icn3d 3.31.12 → 3.32.0

package/icn3d.module.js

@@ -9919,7 +9919,7 @@ class ClickMenu {
         });
 
         me.myEventCls.onIds("#" + me.pre + "mn1_mmciffile", "click", function(e) { me.icn3d; //e.preventDefault();
-           me.htmlCls.dialogCls.openDlg('dl_mmciffile', 'Please input mmCIF File');
+           me.htmlCls.dialogCls.openDlg('dl_mmciffile', 'Please append mmCIF File');
         });
 
         me.myEventCls.onIds("#" + me.pre + "mn1_mmcifid", "click", function(e) { me.icn3d; //e.preventDefault();
@@ -12585,7 +12585,7 @@ class SetMenu {
 //        html += this.getLink('mn1_pdbfile', 'PDB File');
 //        html += this.getLink('mn1_pdbfile_app', 'PDB File (append)');
         html += this.getLink('mn1_pdbfile_app', 'PDB Files (appendable)', 1, 2);
-        html += this.getLink('mn1_mmciffile', 'mmCIF File', undefined, 2);
+        html += this.getLink('mn1_mmciffile', 'mmCIF File (appendable)', undefined, 2);
         html += this.getLink('mn1_mol2file', 'Mol2 File', undefined, 2);
         html += this.getLink('mn1_sdffile', 'SDF File', undefined, 2);
         html += this.getLink('mn1_xyzfile', 'XYZ File', undefined, 2);
@@ -14929,8 +14929,8 @@ class SetDialog {
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_mmciffile' class='" + dialogClass + "'>";
-        html += this.addNotebookTitle('dl_mmciffile', 'Please input an mmCIF file');
-        html += "mmCIF File: " + me.htmlCls.inputFileStr + "id='" + me.pre + "mmciffile' value='1TUP' size=8> ";
+        html += this.addNotebookTitle('dl_mmciffile', 'Please append mmCIF files');
+        html += "Multiple mmCIF Files: <input type='file' multiple id='" + me.pre + "mmciffile' size=8> ";
         html += me.htmlCls.buttonStr + "reload_mmciffile'>Load</button>";
         html += "</div>";
 
@@ -16185,17 +16185,15 @@ class Events {
         }
     }
 
-    async readFile(bAppend, files, index, dataStrAll) { let me = this.icn3dui, ic = me.icn3d, thisClass = this;
+    async readFile(bAppend, files, index, dataStrAll, bmmCIF) { let me = this.icn3dui, ic = me.icn3d, thisClass = this;
         let file = files[index];
         let commandName = (bAppend) ? 'append': 'load';
+        commandName += (bmmCIF) ? ' mmcif file ': ' pdb file ';
         
         let reader = new FileReader();
         reader.onload = async function(e) {
-            //++ic.loadedFileCnt;
-
             let dataStr = e.target.result; // or = reader.result;
-            //thisClass.setLogCmd(commandName + ' pdb file ' + $("#" + me.pre + fileId).val(), false);
-            thisClass.setLogCmd(commandName + ' pdb file ' + file.name, false);
+            thisClass.setLogCmd(commandName + file.name, false);
 
             if(!bAppend) {
                 ic.init();
@@ -16209,7 +16207,7 @@ class Events {
             }
 
             ic.bInputfile = true;
-            ic.InputfileType = 'pdb';
+            ic.InputfileType = (bmmCIF) ? 'mmcif' : 'pdb';
             ic.InputfileData = (ic.InputfileData) ? ic.InputfileData + '\nENDMDL\n' + dataStr : dataStr;
 
             dataStrAll = (index > 0) ? dataStrAll + '\nENDMDL\n' + dataStr : dataStr;
@@ -16219,15 +16217,21 @@ class Events {
                     ic.hAtoms = {};
                     ic.dAtoms = {};
                 }
-                await ic.pdbParserCls.loadPdbData(dataStrAll, undefined, undefined, bAppend);
+                if(bmmCIF) {
+                    await ic.mmcifParserCls.loadMultipleMmcifData(dataStrAll, undefined, bAppend); 
+                }
+                else {
+                	await ic.pdbParserCls.loadPdbData(dataStrAll, undefined, undefined, bAppend);
+                }
+
+                //ic.InputfileType = undefined; // reset
             }
             else {
-                await thisClass.readFile(bAppend, files, index + 1, dataStrAll);
+                await thisClass.readFile(bAppend, files, index + 1, dataStrAll, bmmCIF);
             }
 
             if(bAppend) {
                 if(ic.bSetChainsAdvancedMenu) ic.definedSetsCls.showSets();
-                //if(ic.bSetChainsAdvancedMenu) ic.legendTableCls.showSets();
 
                 ic.bResetAnno = true;
 
@@ -16244,9 +16248,7 @@ class Events {
         }
     }
 
-    async loadPdbFile(bAppend) { let me = this.icn3dui, ic = me.icn3d;
-       let fileId = (bAppend) ? 'pdbfile_app' : 'pdbfile';
-
+    async loadPdbFile(bAppend, fileId, bmmCIF) { let me = this.icn3dui, ic = me.icn3d;
        //me = ic.setIcn3dui(this.id);
        ic.bInitial = true;
        if(!me.cfg.notebook) dialog.dialog( "close" );
@@ -16270,7 +16272,7 @@ class Events {
 
             ic.dataStrAll = '';
 
-            await this.readFile(bAppend, files, 0, '');
+            await this.readFile(bAppend, files, 0, '', bmmCIF);
        }
     }
 
@@ -17627,14 +17629,14 @@ class Events {
            e.preventDefault();
 
            let bAppend = false;
-           await thisClass.loadPdbFile(bAppend);
+           await thisClass.loadPdbFile(bAppend, 'pdbfile');
         });
 
         me.myEventCls.onIds("#" + me.pre + "reload_pdbfile_app", "click", async function(e) { let ic = me.icn3d;
            e.preventDefault();
 
            ic.bAppend = true;
-           await thisClass.loadPdbFile(ic.bAppend);
+           await thisClass.loadPdbFile(ic.bAppend, 'pdbfile_app');
         });
 
         me.myEventCls.onIds("#" + me.pre + "reload_mol2file", "click", function(e) { let ic = me.icn3d;
@@ -17818,49 +17820,13 @@ class Events {
            await ic.pdbParserCls.downloadUrl(url, type);
         });
 
-        me.myEventCls.onIds("#" + me.pre + "reload_mmciffile", "click", function(e) { let ic = me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_mmciffile", "click", async function(e) { let ic = me.icn3d;
            e.preventDefault();
-           ic.bInitial = true;
-           if(!me.cfg.notebook) dialog.dialog( "close" );
-           //close all dialog
-           if(!me.cfg.notebook) {
-               $(".ui-dialog-content").dialog("close");
-           }
-           else {
-               ic.resizeCanvasCls.closeDialogs();
-           }
-           let file = $("#" + me.pre + "mmciffile")[0].files[0];
-           if(!file) {
-             alert("Please select a file before clicking 'Load'");
-           }
-           else {
-             me.htmlCls.setHtmlCls.fileSupport();
-             let reader = new FileReader();
-             reader.onload = async function(e) {
-                let dataStr = e.target.result; // or = reader.result;
-                thisClass.setLogCmd('load mmcif file ' + $("#" + me.pre + "mmciffile").val(), false);
-                ic.molTitle = "";
-
-                // let url = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi";
-                // //ic.bCid = undefined;
-
-                // let dataObj = {'mmciffile': dataStr};
-                // let data = await me.getAjaxPostPromise(url, dataObj, true);
-
-                let bText = true;
-                // let bcifData = ic.bcifParserCls.getBcifJson(dataStr, undefined, bText);
-                // let data = JSON.parse(bcifData);
 
-                //ic.initUI();
-                ic.init();
-                ic.bInputfile = true;
-                ic.InputfileData = (ic.InputfileData) ? ic.InputfileData + '\nENDMDL\n' + data : data;
-                ic.InputfileType = 'mmcif';
-                // await ic.mmcifParserCls.loadMmcifData(data); 
-                await ic.opmParserCls.loadOpmData(dataStr, undefined, undefined, 'mmcif', undefined, bText);
-             };
-             reader.readAsText(file);
-           }
+           ic.bAppend = true;
+           let bmmCIF = true;
+           let fileId = 'mmciffile';
+           await thisClass.loadPdbFile(ic.bAppend, fileId, bmmCIF);
         });
 
         me.myEventCls.onIds("#" + me.pre + "applycustomcolor", "click", function(e) { let ic = me.icn3d;
@@ -18509,11 +18475,13 @@ class Events {
             let command;
             if(shape == 'Sphere') {
                 ic.sphereCls.createSphereBase(pos1, color, radius, undefined, undefined, undefined, opacity);
-                command = 'add sphere | x1 ' + pos1.x.toPrecision(4)  + ' y1 ' + pos1.y.toPrecision(4) + ' z1 ' + pos1.z.toPrecision(4) + ' | color ' + colorStr + ' | opacity ' + opacity + ' | radius ' + radius;
+                // command = 'add sphere | x1 ' + pos1.x.toPrecision(4)  + ' y1 ' + pos1.y.toPrecision(4) + ' z1 ' + pos1.z.toPrecision(4) + ' | color ' + colorStr + ' | opacity ' + opacity + ' | radius ' + radius;
+                command = 'add sphere | ' + nameArray + ' | color ' + colorStr + ' | opacity ' + opacity + ' | radius ' + radius;
             }
             else {
                 ic.boxCls.createBox_base(pos1, radius, color, undefined, undefined, undefined, opacity);
-                command = 'add cube | x1 ' + pos1.x.toPrecision(4)  + ' y1 ' + pos1.y.toPrecision(4) + ' z1 ' + pos1.z.toPrecision(4) + ' | color ' + colorStr + ' | opacity ' + opacity + ' | radius ' + radius;
+                // command = 'add cube | x1 ' + pos1.x.toPrecision(4)  + ' y1 ' + pos1.y.toPrecision(4) + ' z1 ' + pos1.z.toPrecision(4) + ' | color ' + colorStr + ' | opacity ' + opacity + ' | radius ' + radius;
+                command = 'add cube | ' + nameArray + ' | color ' + colorStr + ' | opacity ' + opacity + ' | radius ' + radius;
             }
 
             thisClass.setLogCmd(command, true);
@@ -29047,14 +29015,14 @@ class Strand {
         // include the whole sheet or helix when highlighting
         let atomsAdjust = {};
 
-        //if( (bHighlight === 1 || bHighlight === 2) && !ic.bAllAtoms) {
-        //if( !ic.bAllAtoms) {
-        if( Object.keys(atoms).length < Object.keys(ic.atoms).length) {
-            atomsAdjust = this.getSSExpandedAtoms(atoms);
-        }
-        else {
-            atomsAdjust = atoms;
-        }
+        // if( Object.keys(atoms).length < Object.keys(ic.atoms).length) {
+        //     atomsAdjust = this.getSSExpandedAtoms(atoms);
+        // }
+        // else {
+        //     atomsAdjust = atoms;
+        // }
+
+        atomsAdjust = atoms;
 
         if(bHighlight === 2) {
             if(fill) {
@@ -29112,9 +29080,16 @@ class Strand {
 
         let maxDist = 6.0;
 
+        //get the last residue
+        let atomArray = Object.keys(atoms);
+        let lastAtomSerial = atomArray[atomArray.length - 1];
+        let lastAtom = atoms[lastAtomSerial];
+        let lastResid = lastAtom.structure + '_' + lastAtom.chain + '_' + lastAtom.resi;
+
         for (let i in atomsAdjust) {
           atom = atomsAdjust[i];
           let chainid = atom.structure + '_' + atom.chain;
+          let resid = atom.structure + '_' + atom.chain + '_' + atom.resi;
           if ((atom.name === 'O' || atom.name === 'CA') && !atom.het) {
             // "CA" has to appear before "O"
 
@@ -29151,7 +29126,7 @@ class Strand {
                 if(atom.ssend && atom.ss === 'sheet') {
                     bSheetSegment = true;
                 }
-                else if(atom.ssend && atom.ss === 'helix') {
+                else if( (atom.ssend && atom.ss === 'helix') || resid == lastResid) { // partial sheet will draw as helix
                     bHelixSegment = true;
                 }
 
@@ -29258,7 +29233,7 @@ class Strand {
                 // }
 
                 //if ((atom.ssbegin || atom.ssend || (drawnResidueCount === totalResidueCount - 1) || bBrokenSs) && pnts[0].length > 0 && bSameChain) {
-                if ((currentChain !== atom.chain || atom.ssbegin || atom.ssend || (drawnResidueCount === totalResidueCount - 1) || bBrokenSs) && pnts[0].length > 0) {
+                if ((currentChain !== atom.chain || atom.ssbegin || atom.ssend || (drawnResidueCount === totalResidueCount - 1) || bBrokenSs || resid == lastResid) && pnts[0].length > 0) {
                     let atomName = 'CA';
                 
                     let prevone = [], nexttwo = [];
@@ -29401,8 +29376,11 @@ class Strand {
                     bHelixSegment = false;
                 } // end if (atom.ssbegin || atom.ssend)
 
-                // end of a chain
-                if ((currentChain !== atom.chain || ic.ParserUtilsCls.getResiNCBI(atom.structure + '_' + currentChain, currentResi) + 1 !== ic.ParserUtilsCls.getResiNCBI(chainid, atom.resi)) && pnts[0].length > 0) {
+                // end of a chain, or end of selection
+                if ((currentChain !== atom.chain 
+                    || ic.ParserUtilsCls.getResiNCBI(atom.structure + '_' + currentChain, currentResi) + 1 !== ic.ParserUtilsCls.getResiNCBI(chainid, atom.resi)
+                    || resid == lastResid
+                    ) && pnts[0].length > 0) {
                 //if ((currentChain !== atom.chain) && pnts[0].length > 0) {
 
                     let atomName = 'CA';
@@ -40838,9 +40816,24 @@ class AnnoCddSite {
             pssmid2toArray = {};
         }
 
-        let indexl =(domainArray !== undefined) ? domainArray.length : 0;
+        if(domainArray === undefined) domainArray = [];
+        let indexl = domainArray.length;
         let maxTextLen =(type == 'domain') ? 14 : 19;
         let titleSpace =(type == 'domain') ? 100 : 120;
+
+        // sort domainArray
+        domainArray.sort(function(a, b) {
+            let domainRepeatArray = a.locs;
+            let segArray = (type == 'domain' || type == 'ig') ? domainRepeatArray[0].segs : [domainRepeatArray[0]];
+            let domainFrom1 = Math.round(segArray[0].from);
+
+            domainRepeatArray = b.locs;
+            segArray = (type == 'domain' || type == 'ig') ? domainRepeatArray[0].segs : [domainRepeatArray[0]];
+            let domainFrom2 = Math.round(segArray[0].from);
+
+            return domainFrom1 - domainFrom2;
+        });
+
         for(let index = 0; index < indexl; ++index) {
             let pssmid = (type == 'domain') ? domainArray[index].pssmid : 0;
 
@@ -40904,6 +40897,9 @@ class AnnoCddSite {
                 // if(type != 'domain') setname += "_" + index + "_" + r; 
                 if(type != 'domain') setname = chnid + "_" + index + "_" + r  + "_" + domain; 
 
+                //remove space in setname
+                setname = setname.replace(/\s+/g, '');
+
                 if(type == 'domain') pssmid2fromArray[pssmid] = fromArray;
                 if(type == 'domain') pssmid2toArray[pssmid] = toArray;
 
@@ -41706,6 +41702,7 @@ class AnnoIg {
     async showIg(chnid, template) { let ic = this.icn3d; ic.icn3dui;
         // if(!ic.bRunRefnum || Object.keys(ic.atoms).length > Object.keys(ic.hAtoms).length) {
         if(ic.bRunRefnumAgain) {
+            // run for all chains
             await ic.refnumCls.showIgRefNum(template);
             // ic.bRunRefnum = true;    
         }
@@ -42363,9 +42360,7 @@ class AnnoDomain {
 
                     let result = ic.domain3dCls.c2b_NewSplitChain(atoms);
                     let subdomains = result.subdomains;
-                    let pos2resi = result.pos2resi;
-                    //let substruct = result.substruct;
-                    //let jsonStr = ic.domain3dCls.getDomainJsonForAlign(atoms);
+                    // let pos2resi = result.pos2resi;
 
                     for(let i = 0, il = subdomains.length; i < il; ++i) {
                         // domain item: {"sdid":1722375,"intervals":[[1,104],[269,323]]}
@@ -42379,7 +42374,7 @@ class AnnoDomain {
                         data.domains[chainid].domains.push(domain);
                     }
 
-                    data.domains[chainid].pos2resi = pos2resi;
+                    // data.domains[chainid].pos2resi = pos2resi;
                 }
             }
 
@@ -42412,11 +42407,26 @@ class AnnoDomain {
             this.showDomainPerStructure(i);
         }
     }
+
+    getResiFromNnbiresid(ncbiresid) { let ic = this.icn3d; ic.icn3dui;
+        let resid = (ic.ncbi2resid[ncbiresid]) ? ic.ncbi2resid[ncbiresid] : ncbiresid;
+        let resi = resid.substr(resid.lastIndexOf('_') + 1);
+
+        return resi;
+    }
+
+    getNcbiresiFromResid(resid) { let ic = this.icn3d; ic.icn3dui;
+        let ncbiresid = (ic.resid2ncbi[resid]) ? ic.resid2ncbi[resid] : resid;
+        let resi = ncbiresid.substr(ncbiresid.lastIndexOf('_') + 1);
+
+        return resi;
+    }
+
     showDomainWithData(chnid, data, bCalcDirect) { let ic = this.icn3d, me = ic.icn3dui;
         let html = '<div id="' + ic.pre + chnid + '_domainseq_sequence" class="icn3d-dl_sequence">';
         let html2 = html;
         let html3 = html;
-        let domainArray, pos2resi, proteinname;
+        let domainArray, proteinname;
         let pos = chnid.indexOf('_');
         let chain = chnid.substr(pos + 1);
         // MMDB symmetry chain has the form of 'A1'
@@ -42427,7 +42437,7 @@ class AnnoDomain {
         // if(bCalcDirect) {
             proteinname = chnid;
             domainArray = (data.domains[chnid]) ? data.domains[chnid].domains : [];
-            pos2resi = data.domains[chnid].pos2resi;
+            // pos2resi = data.domains[chnid].pos2resi;
 /*            
         }
         else {
@@ -42455,40 +42465,33 @@ class AnnoDomain {
             let title =(fulltitle.length > 17) ? fulltitle.substr(0,17) + '...' : fulltitle;
             let subdomainArray = domainArray[index].intervals;
             // remove duplicate, e.g., at https://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdb_strview.cgi?v=2&program=icn3d&domain&molinfor&uid=1itw
-            let domainFromHash = {}, domainToHash = {};
-            let fromArray = [], toArray = [], posFromArray = [], posToArray = [];
+            // let domainFromHash = {}, domainToHash = {};
+            let fromArray = [], toArray = []; // posFromArray = [], posToArray = [];
             let resiHash = {};
             let resCnt = 0;
 
+            // subdomainArray contains NCBI residue number
             for(let i = 0, il = subdomainArray.length; i < il; ++i) {
-                let domainFrom = Math.round(subdomainArray[i][0]) - 1; // convert 1-based to 0-based
-                let domainTo = Math.round(subdomainArray[i][1]) - 1;
+                // let domainFrom = Math.round(subdomainArray[i][0]) - 1; // convert 1-based to 0-based
+                // let domainTo = Math.round(subdomainArray[i][1]) - 1;
 
-                if(domainFromHash.hasOwnProperty(domainFrom) || domainToHash.hasOwnProperty(domainTo)) {
-                    continue; // do nothing for duplicated "from" or "to", e.g, PDBID 1ITW, 5FWI
-                }
-                else {
-                    domainFromHash[domainFrom] = 1;
-                    domainToHash[domainTo] = 1;
-                }
+                let domainFrom = parseInt(subdomainArray[i][0]);
+                let domainTo = parseInt(subdomainArray[i][1]);
 
-                // use the NCBI residue number, and convert to PDB residue number during selection
-                // if(ic.bNCBI || bCalcDirect) {
-                    fromArray.push(pos2resi[domainFrom]);
-                    toArray.push(pos2resi[domainTo]);
 
-                    posFromArray.push(domainFrom);
-                    posToArray.push(domainTo);
-                // }
-                // else {
-                //     fromArray.push(domainFrom + ic.baseResi[chnid]);
-                //     toArray.push(domainTo + ic.baseResi[chnid]);
-                // }
+                // fromArray.push(pos2resi[domainFrom]);
+                // toArray.push(pos2resi[domainTo]);
+
+                fromArray.push(domainFrom);
+                toArray.push(domainTo);
+
+                // posFromArray.push(domainFrom);
+                // posToArray.push(domainTo);
 
                 resCnt += domainTo - domainFrom + 1;
                 for(let j = domainFrom; j <= domainTo; ++j) {
-                    // resiHash[j+1] = 1;
-                    let resi = pos2resi[j];
+                    // let resi = pos2resi[j];
+                    let resi = this.getResiFromNnbiresid(chnid + '_' + j);
                     resiHash[resi] = 1;
                 }
             }
@@ -42499,21 +42502,22 @@ class AnnoDomain {
                             
                 if(!ic.resid2domain) ic.resid2domain = {};
                 if(!ic.resid2domain[chnid]) ic.resid2domain[chnid] = [];
-                for(let i = 0, il = posFromArray.length; i < il; ++i) {
-                    let from = parseInt(posFromArray[i]);
-                    let to = parseInt(posToArray[i]);
+                // for(let i = 0, il = posFromArray.length; i < il; ++i) {
+                for(let i = 0, il = fromArray.length; i < il; ++i) {
+                    let from = fromArray[i];
+                    let to = toArray[i];
                     for(let j = from; j <= to; ++j) {
                         // 0-based
                         let obj = {};
                         // let resi = ic.ParserUtilsCls.getResi(chnid, j);
-                        let resi = pos2resi[j];
-                        obj[chnid + '_' + resi] = domainName;
+                        let resid = ic.ncbi2resid(chnid + '_' + j);
+                        obj[resid] = domainName;
                         ic.resid2domain[chnid].push(obj);
                     }
                 }
             }
 
-            let htmlTmp2 = '<div class="icn3d-seqTitle icn3d-link icn3d-blue" 3ddomain="' +(index+1).toString() + '" from="' + posFromArray + '" to="' + posToArray + '" shorttitle="' + title + '" index="' + index + '" setname="' + chnid + '_3d_domain_' +(index+1).toString() + '" anno="sequence" chain="' + chnid + '" title="' + fulltitle + '">' + title + ' </div>';
+            let htmlTmp2 = '<div class="icn3d-seqTitle icn3d-link icn3d-blue" 3ddomain="' +(index+1).toString() + '" from="' + fromArray + '" to="' + toArray + '" shorttitle="' + title + '" index="' + index + '" setname="' + chnid + '_3d_domain_' +(index+1).toString() + '" anno="sequence" chain="' + chnid + '" title="' + fulltitle + '">' + title + ' </div>';
             let htmlTmp3 = '<span class="icn3d-residueNum" title="residue count">' + resCnt.toString() + ' Res</span>';
             html3 += htmlTmp2 + htmlTmp3 + '<br>';
             let htmlTmp = '<span class="icn3d-seqLine">';
@@ -42553,12 +42557,12 @@ class AnnoDomain {
             if(ic.seqStartLen && ic.seqStartLen[chnid]) html2 += ic.showSeqCls.insertMulGapOverview(chnid, ic.seqStartLen[chnid]);
 
             if(me.cfg.blast_rep_id != chnid) { // regular             
-                for(let i = 0, il = posFromArray.length; i < il; ++i) {
+                for(let i = 0, il = fromArray.length; i < il; ++i) {
                     // let emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray[i] - ic.baseResi[chnid] - 1) / ic.maxAnnoLength) : Math.round(ic.seqAnnWidth *(fromArray[i] - toArray[i-1] - 1) / ic.maxAnnoLength);
-                    let emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(posFromArray[i]) / ic.maxAnnoLength) : Math.round(ic.seqAnnWidth *(posFromArray[i] - posToArray[i-1] - 1) / ic.maxAnnoLength);
+                    let emptyWidth =(i == 0) ? Math.round(ic.seqAnnWidth *(fromArray[i]) / ic.maxAnnoLength) : Math.round(ic.seqAnnWidth *(fromArray[i] - toArray[i-1] - 1) / ic.maxAnnoLength);
 
                     html2 += '<div style="display:inline-block; width:' + emptyWidth + 'px;">&nbsp;</div>';
-                    html2 += '<div style="display:inline-block; color:white!important; font-weight:bold; background-color:#' + color + '; width:' + Math.round(ic.seqAnnWidth *(posToArray[i] - posFromArray[i] + 1) / ic.maxAnnoLength) + 'px;" class="icn3d-seqTitle icn3d-link icn3d-blue" 3ddomain="' +(index+1).toString() + '" from="' + posFromArray + '" to="' + posToArray + '" shorttitle="' + title + '" index="' + index + '" setname="' + chnid + '_3d_domain_' +(index+1).toString() + '" id="' + chnid + '_3d_domain_' + index + '" anno="sequence" chain="' + chnid + '" title="' + fulltitle + '">3D domain ' +(index+1).toString() + '</div>';
+                    html2 += '<div style="display:inline-block; color:white!important; font-weight:bold; background-color:#' + color + '; width:' + Math.round(ic.seqAnnWidth *(toArray[i] - fromArray[i] + 1) / ic.maxAnnoLength) + 'px;" class="icn3d-seqTitle icn3d-link icn3d-blue" 3ddomain="' +(index+1).toString() + '" from="' + fromArray + '" to="' + toArray + '" shorttitle="' + title + '" index="' + index + '" setname="' + chnid + '_3d_domain_' +(index+1).toString() + '" id="' + chnid + '_3d_domain_' + index + '" anno="sequence" chain="' + chnid + '" title="' + fulltitle + '">3D domain ' +(index+1).toString() + '</div>';
                 }
             }
             else { // with potential gaps 
@@ -44070,6 +44074,7 @@ class Domain3d {
 	//c2b_NewSplitChain(string asymId, let seqLen, let* x0, let* y0, let* z0) { let ic = this.icn3d, me = ic.icn3dui;
 	// x0, y0, z0: array of x,y,z coordinates of C-alpha atoms
 	//c2b_NewSplitChain(chnid, dcut) { let ic = this.icn3d, me = ic.icn3dui;
+	// this function works for a single chain
 	c2b_NewSplitChain(atoms, dcut) { let ic = this.icn3d; ic.icn3dui;
 		this.init3ddomain();
 
@@ -44125,14 +44130,11 @@ class Domain3d {
 			// pos2resi[i+1] = resi;
 			pos2resi[i] = resi;
 
-			ic.posid2resid[atom.structure + '_' + atom.chain + '_' + (i+1).toString()]  = resid;
-			// let residNCBI = ic.resid2ncbi[resid];
-			// let pos = residNCBI.substr(residNCBI.lastIndexOf('_') + 1);
-			// pos2resi[pos] = resi;
-
+			// ic.posid2resid[atom.structure + '_' + atom.chain + '_' + (i+1).toString()]  = resid;
 			if(atom.ssend) {
 				//substructItem.To = parseInt(resi);
 				substructItem.To = i + 1;
+				// substructItem.To = ic.annoDomainCls.getNcbiresiFromResid(resid);
 				substructItem.x2 = atom.coord.x;
 				substructItem.y2 = atom.coord.y;
 				substructItem.z2 = atom.coord.z;
@@ -44147,6 +44149,7 @@ class Domain3d {
 			if(atom.ssbegin) {
 				//substructItem.From = parseInt(resi);
 				substructItem.From = i + 1;
+				// substructItem.From = ic.annoDomainCls.getNcbiresiFromResid(resid);
 				substructItem.x1 = atom.coord.x;
 				substructItem.y1 = atom.coord.y;
 				substructItem.z1 = atom.coord.z;
@@ -44154,17 +44157,19 @@ class Domain3d {
         }
 
 		let nsse = substruct.length;
-
-		if (nsse <= 3)
+		
+		if (nsse <= 3) {
 			// too small, can't split or trim
-			return {subdomains: subdomains, substruct: substruct, pos2resi: pos2resi};
+			substruct = this.standardizeSubstruct(chnid, substruct, pos2resi);
+			return {subdomains: subdomains, substruct: substruct};
+        }
 
 		if (nsse > this.MAX_SSE) {
 			// we have a problem...
-
-			return {subdomains: subdomains, substruct: substruct, pos2resi: pos2resi};
+			substruct = this.standardizeSubstruct(chnid, substruct, pos2resi);
+			return {subdomains: subdomains, substruct: substruct};
 		}
-
+		
 		let seqLen = residueArray.length; // + resiOffset;
 		//let lastResi = resiArray[seqLen - 1];
 		let lastResi = seqLen;
@@ -44485,7 +44490,8 @@ class Domain3d {
 				let k = prts[i] - 1;
 
 				if ((k < 0) || (k >= substruct.length)) {
-					return {subdomains: subdomains, substruct: substruct, pos2resi: pos2resi};
+					substruct = this.standardizeSubstruct(chnid, substruct, pos2resi);
+					return {subdomains: subdomains, substruct: substruct};
 				}
 
 				//SSE_Rec sserec = substruct[k];
@@ -44572,16 +44578,23 @@ class Domain3d {
 
 				if (inseg && (rf == 0)) {
 					// segment ends
-					segments.push(startseg);
-					segments.push(i);
+					// segments.push(startseg);
+					// segments.push(i);
+
+					let resiRangeArray = this.getNcbiresiRangeFromPos(chnid, startseg, i, pos2resi);
+					segments = segments.concat(resiRangeArray);
+
 					inseg = false;
 				}
 			}
 
 			// check for the last segment
 			if (inseg) {
-				segments.push(startseg);
-				segments.push(lastResi);
+				// segments.push(startseg);
+				// segments.push(lastResi);
+
+				let resiRangeArray = this.getNcbiresiRangeFromPos(chnid, startseg, lastResi, pos2resi);
+				segments = segments.concat(resiRangeArray);
 			}
 
 			subdomains.push(segments);
@@ -44602,61 +44615,114 @@ class Domain3d {
 			}
 		}
 
-		return {subdomains: subdomains, substruct: substruct, pos2resi: pos2resi };
+		substruct = this.standardizeSubstruct(chnid, substruct, pos2resi);
+
+		// return {subdomains: subdomains, substruct: substruct};
+		//subdomains contains NCBI residue numbers
+		return {subdomains: subdomains, substruct: substruct};
 	} // end c2b_NewSplitChain
 
-	getDomainJsonForAlign(atoms, bForceOneDomain) { let ic = this.icn3d, me = ic.icn3dui;
+	standardizeSubstruct(chnid, substruct, pos2resi) { let ic = this.icn3d; ic.icn3dui;
+		// adjust substruct to use NCBI residue number
+		for (let i = 0; i < substruct.length; i++) {
+			//SSE_Rec sserec = substruct[i];
+			let sserec = substruct[i];
+			let FromPos = sserec.From;
+			let ToPos = sserec.To;
+			
+			let FromResi = pos2resi[FromPos - 1];
+			let ToResi = pos2resi[ToPos - 1];
+
+			let FromNcbiResid = ic.annoDomainCls.getNcbiresiFromResid(chnid + '_' + FromResi);
+			let ToNcbiResid = ic.annoDomainCls.getNcbiresiFromResid(chnid + '_' + ToResi);
+
+			substruct[i].From = FromNcbiResid.substr(FromNcbiResid.lastIndexOf('_') + 1);
+			substruct[i].To = ToNcbiResid.substr(ToNcbiResid.lastIndexOf('_') + 1);
+
+			substruct[i].From = parseInt(substruct[i].From);
+			substruct[i].To = parseInt(substruct[i].To);
+		}
+
+		return substruct;
+	}
+
+	getNcbiresiRangeFromPos(chnid, startPos, endPos, pos2resi) { let ic = this.icn3d; ic.icn3dui;
+		let resiArray = [];
+		for(let i = startPos; i <= endPos; ++i) {
+			let resi = pos2resi[i - 1];
+			let residNCBI = (ic.resid2ncbi[chnid + '_' + resi]) ? ic.resid2ncbi[chnid + '_' + resi] : chnid + '_' + resi;
+			let ncbiresi = residNCBI.substr(residNCBI.lastIndexOf('_') + 1);
+			resiArray.push(parseInt(ncbiresi));
+		}
+
+		let resiRangeArray = ic.resid2specCls.resi2range(resiArray);
+	
+		return resiRangeArray;
+	}
+
+	/*
+	// this function works for atoms in a single chain
+	// getDomainJsonForAlign(atoms, bForceOneDomain) { let ic = this.icn3d, me = ic.icn3dui;
+	getDomainJsonForAlign(atoms) { let ic = this.icn3d, me = ic.icn3dui;
 		let result = this.c2b_NewSplitChain(atoms);
 
 		let subdomains = result.subdomains;
 		let substruct = result.substruct;
-		let pos2resi = result.pos2resi;
+		// let pos2resi = result.pos2resi;
 
-		let residueHash = ic.firstAtomObjCls.getResiduesFromAtoms(atoms);
-		let residueArray = Object.keys(residueHash);
-		let chnid = residueArray[0].substr(0, residueArray[0].lastIndexOf('_'));
 
-		if(bForceOneDomain) subdomains = [];
+		let residueHash = ic.firstAtomObjCls.getResiduesFromAtoms(atoms);
+		// let residueArray = Object.keys(residueHash);
+		// let chnid = residueArray[0].substr(0, residueArray[0].lastIndexOf('_'));
 
-		//the whole structure is also considered as a large domain
-		//if(subdomains.length == 0) {
-			//subdomains.push([parseInt(ic.chainsSeq[chnid][0].resi), parseInt(ic.chainsSeq[chnid][ic.chainsSeq[chnid].length - 1].resi)]);
+		let firstAtom = ic.firstAtomObjCls.getFirstAtomObj(atoms);
+		let chnid = firstAtom.structure + '_' + firstAtom.chain;
 
-			// subdomains.push([parseInt(residueArray[0].substr(residueArray[0].lastIndexOf('_') + 1)), 
-			//  	parseInt(residueArray[residueArray.length-1].substr(residueArray[residueArray.length-1].lastIndexOf('_') + 1))]);
+		// if(bForceOneDomain) subdomains = [];
 
-			// use position based
-			subdomains.push([1, residueArray.length]);
-				
-		//}	
+		//the whole structure is also considered as a large domain
+		if(subdomains.length == 0) {
+			let resid1 = residueArray[0];
+			let resid2 = residueArray[residueArray.length - 1];
+			let ncbiresid1 = (ic.resid2ncbi[resid1]) ? ic.resid2ncbi[resid1] : resid1;
+			let ncbiresid2 = (ic.resid2ncbi[resid2]) ? ic.resid2ncbi[resid2] : resid2;
+			subdomains.push([parseInt(ncbiresid1.substr(ncbiresid1.lastIndexOf('_') + 1)), parseInt(ncbiresid2.substr(ncbiresid2.lastIndexOf('_') + 1))]);	
+		}	
 
 		// m_domains1: {"data": [ {"ss": [[1,20,30,x,y,z,x,y,z], [2,50,60,x,y,z,x,y,z]], "domain": [[1,43,x,y,z],[2,58,x,y,z], ...]}, {"ss": [[1,20,30,x,y,z,x,y,z], [2,50,60,x,y,z,x,y,z]],"domain": [[1,43,x,y,z],[2,58,x,y,z], ...]} ] }
 		let jsonStr = '{"data": [';
+		//merge all subdomains into one domain
+		jsonStr += '{"ss": ['; //secondary structure
+
+		let ssCnt = 0, startAll = 999, endAll = -999;
 		for(let i = 0, il = subdomains.length; i < il; ++i) {
-			if(i > 0) jsonStr += ', ';
-			//secondary structure
-			jsonStr += '{"ss": [';
-			let ssCnt = 0;
+			// if(i > 0) jsonStr += ', ';
+			// jsonStr += '{"ss": ['; //secondary structure
+			
 			for(let j = 0, jl = subdomains[i].length; j < jl; j += 2) {
 				let start = subdomains[i][j];
 				let end = subdomains[i][j + 1];
-			
+				
+				if(start < startAll) startAll = start;
+				if(end > endAll) endAll = end;
+				
 				for(let k = 0, kl = substruct.length; k < kl; ++k) {
 					//ss: sstype	ss_start	ss_end	x1	y1	z1	x2	y2	z2
 						//sstype: 1 (helix), 2 (sheet)
 					let sstype = (substruct[k].Sheet) ? 2 : 1;
-					let from = pos2resi[substruct[k].From - 1]; // 1-based to 0-based
-					let to = pos2resi[substruct[k].To - 1];
+					// let from = pos2resi[substruct[k].From - 1]; // 1-based to 0-based
+					// let to = pos2resi[substruct[k].To - 1];
 
 					// 1-based residue numbers
 					let fromPos = substruct[k].From;
 					let toPos = substruct[k].To;
 
-					let residFrom = chnid + "_" + from;
+					let residFrom = ic.ncbi2resid[chnid + "_" + fromPos];
 					let atomFrom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.residues[residFrom]);
+
 					if(!atomFrom || !ic.hAtoms.hasOwnProperty(atomFrom.serial)) continue;
 
-					let residTo = chnid + "_" + to;
+					let residTo = ic.ncbi2resid[chnid + "_" + toPos];
 					let atomTo = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.residues[residTo]);
 					if(!atomTo || !ic.hAtoms.hasOwnProperty(atomTo.serial)) continue;
 
@@ -44668,45 +44734,170 @@ class Domain3d {
 					}
 				}				
 			}
-			jsonStr += ']';
+		}
+		jsonStr += ']';
+		
+		// domain
+		jsonStr += ', "domain": [';
+		let domainCnt = 0;
+		let fakeCoord = 0; //-100000;  // the fake corrd is not read anyway
 
-			// domain
-			jsonStr += ', "domain": [';
-			let domainCnt = 0;
-			for(let j = 0, jl = subdomains[i].length; j < jl; j += 2) {
-				let start = subdomains[i][j];
-				let end = subdomains[i][j + 1];
+		// resi should be the continuous number starting from 1. make this correction in the backend
+		for(let j = startAll; j <= endAll; ++j) {
+			let ncbiResid = chnid + '_' + j;
+			let resid = ic.ncbi2resid[ncbiResid];
+
+			let pos = j;
+
+			if(domainCnt > 0) jsonStr += ', ';
+
+			if(!residueHash.hasOwnProperty(resid)) {
+				jsonStr += '[' + pos + ',' + 0 + ',' + fakeCoord + ',' + fakeCoord + ',' + fakeCoord + ']';
+			}
+			else {
+				let atom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.residues[resid]);
+
+				//domain: resi, restype, x, y, z
+				let restype = (me.parasCls.resn2restype[atom.resn]) ? me.parasCls.resn2restype[atom.resn] : 0;
+				
+				jsonStr += '[' + pos + ',' + restype + ',' + atom.coord.x.toFixed(2) + ',' + atom.coord.y.toFixed(2) + ',' + atom.coord.z.toFixed(2) + ']';
+			}
+
+			++domainCnt;		
+		}
+		jsonStr += ']}';
+
+		jsonStr += ']}';
+
+		return jsonStr;
+	} 
+*/
+	// this function works for atoms in a single chain
+	getDomainJsonForAlign(atoms) { let ic = this.icn3d, me = ic.icn3dui;
+		// let result = this.c2b_NewSplitChain(atoms);
+
+		// let subdomains = result.subdomains;
+		// let substruct = result.substruct;
+
+		let residueHash = ic.firstAtomObjCls.getResiduesFromAtoms(atoms);
+		let residueArray = Object.keys(residueHash);
+		let chnid = residueArray[0].substr(0, residueArray[0].lastIndexOf('_'));
+
+		// let resid1 = residueArray[0];
+		// let resid2 = residueArray[residueArray.length - 1];
+		// let ncbiresid1 = (ic.resid2ncbi[resid1]) ? ic.resid2ncbi[resid1] : resid1;
+		// let ncbiresid2 = (ic.resid2ncbi[resid2]) ? ic.resid2ncbi[resid2] : resid2;
+		// let startAll = parseInt(ncbiresid1.substr(ncbiresid1.lastIndexOf('_') + 1));
+		// let endAll = parseInt(ncbiresid2.substr(ncbiresid2.lastIndexOf('_') + 1));	
+
+		let substruct = [];
+		let substructItem = {};
+		let pos2resi = {}; // 0-based
+		let startAll = 999, endAll = -999;
+		for(let i = 0; i < residueArray.length; ++i) {
+			let resid = residueArray[i];
+			let atom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.residues[resid]);
 
-				for(let k = 0, kl = residueArray.length; k < kl; ++k) {
-					let resid = residueArray[k];
+			let resi = resid.substr(resid.lastIndexOf('_') + 1);
+			pos2resi[i] = resi;
+
+			let ncbiresid = (ic.resid2ncbi[resid]) ? ic.resid2ncbi[resid] : resid;
+			let ncbiresi = parseInt(ncbiresid.substr(ncbiresid.lastIndexOf('_') + 1));
+
+			if(ncbiresi < startAll) startAll = ncbiresi;
+			if(ncbiresi > endAll) endAll = ncbiresi;
+
+			if(atom.ssend) {
+				substructItem.To = i + 1;
+				substructItem.x2 = atom.coord.x;
+				substructItem.y2 = atom.coord.y;
+				substructItem.z2 = atom.coord.z;
 
-					// let resi = resid.substr(resid.lastIndexOf('_') + 1);
-					// let residNCBI = ic.resid2ncbi[resid];
-					// let pos = residNCBI.substr(residNCBI.lastIndexOf('_') + 1);
-					let pos = k + 1;
+				substructItem.Sheet = (atom.ss == 'sheet') ? true : false;
+
+				substruct.push(substructItem);
+				substructItem = {};		
+			}
+
+			// a residue could be both start and end. check ssend first, then check ssbegin 
+			if(atom.ssbegin) {
+				substructItem.From = i + 1;
+				substructItem.x1 = atom.coord.x;
+				substructItem.y1 = atom.coord.y;
+				substructItem.z1 = atom.coord.z;
+			}
+        }
+
+		substruct = this.standardizeSubstruct(chnid, substruct, pos2resi);
+
+		// m_domains1: {"data": [ {"ss": [[1,20,30,x,y,z,x,y,z], [2,50,60,x,y,z,x,y,z]], "domain": [[1,43,x,y,z],[2,58,x,y,z], ...]}, {"ss": [[1,20,30,x,y,z,x,y,z], [2,50,60,x,y,z,x,y,z]],"domain": [[1,43,x,y,z],[2,58,x,y,z], ...]} ] }
+		let jsonStr = '{"data": [';
+		//merge all subdomains into one domain
+		jsonStr += '{"ss": ['; //secondary structure
+
+		let ssCnt = 0;
+		for(let k = 0, kl = substruct.length; k < kl; ++k) {
+			//ss: sstype	ss_start	ss_end	x1	y1	z1	x2	y2	z2
+			//sstype: 1 (helix), 2 (sheet)
+			let sstype = (substruct[k].Sheet) ? 2 : 1;
+
+			// 1-based residue numbers
+			let fromPos = substruct[k].From;
+			let toPos = substruct[k].To;
+
+			let residFrom = ic.ncbi2resid[chnid + "_" + fromPos];
+			let atomFrom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.residues[residFrom]);
+			if(!atomFrom || !ic.hAtoms.hasOwnProperty(atomFrom.serial)) continue;
+
+			let residTo = ic.ncbi2resid[chnid + "_" + toPos];
+			let atomTo = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.residues[residTo]);
+			if(!atomTo || !ic.hAtoms.hasOwnProperty(atomTo.serial)) continue;
+
+			// if(fromPos >= start && toPos <= end) {
+				if(ssCnt > 0) jsonStr += ', ';
+				jsonStr += '[' + sstype + ',' + fromPos + ',' + toPos + ',' + substruct[k].x1.toFixed(2) + ',' + substruct[k].y1.toFixed(2) + ',' 
+					+ substruct[k].z1.toFixed(2) + ',' + substruct[k].x2.toFixed(2) + ',' + substruct[k].y2.toFixed(2) + ',' + substruct[k].z2.toFixed(2) + ']';
+				++ssCnt;
+			// }
+		}				
+
+		jsonStr += ']';
 		
-					//let resid = chnid + "_" + resi;
-					let atom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.residues[resid]);
-
-					if(!atom) continue;
-					if(!ic.hAtoms.hasOwnProperty(atom.serial)) continue;
-
-					//domain: resi, restype, x, y, z
-					let restype = me.parasCls.resn2restype[atom.resn];
-					if(restype !== undefined && pos >= start && pos <= end) {
-						if(domainCnt > 0) jsonStr += ', ';
-						jsonStr += '[' + pos + ',' + restype + ',' + atom.coord.x.toFixed(2) + ',' 
-							+ atom.coord.y.toFixed(2) + ',' + atom.coord.z.toFixed(2) + ']';
-						++domainCnt;
-					}
-				}			
+		// domain
+		jsonStr += ', "domain": [';
+		let domainCnt = 0;
+		let fakeCoord = 0; //-100000;  // the fake corrd is not read anyway
+
+		// resi should be the continuous number starting from 1. make this correction in the backend
+		for(let j = startAll; j <= endAll; ++j) {
+			let ncbiResid = chnid + '_' + j;
+			let resid = ic.ncbi2resid[ncbiResid];
+
+			let pos = j;
+
+			if(domainCnt > 0) jsonStr += ', ';
+
+			if(!residueHash.hasOwnProperty(resid)) {
+				jsonStr += '[' + pos + ',' + 0 + ',' + fakeCoord + ',' + fakeCoord + ',' + fakeCoord + ']';
+			}
+			else {
+				let atom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.residues[resid]);
+
+				//domain: resi, restype, x, y, z
+				let restype = (me.parasCls.resn2restype[atom.resn]) ? me.parasCls.resn2restype[atom.resn] : 0;
+				
+				jsonStr += '[' + pos + ',' + restype + ',' + atom.coord.x.toFixed(2) + ',' + atom.coord.y.toFixed(2) + ',' + atom.coord.z.toFixed(2) + ']';
 			}
-			jsonStr += ']}';
+
+			++domainCnt;		
 		}
 		jsonStr += ']}';
 
+		jsonStr += ']}';
+
 		return jsonStr;
 	} 
+
 }
 
 /**
@@ -44804,27 +44995,12 @@ class AddTrack {
         });
 
         // Isoform Alignment
-        me.myEventCls.onIds("#" + ic.pre + "addtrack_button2c", "click", async function(e) { let ic = thisClass.icn3d;
+        me.myEventCls.onIds("#" + ic.pre + "addtrack_button2c", "click", async function(e) { thisClass.icn3d;
             e.stopImmediatePropagation();
             //e.preventDefault();
             dialog.dialog( "close" );
 
-            let chainid = $("#" + ic.pre + "track_chainid").val();    
-            let geneid = $("#" + ic.pre + "track_geneid").val();
-            if(!geneid) {
-                alert("Please fill in the Gene ID...");
-                return;
-            }
-
-            let startpos = $("#" + ic.pre + "fasta_startpos2").val();
-            if(!startpos) startpos = 1;
-
-            //let colorseqby = $("#" + ic.pre + "colorseqby2").val();
-            //let type =(colorseqby == 'identity') ? 'identity' : 'custom';
-
-            let type = 'identity';
-    
-            await thisClass.addExonTracks(chainid, geneid, startpos, type);
+            await thisClass.addExonTracksWrap();
         });
 
         // BED file
@@ -46415,6 +46591,25 @@ class AddTrack {
         return acclistTmp;
     }
 
+    async addExonTracksWrap() { let ic = this.icn3d; ic.icn3dui;
+        let chainid = $("#" + ic.pre + "track_chainid").val();    
+        let geneid = $("#" + ic.pre + "track_geneid").val();
+        if(!geneid) {
+            alert("Please fill in the Gene ID...");
+            return;
+        }
+
+        let startpos = $("#" + ic.pre + "fasta_startpos2").val();
+        if(!startpos) startpos = 1;
+
+        //let colorseqby = $("#" + ic.pre + "colorseqby2").val();
+        //let type =(colorseqby == 'identity') ? 'identity' : 'custom';
+
+        let type = 'identity';
+
+        await thisClass.addExonTracks(chainid, geneid, startpos, type);
+    }
+
     async addExonTracks(chainid, geneid, startpos, type) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
@@ -46808,7 +47003,6 @@ class Annotation {
         if($("#" + ic.pre + "anno_transmem").length) $("#" + ic.pre + "anno_transmem")[0].checked = false;
     }
     async setAnnoTabIg(bSelection, template) {  let ic = this.icn3d; ic.icn3dui;
-
         await this.updateIg(bSelection, template);
 
         $("[id^=" + ic.pre + "ig]").show();
@@ -47149,7 +47343,7 @@ class Annotation {
 
     async updateIg(bSelection, template) { let ic = this.icn3d, me = ic.icn3dui;
         ic.opts['color'] = 'ig strand';
-
+        
         // if(!bSelection && !template) {
         if(!bSelection) {
             // select all protein chains
@@ -47168,11 +47362,13 @@ class Annotation {
         }
 
         ic.bRunRefnumAgain = true;
-        for(let chainid in ic.protein_chainid) {
+        let chainidHash = (!bSelection) ? ic.protein_chainid : ic.firstAtomObjCls.getChainsFromAtoms(ic.hAtoms);
+        for(let chainid in chainidHash) {
+            // showIgRefNum() in showIg() runs for all chains
             await ic.annoIgCls.showIg(chainid, template);
             ic.bRunRefnumAgain = false; // run it once for all chains
         }
-
+        
         if(ic.bShowRefnum) {
             ic.hlUpdateCls.updateHlAll();
             ic.drawCls.draw();
@@ -48609,11 +48805,12 @@ class HlSeq {
                   ic.bAlignSeq = false;
                   ic.bAnnotations = true;
               }
-
+              
               if(ic.bSelectResidue === false && !ic.bShift && !ic.bCtrl) {
+            //   if(!ic.bShift && !ic.bCtrl) {
                   ic.selectionCls.removeSelection();
               }
-
+              
               // select residues
               $("span.ui-selected", this).each(function() {
                   let id = $(this).attr('id');
@@ -48624,11 +48821,12 @@ class HlSeq {
               });
 
               ic.selectionCls.saveSelectionPrep(true);
-              ic.selectionCls.saveSelection(undefined, undefined, true);
+              //ic.selectionCls.saveSelection(undefined, undefined, true);
+              // do not use selected residues, use ic.hAtoms instead
+              ic.selectionCls.saveSelection(undefined, undefined, false);
 
               //ic.residueLabelsCls.addResidueLabels(ic.hAtoms, false, 0.5);
               ic.hlObjectsCls.addHlObjects();  // render() is called
-
               // get all chainid in the selected residues
               let chainHash = {};
               for(let residueid in ic.selectedResidues) {
@@ -48711,7 +48909,9 @@ class HlSeq {
                    thisClass.selectResidues(id, this);
 
                    ic.selectionCls.saveSelectionPrep(true);
-                   ic.selectionCls.saveSelection(undefined, undefined, true);
+                   //ic.selectionCls.saveSelection(undefined, undefined, true);
+                   // do not use selected residues, use ic.hAtoms instead
+                   ic.selectionCls.saveSelection(undefined, undefined, false);
               }
           //});
 
@@ -48915,8 +49115,9 @@ class HlSeq {
                                         residueid = ic.ncbi2resid[residNCBI];
                                     }
                                     else if($(that).attr('3ddomain') !== undefined) {
-                                        // the position of residues with coordinates
-                                        residueid = ic.posid2resid[chainid + '_' + (j+1).toString()];
+                                        // NCBI residue numbers
+                                        // residueid = ic.posid2resid[chainid + '_' + (j+1).toString()];
+                                        residueid = ic.ncbi2resid[chainid + '_' + j];
                                     }
                                     else {
                                         residueid = chainid + '_' + (j+1).toString();
@@ -49036,9 +49237,10 @@ class HlSeq {
       if(me.bNode) return;
 
       if(ic.bSelectResidue === false && !ic.bShift && !ic.bCtrl) {
+    //   if(!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);
@@ -49599,7 +49801,7 @@ class LineGraph {
             // Node for common interaction: {id : "Q24.A.2AJF|Q24", r : "1_1_2AJF_A_24", s: "a", ...}
             let nodeArray1SplitCommon = [], nodeArray2SplitCommon = [], linkArraySplitCommon = [], nameHashSplitCommon = [];
             let nodeArray1SplitDiff = [], nodeArray2SplitDiff = [], linkArraySplitDiff = [], nameHashSplitDiff = [];
-            let linkedNodeCnt = {}, linkedNodeInterDiff = {};
+            let linkedNodeCnt = {}, linkedNodeInterDiff = {}, linkedNodeInterDiffBool = {};
 
             for(let i = 0, il = structureArray.length; i < il; ++i) {   
                 nodeArray1Split[i] = [];
@@ -49658,13 +49860,15 @@ class LineGraph {
                             linkedNodeInterDiff[mappingid] = link.n;
                           }
                           else {                           
-                            ++linkedNodeCnt[mappingid];                            
-                            linkedNodeInterDiff[mappingid] -= link.n; // show difference
+                            ++linkedNodeCnt[mappingid];   
+                            linkedNodeInterDiff[mappingid] += link.n; 
+                            
+                            linkedNodeInterDiffBool[mappingid] = (linkedNodeInterDiff[mappingid] / link.n == linkedNodeCnt[mappingid]) ? 0 : 1; 
                           }
                       }
                 } 
             }
-
+            
             // do not combine with the above section since linkedNodeCnt was pre-populated above
             // set linkArraySplitCommon and nameHashSplitCommon
             // set linkArraySplitDiff and nameHashSplitDiff
@@ -49710,7 +49914,7 @@ class LineGraph {
                           linkDiff.source += separatorDiff + ic.chainsMapping[chainid1][resid1];
                           linkDiff.target += separatorDiff + ic.chainsMapping[chainid2][resid2];
                       
-                          if(linkedNodeCnt[mappingid] == structureArray.length && linkedNodeInterDiff[mappingid] == 0) {
+                          if(linkedNodeCnt[mappingid] == structureArray.length && linkedNodeInterDiffBool[mappingid] == 0) {
                               linkArraySplitCommon[index].push(linkCommon);
                           }  
                           else {
@@ -50407,18 +50611,20 @@ class GetGraph {
         return lineGraphStr;
     }
 
-    updateGraphColor() { let ic = this.icn3d, me = ic.icn3dui;
+    updateGraphColor() { let ic = this.icn3d; ic.icn3dui;
       // change graph color
 
+      // do not update the graph for now
+      /*
       if(ic.graphStr !== undefined) {
           let graphJson = JSON.parse(ic.graphStr);
-          let resid2color = {};
+          let resid2color = {}
           for(let resid in ic.residues) {
               let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
               resid2color[resid] = atom.color.getHexString().toUpperCase();
           }
 
-          let target2resid = {};
+          let target2resid = {}
           for(let i = 0, il = graphJson.nodes.length; i < il; ++i) {
               let node = graphJson.nodes[i];
               //node.r: 1_1_1KQ2_A_1
@@ -50447,6 +50653,7 @@ class GetGraph {
       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);
+      */
     }
 
     handleForce() { let ic = this.icn3d, me = ic.icn3dui;
@@ -52610,7 +52817,7 @@ class ContactMap {
 
         let graphStr = '{\n';
 
-        let struc1 = (ic.structures.length > 0) ? ic.structures[0] : ic.defaultPdbId;
+        let struc1 = (Object.keys(ic.structures).length > 0) ? ic.structures[0] : ic.defaultPdbId;
         let len1 = nodeArray1.length,
             len2 = nodeArray2.length;
         let factor = 1;
@@ -53144,6 +53351,7 @@ class ChainalignParser {
                 let allPromise = Promise.allSettled(ajaxArray);
                 // try {
                     let dataArray = await allPromise;
+                    
                     await thisClass.downloadChainalignmentPart2b(chainresiCalphaHash2, chainidArray, hAtoms, dataArray, indexArray, mmdbid_t, struArray);
                 // }
                 // catch(err) {
@@ -53747,13 +53955,13 @@ class ChainalignParser {
         if(queryData !== undefined && JSON.stringify(queryData).indexOf('Oops there was a problem') === -1
             && align !== undefined && JSON.stringify(align).indexOf('Oops there was a problem') === -1
         ) {
-            if((align === undefined || align.length == 0) && bEqualMmdbid && bEqualChain) {
+            if((align === "error" || align === undefined || align.length == 0) && bEqualMmdbid && bEqualChain) {
                 ic.t_trans_add[index] = {"x":0, "y":0, "z":0};
                 ic.q_trans_sub[index] = {"x":0, "y":0, "z":0};
                 ic.q_rotation[index] = {"x1":1, "y1":0, "z1":0, "x2":0, "y2":1, "z2":0, "x3":0, "y3":0, "z3":1};
                 ic.qt_start_end[index] = undefined;
             }
-            else if(align === undefined || align.length == 0) {
+            else if(align === "error" || align === undefined || align.length == 0) {
                 if(!me.cfg.command && !bNoAlert) alert('These two chains can not align to each other. ' + 'Please select sequences from these two chains in the "Sequences & Annotations" window, ' + 'and click "Realign Selection" in the "File" menu to align your selection.');
 
                 ic.t_trans_add[index] = {"x":0, "y":0, "z":0};
@@ -53784,14 +53992,16 @@ class ChainalignParser {
                 ic.qt_start_end[index] = align[0].segs;
 
                 let rmsd = align[0].super_rmsd;
+                let rmsdStr = (rmsd) ? rmsd.toPrecision(4) : rmsd;
+                let scoreStr = (align[0].score) ? align[0].score.toPrecision(4) : align[0].score;
 
-                let logStr = "alignment RMSD: " + rmsd.toPrecision(4);
-                if(me.cfg.aligntool == 'tmalign') logStr += "; TM-score: " + align[0].score.toPrecision(4);
+                let logStr = "alignment RMSD: " + rmsdStr;
+                if(me.cfg.aligntool == 'tmalign') logStr += "; TM-score: " + scoreStr;
                 me.htmlCls.clickMenuCls.setLogCmd(logStr, false);
-                let html = "<br><b>Alignment RMSD</b>: " + rmsd.toPrecision(4) + " &#8491;<br>";
+                let html = "<br><b>Alignment RMSD</b>: " + rmsdStr + " &#8491;<br>";
                 if(me.cfg.aligntool == 'tmalign') {
-                    html += "<b>TM-score</b>: " + align[0].score.toPrecision(4) + "<br><br>";
-                    ic.tmscore = align[0].score.toPrecision(4);
+                    html += "<b>TM-score</b>: " + scoreStr + "<br><br>";
+                    ic.tmscore = scoreStr;
                 }
 
                 $("#" + ic.pre + "dl_rmsd_html").html(html);
@@ -53938,6 +54148,7 @@ class ChainalignParser {
         let allPromise = Promise.allSettled(ajaxArray);
         // try {
             let dataArray = await allPromise;
+
             await thisClass.parseMMdbAfData(dataArray, structArray, bQuery, vastplusAtype);
             if(vastplusAtype === undefined) ic.ParserUtilsCls.hideLoading();
         // }
@@ -53970,13 +54181,9 @@ class ChainalignParser {
 
         //if(!ic.bCommandLoad && !bQuery) ic.init(); // remove all previously loaded data
         
-        let hAtoms = {}, hAtomsTmp = {};
+        let hAtoms = {};
         let bLastQuery = false;
 
-        let opts = {};
-
-        opts['color'] = (structArray.length > 1) ? 'structure' : ((structArray[0].length > 5) ? 'confidence' : 'chain');
-
         for(let i = 0, il = structArray.length; i < il; ++i) {
             if(i == structArray.length - 1) bLastQuery = true;
 
@@ -53991,24 +54198,30 @@ class ChainalignParser {
                 targetOrQuery = 'query';
                 bAppend = true; 
             }
-            
+
             //if(structArray[i].length > 4) {
             if(isNaN(structArray[i]) && structArray[i].length > 5) {  // PDB ID plus postfix could be 5 
                 //let bNoDssp = true;
                 let bNoDssp = false; // get secondary structure info
-                hAtomsTmp = await ic.pdbParserCls.loadPdbData(queryDataArray[i], structArray[i], false, bAppend, targetOrQuery, bLastQuery, bNoDssp);
+                await ic.pdbParserCls.loadPdbData(queryDataArray[i], structArray[i], false, bAppend, targetOrQuery, bLastQuery, bNoDssp);
             }
             else {
                 let bNoSeqalign = true;
                 let pdbid = structArray[i];
-                hAtomsTmp = await ic.mmdbParserCls.parseMmdbData(queryDataArray[i], targetOrQuery, undefined, undefined, bLastQuery, bNoSeqalign, pdbid);
+
+                //hAtomsTmp contains all atoms
+                await ic.mmdbParserCls.parseMmdbData(queryDataArray[i], targetOrQuery, undefined, undefined, bLastQuery, bNoSeqalign, pdbid);
             }
                     
-            hAtoms = me.hashUtilsCls.unionHash(hAtoms, hAtomsTmp);
+            // hAtoms = me.hashUtilsCls.unionHash(hAtoms, hAtomsTmp);
         }
 
-        // add color only for the newly loaded structures
-        ic.setColorCls.setColorByOptions(opts, hAtoms);
+        let structArrayAll = Object.keys(ic.structures);
+
+        ic.opts['color'] = (structArrayAll.length > 1) ? 'structure' : ((structArrayAll[0].length > 5) ? 'confidence' : 'chain');
+
+        // add color for all structures
+        ic.setColorCls.setColorByOptions(ic.opts, hAtoms);
 
         await ic.ParserUtilsCls.renderStructure();
 
@@ -54038,15 +54251,6 @@ class ChainalignParser {
             if(vastplusAtype == 2) me.cfg.aligntool = 'tmalign';
             await ic.vastplusCls.vastplusAlign(structArray, vastplusAtype);
         }
-
-        // /// if(ic.deferredMmdbaf !== undefined) ic.deferredMmdbaf.resolve();
-
-        // if(Object.keys(ic.structures).length == 1 && me.cfg.mmdbafid.length > 5) {
-        //     ic.ParserUtilsCls.checkMemProtein(me.cfg.mmdbafid);
-        // }
-        // else {
-        //     /// if(ic.deferredMmdbaf !== undefined) ic.deferredMmdbaf.resolve();
-        // }
     }
 }
 
@@ -55514,24 +55718,32 @@ class MmcifParser {
             if(data.emd !== undefined) ic.emd = data.emd;
             if(data.organism !== undefined) ic.organism = data.organism;
 
-            if(ic.emd !== undefined) {
-              $("#" + ic.pre + "mapWrapper1").hide();
-              $("#" + ic.pre + "mapWrapper2").hide();
-              $("#" + ic.pre + "mapWrapper3").hide();
-            }
-            else {
-              $("#" + ic.pre + "emmapWrapper1").hide();
-              $("#" + ic.pre + "emmapWrapper2").hide();
-              $("#" + ic.pre + "emmapWrapper3").hide();
-            }
-
             await ic.opmParserCls.loadOpmData(data, mmcifid, undefined, 'mmcif');
+
+            ic.opmParserCls.modifyUIMapAssembly();
         }
         else {
-            //alert('invalid atoms data.');
             return false;
         }
     }
+
+    async loadMultipleMmcifData(data, mmcifid, bAppend) { let ic = this.icn3d; ic.icn3dui;
+        let bText = true;
+        ic.loadCIFCls.loadCIF(data, mmcifid, bText, bAppend);
+        
+        if(Object.keys(ic.structures).length > 1) {
+            ic.opts['color'] = 'structure';
+        }
+
+        ic.opmParserCls.modifyUIMapAssembly();
+
+        ic.pdbParserCls.addSecondary(bAppend);
+
+        // ic.setStyleCls.setAtomStyleByOptions(ic.opts);
+        // ic.setColorCls.setColorByOptions(ic.opts, ic.atoms);
+
+        // await ic.ParserUtilsCls.renderStructure();
+    }
 }
 
 /**
@@ -56374,26 +56586,26 @@ class BcifParser {
                 let molecueType;
                 if(atom_hetatm == "ATOM") {
                     if(resn.length == 3) {
-                        molecueType = "p"; // protein
+                        molecueType = "protein"; //"p"; // protein
                     }
                     else {
-                        molecueType = "n"; // nucleotide
+                        molecueType = "nucleotide"; //"n"; // nucleotide
                     }
                 }
                 else {
                     if(resn == "WAT" || resn == "HOH") {
-                        molecueType = "s"; // solvent
+                        molecueType = "solvent"; //"s"; // solvent
                         chain = 'Misc';
                     }
                     else {
-                        molecueType = "l"; // ligands or ions
+                        molecueType = "ligand"; //"l"; // ligands or ions
                         chain = resn;
                     }
                 }
 
                 // C-alpha only for large structure
-                if(!bFull && ((molecueType == "p" && !(elem == 'C' && name == 'CA')) 
-                    || (molecueType == "n" && !(name == "P")) ) ) continue;
+                if(!bFull && ((molecueType == "protein" && !(elem == 'C' && name == 'CA')) 
+                    || (molecueType == "nucleotide" && !(name == "P")) ) ) continue;
                 // skip alternative atoms
                 if(alt == "B") continue;
 
@@ -56416,7 +56628,7 @@ class BcifParser {
                     // }
                 }
     
-                if(molecueType == 's' || molecueType == "l") {
+                if(molecueType == 'solvent' || molecueType == "ligand") {
                     let seq = {};
                     if(!ligSeqHash.hasOwnProperty(chain)) {
                         ligSeqHash[chain] = [];
@@ -56554,26 +56766,26 @@ class BcifParser {
                 let molecueType;
                 if(atom_hetatm == "ATOM") {
                     if(resn.length == 3) {
-                        molecueType = "p"; // protein
+                        molecueType = "protein"; // protein
                     }
                     else {
-                        molecueType = "n"; // nucleotide
+                        molecueType = "nucleotide"; // nucleotide
                     }
                 }
                 else {
                     if(resn == "WAT" || resn == "HOH") {
-                        molecueType = "s"; // solvent
+                        molecueType = "solvent"; // solvent
                         chain = 'Misc';
                     }
                     else {
-                        molecueType = "l"; // ligands or ions
+                        molecueType = "ligand"; // ligands or ions
                         chain = resn;
                     }
                 }
 
                 // C-alpha only for large structure
-                if(!bFull && ((molecueType == "p" && !(elem == 'C' && name == 'CA')) 
-                    || (molecueType == "n" && !(name == "P")) ) ) continue;
+                if(!bFull && ((molecueType == "protein" && !(elem == 'C' && name == 'CA')) 
+                    || (molecueType == "nucleotide" && !(name == "P")) ) ) continue;
                 // skip alternative atoms
                 if(alt == "B") continue;
 
@@ -57123,6 +57335,43 @@ class OpmParser {
         }
     }
 
+    modifyUIMapAssembly() { let ic = this.icn3d, me = ic.icn3dui;
+        if(!me.bNode) {
+            if(ic.emd !== undefined) {
+                $("#" + ic.pre + "mapWrapper1").hide();
+                $("#" + ic.pre + "mapWrapper2").hide();
+                $("#" + ic.pre + "mapWrapper3").hide();
+              }
+              else {
+                $("#" + ic.pre + "emmapWrapper1").hide();
+                $("#" + ic.pre + "emmapWrapper2").hide();
+                $("#" + ic.pre + "emmapWrapper3").hide();
+              }
+  
+              if(Object.keys(ic.structures).length == 1) {
+                  $("#" + ic.pre + "alternateWrapper").hide();
+              }
+  /*    
+              // load assembly info
+              if(type === 'mmcif') {
+                  let assembly =(data.assembly !== undefined) ? data.assembly : [];
+                  for(let i = 0, il = assembly.length; i < il; ++i) {
+                      if(ic.biomtMatrices[i] == undefined) ic.biomtMatrices[i] = new THREE.Matrix4().identity();
+          
+                      for(let j = 0, jl = assembly[i].length; j < jl; ++j) {
+                          ic.biomtMatrices[i].elements[j] = assembly[i][j];
+                      }
+                  }
+              }
+  */        
+              if(ic.biomtMatrices !== undefined && ic.biomtMatrices.length > 1) {
+                  $("#" + ic.pre + "assemblyWrapper").show();
+      
+                  ic.asuCnt = ic.biomtMatrices.length;
+              }
+        }
+    }
+
     async parseAtomData(data, pdbid, bFull, type, pdbid2, bText) { let ic = this.icn3d, me = ic.icn3dui;
         /*
         if(type === 'mmtf') {
@@ -57139,38 +57388,7 @@ class OpmParser {
                 ic.loadCIFCls.loadCIF(data, pdbid, bText);
             // }
 
-            if(ic.emd !== undefined) {
-              $("#" + ic.pre + "mapWrapper1").hide();
-              $("#" + ic.pre + "mapWrapper2").hide();
-              $("#" + ic.pre + "mapWrapper3").hide();
-            }
-            else {
-              $("#" + ic.pre + "emmapWrapper1").hide();
-              $("#" + ic.pre + "emmapWrapper2").hide();
-              $("#" + ic.pre + "emmapWrapper3").hide();
-            }
-
-            if(Object.keys(ic.structures).length == 1) {
-                $("#" + ic.pre + "alternateWrapper").hide();
-            }
-/*    
-            // load assembly info
-            if(type === 'mmcif') {
-                let assembly =(data.assembly !== undefined) ? data.assembly : [];
-                for(let i = 0, il = assembly.length; i < il; ++i) {
-                    if(ic.biomtMatrices[i] == undefined) ic.biomtMatrices[i] = new THREE.Matrix4().identity();
-        
-                    for(let j = 0, jl = assembly[i].length; j < jl; ++j) {
-                        ic.biomtMatrices[i].elements[j] = assembly[i][j];
-                    }
-                }
-            }
-*/        
-            if(ic.biomtMatrices !== undefined && ic.biomtMatrices.length > 1) {
-                $("#" + ic.pre + "assemblyWrapper").show();
-    
-                ic.asuCnt = ic.biomtMatrices.length;
-            }
+            this.modifyUIMapAssembly();
     
             ic.setStyleCls.setAtomStyleByOptions(ic.opts);
             ic.setColorCls.setColorByOptions(ic.opts, ic.atoms);
@@ -57364,6 +57582,12 @@ class PdbParser {
             }
         }
 
+        await this.addSecondary(bAppend, bNoDssp);
+
+        return hAtoms;
+    }
+
+    async addSecondary(bAppend, bNoDssp) { let ic = this.icn3d, me = ic.icn3dui;
         // calculate secondary structures if not available
         // DSSP only works for structures with all atoms. The Calpha only structures didn't work
         //if(!ic.bSecondaryStructure && !bCalphaOnly) {
@@ -57387,8 +57611,6 @@ class PdbParser {
 
             /// if(ic.deferredOpm !== undefined) ic.deferredOpm.resolve();
         }
-
-        return hAtoms;
     }
 
     async applyCommandDssp(bAppend) { let ic = this.icn3d, me = ic.icn3dui;
@@ -58226,23 +58448,27 @@ class RealignParser {
 
         for(let s = 0, sl = structArray.length; s < sl; ++s) {
             let struct1 = structArray[s];
+
             let chainidArray1 = Object.keys(struct2domain[struct1]);
             if(chainidArray1.length == 0) continue;
-            for(let t = s+1, tl = structArray.length; t < tl; ++t) {
-                let struct2 = structArray[t];
-                let chainidArray2 = Object.keys(struct2domain[struct2]);
-                if(chainidArray2.length == 0) continue;
-
-                for(let i = 0, il = chainidArray1.length; i < il; ++i) {
-                    let chainid1 = chainidArray1[i];
-                    let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(struct2domain[struct1][chainid1]);
+
+            for(let i = 0, il = chainidArray1.length; i < il; ++i) {
+                let chainid1 = chainidArray1[i];
+                let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(struct2domain[struct1][chainid1]);
+
+                for(let t = s+1, tl = structArray.length; t < tl; ++t) {
+                    let struct2 = structArray[t];
+
+                    let chainidArray2 = Object.keys(struct2domain[struct2]);
+                    if(chainidArray2.length == 0) continue;
+
                     for(let j = 0, jl = chainidArray2.length; j < jl; ++j) {
                         let chainid2 = chainidArray2[j];
 
                         let alignAjax;
                         if(me.cfg.aligntool != 'tmalign') {
                             let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(struct2domain[struct2][chainid2]);
-                        
+           
                             let dataObj = {'domains1': jsonStr_q, 'domains2': jsonStr_t};
                             alignAjax = me.getAjaxPostPromise(urlalign, dataObj);
                         }
@@ -58267,7 +58493,14 @@ class RealignParser {
 
         let allPromise = Promise.allSettled(ajaxArray);
         // try {
+            // let dataArray = await allPromise;
+
+            let startDate = new Date();
             let dataArray = await allPromise;
+            let endDate   = new Date();
+            let miliseconds = (endDate.getTime() - startDate.getTime());
+            console.log("vastdyn time: " + miliseconds + " miliseconds");
+          
             ic.qt_start_end = []; // reset the alignment
             await ic.chainalignParserCls.downloadChainalignmentPart2bRealign(dataArray, chainidPairArray, bReverse);  
         // }
@@ -60491,6 +60724,7 @@ class LoadAtomData {
 
     //This function was used to parse atom "data" to set up parameters for the 3D viewer. "type" is mmcifid or mmdbid.
     //"id" is the MMDB ID or mmCIF ID.
+    // thi sfunction is NOT used for mmCIF loading any more
     loadAtomDataIn(data, id, type, seqalign, alignType, chainidInput, chainIndex, bLastQuery, bNoSeqalign) { let ic = this.icn3d, me = ic.icn3dui;
         //ic.init();
         ic.pmin = new THREE.Vector3( 9999, 9999, 9999);
@@ -60634,13 +60868,6 @@ class LoadAtomData {
                   if(ic.pdbid_chain2title === undefined) ic.pdbid_chain2title = {};
                   ic.pdbid_chain2title[chainid] = data.moleculeInfor[molid].name;
 
-                  //if(alignType == 'query' && chain == ic.chain_q) {
-                  //    ic.alignmolid2color[0][molid] = molidCnt.toString();
-                  //}
-                  //else if(alignType == 'target' && chain == ic.chain_t) {
-                  //    ic.alignmolid2color[1][molid] = molidCnt.toString();
-                  //}
-
                   if(chain == chainid.substr(chainid.lastIndexOf('_')) ) {
                       let tmpHash = {};
                       tmpHash[molid] = molidCnt.toString();
@@ -60832,17 +61059,15 @@ class LoadAtomData {
             ic.pmin.min(atm.coord);
             ic.pmax.max(atm.coord);
             ic.psum.add(atm.coord);
-
-            let bNonMmcif = (me.cfg.mmcifid === undefined && me.cfg.mmtfid === undefined && me.cfg.bcifid === undefined && ic.InputfileType != 'mmcif');
-            let bProtein = (bNonMmcif) ? chainid2kind[chainNum] === 'protein' : atm.mt === 'p';
-            let bNucleotide = (bNonMmcif) ? chainid2kind[chainNum] === 'nucleotide' : atm.mt === 'n';
-            let bSolvent = (bNonMmcif) ? chainid2kind[chainNum] === 'solvent' : atm.mt === 's';
+            let bProtein = chainid2kind[chainNum] === 'protein' ;
+            let bNucleotide = chainid2kind[chainNum] === 'nucleotide' ;
+            let bSolvent = chainid2kind[chainNum] === 'solvent' ;
             // in vastplus.cgi, ions arenotlisted in alignedStructures...molecules, thus chainid2kind[chainNum] === undefined is used.
             // ions will be separated from chemicals later.
             // here "ligand" is used in the cgi output
             //var bChemicalIons =(me.cfg.mmcifid === undefined) ?(chainid2kind[chainNum] === 'ligand' || chainid2kind[chainNum] === 'otherPolymer' || chainid2kind[chainNum] === undefined) : atm.mt === 'l';
             // kind: other, otherPolymer, etc
-            let bChemicalIons = (bNonMmcif) ? (chainid2kind[chainNum] === 'ligand' ||(chainid2kind[chainNum] !== undefined && chainid2kind[chainNum].indexOf('other') !== -1) || chainid2kind[chainNum] === undefined) : atm.mt === 'l';
+            let bChemicalIons = (chainid2kind[chainNum] === 'ligand' ||(chainid2kind[chainNum] !== undefined && chainid2kind[chainNum].indexOf('other') !== -1) || chainid2kind[chainNum] === undefined) ;
 
             if((atm.chain === 'Misc' || chainid2kind[chainNum] === 'other') && biopolymerChainsHash[chainNum] !== 'protein' && biopolymerChainsHash[chainNum] !== 'nucleotide') { // biopolymer, could be protein or nucleotide
                 if(atm.name === 'CA' && atm.elem === 'C') {
@@ -61106,18 +61331,17 @@ class LoadAtomData {
 
         // update bonds info
         if(type !== 'mmcifid') {
-        //for(let i in ic.atoms) {
-        for(let i in atoms) {
-            let currSerial = atomid2serial[i];
+            //for(let i in ic.atoms) {
+            for(let i in atoms) {
+                let currSerial = atomid2serial[i];
 
-            let bondLength =(ic.atoms[currSerial].bonds === undefined) ? 0 : ic.atoms[currSerial].bonds.length;
+                let bondLength =(ic.atoms[currSerial].bonds === undefined) ? 0 : ic.atoms[currSerial].bonds.length;
 
-            for(let j = 0; j < bondLength; ++j) {
-                ic.atoms[currSerial].bonds[j] = atomid2serial[ic.atoms[currSerial].bonds[j]];
+                for(let j = 0; j < bondLength; ++j) {
+                    ic.atoms[currSerial].bonds[j] = atomid2serial[ic.atoms[currSerial].bonds[j]];
+                }
             }
         }
-        }
-
         // remove the reference
         data.atoms = {};
 
@@ -61213,7 +61437,7 @@ class LoadAtomData {
         // display the structure right away. load the mns and sequences later
     //        setTimeout(function(){
         let hAtoms = {};
-    
+
         if(type === 'align' && seqalign !== undefined && ic.bFullUi) {
             ic.setSeqAlignCls.setSeqAlign(seqalign, data.alignedStructures);
         } // if(align
@@ -61236,7 +61460,7 @@ class LoadAtomData {
                 hAtoms = ic.hAtoms;
             }
         }
-        else if(type === 'mmdbid' && alignType === 'target') {
+        else { //if(type === 'mmdbid' && alignType === 'target') {
             hAtoms = ic.hAtoms;
         }
 
@@ -61570,13 +61794,19 @@ class SetSeqAlign {
           resi = pos;
         }
         else {
-          if(ic.posid2resid) {
-              let resid = ic.posid2resid[chainid + '_' + pos];
-              resi = resid.substr(resid.lastIndexOf('_') + 1);
-          }
-          else {
+        //   if(ic.posid2resid) {
+        //       let resid = ic.posid2resid[chainid + '_' + pos];
+        //       resi = resid.substr(resid.lastIndexOf('_') + 1);
+        //   }
+        //   else {
+            //   resi = (ic.chainsSeq[chainid][pos].resi) ? ic.chainsSeq[chainid][pos].resi : pos;
+              if(pos > ic.chainsSeq[chainid].length - 1) {
+                console.log("Error: the position " + pos + " exceeds the max index " + (ic.chainsSeq[chainid].length - 1));
+                pos = ic.chainsSeq[chainid].length - 1;
+              }
+
               resi = ic.chainsSeq[chainid][pos].resi;
-          }
+        //   }
         }
 
         return resi;
@@ -63661,17 +63891,6 @@ class LoadCIF {
     loadCIF(bcifData, bcifid, bText, bAppend) { let ic = this.icn3d, me = ic.icn3dui;
         let hAtoms = {};
 
-        // bcifData could be binary or text
-        let parsed = (bText) ? CIFTools.Text.parse(bcifData) : CIFTools.Binary.parse(bcifData);
-
-        if (parsed.isError) {
-            // report error:
-            alert("The Binary CIF data can NOT be parsed: " + parsed.toString());
-            return;
-        }
-
-        let block = parsed.result.dataBlocks[0];
-
         let bNMR = false;
         // let lines = src.split('\n');
 
@@ -63707,92 +63926,152 @@ class LoadCIF {
         
         let bFirstAtom = true;
 
-        if(block.getCategory("_entry")) {
-            id = block.getCategory("_entry").getColumn("id").getString(0);
+        let cifArray = bcifData.split('ENDMDL\n');
 
-            if(id == '') {
-                if(bAppend) {
-                    id = ic.defaultPdbId;
-                }
-                else {
-                    //if(!ic.inputid) ic.inputid = ic.defaultPdbId;
-                    id = (ic.inputid && ic.inputid.indexOf('/') == -1) ? ic.inputid.substr(0, 10) : ic.defaultPdbId; //ic.filename.substr(0, 4);
-                }
-            }
+        for(let index = 0, indexl = cifArray.length; index  < indexl; ++index) {
+            ++moleculeNum;
+            id = ic.defaultPdbId;
 
             structure = ic.loadPDBCls.getStructureId(id, moleculeNum);
 
-            ic.molTitle = '';
-            ic.molTitleHash = {};
-        }
-        
-        if(block.getCategory("_struct")) {
-            let title = block.getCategory("_struct").getColumn("title").getString(0);
-            title = title.replace(/"/, "'");
-            let name = title.replace(/ALPHAFOLD MONOMER V2.0 PREDICTION FOR /gi, '');
-            ic.molTitle += name.trim() + " ";
-            // if(bEsmfold && ic.esmTitle) ic.molTitle = ic.esmTitle;
+            // if(!bNMR) {
+                sheetArray = [];
+                sheetStart = [];
+                sheetEnd = [];
+                helixArray = [];
+                helixStart = [];
+                helixEnd = [];
 
-            if(!ic.molTitleHash) ic.molTitleHash = {};
-            ic.molTitleHash[structure] = ic.molTitle;
 
-        }
+            // bcifData could be binary or text
+            let parsed = (bText) ? CIFTools.Text.parse(cifArray[index]) : CIFTools.Binary.parse(cifArray[index]);
 
-        if(block.getCategory("_entity_src_gen")) {
-            ic.organism = block.getCategory("_entity_src_gen").getColumn("gene_src_common_name").getString(0);
-        }
-        
-        if(block.getCategory("_database_2")) {
-            let database_2 = block.getCategory("_database_2");
-        
-            // Iterate through every row in the table
-            let db2Size = database_2.rowCount ;
-            for (let i = 0; i < db2Size; ++i) {
-                let db_id = database_2.getColumn("database_id").getString(0);
-                let db_code = database_2.getColumn("database_code").getString(0);
+            if (parsed.isError) {
+                // report error:
+                alert("The Binary CIF data can NOT be parsed: " + parsed.toString());
+                return;
+            }
+
+            let block = parsed.result.dataBlocks[0];
             
-                if(db_id == "EMDB") {
-                    ic.emd = db_code;
-                    break;
+            if(block.getCategory("_entry")) {
+                id = block.getCategory("_entry").getColumn("id").getString(0);
+
+                if(id == '') {
+                    if(bAppend) {
+                        id = ic.defaultPdbId;
+                    }
+                    else {
+                        //if(!ic.inputid) ic.inputid = ic.defaultPdbId;
+                        id = (ic.inputid && ic.inputid.indexOf('/') == -1) ? ic.inputid.substr(0, 10) : ic.defaultPdbId; //ic.filename.substr(0, 4);
+                    }
                 }
+
+                structure = ic.loadPDBCls.getStructureId(id, moleculeNum);
+
+                ic.molTitle = '';
+                ic.molTitleHash = {};
             }
-        }
+            
+            if(block.getCategory("_struct")) {
+                let title = block.getCategory("_struct").getColumn("title").getString(0);
+                title = title.replace(/"/, "'");
+                let name = title.replace(/ALPHAFOLD MONOMER V2.0 PREDICTION FOR /gi, '');
+                ic.molTitle += name.trim() + " ";
+                // if(bEsmfold && ic.esmTitle) ic.molTitle = ic.esmTitle;
 
-        if(block.getCategory("_struct_conf")) {
-            ic.bSecondaryStructure = true;
+                if(!ic.molTitleHash) ic.molTitleHash = {};
+                ic.molTitleHash[structure] = ic.molTitle;
 
-            // Retrieve the table corresponding to the struct_conf category, which delineates mainly helix
-            let struct_conf = block.getCategory("_struct_conf");
-        
-            let conf_type_idArray = struct_conf.getColumn("conf_type_id");
-        
-            let chain1Array = struct_conf.getColumn("beg_auth_asym_id");
-            // let resi1Array = struct_conf.getColumn("beg_label_seq_id");
-            let resi1Array = struct_conf.getColumn("beg_auth_seq_id");
-        
-            struct_conf.getColumn("end_auth_asym_id");
-            // let resi2Array = struct_conf.getColumn("end_label_seq_id");
-            let resi2Array = struct_conf.getColumn("end_auth_seq_id");
-        
-            // Iterate through every row in the struct_conf category table, where each row delineates an interatomic connection
-            let confSize = struct_conf.rowCount;
-            for (let i = 0; i < confSize; ++i) {
-                let conf_type_id = conf_type_idArray.getString(i);
+            }
+
+            if(block.getCategory("_entity_src_gen")) {
+                ic.organism = block.getCategory("_entity_src_gen").getColumn("gene_src_common_name").getString(0);
+            }
             
-                let startChain = chain1Array.getString(i);
-                let startResi = parseInt(resi1Array.getString(i));
-                let endResi = parseInt(resi2Array.getString(i));
+            if(block.getCategory("_database_2")) {
+                let database_2 = block.getCategory("_database_2");
             
-                if(conf_type_id.substr(0, 4) == "HELX") {
-                    for(let j = parseInt(startResi); j <= parseInt(endResi); ++j) {
-                        let resid = structure + "_" + startChain + "_" + j;
-                        helixArray.push(resid);
-        
-                        if(j == startResi) helixStart.push(resid);
-                        if(j == endResi) helixEnd.push(resid);
-                    } 
+                // Iterate through every row in the table
+                let db2Size = database_2.rowCount ;
+                for (let i = 0; i < db2Size; ++i) {
+                    let db_id = database_2.getColumn("database_id").getString(0);
+                    let db_code = database_2.getColumn("database_code").getString(0);
+                
+                    if(db_id == "EMDB") {
+                        ic.emd = db_code;
+                        break;
+                    }
                 }
-                else if(conf_type_id.substr(0, 4) == "STRN") {
+            }
+
+            if(block.getCategory("_struct_conf")) {
+                ic.bSecondaryStructure = true;
+
+                // Retrieve the table corresponding to the struct_conf category, which delineates mainly helix
+                let struct_conf = block.getCategory("_struct_conf");
+            
+                let conf_type_idArray = struct_conf.getColumn("conf_type_id");
+            
+                let chain1Array = struct_conf.getColumn("beg_auth_asym_id");
+                // let resi1Array = struct_conf.getColumn("beg_label_seq_id");
+                let resi1Array = struct_conf.getColumn("beg_auth_seq_id");
+            
+                struct_conf.getColumn("end_auth_asym_id");
+                // let resi2Array = struct_conf.getColumn("end_label_seq_id");
+                let resi2Array = struct_conf.getColumn("end_auth_seq_id");
+            
+                // Iterate through every row in the struct_conf category table, where each row delineates an interatomic connection
+                let confSize = struct_conf.rowCount;
+                for (let i = 0; i < confSize; ++i) {
+                    let conf_type_id = conf_type_idArray.getString(i);
+                
+                    let startChain = chain1Array.getString(i);
+                    let startResi = parseInt(resi1Array.getString(i));
+                    let endResi = parseInt(resi2Array.getString(i));
+                
+                    if(conf_type_id.substr(0, 4) == "HELX") {
+                        for(let j = parseInt(startResi); j <= parseInt(endResi); ++j) {
+                            let resid = structure + "_" + startChain + "_" + j;
+                            helixArray.push(resid);
+            
+                            if(j == startResi) helixStart.push(resid);
+                            if(j == endResi) helixEnd.push(resid);
+                        } 
+                    }
+                    else if(conf_type_id.substr(0, 4) == "STRN") {
+                        for(let j = startResi; j <= endResi; ++j) {
+                            let resid = structure + "_" + startChain + "_" + j;
+                            sheetArray.push(resid);
+            
+                            if(j == startResi) sheetStart.push(resid);
+                            if(j == endResi) sheetEnd.push(resid);
+                        } 
+                    }
+                }
+            
+                conf_type_idArray = chain1Array = resi1Array = resi2Array = [];
+            }
+
+            if(block.getCategory("_struct_sheet_range")) {
+                // Retrieve the table corresponding to the struct_sheet_range category, which delineates mainly beta sheet
+                let struct_sheet_range = block.getCategory("_struct_sheet_range");
+            
+                let chain1Array = struct_sheet_range.getColumn("beg_auth_asym_id");
+                // let resi1Array = struct_sheet_range.getColumn("beg_label_seq_id");
+                let resi1Array = struct_sheet_range.getColumn("beg_auth_seq_id");
+            
+                struct_sheet_range.getColumn("end_auth_asym_id");
+                // let resi2Array = struct_sheet_range.getColumn("end_label_seq_id");
+                let resi2Array = struct_sheet_range.getColumn("end_auth_seq_id");
+            
+                // Iterate through every row in the struct_sheet_range category table, where each row delineates an interatomic connection
+                let sheetSize = struct_sheet_range.rowCount;
+                for (let i = 0; i < sheetSize; ++i) {
+                    let startChain = chain1Array.getString(i);
+                    let startResi = parseInt(resi1Array.getString(i));
+                    let endResi = parseInt(resi2Array.getString(i));
+
                     for(let j = startResi; j <= endResi; ++j) {
                         let resid = structure + "_" + startChain + "_" + j;
                         sheetArray.push(resid);
@@ -63801,500 +64080,469 @@ class LoadCIF {
                         if(j == endResi) sheetEnd.push(resid);
                     } 
                 }
+            
+                chain1Array = resi1Array = resi2Array = [];
             }
-        
-            conf_type_idArray = chain1Array = resi1Array = resi2Array = [];
-        }
-
-        if(block.getCategory("_struct_sheet_range")) {
-            // Retrieve the table corresponding to the struct_sheet_range category, which delineates mainly beta sheet
-            let struct_sheet_range = block.getCategory("_struct_sheet_range");
-        
-            let chain1Array = struct_sheet_range.getColumn("beg_auth_asym_id");
-            // let resi1Array = struct_sheet_range.getColumn("beg_label_seq_id");
-            let resi1Array = struct_sheet_range.getColumn("beg_auth_seq_id");
-        
-            struct_sheet_range.getColumn("end_auth_asym_id");
-            // let resi2Array = struct_sheet_range.getColumn("end_label_seq_id");
-            let resi2Array = struct_sheet_range.getColumn("end_auth_seq_id");
-        
-            // Iterate through every row in the struct_sheet_range category table, where each row delineates an interatomic connection
-            let sheetSize = struct_sheet_range.rowCount;
-            for (let i = 0; i < sheetSize; ++i) {
-                let startChain = chain1Array.getString(i);
-                let startResi = parseInt(resi1Array.getString(i));
-                let endResi = parseInt(resi2Array.getString(i));
-
-                for(let j = startResi; j <= endResi; ++j) {
-                    let resid = structure + "_" + startChain + "_" + j;
-                    sheetArray.push(resid);
-    
-                    if(j == startResi) sheetStart.push(resid);
-                    if(j == endResi) sheetEnd.push(resid);
-                } 
-            }
-        
-            chain1Array = resi1Array = resi2Array = [];
-        }
 
-        if(block.getCategory("_struct_conn")) {
-            ic.bSsbondProvided = true;
+            if(block.getCategory("_struct_conn")) {
+                ic.bSsbondProvided = true;
 
-            // Retrieve the table corresponding to the struct_conn category, which delineates connections1
-            let struct_conn = block.getCategory("_struct_conn");
-        
-            let conn_type_idArray = struct_conn.getColumn("conn_type_id");
-        
-            let chain1Array = struct_conn.getColumn("ptnr1_auth_asym_id");
-            let name1Array = struct_conn.getColumn("ptnr1_label_atom_id");
-            let resi1Array = struct_conn.getColumn("ptnr1_label_seq_id");
-        
-            let chain2Array = struct_conn.getColumn("ptnr2_auth_asym_id");
-            let name2Array = struct_conn.getColumn("ptnr2_label_atom_id");
-            let resi2Array = struct_conn.getColumn("ptnr2_label_seq_id");
-        
-            let connSize = struct_conn.rowCount;
-            for (let i = 0; i < connSize; ++i) {
-                let conn_type_id = conn_type_idArray.getString(i);
+                // Retrieve the table corresponding to the struct_conn category, which delineates connections1
+                let struct_conn = block.getCategory("_struct_conn");
             
-                let chain1 = chain1Array.getString(i);
-                name1Array.getString(i);
-                let resi1 = resi1Array.getString(i);
-                let id1 = structure + '_' + chain1 + "_" + resi1;
+                let conn_type_idArray = struct_conn.getColumn("conn_type_id");
             
-                let chain2 = chain2Array.getString(i);
-                name2Array.getString(i);
-                let resi2 = resi2Array.getString(i);
-                let id2 = structure + '_' + chain2 + "_" + resi2;
+                let chain1Array = struct_conn.getColumn("ptnr1_auth_asym_id");
+                let name1Array = struct_conn.getColumn("ptnr1_label_atom_id");
+                let resi1Array = struct_conn.getColumn("ptnr1_label_seq_id");
             
-                // Verify that the linkage is covalent, as indicated by the conn_type_id attribute2
+                let chain2Array = struct_conn.getColumn("ptnr2_auth_asym_id");
+                let name2Array = struct_conn.getColumn("ptnr2_label_atom_id");
+                let resi2Array = struct_conn.getColumn("ptnr2_label_seq_id");
             
-                // if (conn_type_id == "covale") {
-                //     vBonds.push(id1);
-                //     vBonds.push(id2);
-                // }
+                let connSize = struct_conn.rowCount;
+                for (let i = 0; i < connSize; ++i) {
+                    let conn_type_id = conn_type_idArray.getString(i);
                 
-                if(conn_type_id == "disulf") {
-                    if(ic.ssbondpnts[structure] === undefined) ic.ssbondpnts[structure] = [];
+                    let chain1 = chain1Array.getString(i);
+                    name1Array.getString(i);
+                    let resi1 = resi1Array.getString(i);
+                    let id1 = structure + '_' + chain1 + "_" + resi1;
+                
+                    let chain2 = chain2Array.getString(i);
+                    name2Array.getString(i);
+                    let resi2 = resi2Array.getString(i);
+                    let id2 = structure + '_' + chain2 + "_" + resi2;
+                
+                    // Verify that the linkage is covalent, as indicated by the conn_type_id attribute2
+                
+                    // if (conn_type_id == "covale") {
+                    //     vBonds.push(id1);
+                    //     vBonds.push(id2);
+                    // }
+                    
+                    if(conn_type_id == "disulf") {
+                        if(ic.ssbondpnts[structure] === undefined) ic.ssbondpnts[structure] = [];
 
-                    ic.ssbondpnts[structure].push(id1);
-                    ic.ssbondpnts[structure].push(id2);
+                        ic.ssbondpnts[structure].push(id1);
+                        ic.ssbondpnts[structure].push(id2);
+                    }
                 }
+            
+                conn_type_idArray = chain1Array = name1Array = resi1Array = chain2Array = name2Array = resi2Array = [];
             }
-        
-            conn_type_idArray = chain1Array = name1Array = resi1Array = chain2Array = name2Array = resi2Array = [];
-        }
 
-        if(block.getCategory("_exptl")) {
-            let method = block.getCategory("_exptl").getColumn("method").getString(0);
-            if(method.indexOf('NMR') != -1) {
-                bNMR = true;
+            if(block.getCategory("_exptl")) {
+                let method = block.getCategory("_exptl").getColumn("method").getString(0);
+                if(method.indexOf('NMR') != -1) {
+                    bNMR = true;
+                }
             }
-        }
 
-        if(block.getCategory("_pdbx_struct_oper_list")) {
-            // Retrieve the table corresponding to the struct_oper_list category, which delineates assembly
-            let struct_oper_list = block.getCategory("_pdbx_struct_oper_list");
-        
-            let struct_oper_idArray = struct_oper_list.getColumn("id");
-            let m11Array = struct_oper_list.getColumn("matrix[1][1]");
-            let m12Array = struct_oper_list.getColumn("matrix[1][2]");
-            let m13Array = struct_oper_list.getColumn("matrix[1][3]");
-            let m14Array = struct_oper_list.getColumn("vector[1]");
-        
-            let m21Array = struct_oper_list.getColumn("matrix[2][1]");
-            let m22Array = struct_oper_list.getColumn("matrix[2][2]");
-            let m23Array = struct_oper_list.getColumn("matrix[2][3]");
-            let m24Array = struct_oper_list.getColumn("vector[2]");
-        
-            let m31Array = struct_oper_list.getColumn("matrix[3][1]");
-            let m32Array = struct_oper_list.getColumn("matrix[3][2]");
-            let m33Array = struct_oper_list.getColumn("matrix[3][3]");
-            let m34Array = struct_oper_list.getColumn("vector[3]");
-        
-            let assemblySize = struct_oper_list.rowCount;
-            for (let i = 0; i < assemblySize; ++i) {
-                let struct_oper_id = struct_oper_idArray.getString(i);
-                if(struct_oper_id == "X0") continue;
+            if(block.getCategory("_pdbx_struct_oper_list")) {
+                // Retrieve the table corresponding to the struct_oper_list category, which delineates assembly
+                let struct_oper_list = block.getCategory("_pdbx_struct_oper_list");
+            
+                let struct_oper_idArray = struct_oper_list.getColumn("id");
+                let m11Array = struct_oper_list.getColumn("matrix[1][1]");
+                let m12Array = struct_oper_list.getColumn("matrix[1][2]");
+                let m13Array = struct_oper_list.getColumn("matrix[1][3]");
+                let m14Array = struct_oper_list.getColumn("vector[1]");
+            
+                let m21Array = struct_oper_list.getColumn("matrix[2][1]");
+                let m22Array = struct_oper_list.getColumn("matrix[2][2]");
+                let m23Array = struct_oper_list.getColumn("matrix[2][3]");
+                let m24Array = struct_oper_list.getColumn("vector[2]");
+            
+                let m31Array = struct_oper_list.getColumn("matrix[3][1]");
+                let m32Array = struct_oper_list.getColumn("matrix[3][2]");
+                let m33Array = struct_oper_list.getColumn("matrix[3][3]");
+                let m34Array = struct_oper_list.getColumn("vector[3]");
+            
+                let assemblySize = struct_oper_list.rowCount;
+                for (let i = 0; i < assemblySize; ++i) {
+                    let struct_oper_id = struct_oper_idArray.getString(i);
+                    if(struct_oper_id == "X0") continue;
 
-                if (ic.biomtMatrices[i] == undefined) ic.biomtMatrices[i] = new THREE.Matrix4().identity();
-                ic.biomtMatrices[i].set(m11Array.getString(i), m12Array.getString(i), m13Array.getString(i), m14Array.getString(i), 
-                    m21Array.getString(i), m22Array.getString(i), m23Array.getString(i), m24Array.getString(i), 
-                    m31Array.getString(i), m32Array.getString(i), m33Array.getString(i), m34Array.getString(i), 
-                    0, 0, 0, 1);
+                    if (ic.biomtMatrices[i] == undefined) ic.biomtMatrices[i] = new THREE.Matrix4().identity();
+                    ic.biomtMatrices[i].set(m11Array.getString(i), m12Array.getString(i), m13Array.getString(i), m14Array.getString(i), 
+                        m21Array.getString(i), m22Array.getString(i), m23Array.getString(i), m24Array.getString(i), 
+                        m31Array.getString(i), m32Array.getString(i), m33Array.getString(i), m34Array.getString(i), 
+                        0, 0, 0, 1);
+                }
+            
+                struct_oper_idArray = m11Array = m12Array = m13Array = m14Array = m21Array = m22Array = m23Array 
+                = m24Array = m31Array = m32Array = m33Array = m34Array = [];
             }
-        
-            struct_oper_idArray = m11Array = m12Array = m13Array = m14Array = m21Array = m22Array = m23Array 
-            = m24Array = m31Array = m32Array = m33Array = m34Array = [];
-        }
 
-        // if (record === 'ENDMDL') {
-        //     ++moleculeNum;
-        //     id = ic.defaultPdbId;
+            // if (record === 'ENDMDL') {
+            //     ++moleculeNum;
+            //     id = ic.defaultPdbId;
 
-        //     structure = ic.loadPDBCls.getStructureId(id, moleculeNum);
+            //     structure = ic.loadPDBCls.getStructureId(id, moleculeNum);
 
-        //     //helices = [];
-        //     //sheets = [];
-        //     if(!bNMR) {
-        //         sheetArray = [];
-        //         sheetStart = [];
-        //         sheetEnd = [];
-        //         helixArray = [];
-        //         helixStart = [];
-        //         helixEnd = [];
-        //     }
+            //     //helices = [];
+            //     //sheets = [];
+            //     if(!bNMR) {
+            //         sheetArray = [];
+            //         sheetStart = [];
+            //         sheetEnd = [];
+            //         helixArray = [];
+            //         helixStart = [];
+            //         helixEnd = [];
+            //     }
 
-        //     bHeader = false; // reinitialize to read structure name from the header
-        // }
+            //     bHeader = false; // reinitialize to read structure name from the header
+            // }
 
-        if(block.getCategory("_citation")) {
-            ic.pmid = block.getCategory("_citation").getColumn("pdbx_database_id_PubMed").getString(0);
-        }
+            if(block.getCategory("_citation")) {
+                ic.pmid = block.getCategory("_citation").getColumn("pdbx_database_id_PubMed").getString(0);
+            }
 
-        // Retrieve the table corresponding to the atom_site category, which delineates atomic constituents
-        let atom_site = block.getCategory("_atom_site");
-        let atomSize = atom_site.rowCount;
-        // let bFull = (atomSize * 10 > ic.maxatomcnt) ? false : true;
-        let bFull = (atomSize > ic.maxatomcnt) ? false : true;
+            // Retrieve the table corresponding to the atom_site category, which delineates atomic constituents
+            let atom_site = block.getCategory("_atom_site");
+            let atomSize = atom_site.rowCount;
+            // let bFull = (atomSize * 10 > ic.maxatomcnt) ? false : true;
+            let bFull = (atomSize > ic.maxatomcnt) ? false : true;
 
-        if(!bFull) {
-            ic.opts['proteins'] = 'c alpha trace'; //ribbon, strand, cylinder and plate, schematic, c alpha trace, b factor tube, lines, stick, ball and stick, sphere, nothing
-            ic.opts['nucleotides'] = 'o3 trace'; //nucleotide cartoon, o3 trace, schematic, lines, stick,
-        }
+            if(!bFull) {
+                ic.opts['proteins'] = 'c alpha trace'; //ribbon, strand, cylinder and plate, schematic, c alpha trace, b factor tube, lines, stick, ball and stick, sphere, nothing
+                ic.opts['nucleotides'] = 'o3 trace'; //nucleotide cartoon, o3 trace, schematic, lines, stick,
+            }
 
-        let atom_hetatmArray = atom_site.getColumn("group_PDB");
-        let resnArray = atom_site.getColumn("label_comp_id");
-        let elemArray = atom_site.getColumn("type_symbol");
-        let nameArray = atom_site.getColumn("label_atom_id");
+            let atom_hetatmArray = atom_site.getColumn("group_PDB");
+            let resnArray = atom_site.getColumn("label_comp_id");
+            let elemArray = atom_site.getColumn("type_symbol");
+            let nameArray = atom_site.getColumn("label_atom_id");
 
-        let chainArray = atom_site.getColumn("auth_asym_id");
+            let chainArray = atom_site.getColumn("auth_asym_id");
 
-        let resiArray = atom_site.getColumn("label_seq_id");
-        let resiOriArray = atom_site.getColumn("auth_seq_id");
-        let altArray = atom_site.getColumn("label_alt_id");
+            let resiArray = atom_site.getColumn("label_seq_id");
+            let resiOriArray = atom_site.getColumn("auth_seq_id");
+            let altArray = atom_site.getColumn("label_alt_id");
 
-        let bArray = atom_site.getColumn("B_iso_or_equiv");
+            let bArray = atom_site.getColumn("B_iso_or_equiv");
 
-        let xArray = atom_site.getColumn("Cartn_x");
-        let yArray = atom_site.getColumn("Cartn_y");
-        let zArray = atom_site.getColumn("Cartn_z");
+            let xArray = atom_site.getColumn("Cartn_x");
+            let yArray = atom_site.getColumn("Cartn_y");
+            let zArray = atom_site.getColumn("Cartn_z");
 
-        let autochainArray = atom_site.getColumn("label_asym_id");
+            let autochainArray = atom_site.getColumn("label_asym_id");
 
-        // get the bond info
-        let ligSeqHash = {}, prevAutochain = '';
-        let prevResn;
-        let sChain = {};
-        for (let i = 0; i < atomSize; ++i) {
-            let atom_hetatm = atom_hetatmArray.getString(i);
-            let resn = resnArray.getString(i);
-            let elem = elemArray.getString(i);
-            let atom = nameArray.getString(i);
-            let chain = chainArray.getString(i);
-            let resi = resiArray.getString(i);
-            let oriResi = resiOriArray.getString(i); 
-            let alt = altArray.getString(i);
-            let bFactor = bArray.getString(i);
+            // get the bond info
+            let ligSeqHash = {}, prevAutochain = '';
+            let prevResn;
+            let sChain = {};
+            for (let i = 0; i < atomSize; ++i) {
+                let atom_hetatm = atom_hetatmArray.getString(i);
+                let resn = resnArray.getString(i);
+                let elem = elemArray.getString(i);
+                let atom = nameArray.getString(i);
+                let chain = chainArray.getString(i);
+                let resi = resiArray.getString(i);
+                let oriResi = resiOriArray.getString(i); 
+                let alt = altArray.getString(i);
+                let bFactor = bArray.getString(i);
 
-            let autochain = autochainArray.getString(i);
+                let autochain = autochainArray.getString(i);
 
 
-            resi = oriResi;
+                resi = oriResi;
 
-            let molecueType;
-            if(atom_hetatm == "ATOM") {
-                if(resn.length == 3) {
-                    molecueType = "p"; // protein
-                }
-                else {
-                    molecueType = "n"; // nucleotide
-                }
-            }
-            else {
-                if(resn == "WAT" || resn == "HOH") {
-                    molecueType = "s"; // solvent
-                    chain = 'Misc';
+                let molecueType;
+                if(atom_hetatm == "ATOM") {
+                    if(resn.length == 3) {
+                        molecueType = "protein"; // protein
+                    }
+                    else {
+                        molecueType = "nucleotide"; // nucleotide
+                    }
                 }
                 else {
-                    molecueType = "l"; // ligands or ions
-                    chain = resn;
+                    if(resn == "WAT" || resn == "HOH") {
+                        molecueType = "solvent"; // solvent
+                        chain = 'Misc';
+                    }
+                    else {
+                        molecueType = "ligand"; // ligands or ions
+                        chain = resn;
+                    }
                 }
-            }
-            if(chain === '') chain = 'A';
-
-            // C-alpha only for large structure
-            if(!bFull && ((molecueType == "p" && !(elem == 'C' && atom == 'CA')) || (molecueType == "n" && !(atom == "P")) ) ) continue;
-            
-            // skip alternative atoms
-            if(alt == "B") continue;
-
-            sChain[chain] = 1;
+                if(chain === '') chain = 'A';
 
-            if(bFirstAtom) {
-                structure = ic.loadPDBCls.getStructureId(id, moleculeNum);
+                // C-alpha only for large structure
+                if(!bFull && ((molecueType == "protein" && !(elem == 'C' && atom == 'CA')) || (molecueType == "nucleotide" && !(atom == "P")) ) ) continue;
+                
+                // skip alternative atoms
+                if(alt == "B") continue;
 
-                bFirstAtom = false;
-            }
+                sChain[chain] = 1;
 
-            // "CA" has to appear before "O". Otherwise the cartoon of secondary structure will have breaks
-            // Concatenation of two pdbs will have several atoms for the same serial
-            ++serial;
+                if(bFirstAtom) {
+                    structure = ic.loadPDBCls.getStructureId(id, moleculeNum);
 
-            // if(oriResi != resi || bModifyResi) { // e.g., 99A and 99
-            //     bModifyResi = true;
-            // }
+                    bFirstAtom = false;
+                }
 
-            if(resi == "?" || resi == "." || resi == "0") {
-                resi = oriResi;
+                // "CA" has to appear before "O". Otherwise the cartoon of secondary structure will have breaks
+                // Concatenation of two pdbs will have several atoms for the same serial
+                ++serial;
 
-                // if(resn.length != 3 || resn == "HOH" || resn == "WAT") {
-                //     if(resn.length != 3 || (elem == 'O' && (resn == "HOH" || resn == "WAT"))) {
-                //         resi = (++tmpResi).toString();
-                //     }
-                // }
-                // else {
-                //     if(chain + "_" + resn != prevResn || prevAutochain != autochain) {
-                //         resi = (++tmpResi).toString();
-                //     }
-                //     else {
-                //         resi = (tmpResi).toString();
-                //     }
+                // if(oriResi != resi || bModifyResi) { // e.g., 99A and 99
+                //     bModifyResi = true;
                 // }
-            }
 
-            if(molecueType == 's' || molecueType == "l") {
-                let seq = {};
-                if(!ligSeqHash.hasOwnProperty(chain)) {
-                    ligSeqHash[chain] = [];
+                if(resi == "?" || resi == "." || resi == "0") {
+                    resi = oriResi;
+
+                    // if(resn.length != 3 || resn == "HOH" || resn == "WAT") {
+                    //     if(resn.length != 3 || (elem == 'O' && (resn == "HOH" || resn == "WAT"))) {
+                    //         resi = (++tmpResi).toString();
+                    //     }
+                    // }
+                    // else {
+                    //     if(chain + "_" + resn != prevResn || prevAutochain != autochain) {
+                    //         resi = (++tmpResi).toString();
+                    //     }
+                    //     else {
+                    //         resi = (tmpResi).toString();
+                    //     }
+                    // }
                 }
 
-                if(resn.length != 3 || resn == "HOH" || resn == "WAT") {
-                    if(resn.length != 3 || (elem == 'O' && (resn == "HOH" || resn == "WAT"))) {
-                        seq.resi = resi;
-                        seq.name = me.utilsCls.residueName2Abbr(resn);
-                        ligSeqHash[chain].push(seq);
+                if(molecueType == 'solvent' || molecueType == "ligand") {
+                    let seq = {};
+                    if(!ligSeqHash.hasOwnProperty(chain)) {
+                        ligSeqHash[chain] = [];
                     }
-                }
-                else {
-                    if(chain + "_" + resn != prevResn || prevAutochain != autochain) {
-                        seq.resi = resi;
-                        seq.name = me.utilsCls.residueName2Abbr(resn);
-                        ligSeqHash[chain].push(seq);
+
+                    if(resn.length != 3 || resn == "HOH" || resn == "WAT") {
+                        if(resn.length != 3 || (elem == 'O' && (resn == "HOH" || resn == "WAT"))) {
+                            seq.resi = resi;
+                            seq.name = me.utilsCls.residueName2Abbr(resn);
+                            ligSeqHash[chain].push(seq);
+                        }
+                    }
+                    else {
+                        if(chain + "_" + resn != prevResn || prevAutochain != autochain) {
+                            seq.resi = resi;
+                            seq.name = me.utilsCls.residueName2Abbr(resn);
+                            ligSeqHash[chain].push(seq);
+                        }
                     }
                 }
-            }
 
-            // if(bOpm && resn === 'DUM') {
-            //     elem = atom;
-            //     chain = 'MEM';
-            //     resi = 1;
-            //     oriResi = 1;
-            // }
+                // if(bOpm && resn === 'DUM') {
+                //     elem = atom;
+                //     chain = 'MEM';
+                //     resi = 1;
+                //     oriResi = 1;
+                // }
 
-            // if(bVector && resn === 'DUM') break; // just need to get the vector of the largest chain
+                // if(bVector && resn === 'DUM') break; // just need to get the vector of the largest chain
 
-            chainNum = structure + "_" + chain;
-            oriResidueNum = chainNum + "_" + oriResi;
+                chainNum = structure + "_" + chain;
+                oriResidueNum = chainNum + "_" + oriResi;
 
-            residueNum = chainNum + "_" + resi;
+                residueNum = chainNum + "_" + resi;
 
-            //let chain_resi = chain + "_" + resi;
+                //let chain_resi = chain + "_" + resi;
 
-            let x = xArray.getFloat(i);
-            let y = yArray.getFloat(i);
-            let z = zArray.getFloat(i);
-            let coord = new THREE.Vector3(x, y, z);
+                let x = xArray.getFloat(i);
+                let y = yArray.getFloat(i);
+                let z = zArray.getFloat(i);
+                let coord = new THREE.Vector3(x, y, z);
 
-            let atomDetails = {
-                het: (atom_hetatm == "HETATM"), // optional, used to determine chemicals, water, ions, etc
-                serial: serial,         // required, unique atom id
-                name: atom,             // required, atom name
-                alt: alt,               // optional, some alternative coordinates
-                resn: resn,         // optional, used to determine protein or nucleotide
-                structure: structure,   // optional, used to identify structure
-                chain: chain,           // optional, used to identify chain
-                resi: resi,             // optional, used to identify residue ID
-                //insc: line.substr(26, 1),
-                coord: coord,           // required, used to draw 3D shape
-                b: bFactor,             // optional, used to draw B-factor tube
-                elem: elem,             // optional, used to determine hydrogen bond
-                bonds: [],              // required, used to connect atoms
-                ss: 'coil',             // optional, used to show secondary structures
-                ssbegin: false,         // optional, used to show the beginning of secondary structures
-                ssend: false            // optional, used to show the end of secondary structures
-            };
+                let atomDetails = {
+                    het: (atom_hetatm == "HETATM"), // optional, used to determine chemicals, water, ions, etc
+                    serial: serial,         // required, unique atom id
+                    name: atom,             // required, atom name
+                    alt: alt,               // optional, some alternative coordinates
+                    resn: resn,         // optional, used to determine protein or nucleotide
+                    structure: structure,   // optional, used to identify structure
+                    chain: chain,           // optional, used to identify chain
+                    resi: resi,             // optional, used to identify residue ID
+                    //insc: line.substr(26, 1),
+                    coord: coord,           // required, used to draw 3D shape
+                    b: bFactor,             // optional, used to draw B-factor tube
+                    elem: elem,             // optional, used to determine hydrogen bond
+                    bonds: [],              // required, used to connect atoms
+                    ss: 'coil',             // optional, used to show secondary structures
+                    ssbegin: false,         // optional, used to show the beginning of secondary structures
+                    ssend: false            // optional, used to show the end of secondary structures
+                };
 
-            if(!atomDetails.het && atomDetails.name === 'C') ;
-            if(!atomDetails.het && atomDetails.name === 'O') ;
+                if(!atomDetails.het && atomDetails.name === 'C') ;
+                if(!atomDetails.het && atomDetails.name === 'O') ;
 
-            // from DSSP C++ code
-            // if(!atomDetails.het && atomDetails.name === 'N' && prevCSerial !== undefined && prevOSerial !== undefined) {
-            //     let dist = ic.atoms[prevCSerial].coord.distanceTo(ic.atoms[prevOSerial].coord);
+                // from DSSP C++ code
+                // if(!atomDetails.het && atomDetails.name === 'N' && prevCSerial !== undefined && prevOSerial !== undefined) {
+                //     let dist = ic.atoms[prevCSerial].coord.distanceTo(ic.atoms[prevOSerial].coord);
 
-            //     let x2 = atomDetails.coord.x + (ic.atoms[prevCSerial].coord.x - ic.atoms[prevOSerial].coord.x) / dist;
-            //     let y2 = atomDetails.coord.y + (ic.atoms[prevCSerial].coord.y - ic.atoms[prevOSerial].coord.y) / dist;
-            //     let z2 = atomDetails.coord.z + (ic.atoms[prevCSerial].coord.z - ic.atoms[prevOSerial].coord.z) / dist;
+                //     let x2 = atomDetails.coord.x + (ic.atoms[prevCSerial].coord.x - ic.atoms[prevOSerial].coord.x) / dist;
+                //     let y2 = atomDetails.coord.y + (ic.atoms[prevCSerial].coord.y - ic.atoms[prevOSerial].coord.y) / dist;
+                //     let z2 = atomDetails.coord.z + (ic.atoms[prevCSerial].coord.z - ic.atoms[prevOSerial].coord.z) / dist;
 
-            //     atomDetails.hcoord = new THREE.Vector3(x2, y2, z2);
-            // }
+                //     atomDetails.hcoord = new THREE.Vector3(x2, y2, z2);
+                // }
 
-            ic.atoms[serial] = atomDetails;
+                ic.atoms[serial] = atomDetails;
 
-            ic.dAtoms[serial] = 1;
-            ic.hAtoms[serial] = 1;
-            hAtoms[serial] = 1;
+                ic.dAtoms[serial] = 1;
+                ic.hAtoms[serial] = 1;
+                hAtoms[serial] = 1;
 
-            // Assign secondary structures from the input
-            // if a residue is assigned both sheet and helix, it is assigned as sheet
-            if(ic.loadPDBCls.isSecondary(residueNum, sheetArray, bNMR, !bFull)) {
-                ic.atoms[serial].ss = 'sheet';
-                if(ic.loadPDBCls.isSecondary(residueNum, sheetStart, bNMR, !bFull)) {
-                ic.atoms[serial].ssbegin = true;
-                }
+                // Assign secondary structures from the input
+                // if a residue is assigned both sheet and helix, it is assigned as sheet
+                if(ic.loadPDBCls.isSecondary(residueNum, sheetArray, bNMR, !bFull)) {
+                    ic.atoms[serial].ss = 'sheet';
+                    if(ic.loadPDBCls.isSecondary(residueNum, sheetStart, bNMR, !bFull)) {
+                    ic.atoms[serial].ssbegin = true;
+                    }
 
-                // do not use else if. Some residues are both start and end of secondary structure
-                if(ic.loadPDBCls.isSecondary(residueNum, sheetEnd, bNMR, !bFull)) {
-                ic.atoms[serial].ssend = true;
+                    // do not use else if. Some residues are both start and end of secondary structure
+                    if(ic.loadPDBCls.isSecondary(residueNum, sheetEnd, bNMR, !bFull)) {
+                    ic.atoms[serial].ssend = true;
+                    }
                 }
-            }
-            else if(ic.loadPDBCls.isSecondary(residueNum, helixArray, bNMR, !bFull)) {
-                ic.atoms[serial].ss = 'helix';
+                else if(ic.loadPDBCls.isSecondary(residueNum, helixArray, bNMR, !bFull)) {
+                    ic.atoms[serial].ss = 'helix';
 
-                if(ic.loadPDBCls.isSecondary(residueNum, helixStart, bNMR, !bFull)) {
-                ic.atoms[serial].ssbegin = true;
+                    if(ic.loadPDBCls.isSecondary(residueNum, helixStart, bNMR, !bFull)) {
+                    ic.atoms[serial].ssbegin = true;
+                    }
+
+                    // do not use else if. Some residues are both start and end of secondary structure
+                    if(ic.loadPDBCls.isSecondary(residueNum, helixEnd, bNMR, !bFull)) {
+                    ic.atoms[serial].ssend = true;
+                    }
                 }
 
-                // do not use else if. Some residues are both start and end of secondary structure
-                if(ic.loadPDBCls.isSecondary(residueNum, helixEnd, bNMR, !bFull)) {
-                ic.atoms[serial].ssend = true;
+                let secondaries = '-';
+                if(ic.atoms[serial].ss === 'helix') {
+                    secondaries = 'H';
+                }
+                else if(ic.atoms[serial].ss === 'sheet') {
+                    secondaries = 'E';
+                }
+                //else if(ic.atoms[serial].ss === 'coil') {
+                //    secondaries = 'c';
+                //}
+                else if(!ic.atoms[serial].het && me.parasCls.residueColors.hasOwnProperty(ic.atoms[serial].resn.toUpperCase()) ) {
+                    secondaries = 'c';
+                }
+                else {
+                    secondaries = 'o';
                 }
-            }
 
-            let secondaries = '-';
-            if(ic.atoms[serial].ss === 'helix') {
-                secondaries = 'H';
-            }
-            else if(ic.atoms[serial].ss === 'sheet') {
-                secondaries = 'E';
-            }
-            //else if(ic.atoms[serial].ss === 'coil') {
-            //    secondaries = 'c';
-            //}
-            else if(!ic.atoms[serial].het && me.parasCls.residueColors.hasOwnProperty(ic.atoms[serial].resn.toUpperCase()) ) {
-                secondaries = 'c';
-            }
-            else {
-                secondaries = 'o';
-            }
+                ic.secondaries[residueNum] = secondaries;
 
-            ic.secondaries[residueNum] = secondaries;
+                // different residue
+                //if(residueNum !== prevResidueNum) {
+                    
+                // if(oriResidueNum !== prevOriResidueNum) {
+                if(oriResidueNum !== prevOriResidueNum || chain + "_" + resn != prevResn || prevAutochain != autochain) {
+                    let residue = me.utilsCls.residueName2Abbr(resn);
+                    
+                    ic.residueId2Name[residueNum] = residue;
 
-            // different residue
-            //if(residueNum !== prevResidueNum) {
-                
-            // if(oriResidueNum !== prevOriResidueNum) {
-            if(oriResidueNum !== prevOriResidueNum || chain + "_" + resn != prevResn || prevAutochain != autochain) {
-                let residue = me.utilsCls.residueName2Abbr(resn);
-                
-                ic.residueId2Name[residueNum] = residue;
+                    if(serial !== 1 && prevResidueNum !== '') {
+                        ic.residues[prevResidueNum] = residuesTmp;
+                    }
 
-                if(serial !== 1 && prevResidueNum !== '') {
-                    ic.residues[prevResidueNum] = residuesTmp;
-                }
+                    if(residueNum !== prevResidueNum) {
+                        residuesTmp = {};
+                    }
 
-                if(residueNum !== prevResidueNum) {
-                    residuesTmp = {};
-                }
+                    // different chain
+                    if(chainNum !== prevChainNum) {
 
-                // different chain
-                if(chainNum !== prevChainNum) {
+                        // a chain could be separated in two sections
+                        if(serial !== 1 && prevChainNum !== '') {
+                            if(ic.chains[prevChainNum] === undefined) ic.chains[prevChainNum] = {};
+                            ic.chains[prevChainNum] = me.hashUtilsCls.unionHash(ic.chains[prevChainNum], chainsTmp);
+                        }
 
-                    // a chain could be separated in two sections
-                    if(serial !== 1 && prevChainNum !== '') {
-                        if(ic.chains[prevChainNum] === undefined) ic.chains[prevChainNum] = {};
-                        ic.chains[prevChainNum] = me.hashUtilsCls.unionHash(ic.chains[prevChainNum], chainsTmp);
-                    }
+                        chainsTmp = {};
 
-                    chainsTmp = {};
+                        if(ic.structures[structure.toString()] === undefined) ic.structures[structure.toString()] = [];
+                        if(!ic.structures[structure.toString()].includes(chainNum)) ic.structures[structure.toString()].push(chainNum);
 
-                    if(ic.structures[structure.toString()] === undefined) ic.structures[structure.toString()] = [];
-                    if(!ic.structures[structure.toString()].includes(chainNum)) ic.structures[structure.toString()].push(chainNum);
+                        if(ic.chainsSeq[chainNum] === undefined) ic.chainsSeq[chainNum] = [];
 
-                    if(ic.chainsSeq[chainNum] === undefined) ic.chainsSeq[chainNum] = [];
+                        let resObject = {};
+                        resObject.resi = resi;
+                        resObject.name = residue;
 
-                    let resObject = {};
-                    resObject.resi = resi;
-                    resObject.name = residue;
+                        ic.chainsSeq[chainNum].push(resObject);
+                    }
+                    else {
+
+                        let resObject = {};
+                        resObject.resi = resi;
+                        resObject.name = residue;
 
-                    ic.chainsSeq[chainNum].push(resObject);
+                        ic.chainsSeq[chainNum].push(resObject);
+                    }
                 }
-                else {
 
-                    let resObject = {};
-                    resObject.resi = resi;
-                    resObject.name = residue;
+                chainsTmp[serial] = 1;
+                residuesTmp[serial] = 1;
 
-                    ic.chainsSeq[chainNum].push(resObject);
-                }
-            }
+                prevChainNum = chainNum;
+                prevResidueNum = residueNum;
+                prevOriResidueNum = oriResidueNum;
 
-            chainsTmp[serial] = 1;
-            residuesTmp[serial] = 1;
+                prevResn = chain + "_" + resn;
+                prevAutochain = autochain;
+            }
 
-            prevChainNum = chainNum;
-            prevResidueNum = residueNum;
-            prevOriResidueNum = oriResidueNum;
+            // add the last residue set
+            ic.residues[residueNum] = residuesTmp;
+            if(ic.chains[chainNum] === undefined) ic.chains[chainNum] = {};
+            ic.chains[chainNum] = me.hashUtilsCls.unionHash2Atoms(ic.chains[chainNum], chainsTmp, ic.atoms);
 
-            prevResn = chain + "_" + resn;
-            prevAutochain = autochain;
-        }
+            // clear memory
+            atom_hetatmArray = resnArray = elemArray = nameArray = chainArray = resiArray = resiOriArray 
+                = altArray = bArray = xArray = yArray = zArray = autochainArray = [];
 
-        // add the last residue set
-        ic.residues[residueNum] = residuesTmp;
-        if(ic.chains[chainNum] === undefined) ic.chains[chainNum] = {};
-        ic.chains[chainNum] = me.hashUtilsCls.unionHash2Atoms(ic.chains[chainNum], chainsTmp, ic.atoms);
+            let mChainSeq = {};
+            if(block.getCategory("_pdbx_poly_seq_scheme")) {
+                let poly_seq_scheme = block.getCategory("_pdbx_poly_seq_scheme");
 
-        // clear memory
-        atom_hetatmArray = resnArray = elemArray = nameArray = chainArray = resiArray = resiOriArray 
-            = altArray = bArray = xArray = yArray = zArray = autochainArray = [];
+                let resiArray = poly_seq_scheme.getColumn("seq_id");
+                let oriResiArray = poly_seq_scheme.getColumn("pdb_seq_num");
+                let resnArray = poly_seq_scheme.getColumn("mon_id");
+                let chainArray = poly_seq_scheme.getColumn("pdb_strand_id");
 
-        let mChainSeq = {};
-        if(block.getCategory("_pdbx_poly_seq_scheme")) {
-            let poly_seq_scheme = block.getCategory("_pdbx_poly_seq_scheme");
+                let seqSize = poly_seq_scheme.rowCount;
+                let prevChain = "";
+                let seqArray = [];
+                for (let i = 0; i < seqSize; ++i) {
+                    resiArray.getString(i);
+                    let oriResi = oriResiArray.getString(i);
+                    let resn = resnArray.getString(i);
+                    let chain = chainArray.getString(i);
 
-            let resiArray = poly_seq_scheme.getColumn("seq_id");
-            let oriResiArray = poly_seq_scheme.getColumn("pdb_seq_num");
-            let resnArray = poly_seq_scheme.getColumn("mon_id");
-            let chainArray = poly_seq_scheme.getColumn("pdb_strand_id");
+                    if(chain != prevChain && i > 0) {
+                        mChainSeq[prevChain] = seqArray;
 
-            let seqSize = poly_seq_scheme.rowCount;
-            let prevChain = "";
-            let seqArray = [];
-            for (let i = 0; i < seqSize; ++i) {
-                resiArray.getString(i);
-                let oriResi = oriResiArray.getString(i);
-                let resn = resnArray.getString(i);
-                let chain = chainArray.getString(i);
+                        seqArray = [];
+                    }
 
-                if(chain != prevChain && i > 0) {
-                    mChainSeq[prevChain] = seqArray;
+                    // seqArray.push({"resi": resi, "name": me.utilsCls.residueName2Abbr(resn)});
+                    seqArray.push({"resi": oriResi, "name": me.utilsCls.residueName2Abbr(resn)});
 
-                    seqArray = [];
+                    prevChain = chain;
                 }
 
-                // seqArray.push({"resi": resi, "name": me.utilsCls.residueName2Abbr(resn)});
-                seqArray.push({"resi": oriResi, "name": me.utilsCls.residueName2Abbr(resn)});
+                mChainSeq[prevChain] = seqArray;
 
-                prevChain = chain;
+                resiArray = oriResiArray = resnArray = chainArray = [];
             }
-
-            mChainSeq[prevChain] = seqArray;
-
-            resiArray = oriResiArray = resnArray = chainArray = [];
+            
+            this.setSeq(structure, sChain, mChainSeq, ligSeqHash);
         }
-        
-        this.setSeq(structure, sChain, mChainSeq, ligSeqHash);
 
         // copy disulfide bonds
         let structureArray = Object.keys(ic.structures);
@@ -66069,11 +66317,13 @@ class ApplyCommand {
         ic.drawCls.draw();
       }
       else if(command.indexOf('add sphere') == 0) {
-        this.addShape(command, 'sphere');
+        this.addShape(commandOri, 'sphere');
+        ic.shapeCmdHash[commandOri] = 1;
         //ic.drawCls.draw();
       }
       else if(command.indexOf('add cube') == 0) {
-        this.addShape(command, 'cube');
+        this.addShape(commandOri, 'cube');
+        ic.shapeCmdHash[commandOri] = 1;
         //ic.drawCls.draw();
       }
       else if(command.indexOf('clear shape') == 0) {
@@ -66529,8 +66779,8 @@ class ApplyCommand {
 
         ic.hlUpdateCls.updateHlAll();
 
-        // change graph color
-        ic.getGraphCls.updateGraphColor();
+        // change graph color, was done in color command
+        //ic.getGraphCls.updateGraphColor();
       }
       else if(commandOri.indexOf('remove legend') == 0) {
         $("#" + me.pre + "legend").hide();
@@ -66816,7 +67066,7 @@ class ApplyCommand {
     }
 
     addShape(command, shape) { let ic = this.icn3d, me = ic.icn3dui;
-      ic.shapeCmdHash[command] = 1;
+      // ic.shapeCmdHash[command] = 1;
       
       let paraArray = command.split(' | ');
       let p1Array = paraArray[1].split(' ');
@@ -66827,7 +67077,17 @@ class ApplyCommand {
       colorStr = '#' + colorStr.replace(/\#/g, '');
       let color = me.parasCls.thr(colorStr);
 
-      let pos1 = new THREE.Vector3(parseFloat(p1Array[1]), parseFloat(p1Array[3]), parseFloat(p1Array[5]));
+      let pos1;
+
+      if(p1Array[0] == 'x1') { // input position
+        pos1 = new THREE.Vector3(parseFloat(p1Array[1]), parseFloat(p1Array[3]), parseFloat(p1Array[5]));
+      }
+      else { // input sets
+        let nameArray = paraArray[1].split(',');
+        let atomSet1 = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
+        let posArray1 = ic.contactCls.getExtent(atomSet1);
+        pos1 = new THREE.Vector3(posArray1[2][0], posArray1[2][1], posArray1[2][2]);
+      }
 
       if(shape == 'sphere') {
         ic.sphereCls.createSphereBase(pos1, color, parseFloat(radius), undefined, undefined, undefined, parseFloat(opacity));
@@ -67807,7 +68067,7 @@ class SelectCollections {
 
     ic.ssbondpnts = {};
 
-    ic.bShowHighlight = false;
+    ic.bShowHighlight = undefined;
     ic.bResetSets = true;
   }
 
@@ -67938,8 +68198,8 @@ class SelectCollections {
             ic.hAtoms = me.hashUtilsCls.cloneHash(ic.atoms);
           }
           
-        ic.opts["color"] = "structure";
-        ic.setStyleCls.setAtomStyleByOptions();
+        ic.opts["color"] = (Object.keys(ic.structures).length == 1) ? "chain" : "structure";
+        // ic.setStyleCls.setAtomStyleByOptions();
         ic.setColorCls.setColorByOptions(ic.opts, ic.atoms);
 
         ic.transformCls.zoominSelection();
@@ -70189,6 +70449,34 @@ class Resid2spec {
          return spec;
     }
 
+    resi2range(resiArray) {var ic = this.icn3d; ic.icn3dui;
+        let range = [];
+    
+        let resiArraySorted = resiArray.sort(function(a, b) {
+           return parseInt(a) - parseInt(b);
+        });
+        
+        let startResi = resiArraySorted[0];
+        let prevResi, resi;
+        for(let j = 0, jl = resiArraySorted.length; j < jl; ++j) {
+            resi = resiArraySorted[j];
+    
+            if(j != 0 && resi != prevResi + 1) {
+                range.push(startResi);
+                range.push(prevResi);
+                startResi = resi;
+            }
+    
+            prevResi = resi;
+        }
+        
+        // last residue
+        range.push(startResi);
+        range.push(prevResi);
+    
+        return range;
+    }
+
     atoms2spec(atomHash) {var ic = this.icn3d; ic.icn3dui;
         let spec = "";
         let i = 0;
@@ -71651,8 +71939,6 @@ class Dssp {
                     bNoMoreIg = false;
 
                     let pdb_target = ic.saveFileCls.getAtomPDB(domainAtomsArray[k], undefined, undefined, undefined, undefined, struct);
-                    //let bForceOneDomain = true;
-                    //let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(domainAtomsArray[k], bForceOneDomain);
 
                     // ig strand for any subset will have the same k, use the number of residue to separate them
                     let atomFirst = ic.firstAtomObjCls.getFirstAtomObj(domainAtomsArray[k]);
@@ -71812,20 +72098,24 @@ class Dssp {
         // assign ref numbers to selected residues
         let result = ic.domain3dCls.c2b_NewSplitChain(currAtoms, undefined);
         let subdomains = result.subdomains;
-        let pos2resi = result.pos2resi;
+        // let pos2resi = result.pos2resi;
 
         if(subdomains.length >= 1) {
             for(let k = 0, kl = subdomains.length; k < kl; ++k) {
                 let domainAtoms = {};
                 let segArray = subdomains[k];
 
-                let resCnt = 0;
+                let resCnt = 0; // minResi = 999, maxResi = -999;
                 for(let m = 0, ml = segArray.length; m < ml; m += 2) {
                     let startResi = parseInt(segArray[m]);
                     let endResi = parseInt(segArray[m+1]);
 
+                    // if(startResi < minResi) minResi = startResi;
+                    // if(endResi > maxResi) maxResi = endResi;
+
                     for(let n = startResi; n <= endResi; ++n) {
-                        let resid = chainid + '_' + pos2resi[n - 1];
+                        // let resid = chainid + '_' + pos2resi[n - 1];
+                        let resid = ic.ncbi2resid[chainid + '_' + n];
                         ++resCnt;
                         domainAtoms = me.hashUtilsCls.unionHash(domainAtoms, ic.residues[resid]);
 
@@ -71841,6 +72131,9 @@ class Dssp {
                 domainAtomsArray.push(domainAtoms);
             }
         }
+        // else { // no domain
+        //     domainAtomsArray = [currAtoms];
+        // }
 
         return domainAtomsArray;
     }
@@ -71977,7 +72270,6 @@ class Dssp {
                         continue;  
                   }
                 // }
-
             }
 
             if(!bRound1) {
@@ -72525,15 +72817,21 @@ class Dssp {
 
                 let resi = refAA[i][j].trim();
                 let refnum = refAA[refI][j].trim();
+
+                if(!ic.chainsMapping.hasOwnProperty(chainid)) {
+                    ic.chainsMapping[chainid] = {};
+                }
+
+                let resid = chainid + '_' + resi;
+
                 if(resi && refnum) {
-                    let resid = chainid + '_' + resi;
                     ic.resid2refnum[resid] = refnum;
 
-                    if(!ic.chainsMapping.hasOwnProperty(chainid)) {
-                        ic.chainsMapping[chainid] = {};
-                    }
                     ic.chainsMapping[chainid][resid] = refnum;
                 }
+                else {
+                    ic.chainsMapping[chainid][resid] = resi;
+                }
             }
         }
 
@@ -73009,17 +73307,18 @@ class Dssp {
                 }
                 
                 // assign before removing
-                let resid = chnid + '_' + strandArray[i].startResi;
+                chnid + '_' + strandArray[i].startResi;
 
                 strandArray.splice(i, 1);
 
-                if(strandTmp == 'B' || strandTmp == 'C' || strandTmp == 'E' || strandTmp == 'F') {
-                    if(!me.bNode) console.log("Ig strand " + strandTmp + " is removed since it is too short...");
+                // do not remove BCEF strands even though they are short
+                // if(strandTmp == 'B' || strandTmp == 'C' || strandTmp == 'E' || strandTmp == 'F') {
+                //     if(!me.bNode) console.log("Ig strand " + strandTmp + " is removed since it is too short...");
                     
-                    let domainid = ic.resid2domainid[resid];
-                    removeDomainidHash[domainid] = 1;
-                    continue;
-                }   
+                //     let domainid = ic.resid2domainid[resid];
+                //     removeDomainidHash[domainid] = 1;
+                //     continue;
+                // }   
             }
         }
 
@@ -73237,7 +73536,7 @@ class Dssp {
 
                 // remove the postfix when comparing interactions
                 //ic.chainsMapping[chnid][residueid] = refnumLabel;
-                ic.chainsMapping[chnid][residueid] = refnumLabelNoPostfix;
+                ic.chainsMapping[chnid][residueid] = (refnumLabelNoPostfix) ? refnumLabelNoPostfix : currResi;
             }
         }
 
@@ -81390,7 +81689,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.31.3';
+    this.REVISION = '3.32.0';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;