icn3d 3.29.5 → 3.29.6

package/icn3d.js

@@ -7611,6 +7611,13 @@ class ClickMenu {
            //}
         });
 
+        $(document).on("click", "#" + me.pre + "mn2_translate", function(e) { me.icn3d; //e.preventDefault();
+           me.htmlCls.dialogCls.openDlg('dl_translate', 'Translate the X,Y,Z coordinates of the structure');
+        });
+
+        $(document).on("click", "#" + me.pre + "mn2_matrix", function(e) { me.icn3d; //e.preventDefault();
+           me.htmlCls.dialogCls.openDlg('dl_matrix', 'Apply matrix to the X,Y,Z coordinates of the structure');
+        });
 
         $(document).on("click", "." + me.pre + "mn6_rotate", function(e) { let ic = me.icn3d; //e.preventDefault();
            let value = $(this).attr('v').toLowerCase();
@@ -8667,14 +8674,14 @@ class SetMenu {
         }
 
         //!!!
-/*
+
         html += this.getMenuText('m1_exportrefnum', 'Reference Numbers', undefined, undefined, 2);
         html += "<ul>";
         html += this.getLink('mn1_exportIgstrand', 'Ig Strand', undefined, 3);
         html += this.getLink('mn1_exportKabat', 'Kabat', undefined, 3);
         html += this.getLink('mn1_exportImgt', 'IMGT', undefined, 3);
         html += "</ul>";
-*/
+
 
         html += "<li><br/></li>";
 
@@ -8894,6 +8901,9 @@ class SetMenu {
         html += "</ul>";
         html += "</li>";
 
+        html += this.getLink('mn2_translate', 'Translate XYZ', undefined, 1);
+        html += this.getLink('mn2_matrix', 'Apply Matrix', undefined, 1);
+
         html += this.getMenuText('mn2_camera', 'Camera', undefined, undefined, 1);
         html += "<ul>";
         html += this.getRadio('mn6_camera', 'mn6_cameraPers', 'Perspective', true, undefined, 2);
@@ -9515,8 +9525,8 @@ class SetMenu {
             //}
 
             //!!!
-            //html += this.getRadio('mn4_clr', 'mn4_clrIgstrand', 'Ig Strand', undefined, undefined, 2);
-            //html += this.getRadio('mn4_clr', 'mn4_clrIgproto', 'Ig Protodomain', undefined, undefined, 2);
+            html += this.getRadio('mn4_clr', 'mn4_clrIgstrand', 'Ig Strand', undefined, undefined, 2);
+            html += this.getRadio('mn4_clr', 'mn4_clrIgproto', 'Ig Protodomain', undefined, undefined, 2);
         }
         else {
             //if(!me.cfg.hidelicense) html += this.getRadio('mn4_clr', 'mn1_delphi2', 'DelPhi<br><span style="padding-left:1.5em;">Potential ' + me.htmlCls.licenseStr + '</span>');
@@ -9647,7 +9657,7 @@ class SetMenu {
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelResidues', 'per Residue', undefined, 1, 2);
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelResnum', 'per Residue & Number', undefined, 1, 2);
             //!!!
-            //html += this.getRadio('mn6_addlabel', 'mn6_addlabelRefnum', 'per Reference Number', undefined, 1, 2);
+            html += this.getRadio('mn6_addlabel', 'mn6_addlabelRefnum', 'per Reference Number', undefined, 1, 2);
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelChains', 'per Chain', undefined, undefined, 2);
             html += this.getRadio('mn6_addlabel', 'mn6_addlabelTermini', 'N- & C-Termini', undefined, 1, 2);
         }
@@ -9739,13 +9749,13 @@ class SetMenu {
 
             html += "<ul>";
 //!!!
-/*
+
             html += this.getLink('mn6_igrefYes', 'Show Ig Ref. Number', undefined, 2);
             html += this.getLink('mn6_igrefTpl', 'Ig w/ Specified Template', undefined, 2);
             html += this.getLink('mn6_igrefNo', 'Hide Ig Ref. Number', undefined, 2);
 
             html += this.getMenuSep();
-*/
+
             html += this.getLink('mn6_customref', 'Custom Ref. Number', undefined, 2);
             html += "</ul>";
             html += "</li>";
@@ -11855,6 +11865,39 @@ class SetDialog {
         html += this.addNotebookTitle('dl_disttable', 'Distance Table', true);
         html += "</div>";
 
+        html += me.htmlCls.divStr + "dl_translate' class='" + dialogClass + "'>";
+        html += this.addNotebookTitle('dl_translate', 'Translate the X,Y,Z coordinates of the structure');
+        html += "X: " + me.htmlCls.inputTextStr + "id='" + me.pre + "translateX' value='' size=4> ";
+        html += "Y: " + me.htmlCls.inputTextStr + "id='" + me.pre + "translateY' value='' size=4> ";
+        html += "Z: " + me.htmlCls.inputTextStr + "id='" + me.pre + "translateZ' value='' size=4> ";
+        html += me.htmlCls.buttonStr + "translate_pdb'>Translate</button>";
+        html += "</div>";
+
+        html += me.htmlCls.divStr + "dl_matrix' class='" + dialogClass + "'>";
+        html += this.addNotebookTitle('dl_matrix', 'Apply matrix to the X,Y,Z coordinates of the structure');
+        html += "0: " + me.htmlCls.inputTextStr + "id='" + me.pre + "matrix0' value='1' size=2> ";
+        html += "4: " + me.htmlCls.inputTextStr + "id='" + me.pre + "matrix4' value='0' size=2> ";
+        html += "8: " + me.htmlCls.inputTextStr + "id='" + me.pre + "matrix8' value='0' size=2> ";
+        html += "12: " + me.htmlCls.inputTextStr + "id='" + me.pre + "matrix12' value='0' size=2><br>";
+
+        html += "1: " + me.htmlCls.inputTextStr + "id='" + me.pre + "matrix1' value='0' size=2> ";
+        html += "5: " + me.htmlCls.inputTextStr + "id='" + me.pre + "matrix5' value='1' size=2> ";
+        html += "9: " + me.htmlCls.inputTextStr + "id='" + me.pre + "matrix9' value='0' size=2> ";
+        html += "13: " + me.htmlCls.inputTextStr + "id='" + me.pre + "matrix13' value='0' size=2><br>";
+
+        html += "2: " + me.htmlCls.inputTextStr + "id='" + me.pre + "matrix2' value='0' size=2> ";
+        html += "6: " + me.htmlCls.inputTextStr + "id='" + me.pre + "matrix6' value='0' size=2> ";
+        html += "10: " + me.htmlCls.inputTextStr + "id='" + me.pre + "matrix10' value='1' size=2> ";
+        html += "14: " + me.htmlCls.inputTextStr + "id='" + me.pre + "matrix14' value='0' size=2><br>";
+
+        html += "3: " + me.htmlCls.inputTextStr + "id='" + me.pre + "matrix3' value='0' size=2> ";
+        html += "7: " + me.htmlCls.inputTextStr + "id='" + me.pre + "matrix7' value='0' size=2> ";
+        html += "11: " + me.htmlCls.inputTextStr + "id='" + me.pre + "matrix11' value='0' size=2> ";
+        html += "15: " + me.htmlCls.inputTextStr + "id='" + me.pre + "matrix15' value='1' size=2><br>";
+
+        html += me.htmlCls.buttonStr + "matrix_pdb'>Apply Matrix</button>";
+        html += "</div>";
+
         html += me.htmlCls.divStr + "dl_igrefTpl' class='" + dialogClass + "'>";
         html += this.addNotebookTitle('dl_igrefTpl', 'Choose an Ig template');
         html += "<span style='white-space:nowrap;font-weight:bold;'>Choose an Ig template for selected residues:</span> <br><br><select id='" + me.pre + "igrefTpl'>";
@@ -12580,6 +12623,33 @@ class Events {
            window.open(hostUrl + '?pdbid=' + $("#" + me.pre + "pdbid").val(), urlTarget);
         });
 
+        me.myEventCls.onIds("#" + me.pre + "translate_pdb", "click", function(e) { let ic = me.icn3d;
+            e.preventDefault();
+            if(!me.cfg.notebook) dialog.dialog( "close" );
+            let dx = $("#" + me.pre + "translateX").val();
+            let dy = $("#" + me.pre + "translateY").val();
+            let dz = $("#" + me.pre + "translateZ").val();
+
+            ic.transformCls.translateCoord(ic.hAtoms, parseFloat(dx), parseFloat(dy), parseFloat(dz));
+            ic.drawCls.draw();
+
+            thisClass.setLogCmd("translate pdb " + dx + " " + dy + " "  + dz, true);
+        });
+
+        me.myEventCls.onIds("#" + me.pre + "matrix_pdb", "click", function(e) { let ic = me.icn3d;
+            e.preventDefault();
+            if(!me.cfg.notebook) dialog.dialog( "close" );
+            let mArray = [];
+            for(let i = 0; i< 16; ++i) {
+                mArray.push(parseFloat($("#" + me.pre + "matrix" + i).val()));
+            }
+
+            ic.transformCls.rotateCoord(ic.hAtoms, mArray);
+            ic.drawCls.draw();
+
+            thisClass.setLogCmd("rotate pdb " + mArray, true);
+        });
+
         me.myEventCls.onIds("#" + me.pre + "pdbid", "keyup", function(e) { let ic = me.icn3d;
            if (e.keyCode === 13) {
                e.preventDefault();
@@ -39260,6 +39330,7 @@ class Domain3d {
 				substructItem.z2 = atom.coord.z;
 
 				substructItem.Sheet = (atom.ss == 'sheet') ? true : false;
+
 				substruct.push(substructItem);
 				substructItem = {};		
 			}
@@ -42985,8 +43056,8 @@ class ShowSeq {
         }
         giSeq = giSeqTmp;
 
-        //let divLength = me.htmlCls.RESIDUE_WIDTH * ic.giSeq[chnid].length + 200;
-        let divLength = me.htmlCls.RESIDUE_WIDTH * (ic.giSeq[chnid].length + ic.nTotalGap) + 200;
+        //let divLength = me.htmlCls.RESIDUE_WIDTH * (ic.giSeq[chnid].length + ic.nTotalGap) + 200;
+        let divLength = me.htmlCls.RESIDUE_WIDTH * (giSeq.length + ic.nTotalGap) + 200;
 
         // let seqLength = ic.giSeq[chnid].length
         // if(seqLength > ic.maxAnnoLength) {
@@ -43006,7 +43077,7 @@ class ShowSeq {
         // html to display protein positions(10, 20, etc)
         //if(Object.keys(ic.chains[chnid]).length > 10) {
 
-        if(ic.giSeq[chnid].length > 10) {
+        if(giSeq.length > 10) {
             htmlTmp = '<div class="icn3d-residueLine" style="white-space:nowrap;">';
             let atom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.chains[chnid]);
             //if(ic.baseResi[chnid] != 0 &&(me.cfg.mmdbid !== undefined || me.cfg.gi !== undefined || me.cfg.align !== undefined)) {
@@ -43368,7 +43439,7 @@ class ShowSeq {
         html3 += '</div>';
         
         //if(Object.keys(ic.chains[chnid]).length > 10) {
-        if(ic.giSeq[chnid].length > 10) {
+        if(giSeq.length > 10) {
             let atom = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.chains[chnid]);
             //if(ic.baseResi[chnid] != 0 &&(me.cfg.mmdbid !== undefined || me.cfg.gi !== undefined || me.cfg.align !== undefined)) {
             if((me.cfg.mmdbid !== undefined || me.cfg.gi !== undefined || me.cfg.blast_rep_id !== undefined || me.cfg.align !== undefined || me.cfg.chainalign !== undefined || me.cfg.mmdbafid !== undefined) && atom.resi_ori !== undefined && atom.resi_ori != atom.resi && chnid.indexOf('Misc') == -1 ) {
@@ -43555,12 +43626,12 @@ class ShowSeq {
             // reset ic.residIgLoop for the current selection, which could be the second round of ref num assignment
             // just current chain
             let atomHash = me.hashUtilsCls.intHash(ic.chains[chnid], ic.hAtoms);
-            let residHash = ic.firstAtomObjCls.getResiduesFromAtoms(atomHash);
+            ic.firstAtomObjCls.getResiduesFromAtoms(atomHash);
             
-            for(let resid in residHash) {
-                // not in loop any more if you assign ref numbers multiple times
-                delete ic.residIgLoop[resid];
-            }
+            // for(let resid in residHash) {
+            //     // not in loop any more if you assign ref numbers multiple times
+            //     delete ic.residIgLoop[resid];
+            // }
         }
 
         // 1. get the range of each strand excluding loops
@@ -43690,6 +43761,76 @@ class ShowSeq {
                 }
             }
 
+            // 2b. extend the strand to end of sheet
+            let maxExtend = 8;
+            for(let i = 0, il = strandArray.length; i < il; ++i) {
+                let startAtom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[chnid + '_' + strandArray[i].startResi]);
+                let endAtom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[chnid + '_' + strandArray[i].endResi]);
+
+                let startPos = ic.setSeqAlignCls.getPosFromResi(chnid, strandArray[i].startResi);
+                let endPos = ic.setSeqAlignCls.getPosFromResi(chnid, strandArray[i].endResi);
+
+                if(startAtom.ss == 'sheet' && !startAtom.ssbegin) {
+                    for(let j = 1; j <= maxExtend; ++j) {
+                        let currPos = startPos - j;
+                        let currResi = ic.ParserUtilsCls.getResi(chnid, currPos);
+                        if(i > 0 && parseInt(currResi) <= parseInt(strandArray[i-1].endResi)) break;
+
+                        let currResid = chnid + '_' + currResi;
+                        let currAtom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[currResid]);
+                        if(currAtom.ssbegin) { // find the start of the sheet
+                            // update the following: startResi,startRefnum,endResi,endRefnum,loopResCnt,resCntBfAnchor,resCntAtAnchor
+                            strandArray[i].startResi = currResi;
+                            strandArray[i].startRefnum -= j;
+                            strandArray[i].loopResCnt -= j;
+                            if(strandArray[i].loopResCnt < 0) strandArray[i].loopResCnt = 0;
+                            strandArray[i].resCntBfAnchor += j;
+
+                            // update ic.resid2refnum
+                            for(let k = 1; k <= j; ++k) {
+                                currPos = startPos - k;
+                                currResi = ic.ParserUtilsCls.getResi(chnid, currPos);
+                                let currResid = chnid + '_' + currResi;
+                                delete ic.residIgLoop[currResid];
+                            }
+
+                            break;
+                        }
+                    }
+                }
+
+                if(endAtom.ss == 'sheet' && !endAtom.ssend) {
+                    for(let j = 1; j <= maxExtend; ++j) {
+                        let currPos = endPos + j;
+                        let currResi = ic.ParserUtilsCls.getResi(chnid, currPos);
+                        if(i < il - 1 && parseInt(currResi) >= parseInt(strandArray[i+1].startResi)) break; 
+
+                        let currResid = chnid + '_' + currResi;
+                        let currAtom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[currResid]);
+                        if(currAtom.ssend) { // find the end of the sheet
+                            // update the following: startResi,startRefnum,endResi,endRefnum,loopResCnt,resCntBfAnchor,resCntAtAnchor
+                            strandArray[i].endResi = currResi;
+                            strandArray[i].endRefnum += j;
+                            if(i < il - 1) {
+                                strandArray[i + 1].loopResCnt -= j;
+                                if(strandArray[i + 1].loopResCnt < 0) strandArray[i + 1].loopResCnt = 0;
+                            }
+                            strandArray[i].resCntAtAnchor += j;
+
+                            // update ic.residIgLoop[resid];
+                            for(let k = 1; k <= j; ++k) {
+                                currPos = endPos + k;
+                                currResi = ic.ParserUtilsCls.getResi(chnid, currPos);
+                                let currResid = chnid + '_' + currResi;
+                                delete ic.residIgLoop[currResid];
+                            }
+
+                            break;
+                        }
+                    }
+                }
+            }
+            
             // 3. assign refnumLabel for each resid
             strandCnt = 0;
             let loopCnt = 0;
@@ -45872,7 +46013,15 @@ class LineGraph {
 
                 ic.pdbDataArray = await this.promiseWithFixedJobs(pdbAjaxArray);
 
-                await thisClass.parseRefPdbData(ic.pdbDataArray, template);
+                let bNoMoreIg = await thisClass.parseRefPdbData(ic.pdbDataArray, template);
+                let numRound = 0;
+
+                //while(!bNoMoreIg) {
+                while(!bNoMoreIg && numRound < 10) {
+                    let bRerun = true;
+                    bNoMoreIg = await thisClass.parseRefPdbData(ic.pdbDataArray, template, bRerun);
+                    ++numRound;
+                }
             }
             else {
                 await thisClass.parseRefPdbData(undefined, template);
@@ -45884,7 +46033,7 @@ class LineGraph {
         // }
     }
 
-    async parseRefPdbData(dataArray, template) { let ic = this.icn3d, me = ic.icn3dui;
+    async parseRefPdbData(dataArray, template, bRerun) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
         let struArray = Object.keys(ic.structures);
@@ -45899,6 +46048,7 @@ class LineGraph {
         //ic.resid2domainid = {};
         ic.domainid2pdb = {};
 
+        let bNoMoreIg = true;
         for(let i = 0, il = struArray.length; i < il; ++i) {
             let struct = struArray[i];
             let chainidArray = ic.structures[struct];
@@ -45906,12 +46056,14 @@ class LineGraph {
             for(let j = 0, jl = chainidArray.length; j < jl; ++j) {
                 let chainid = chainidArray[j];
 
-                let domainAtomsArray = this.getDomainAtomsArray(chainid);
-                    
+                let domainAtomsArray = this.getDomainAtomsArray(chainid, bRerun);
+
                 if(!ic.domainid2refpdbname) ic.domainid2refpdbname = {};
                 if(!ic.domainid2score) ic.domainid2score = {};
 
                 for(let k = 0, kl = domainAtomsArray.length; k < kl; ++k) {
+                    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);
@@ -46012,6 +46164,8 @@ class LineGraph {
     
                 await thisClass.parseAlignData(dataArray3, domainidpairArray3);
             }
+
+            return bNoMoreIg;
             /*
         }
         catch(err) {
@@ -46028,10 +46182,12 @@ class LineGraph {
         */           
     }
 
-    getDomainAtomsArray(chainid) { let ic = this.icn3d, me = ic.icn3dui;
+    getDomainAtomsArray(chainid, bRerunDomain) { let ic = this.icn3d, me = ic.icn3dui;
         let domainAtomsArray = [];
 
-        let minResidues = 20;
+        let minResidues = 20, minAtoms = 200;
+
+        if(!ic.chainid2atomsLeft) ic.chainid2atomsLeft = {};
 
         if(!ic.proteins.hasOwnProperty(ic.firstAtomObjCls.getFirstAtomObj(ic.chains[chainid]).serial)
         && !ic.proteins.hasOwnProperty(ic.firstAtomObjCls.getMiddleAtomObj(ic.chains[chainid]).serial)) return domainAtomsArray;
@@ -46040,18 +46196,37 @@ class LineGraph {
         let currAtoms = me.hashUtilsCls.intHash(ic.chains[chainid], ic.hAtoms);
         if(Object.keys(currAtoms).length == 0) return domainAtomsArray;
 
+        if(bRerunDomain) {
+            let atomsAssigned = {};
+            // for(let resid in ic.resid2refnum_ori) {
+            //     atomsAssigned = me.hashUtilsCls.unionHash(atomsAssigned, ic.residues[resid]);
+            // }
+            for(let resid in ic.resid2refnum) {
+                if(ic.resid2refnum[resid]) atomsAssigned = me.hashUtilsCls.unionHash(atomsAssigned, ic.residues[resid]);
+            }
+
+            currAtoms = me.hashUtilsCls.exclHash(currAtoms, atomsAssigned);
+
+            // no need to rerun the rest residues any more
+            if(ic.chainid2atomsLeft[chainid] == Object.keys(currAtoms).length) {
+                return domainAtomsArray;
+            }
+
+            ic.chainid2atomsLeft[chainid] = Object.keys(currAtoms).length;
+
+            if(Object.keys(currAtoms).length < minAtoms) return domainAtomsArray;
+        }
+
         // align each 3D domain with reference structure
         //let result = ic.domain3dCls.c2b_NewSplitChain(ic.chains[chainid]);
         // assign ref numbers to selected residues
-        let result = ic.domain3dCls.c2b_NewSplitChain(currAtoms);
+        let result = ic.domain3dCls.c2b_NewSplitChain(currAtoms, undefined);
         let subdomains = result.subdomains;  
         let pos2resi = result.pos2resi;
 
         if(subdomains.length <= 1) {
-            //domainAtomsArray.push(ic.chains[chainid]);
-            domainAtomsArray.push(currAtoms);
-
             let residueArray = ic.resid2specCls.atoms2residues(Object.keys(currAtoms));
+            if(residueArray.length < minResidues) return domainAtomsArray;
 
             let atomFirst = ic.firstAtomObjCls.getFirstAtomObj(currAtoms);
             let atomLast = ic.firstAtomObjCls.getLastAtomObj(currAtoms);
@@ -46062,31 +46237,41 @@ class LineGraph {
                 ic.resid2domainid[resid] = chainid + '-0' + '_' + resiSum; 
 
                 // clear previous refnum assignment if any
-                if(ic.resid2refnum && ic.resid2refnum[resid]) {
+                // if(!bRerunDomain && ic.resid2refnum && ic.resid2refnum[resid]) {
+                // if(ic.resid2refnum && ic.resid2refnum[resid]) {
                     delete ic.resid2refnum[resid];
-                }
+                    delete ic.residIgLoop[resid];
+                // }
             }
+
+            domainAtomsArray.push(currAtoms);
         }
         else {                 
             for(let k = 0, kl = subdomains.length; k < kl; ++k) {
                 let domainAtoms = {};
                 let segArray = subdomains[k];
 
+                let resCnt = 0;
                 for(let m = 0, ml = segArray.length; m < ml; m += 2) {
                     let startResi = segArray[m];
                     let endResi = segArray[m+1];
                     for(let n = parseInt(startResi); n <= parseInt(endResi); ++n) {
                         let resid = chainid + '_' + pos2resi[n];
+                        ++resCnt;
                         domainAtoms = me.hashUtilsCls.unionHash(domainAtoms, ic.residues[resid]);
                         //ic.resid2domainid[resid] = chainid + '-' + k;
 
                         // clear previous refnum assignment if any
-                        if(ic.resid2refnum && ic.resid2refnum[resid]) {
+                        // if(!bRerunDomain && ic.resid2refnum && ic.resid2refnum[resid]) {
+                        // if(ic.resid2refnum && ic.resid2refnum[resid]) {
                             delete ic.resid2refnum[resid];
-                        }
+                            delete ic.residIgLoop[resid];
+                        // }
                     }
                 }
 
+                if(resCnt < minResidues) continue;
+
                 domainAtomsArray.push(domainAtoms);
 
                 let atomFirst = ic.firstAtomObjCls.getFirstAtomObj(domainAtoms);
@@ -46209,31 +46394,45 @@ class LineGraph {
 
             // Ig-like domains: B (2150, 2150a, 2150b), C (3150, 3250), E (7150, 7250), F (8150, 8250) strands
             // Ig domain may require G (7050). But we'll leave that out for now.
-            if(!bRound1) {
+            if(!bRound1 && queryData[0].segs) {
                 let bBstrand = false, bCstrand = false, bEstrand = false, bFstrand = false;
-                for(let i = 0, il = queryData[0].segs.length; i < il; ++i) {
-                    let seg = queryData[0].segs[i];
+                let bBSheet = true, bCSheet = true, bESheet = true, bFSheet = true;
+                let chainid = domainid.split(',')[0];
+
+                for(let j = 0, jl = queryData[0].segs.length; j < jl; ++j) {
+                    let seg = queryData[0].segs[j];
+                    let resi = seg.t_start;
+                    let resid = chainid + '_' + resi;
 
                     if(seg.q_start.indexOf('2550') != -1) {
                         bBstrand = true;
+                        let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
+                        bBSheet = (atom.ss == 'sheet');
                     }
                     else if(seg.q_start.indexOf('3550') != -1) {
                         bCstrand = true;
+                        let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
+                        bBSheet = (atom.ss == 'sheet');
                     }
                     else if(seg.q_start.indexOf('7550') != -1) {
                         bEstrand = true;
+                        let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
+                        bBSheet = (atom.ss == 'sheet');
                     }
                     else if(seg.q_start.indexOf('8550') != -1) {
                         bFstrand = true;
+                        let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
+                        bBSheet = (atom.ss == 'sheet');
                     }
 
                     //if(bBstrand && bCstrand && bEstrand && bFstrand && bGstrand) break;
                     if(bBstrand && bCstrand && bEstrand && bFstrand) break;
                 }
 
-                //if(!(bBstrand && bCstrand && bEstrand && bFstrand && bGstrand)) continue;
-                if(!(bBstrand && bCstrand && bEstrand && bFstrand)) {
-                    if(!me.bNode) console.log("Some of the Ig strands B, C, E, F are missing in the domain " + domainid + "...");
+                if(!(bBstrand && bCstrand && bEstrand && bFstrand) || !(bBSheet && bCSheet && bESheet && bFSheet)) {
+                //if(!(bBstrand && bCstrand && bEstrand && bFstrand)) {
+                    if(!me.bNode && !(bBstrand && bCstrand && bEstrand && bFstrand)) console.log("Some of the Ig strands B, C, E, F are missing in the domain " + domainid + "...");
+                    if(!me.bNode && !(bBSheet && bCSheet && bESheet && bFSheet)) console.log("Some of the Ig strands B, C, E, F are not beta sheets...");
                     if(ic.domainid2refpdbname[domainid] == refpdbname) {
                         delete ic.domainid2refpdbname[domainid];
                         delete ic.domainid2score[domainid];
@@ -46370,11 +46569,12 @@ class LineGraph {
 
         // assign ic.resid2refnum, ic.refnum2residArray, ic.chainsMapping
         if(!ic.resid2refnum) ic.resid2refnum = {};
+        // if(!ic.resid2refnum_ori) ic.resid2refnum_ori = {};
         if(!ic.refnum2residArray) ic.refnum2residArray = {};
         if(!ic.chainsMapping) ic.chainsMapping = {};
 
         if(!ic.refPdbList) ic.refPdbList = [];
-
+        
         for(let chainid in chainid2segs) {
             let segArray = chainid2segs[chainid];
 
@@ -46393,10 +46593,66 @@ class LineGraph {
             }
             ic.refPdbList.push(message);
 
+            // adjust C' and D strands ======start
+            let bCstrand = false, bCpstrand = false, bCppstrand = false, bDstrand = false, bEstrand = false;
+            let CAtom, CpAtom, DAtom, EAtom;
+            //let chainid = domainid.split(',')[0];
+
+            let cntBtCE = 0;
+            for(let i = 0, il = segArray.length; i < il; ++i) {
+                let seg = segArray[i];
+                if(!seg) continue;
+
+                let resi = seg.t_start;
+                let resid = chainid + '_' + resi;
+
+                if(seg.q_start.indexOf('3550') != -1) {
+                    bCstrand = true;
+                    CAtom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
+                }
+                else if(seg.q_start.indexOf('4550') != -1) {
+                    bCpstrand = true;
+                    CpAtom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
+                    ++cntBtCE;
+                }
+                // else if(seg.q_start.indexOf('5550') != -1) {
+                //     bCppstrand = true;
+                //     CppAtom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
+                //     ++cntBtCE;
+                // }
+                else if(seg.q_start.indexOf('6550') != -1) {
+                    bDstrand = true;
+                    DAtom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
+                    ++cntBtCE;
+                }
+                else if(seg.q_start.indexOf('7550') != -1) {
+                    bEstrand = true;
+                    EAtom = ic.firstAtomObjCls.getFirstAtomObj(ic.residues[resid]);
+                }
+
+                if(bCstrand && bCpstrand && bCppstrand && bDstrand && bEstrand) break;
+            }
+
+            let CpToDResi, DToCpResi;
+            if(cntBtCE == 1) {
+                let distToC = (bCpstrand) ? CpAtom.coord.distanceTo(CAtom.coord) : DAtom.coord.distanceTo(CAtom.coord);
+                let distToE = (bCpstrand) ? CpAtom.coord.distanceTo(EAtom.coord) : DAtom.coord.distanceTo(EAtom.coord);
+
+                if(bCpstrand && distToC > distToE) { // rename C' to D
+                    CpToDResi = CAtom.resi;
+                }
+                else if(bDstrand && distToC < distToE) { // rename D to C'
+                    DToCpResi = DAtom.resi;
+                }
+            }
+            // adjust C' and D strands ======end
+
             let prevStrand;
             let bCd19 = refpdbnameArray.length == 1 && refpdbnameArray[0] == 'CD19_6al5A_human_C2orV-n1';
             for(let i = 0, il = segArray.length; i < il; ++i) {
                 let seg = segArray[i];
+                if(!seg) continue;
+                
                 let qStart = seg.q_start;
                 parseInt(seg.q_start);
                 if(isNaN(seg.q_start)) seg.q_start.substr(seg.q_start.length - 1, 1);
@@ -46413,10 +46669,21 @@ class LineGraph {
                     //let refnum = qStart + postfix;
                     let refnum = qStart;
 
-                    let refnumLabel = this.getLabelFromRefnum(refnum, prevStrand, bCd19);
+                    let prevStrandFinal = prevStrand;
+                    if(prevStrand == "C'" && CpToDResi && parseInt(seg.t_start) < parseInt(CpToDResi) + 10 
+                        && parseInt(seg.t_start) > parseInt(CpToDResi) - 10 ) {
+                        prevStrandFinal = "D";
+                    }
+                    else if(prevStrand == "D" && DToCpResi && parseInt(seg.t_start) < parseInt(DToCpResi) + 10 
+                        && parseInt(seg.t_start) > parseInt(DToCpResi) - 10 ) {
+                        prevStrandFinal = "C'";
+                    }
+
+                    let refnumLabel = this.getLabelFromRefnum(refnum, prevStrandFinal, bCd19);
                     prevStrand = (refnumLabel) ? refnumLabel.replace(new RegExp(refnum,'g'), '') : undefined;
 
                     ic.resid2refnum[resid] = refnumLabel;
+                    // ic.resid2refnum_ori[resid] = refnumLabel;
 
                     // final reference numbers will be assign in ic.showSeqCls.showRefNum()
 
@@ -50642,7 +50909,7 @@ class Dsn6Parser {
         return sigma;
     }
 
-    loadDsn6Data(dsn6data, type, sigma, location, bInputSigma) { let ic = this.icn3d; ic.icn3dui;
+    loadDsn6Data(dsn6data, type, sigma, location, bInputSigma) { let ic = this.icn3d, me = ic.icn3dui;
         // DSN6 http://www.uoxray.uoregon.edu/tnt/manual/node104.html
         // BRIX http://svn.cgl.ucsf.edu/svn/chimera/trunk/libs/VolumeData/dsn6/brix-1.html
 
@@ -50719,6 +50986,8 @@ class Dsn6Parser {
           summand = intView[ 16 ];
         }
 
+        if(!me.bNode) console.log("header: " + JSON.stringify(header));
+
         let data = new Float32Array(
           header.xExtent * header.yExtent * header.zExtent
         );
@@ -51917,7 +52186,9 @@ class MmcifParser {
 
     async downloadMmcifSymmetry(mmcifid, type) { let ic = this.icn3d, me = ic.icn3dui;
         // https://files.rcsb.org/header/ is not accessible in Node.js and Mac
-        let url = (me.bNode || me.utilsCls.isMac()) ? "https://files.rcsb.org/view/" + mmcifid + ".cif" : "https://files.rcsb.org/header/" + mmcifid + ".cif";
+        // Some header files are in the wrong format. So we use the full mmCIF file
+        //let url = (me.bNode || me.utilsCls.isMac()) ? "https://files.rcsb.org/view/" + mmcifid + ".cif" : "https://files.rcsb.org/header/" + mmcifid + ".cif";
+        let url = "https://files.rcsb.org/view/" + mmcifid + ".cif";
 
         //ic.bCid = undefined;
         let data1 = await me.getAjaxPromise(url, 'text', false, "The structure " + mmcifid + " was not found...");
@@ -58800,6 +59071,8 @@ class LoadPDB {
         
         let bHeader = false, bFirstAtom = true;
 
+        let segId, prevSegId;
+
         for (let i in lines) {
             let line = lines[i];
             let record = line.substr(0, 6);
@@ -58959,11 +59232,36 @@ class LoadPDB {
                     ic.pmid = line.substr(19).trim();
                 }
             } else if (record === 'ATOM  ' || record === 'HETATM') {
+                //73 - 76 LString(4) segID Segment identifier, left-justified.
+                // deal with PDBs from MD trajectories
+                segId = line.substr(72, 4).trim();
+
                 if(bFirstAtom) {
                     structure = this.getStructureId(id, moleculeNum, bMutation);
 
                     bFirstAtom = false;
                 }
+                else if(segId != prevSegId) {
+                    ++moleculeNum;
+                    id = ic.defaultPdbId;
+    
+                    structure = this.getStructureId(id, moleculeNum, bMutation);
+    
+                    //helices = [];
+                    //sheets = [];
+                    if(!bNMR) {
+                        sheetArray = [];
+                        sheetStart = [];
+                        sheetEnd = [];
+                        helixArray = [];
+                        helixStart = [];
+                        helixEnd = [];
+                    }
+    
+                    bHeader = false; // reinitialize to read structure name from the header
+                }
+
+                prevSegId = segId;
 
                 let alt = line.substr(16, 1);
                 //if (alt !== " " && alt !== "A") continue;
@@ -61733,6 +62031,22 @@ class ApplyCommand {
       else if(command.indexOf('hide ref number') == 0) {
         ic.bShownRefnum = false;
       }
+      else if(command.indexOf('translate pdb') == 0) {
+        let xyz = command.substr(14 + 1).split(' ');
+
+        ic.transformCls.translateCoord(ic.hAtoms, parseFloat(xyz[0]), parseFloat(xyz[1]), parseFloat(xyz[2]));
+        ic.drawCls.draw();
+      }
+      else if(command.indexOf('rotate pdb') == 0) {
+        let mArray = command.substr(10 + 1).split(',');
+        let mArrayFloat = [];
+        for(let i = 0, il = mArray.length; i < il; ++i) {
+          mArrayFloat.push(parseFloat(mArray[i]));
+        }
+
+        ic.transformCls.rotateCoord(ic.hAtoms, mArrayFloat);
+        ic.drawCls.draw();
+      }
 
     // special, select ==========
 
@@ -62913,6 +63227,14 @@ class SelectCollections {
         ic.transformCls.zoominSelection();
         ic.definedSetsCls.showSets();
 
+        ic.bResetAnno = true;
+        if(ic.bAnnoShown) {
+          await ic.showAnnoCls.showAnnotations();
+
+          ic.hlUpdateCls.updateHlAll(nameArray);
+          // show selected chains in annotation window
+          ic.annotationCls.showAnnoSelectedChains();
+        }
 
         await ic.drawCls.draw();
         ic.saveFileCls.showTitle();
@@ -69861,7 +70183,7 @@ class ResizeCanvas {
         //let itemArray = ['dl_selectannotations', 'dl_alignment', 'dl_2ddgm', 'dl_definedsets', 'dl_graph',
         //    'dl_linegraph', 'dl_scatterplot', 'dl_contactmap', 'dl_allinteraction', 'dl_copyurl',
         //    'dl_symmetry', 'dl_symd', 'dl_rmsd', 'dl_legend', 'dl_disttable'];
-        let itemArray = ['dl_2ddgm', 'dl_2dctn', 'dl_alignment', 'dl_sequence2', 'dl_definedsets', 'dl_setsmenu', 'dl_command', 'dl_setoperations', 'dl_vast', 'dl_foldseek', 'dl_mmtfid', 'dl_pdbid', 'dl_afid', 'dl_opmid', 'dl_pdbfile', 'dl_pdbfile_app', 'dl_rescolorfile', 'dl_customcolor', 'dl_align', 'dl_alignaf', 'dl_chainalign', 'dl_chainalign2', 'dl_chainalign3', 'dl_mutation', 'dl_mol2file', 'dl_sdffile', 'dl_xyzfile', 'dl_afmapfile', 'dl_urlfile', 'dl_mmciffile', 'dl_mmcifid', 'dl_mmdbid', 'dl_mmdbafid', 'dl_blast_rep_id', 'dl_yournote', 'dl_proteinname', 'dl_refseqid', 'dl_cid', 'dl_pngimage', 'dl_state', 'dl_fixedversion', 'dl_selection', 'dl_dsn6', 'dl_dsn6url', 'dl_clr', 'dl_symmetry', 'dl_symd', 'dl_contact', 'dl_hbonds', 'dl_realign', 'dl_realignbystruct', 'dl_allinteracton', 'dl_interactionsorted', 'dl_linegraph', 'dl_linegraphcolor', 'dl_scatterplot', 'dl_scatterploitcolor', 'dl_contactmap', 'dl_alignerrormap', 'dl_elecmap2fofc', 'dl_elecmapfofc', 'dl_emmap', 'dl_aroundsphere', 'dl_adjustmem', 'dl_selectplane', 'dl_addlabel', 'dl_addlabelselection', 'dl_labelColor', 'dl_distance', 'dl_stabilizer', 'dl_disttwosets', 'dl_distmanysets', 'dl_stabilizer_rm', 'dl_thickness', 'dl_thickness2', 'dl_addtrack', 'dl_addtrack_tabs', 'dl_saveselection', 'dl_copyurl', 'dl_selectannotations', 'dl_annotations_tabs', 'dl_anno_view_tabs', 'dl_annotations', 'dl_graph', 'dl_svgcolor', 'dl_area', 'dl_colorbyarea', 'dl_rmsd', 'dl_buriedarea', 'dl_propbypercentout', 'dl_propbybfactor', 'dl_legend', 'dl_disttable'];
+        let itemArray = ['dl_2ddgm', 'dl_2dctn', 'dl_alignment', 'dl_sequence2', 'dl_definedsets', 'dl_setsmenu', 'dl_command', 'dl_setoperations', 'dl_vast', 'dl_foldseek', 'dl_mmtfid', 'dl_pdbid', 'dl_afid', 'dl_opmid', 'dl_pdbfile', 'dl_pdbfile_app', 'dl_rescolorfile', 'dl_customcolor', 'dl_align', 'dl_alignaf', 'dl_chainalign', 'dl_chainalign2', 'dl_chainalign3', 'dl_mutation', 'dl_mol2file', 'dl_sdffile', 'dl_xyzfile', 'dl_afmapfile', 'dl_urlfile', 'dl_mmciffile', 'dl_mmcifid', 'dl_mmdbid', 'dl_mmdbafid', 'dl_blast_rep_id', 'dl_yournote', 'dl_proteinname', 'dl_refseqid', 'dl_cid', 'dl_pngimage', 'dl_state', 'dl_fixedversion', 'dl_selection', 'dl_dsn6', 'dl_dsn6url', 'dl_clr', 'dl_symmetry', 'dl_symd', 'dl_contact', 'dl_hbonds', 'dl_realign', 'dl_realignbystruct', 'dl_allinteracton', 'dl_interactionsorted', 'dl_linegraph', 'dl_linegraphcolor', 'dl_scatterplot', 'dl_scatterploitcolor', 'dl_contactmap', 'dl_alignerrormap', 'dl_elecmap2fofc', 'dl_elecmapfofc', 'dl_emmap', 'dl_aroundsphere', 'dl_adjustmem', 'dl_selectplane', 'dl_addlabel', 'dl_addlabelselection', 'dl_labelColor', 'dl_distance', 'dl_stabilizer', 'dl_disttwosets', 'dl_distmanysets', 'dl_stabilizer_rm', 'dl_thickness', 'dl_thickness2', 'dl_addtrack', 'dl_addtrack_tabs', 'dl_saveselection', 'dl_copyurl', 'dl_selectannotations', 'dl_annotations_tabs', 'dl_anno_view_tabs', 'dl_annotations', 'dl_graph', 'dl_svgcolor', 'dl_area', 'dl_colorbyarea', 'dl_rmsd', 'dl_buriedarea', 'dl_propbypercentout', 'dl_propbybfactor', 'dl_legend', 'dl_disttable', 'dl_translate'];
 
         for(let i in itemArray) {
             let item = itemArray[i];
@@ -70025,6 +70347,8 @@ class Transform {
     }
 
     setRotation(axis, angle) { let ic = this.icn3d, me = ic.icn3dui;
+      if(!axis) return;
+
       if(ic.bControlGl && !me.bNode && window.cam) {
           axis.applyQuaternion( window.cam.quaternion ).normalize();
       }
@@ -70089,6 +70413,25 @@ class Transform {
       if(ic.bRender) ic.drawCls.render();
     }
 
+    translateCoord(atoms, dx, dy, dz) { let ic = this.icn3d; ic.icn3dui;
+        for(let i in atoms) {
+            let atom = ic.atoms[i];
+            atom.coord.x += dx;
+            atom.coord.y += dy;
+            atom.coord.z += dz;
+        }
+    }
+
+    rotateCoord(atoms, mArray) { let ic = this.icn3d; ic.icn3dui;
+        const m = new THREE.Matrix4(); 
+        m.elements = mArray;
+
+        for(let i in atoms) {
+            let atom = ic.atoms[i];
+            atom.coord = atom.coord.applyMatrix4(m);
+        }
+    }
+
     //Center on the selected atoms and zoom in.
     zoominSelection(atoms) { let ic = this.icn3d, me = ic.icn3dui;
        let para = {};
@@ -70646,7 +70989,7 @@ class SaveFile {
 //        }
 
         // export assembly symmetry matrix "BIOMT"
-        if(ic.biomtMatrices) {
+        if(ic.biomtMatrices && Object.keys(atomHash).length == Object.keys(ic.atoms).length) {
             let stru = Object.keys(ic.structures)[0];
             for(let m = 0, ml = ic.biomtMatrices.length; m < ml; ++m) {
                 let mNum = m + 1;
@@ -74416,7 +74759,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.29.2';
+    this.REVISION = '3.29.3';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;