.icn3dui;
         if(!bAppend && (type === undefined || type === 'target')) {
             // if a command contains "load...", the commands should not be cleared with init()
-            let bKeepCmd = (ic.bCommandLoad) ? true : false;
-            if(!ic.bStatefile) ic.init(bKeepCmd);
+            let bClearCmd = (ic.bCommandLoad) ? false : true;
+            if(!ic.bStatefile) ic.init(bClearCmd);
         }
 
         let hAtoms = await ic.loadPDBCls.loadPDB(data, pdbid, bOpm, undefined, undefined, bAppend, type, bEsmfold); // defined in the core library
@@ -129097,6 +129092,7 @@ let resRangeArray = (me.cfg.resrange) ? decodeURIComponent(me.cfg.resrange).spli
         let predefinedResArray, predefinedResPair;
 
         if(bPredefined) {
+            me.cfg.resdef = decodeURIComponent(me.cfg.resdef).trim();
             let tmpStr = me.cfg.resdef.replace(/; /gi, ': ');
             // predefinedResArray = decodeURIComponent(tmpStr).trim().replace(/\+/gi, ' ').split(': ');
             predefinedResArray = tmpStr.replace(/\+/gi, ' ').split(': ');
@@ -132037,45 +132033,6 @@ class SetSeqAlign {
           ic.nconsHash2 = {};
           ic.nalignHash2 = {};
 
-        //   let msaSameColor = [];
-        //   // assume all aligned seq are the same. If any aligned res is different,set it to false (0)
-        //   for(let i = 0, il = seqalign[0].length; i < il; ++i) {
-        //     msaSameColor.push(1);
-        //   }
-
-          for(let i = 0, il = seqalign.length; i < il; ++i) {
-            // first sequence
-            let alignData = seqalign[i][0];
-            let molid1 = alignData.moleculeId;
-
-            let chain1 = ic.pdbid_molid2chain[mmdbid1 + '_' + molid1];
-            chainid1 = mmdbid1 + '_' + chain1;
-            alignData.sequence.length;
-            for(let j = 0, jl = alignData.sequence.length; j < jl; ++j) {
-                // 0: internal resi id, 1: pdb resi id, 2: resn, 3: aligned or not
-                (ic.bUsePdbNum) ? ic.ParserUtilsCls.getResi(chainid1, alignData.sequence[j][0] - 1) : alignData.sequence[j][0];
-                (alignData.sequence[j][2] === '~') ? '-' : alignData.sequence[j][2];
-
-                (alignData.sequence[j][3]) ? 1 : 0;
-            }
-
-            // second sequence
-            alignData = seqalign[i][1];
-
-            // for(let j = start; j <= end; ++j) {
-            //     // 0: internal resi id, 1: pdb resi id, 2: resn, 3: aligned or not
-            //     let alignedTmp =(alignData.sequence[j][3]) ? 1 : 0; 
-
-            //     let aligned = id2aligninfo[j].aligned + alignedTmp; // 0 or 2
-
-            //     if(aligned === 2) { // aligned
-            //         if(id2aligninfo[j].resn != resn) {
-            //             msaSameColor[j] = 0;
-            //         }
-            //     }
-            // }
-          }
-
           for(let i = 0, il = seqalign.length; i < il; ++i) {
               // first sequence
               let alignData = seqalign[i][0];
@@ -132172,8 +132129,6 @@ class SetSeqAlign {
                           ic.nconsHash2[chainid2 + '_' + resi] = 1;
                       }
 
-                    //   color = (msaSameColor[j] == 0) ? '#0000FF' : '#FF0000';
-
                       // 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;
@@ -132190,8 +132145,6 @@ class SetSeqAlign {
 
                       ic.nalignHash1[chainid1 + '_' + id2aligninfo[j].resi] = 1;
                       ic.nalignHash2[chainid2 + '_' + resi] = 1;
-
-                    //   msaSameColor[j] = 2; // not aligned
                   }
 
                   // chain1
@@ -132316,7 +132269,8 @@ class SetSeqAlign {
         return pos;
     }
 
-    getResnFromResi(chainid, resi) { let ic = this.icn3d, me = ic.icn3dui;
+    getResnFromResi(chainid, resi) { let ic = this.icn3d; ic.icn3dui;
+        /*
         let pos = this.getPosFromResi(chainid, resi);
         if(!pos) return '?';
 
@@ -132331,8 +132285,8 @@ class SetSeqAlign {
         }
 
         return resn;
+        */
 
-/*
         let resid = chainid + '_' + resi;
         let resn = ic.residueId2Name[resid];
         if(!resn) {
@@ -132340,7 +132294,6 @@ class SetSeqAlign {
         }
 
         return resn;
-*/
     }
 
     getResiAferAlign(chainid, bRealign, pos) { let ic = this.icn3d, me = ic.icn3dui;
@@ -132571,7 +132524,7 @@ class SetSeqAlign {
                       }
                   }
               }
-
+            
               for(let j = 0; j <= end1 - start1; ++j) {
                   ///if(ic.chainsSeq[chainid1] === undefined || ic.chainsSeq[chainid2] === undefined) break;
 
@@ -132684,29 +132637,43 @@ class SetSeqAlign {
             for(let i = 0, il = ic.qt_start_end[chainIndex].length; i < il; ++i) {
                 let start1, end1;
                 
-                //ic.qt_start_end is zero-based
-                if(!bRealign && me.cfg.aligntool != 'tmalign') { // vast alignment or seqalign
-                    start1 = parseInt(ic.qt_start_end[chainIndex][i].t_start) - 1;
-                    end1 = parseInt(ic.qt_start_end[chainIndex][i].t_end) - 1;
-                }
-                else {
-                    start1 = ic.ParserUtilsCls.getResiNCBI(chainid1, ic.qt_start_end[chainIndex][i].t_start) - 1;
-                    end1 = ic.ParserUtilsCls.getResiNCBI(chainid1, ic.qt_start_end[chainIndex][i].t_end) - 1;
-                }
-
+                // if(bRealign) { // real residue numbers are stored
+                //     start1 = ic.qt_start_end[chainIndex][i].t_start;
+                //     end1 = ic.qt_start_end[chainIndex][i].t_end;
+                // }
+                // else {
+                    //ic.qt_start_end is zero-based
+                    if(!bRealign && me.cfg.aligntool != 'tmalign') { // vast alignment
+                        start1 = parseInt(ic.qt_start_end[chainIndex][i].t_start) - 1;
+                        end1 = parseInt(ic.qt_start_end[chainIndex][i].t_end) - 1;
+                    }
+                    else {
+                        start1 = ic.ParserUtilsCls.getResiNCBI(chainid1, ic.qt_start_end[chainIndex][i].t_start) - 1;
+                        end1 = ic.ParserUtilsCls.getResiNCBI(chainid1, ic.qt_start_end[chainIndex][i].t_end) - 1;
+                    }
+                // }
                 for(let j = start1; j <= end1; ++j) {
                     let resi, resid;
 
-                    // let resiPos;
-                    // if(me.cfg.aligntool == 'tmalign') {
-                    //     resiPos = j - baseResi;
+                    // if(me.cfg.aligntool == 'tmalign') { // tmalign: just one residue in this for loop
+                    //     resi = ic.qt_start_end[chainIndex][i].t_start;
                     // }
                     // else {
-                    //     resiPos = j;
+                        // let resiPos = (bRealign || me.cfg.aligntool != 'tmalign') ? j : j - baseResi;
+                        // let resiPos;
+                        // if(me.cfg.aligntool == 'tmalign') {
+                        //     resiPos = j - baseResi;
+                        // }
+                        // else {
+                        //     // resiPos = (bRealign) ? j : j - baseResi;
+                        //     resiPos = j;
+                        // }
+
+                        let resiPos = j;
+
+                        resi = ic.ParserUtilsCls.getResi(chainidArray[0], resiPos);
+                        resid = chainidArray[0] + '_' + resi;
                     // }
-                    let resiPos = j;
-                    resi = ic.ParserUtilsCls.getResi(chainidArray[0], resiPos);
-                    resid = chainidArray[0] + '_' + resi;
 
                     resid2range_t[resid] = 1;
                     if(j < start_t) start_t = j;
@@ -132720,6 +132687,7 @@ class SetSeqAlign {
 
         let resid2rangeArray = Object.keys(resid2range_t);
         resid2rangeArray.sort(function(a, b) {
+            // return parseInt(a.split('_')[2]) - parseInt(b.split('_')[2]);
             let idArray1 = me.utilsCls.getIdArray(a);
             let idArray2 = me.utilsCls.getIdArray(b);
             return parseInt(idArray1[2]) - parseInt(idArray2[2]);
@@ -132731,7 +132699,7 @@ class SetSeqAlign {
             let resid = resid2rangeArray[i];
             let idArray = me.utilsCls.getIdArray(resid);
             let resi = idArray[2];
-
+            
             if(i == 0) {
                 start = resi;
             }
@@ -132770,9 +132738,7 @@ class SetSeqAlign {
             let resid = chainid1 + '_' + resi;
 
             // let jAdjusted = (me.cfg.aligntool != 'tmalign') ? j : j + baseResi;
-            //let jAdjusted = ic.ParserUtilsCls.getResiNCBI(chainid1, resi) - 1;
-            //!!!
-            let jAdjusted = (me.cfg.aligntool != 'tmalign') ? j : ic.ParserUtilsCls.getResiNCBI(chainid1, resi) - 1;
+            let jAdjusted = (me.cfg.aligntool == 'seqalign') ? j : ic.ParserUtilsCls.getResiNCBI(chainid1, resi) - 1;
 
             //if(j + baseResi < start_t || j + baseResi > end_t) {
             if(jAdjusted < start_t || jAdjusted > end_t) {    
@@ -132790,6 +132756,7 @@ class SetSeqAlign {
             resObject.color2 = (resid2range_t[resid]) ? '#FF0000' : me.htmlCls.GREYC; // color by conservation
             // resObject.class = (resid2range_t[resid]) ? 'icn3d-align' : 'icn3d-nalign';
             resObject.class = (resid2range_t[resid]) ? 'icn3d-cons' : 'icn3d-nalign';
+    
             ic.alnChainsSeq[chainid1].push(resObject);
 
             if(resid2range_t[resid]) {
@@ -132923,7 +132890,7 @@ class SetSeqAlign {
         if(ic.alnChainsSeq[chainid1]) {
             for(let j = 0, jl = ic.alnChainsSeq[chainid1].length; j < jl; ++j) {
                 //add gap before the mapping region       
-                //if(parseInt(ic.alnChainsSeq[chainid1][j].resi) == parseInt(resi_t)) {
+                // if(parseInt(ic.alnChainsSeq[chainid1][j].resi) == parseInt(resi_t)) {
                 if(ic.alnChainsSeq[chainid1][j].resi == resi_t) {
                     pos_t = j;
                     break;
@@ -132949,7 +132916,6 @@ class SetSeqAlign {
         for(let j = 0, jl = alignedChainIndice.length - 1; j < jl; ++j) {
             let chainidTmp = chainidArray[alignedChainIndice[j]];
             let gapResObject = this.getResObject(chainidTmp, true);
-            
             //for(let k = 0, kl = len - nGap; k < kl; ++k) {
             for(let k = 0, kl = len; k < kl; ++k) {
                 ic.alnChainsSeq[chainidTmp].splice(pos_t, 0, gapResObject);
@@ -132966,6 +132932,7 @@ class SetSeqAlign {
             // let resn2 = this.getResn(chainid, start + j);
             let resi2 = (bRealign && me.cfg.aligntool == 'tmalign') ? start + j : ic.ParserUtilsCls.getResi(chainid, start + j);
             let resn2 = this.getResnFromResi(chainid, resi2);
+
             let resn1 = '-';
             let bAlign = false;
             let resObject = this.getResObject(chainid, false, bAlign, resi2, resn2, resn1);
@@ -132974,22 +132941,28 @@ class SetSeqAlign {
     }
 
     getTemplatePosFromOriPos(chainid1, start, end, bRealign) { let ic = this.icn3d; ic.icn3dui;
-        //!!!
         let startResi = ic.ParserUtilsCls.getResi(chainid1, start);
         let endResi = ic.ParserUtilsCls.getResi(chainid1, end);
+            
+        let result1 = this.getResiPosInTemplate(chainid1, startResi);
+        let result2 = this.getResiPosInTemplate(chainid1, endResi);
+        
+        return {"pos1": result1.pos, "pos2": result2.pos};
+    }
 
-        // if(bRealign && me.cfg.aligntool == 'tmalign') { // vast alignment
-        //     let startResi = start;
-        //     let endResi = end;
+    getTemplatePosFromOriResi(chainid1, start, end, bRealign) { let ic = this.icn3d, me = ic.icn3dui;
+        if(bRealign && me.cfg.aligntool == 'tmalign') { // vast alignment
+            let startResi = start;
+            let endResi = end;
 
             let result1 = this.getResiPosInTemplate(chainid1, startResi);
             let result2 = this.getResiPosInTemplate(chainid1, endResi);
     
             return {"pos1": result1.pos, "pos2": result2.pos};
-        // }
-        // else {
-        //    return {"pos1": start, "pos2": end};
-        // }
+        }
+        else {
+            return {"pos1": start, "pos2": end};
+        }
     }
 
     mergeTwoSeqForAll(chainidArray, index, alignedChainIndice, resid2range_t, start_t, end_t, bRealign) { let ic = this.icn3d, me = ic.icn3dui;
@@ -133051,9 +133024,6 @@ class SetSeqAlign {
         if(!ic.chainsMapping[chainid2]) ic.chainsMapping[chainid2] = {};
 
         let result;
-
-        let nGapInTemplate = 0; // number of gaps inserted into the template sequence
-        let startPosInTemplate = 0; // position in the template sequence to start the mapping
         
         // need to improve when tmalign with residue number with postfix such as 52A in 4ORZ_C,5ESV_H
         // start and end should be positions, not original residue numbers.
@@ -133061,11 +133031,10 @@ class SetSeqAlign {
             start_t = ic.ParserUtilsCls.getResi(chainid1, start_t);
             end_t = ic.ParserUtilsCls.getResi(chainid1, end_t);
         }
-console.log("### me.cfg.aligntool " + me.cfg.aligntool + " bRealign " + bRealign );
+
         for(let i = 0, il = ic.qt_start_end[chainIndex].length; i < il; ++i) {
             let start1, start2, end1, end2, resiStart1, start1Pos, end1Pos;
-          
-            if(bRealign && (me.cfg.aligntool == 'tmalign')) { // real residue numbers are stored
+            if(bRealign && me.cfg.aligntool == 'tmalign') { // real residue numbers are stored
                 start1 = parseInt(ic.qt_start_end[chainIndex][i].t_start);
                 start2 = parseInt(ic.qt_start_end[chainIndex][i].q_start);
                 end1 = parseInt(ic.qt_start_end[chainIndex][i].t_end);
@@ -133093,28 +133062,46 @@ console.log("### me.cfg.aligntool " + me.cfg.aligntool + " bRealign " + bRealign
                 end1Pos = end1;
             }
             //let range = resid2range_t[chainid1 + '_' + resiStart1];
-
+  
             // if the mapping does not start from start_t, add gaps to the query seq
             if(i == 0) {
-                startPosInTemplate = start1Pos;
 
-                //!!!
-                // result = this.getTemplatePosFromOriPos(chainid1, start_t, start1, bRealign);
-                result = this.getTemplatePosFromOriPos(chainid1, start_t, start1Pos, bRealign);
-                pos1 = result.pos1;
-                pos2 = result.pos2;
+                if(me.cfg.aligntool == 'seqalign') {
+                    result = this.getTemplatePosFromOriPos(chainid1, start_t, start1Pos, bRealign);
 
-                //!!!
-                // if(start1 > start_t) {
-                if(start1Pos > start_t) {
-                    for(let j = 0, jl = pos2 - pos1; j < jl; ++j) {
-                        ic.alnChainsSeq[chainid2].push(gapResObject2);
+                    pos1 = result.pos1;
+                    pos2 = result.pos2;
+                    
+                    //if(start1 > start_t) {
+                    if(start1Pos > start_t) {
+                        for(let j = 0, jl = pos2 - pos1; j < jl; ++j) {
+                            ic.alnChainsSeq[chainid2].push(gapResObject2);
+                        }
+                    }
+                }
+                else {
+                    result = this.getTemplatePosFromOriResi(chainid1, start_t, start1, bRealign);
+
+                    pos1 = result.pos1;
+                    pos2 = result.pos2;
+                    
+                    if(start1 > start_t) {
+                    //if(start1Pos > start_t) {
+                        for(let j = 0, jl = pos2 - pos1; j < jl; ++j) {
+                            ic.alnChainsSeq[chainid2].push(gapResObject2);
+                        }
                     }
                 }
             }
             else {
                 //let notAlnLen1 = start1 - (prevIndex1 + 1);
-                result = this.getTemplatePosFromOriPos(chainid1, prevIndex1, start1, bRealign);
+                //!!!
+                if(me.cfg.aligntool == 'seqalign') {
+                    result = this.getTemplatePosFromOriPos(chainid1, prevIndex1, start1Pos, bRealign);
+                }
+                else {
+                    result = this.getTemplatePosFromOriResi(chainid1, prevIndex1, start1, bRealign);
+                }
                 pos1 = result.pos1;
                 pos2 = result.pos2;
                 let notAlnLen1 = pos2 - (pos1 + 1);
@@ -133125,47 +133112,48 @@ console.log("### me.cfg.aligntool " + me.cfg.aligntool + " bRealign " + bRealign
 
                 // insert non-aligned residues in query seq
                 this.insertNotAlignRes(chainid2, prevIndex2+1, notAlnLen2, bRealign);
+
                 if(notAlnLen1 >= notAlnLen2) {
                     // add gaps before the query sequence
                     for(let j = 0, jl = notAlnLen1 - notAlnLen2; j < jl; ++j) {
                         ic.alnChainsSeq[chainid2].push(gapResObject2);
-                    }
+                    }                       
                 }
                 else {
                     // check the number of gaps before resiStart1 (n), and insert 'notAlnLen2 - notAlnLen1 - n' gaps
                     this.addGapAllAlnChains(chainidArray, alignedChainIndice, chainid1, resiStart1, notAlnLen2 - notAlnLen1);
-                    nGapInTemplate += (notAlnLen2 - notAlnLen1);
                 }                           
             }
 
             // 2. In the mapped residues
-            // result = this.getTemplatePosFromOriPos(chainid1, start1, end1, bRealign);
-            result = this.getTemplatePosFromOriPos(chainid1, start1Pos, end1Pos, bRealign);
+            if(me.cfg.aligntool == 'seqalign') {
+                result = this.getTemplatePosFromOriPos(chainid1, start1Pos, end1Pos, bRealign);
+            }
+            else {
+                result = this.getTemplatePosFromOriResi(chainid1, start1, end1, bRealign);
+            }
             pos1 = result.pos1;
             pos2 = result.pos2;
-
+            
             let k = 0;    
             if(!ic.chainsMapping[chainid1]) ic.chainsMapping[chainid1] = {};
             if(!ic.chainsMapping[chainid2]) ic.chainsMapping[chainid2] = {};
-            //!!!!!!
-            let resiAdjust = ((bRealign && me.cfg.aligntool == 'tmalign') || me.cfg.aligntool == 'seqalign') ? 0 : - startPosInTemplate + nGapInTemplate; 
             for(let j = pos1; j <= pos2; ++j) {
                 // inherit the gaps from the template
-                if(ic.alnChainsSeq[chainid1][j + resiAdjust].resn == '-') {
+                if(ic.alnChainsSeq[chainid1][j].resn == '-') {
                     ic.alnChainsSeq[chainid2].push(gapResObject2);
                 }
                 else {                   
                     let resi1 = (bRealign && me.cfg.aligntool == 'tmalign') ? start1 + k : ic.ParserUtilsCls.getResi(chainid1, start1 + k);
                     let resi2 = (bRealign && me.cfg.aligntool == 'tmalign') ? start2 + k : ic.ParserUtilsCls.getResi(chainid2, start2 + k);
-
                     let resn1 = this.getResnFromResi(chainid1, resi1); //this.getResn(chainid1, start1 + k);
                     let resn2 = this.getResnFromResi(chainid2, resi2); //this.getResn(chainid2, start2 + k);
-
+                    
                     let bAlign = true;
                     let resObject = this.getResObject(chainid2, false, bAlign, resi2, resn2, resn1);
                     ic.alnChainsSeq[chainid2].push(resObject);
                     // update color in the template
-                    ic.alnChainsSeq[chainid1][j + resiAdjust].color = resObject.color;
+                    ic.alnChainsSeq[chainid1][j].color = resObject.color;
 
                     ic.chainsMapping[chainid1][chainid1 + '_' + resi1] = resn1 + resi1;
                     ic.chainsMapping[chainid2][chainid2 + '_' + resi2] = resn1 + resi1;  
@@ -133183,7 +133171,12 @@ console.log("### me.cfg.aligntool " + me.cfg.aligntool + " bRealign " + bRealign
         } 
 
         // add gaps at the end
-        result = this.getTemplatePosFromOriPos(chainid1, prevIndex1, end_t, bRealign);
+        if(me.cfg.aligntool == 'seqalign') {
+            result = this.getTemplatePosFromOriPos(chainid1, prevIndex1, end_t, bRealign);
+        }
+        else {
+            result = this.getTemplatePosFromOriResi(chainid1, prevIndex1, end_t, bRealign);
+        }
         pos1 = result.pos1;
         pos2 = result.pos2;
         for(let i = pos1; i < pos2; ++i) {
@@ -133203,7 +133196,7 @@ console.log("### me.cfg.aligntool " + me.cfg.aligntool + " bRealign " + bRealign
 
         for(let i = 0, il = ic.qt_start_end[index].length; i < il; ++i) {
             let start1, start2, end1, end2, resiStart1, start1Pos, end1Pos;
-
+            
             start1 = ic.qt_start_end[index][i].t_start;
             start2 = ic.qt_start_end[index][i].q_start;
             end1 = ic.qt_start_end[index][i].t_end;
@@ -133519,10 +133512,10 @@ console.log("### me.cfg.aligntool " + me.cfg.aligntool + " bRealign " + bRealign
         }
     }   
 
-    setMsaFormat(chainidArray) { let ic = this.icn3d, me = ic.icn3dui;
+    setMsaFormat(chainidArray) { let ic = this.icn3d; ic.icn3dui;
         //set MSA
-        let fastaFormat = '', clustalwFormat = 'CLUSTALWW\n\n', resbyresFormat = '';
-        let chainArrayClustal = [];
+        let fastaFormat = '', clustalwFormat = 'CLUSTALW\n\n', resbyresFormat = '';
+        let chainArrayClustalw = [];
         
         let consArray = [], resiArrayTemplate = [];
         let chainidTemplate = chainidArray[0];
@@ -133531,9 +133524,7 @@ console.log("### me.cfg.aligntool " + me.cfg.aligntool + " bRealign " + bRealign
             fastaFormat += '>' + chainid + '\n';
 
             let clustalwArray = [];
-            let itemArray = me.utilsCls.getIdArray(chainid);
-            let chainidStr = 'pdb|' + itemArray[0] + '|' + itemArray[1];
-            let clustalwLine = chainidStr.padEnd(20, ' ');
+            let clustalwLine = chainid.padEnd(20, ' ');
             let consLine = ''.padEnd(20, ' ');
 
             let resiArrayTarget = [], resiArrayQuery = [];
@@ -133593,8 +133584,8 @@ console.log("### me.cfg.aligntool " + me.cfg.aligntool + " bRealign " + bRealign
 
             fastaFormat += '\n';
 
-            chainArrayClustal.push(clustalwArray);
-            if(i == il - 1) chainArrayClustal.push(consArray);
+            chainArrayClustalw.push(clustalwArray);
+            if(i == il - 1) chainArrayClustalw.push(consArray);
 
             // residue by residue
             let resiRangeStr1 = ic.resid2specCls.resi2range(resiArrayTarget, true);
@@ -133603,10 +133594,10 @@ console.log("### me.cfg.aligntool " + me.cfg.aligntool + " bRealign " + bRealign
             if(i > 0) resbyresFormat += resiRangeStr1 + ' | ' + resiRangeStr2 + '\n';
         }
 
-        // CLUSTALWW
-        for(let j = 0, jl = chainArrayClustal[0].length; j < jl; ++j) {
-            for(let i = 0, il = chainArrayClustal.length; i < il; ++i) {
-                clustalwFormat += chainArrayClustal[i][j] + '\n';
+        // CLUSTALW
+        for(let j = 0, jl = chainArrayClustalw[0].length; j < jl; ++j) {
+            for(let i = 0, il = chainArrayClustalw.length; i < il; ++i) {
+                clustalwFormat += chainArrayClustalw[i][j] + '\n';
             }
             clustalwFormat += '\n';
         }
@@ -141730,6 +141721,15 @@ class Resid2spec {
          return Object.keys(residueHash);
     }
 
+    atoms2chains(atoms) {var ic = this.icn3d; ic.icn3dui;
+         let chains = {};
+         for(let i in atoms) {
+             let atom = ic.atoms[i];
+             chains[atom.structure + '_' + atom.chain] = 1;
+         }
+         return chains;
+    }
+
     atoms2structureArray(atoms) {var ic = this.icn3d; ic.icn3dui;
          let structures = {};
          for(let i in atoms) {
@@ -149345,11 +149345,10 @@ class ResizeCanvas {
                 //me.htmlCls.HEIGHT = $( window ).height();
                 me.utilsCls.setViewerWidthHeight(ic.icn3dui);
 
-                let width = me.htmlCls.WIDTH; // - me.htmlCls.LESSWIDTH_RESIZE;
-                let height = me.htmlCls.HEIGHT; // - me.htmlCls.LESSHEIGHT - me.htmlCls.EXTRAHEIGHT;
+                me.htmlCls.WIDTH; // - me.htmlCls.LESSWIDTH_RESIZE;
+                me.htmlCls.HEIGHT; // - me.htmlCls.LESSHEIGHT - me.htmlCls.EXTRAHEIGHT;
 
-                // if(ic !== undefined && !ic.bFullscreen) thisClass.resizeCanvas(width, height);
-                if(ic !== undefined && !ic.bFullscreen) thisClass.resizeCanvas(width, height, true, true);
+                //if(ic !== undefined && !ic.bFullscreen) thisClass.resizeCanvas(width, height, true, true);
             });
         }
     }
@@ -154099,8 +154098,8 @@ class iCn3D {
   }
 }
 //When users first load a structure, call this function to empty previous settings.
-iCn3D.prototype.init = function (bKeepCmd, bKeepConfig) {
-    this.init_base(bKeepCmd, bKeepConfig);
+iCn3D.prototype.init = function (bClearCmd, bKeepConfig) {
+    this.init_base(bClearCmd, bKeepConfig);
 
     this.molTitle = "";
 
@@ -154120,7 +154119,7 @@ iCn3D.prototype.init = function (bKeepCmd, bKeepConfig) {
     this.axes = [];
 };
 
-iCn3D.prototype.init_base = function (bKeepCmd, bKeepConfig) {
+iCn3D.prototype.init_base = function (bClearCmd, bKeepConfig) {
     if(!bKeepConfig) this.resetConfig();
     
     this.structures = {}; // structure name -> array of chains
@@ -154215,7 +154214,7 @@ iCn3D.prototype.init_base = function (bKeepCmd, bKeepConfig) {
     this.transformCls.rotateCount = 0;
     this.transformCls.rotateCountMax = 20;
 
-    if(bKeepCmd) this.commands = [];
+    if(bClearCmd) this.commands = [];
 
     this.axes = [];
 
@@ -154407,9 +154406,9 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
       resize: function( event, ui ) {
         me.htmlCls.WIDTH = ui.size.width; //$("#" + ic.pre + "canvas").width();
         me.htmlCls.HEIGHT = ui.size.height; //$("#" + ic.pre + "canvas").height();
-        if(ic !== undefined && !me.icn3d.bFullscreen) {
-            ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH, me.htmlCls.HEIGHT, true);
-        }
+        // if(ic !== undefined && !me.icn3d.bFullscreen) {
+        //     ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH, me.htmlCls.HEIGHT, true);
+        // }
       }
     });