icn3d 3.21.3 → 3.22.0

package/icn3d.js

@@ -5986,11 +5986,23 @@ class ClickMenu {
            thisClass.setLogCmd("export pqr", true);
         });
 
-        me.myEventCls.onIds(["#" + me.pre + "delphipdbh", "#" + me.pre + "phipqr", "#" + me.pre + "phiurlpqr"], "click", async function(e) { me.icn3d; //e.preventDefault();
-            let bPdb = true;
-            await me.htmlCls.setHtmlCls.exportPqr(bPdb);
-            thisClass.setLogCmd("export pdbh", false);
-         });
+      //   me.myEventCls.onIds("#" + me.pre + "delphipqbh", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
+      //       let bPdb = true;
+      //       await me.htmlCls.setHtmlCls.exportPqr(bPdb);
+      //       thisClass.setLogCmd("export pdbh", false);
+      //    });
+
+        me.myEventCls.onIds("#" + me.pre + "profixpdb", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
+         let bHydrogen = false;
+         await ic.scapCls.exportPdbProfix(bHydrogen);
+         thisClass.setLogCmd("export pdb missing atoms", true);
+        });
+
+        me.myEventCls.onIds("#" + me.pre + "profixpdbh", "click", async function(e) { let ic = me.icn3d; //e.preventDefault();
+        let bHydrogen = true;
+        await ic.scapCls.exportPdbProfix(bHydrogen);
+        thisClass.setLogCmd("export pdb hydrogen", true);
+       });
 
         me.myEventCls.onIds("#" + me.pre + "mn1_exportStl", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
            thisClass.setLogCmd("export stl file", false);
@@ -8498,7 +8510,8 @@ class SetMenu {
         html += this.getLink('mn1_exportCounts', 'Residue Counts', undefined, 2);
 
         html += this.getLink('mn1_exportPdbRes', 'PDB', 1, 2);
-        html += this.getLink('delphipdbh', 'PDB with Hydrogens', undefined, 2);
+        html += this.getLink('profixpdb', 'PDB with Missing Atoms', undefined, 2);
+        html += this.getLink('profixpdbh', 'PDB with Hydrogens', undefined, 2);
 
         if(me.cfg.cid === undefined) {
             html += this.getLink('mn1_exportSecondary', 'Secondary Structure', undefined, 2);
@@ -10907,11 +10920,14 @@ class SetDialog {
 
         html += me.htmlCls.divStr + "dl_realignbystruct' class='" + dialogClass + "'>";
 
-        html += me.htmlCls.divNowrapStr + "1. Select sets in two chains below <br>or use your current selection:</div><br>";
+        html += me.htmlCls.divNowrapStr + "<b>1</b>. Select sets in two chains below <br>or use your current selection:</div><br>";
         html += "<div style='text-indent:1.1em'><select id='" + me.pre + "atomsCustomRealignByStruct' multiple size='5' style='min-width:130px;'>";
         html += "</select></div><br>";
 
-        html += "<div>2. " + me.htmlCls.buttonStr + "applyRealignByStruct_tmalign'>Realign with TM-align</button>" + me.htmlCls.buttonStr + "applyRealignByStruct' style='margin-left:30px'>Realign with VAST</button></div><br>";
+        html += "<div><b>2a</b>. <div style='display:inline-block; width:80px'>MSA:</div> " + me.htmlCls.buttonStr + "applyRealignByStructMsa_tmalign'>Realign with TM-align</button>" + me.htmlCls.buttonStr + "applyRealignByStructMsa' style='margin-left:30px'>Realign with VAST</button></div><br>";
+
+        html += "<div>or <b>2b</b>. <div style='display:inline-block; width:65px'>Pairwise:</div> " + me.htmlCls.buttonStr + "applyRealignByStruct_tmalign'>Realign with TM-align</button>" + me.htmlCls.buttonStr + "applyRealignByStruct' style='margin-left:30px'>Realign with VAST</button></div><br>";
+
         html += "</div>";
 
         html += me.htmlCls.divStr + "dl_realigntwostru' class='" + dialogClass + "'>";
@@ -11584,6 +11600,32 @@ class Events {
        thisClass.setLogCmd('select ' + select + ' | name ' + commandname, true);
     }
 
+    async setRealign(alignType, bMsa) { let me = this.icn3dui, ic = me.icn3d, thisClass = this;
+        let nameArray = $("#" + me.pre + "atomsCustomRealignByStruct").val();
+        if(nameArray.length > 0) {
+            ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
+        }
+
+        me.cfg.aligntool = alignType;
+
+        if(bMsa) {
+            await ic.realignParserCls.realignOnStructAlignMsa(nameArray);
+        }
+        else {
+            await ic.realignParserCls.realignOnStructAlign();
+        }
+
+        let alignStr = (alignType == 'vast') ? 'structure align' : 'tmalign';
+        alignStr += (bMsa) ? ' msa' : '';
+
+        if(nameArray.length > 0) {
+            thisClass.setLogCmd("realign on " + alignStr + " | " + nameArray, true);
+        }
+        else {
+            thisClass.setLogCmd("realign on " + alignStr, true);
+        }
+    }
+
     readFile(bAppend, files, index, dataStrAll) { let me = this.icn3dui, ic = me.icn3d, thisClass = this;
         let file = files[index];
         let commandName = (bAppend) ? 'append': 'load';
@@ -11894,42 +11936,32 @@ class Events {
            }
         });
 
-        me.myEventCls.onIds("#" + me.pre + "applyRealignByStruct", "click", async function(e) { let ic = me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "applyRealignByStruct", "click", async function(e) { me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
-            let nameArray = $("#" + me.pre + "atomsCustomRealignByStruct").val();
-            if(nameArray.length > 0) {
-                ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
-            }
- 
-            me.cfg.aligntool = 'vast';
- 
-            await ic.realignParserCls.realignOnStructAlign();
-            if(nameArray.length > 0) {
-                thisClass.setLogCmd("realign on structure align | " + nameArray, true);
-            }
-            else {
-                thisClass.setLogCmd("realign on structure align", true);
-            }
+
+            await thisClass.setRealign('vast', false);
          });
 
-         me.myEventCls.onIds("#" + me.pre + "applyRealignByStruct_tmalign", "click", async function(e) { let ic = me.icn3d;
+         me.myEventCls.onIds("#" + me.pre + "applyRealignByStruct_tmalign", "click", async function(e) { me.icn3d;
             e.preventDefault();
             if(!me.cfg.notebook) dialog.dialog( "close" );
-            let nameArray = $("#" + me.pre + "atomsCustomRealignByStruct").val();
-            if(nameArray.length > 0) {
-                ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
-            }
 
-            me.cfg.aligntool = 'tmalign';
- 
-            await ic.realignParserCls.realignOnStructAlign();
-            if(nameArray.length > 0) {
-                thisClass.setLogCmd("realign on tmalign | " + nameArray, true);
-            }
-            else {
-                thisClass.setLogCmd("realign on tmalign", true);
-            }
+            await thisClass.setRealign('tmalign', false);
+         });
+
+         me.myEventCls.onIds("#" + me.pre + "applyRealignByStructMsa", "click", async function(e) { me.icn3d;
+            e.preventDefault();
+            if(!me.cfg.notebook) dialog.dialog( "close" );
+
+            await thisClass.setRealign('vast', true);
+         });
+
+         me.myEventCls.onIds("#" + me.pre + "applyRealignByStructMsa_tmalign", "click", async function(e) { me.icn3d;
+            e.preventDefault();
+            if(!me.cfg.notebook) dialog.dialog( "close" );
+
+            await thisClass.setRealign('tmalign', true);
          });
 
          me.myEventCls.onIds("#" + me.pre + "applyRealignByStruct_vastplus", "click", async function(e) { let ic = me.icn3d;
@@ -34014,7 +34046,7 @@ class AnnoCddSite {
     
                     let linkStr = (bCoordinates) ? 'icn3d-link icn3d-blue' : '';
 
-                    let htmlTmp2 = '<div class="icn3d-seqTitle ' + linkStr + '" site="site" posarray="' + adjustedResPosArray.toString() + '" shorttitle="' + title + '" setname="' + chnid + '_site_' + index + '" anno="sequence" chain="' + chnid + '" title="' + fulltitle + '">' + title + ' </div>';
+                    let htmlTmp2 = '<div class="icn3d-seqTitle ' + linkStr + '" site="site" posarray="' + resPosArray.toString() + '" shorttitle="' + title + '" setname="' + chnid + '_site_' + index + '" anno="sequence" chain="' + chnid + '" title="' + fulltitle + '">' + title + ' </div>';
                     let htmlTmp3 = '<span class="icn3d-residueNum" title="residue count">' + resCnt.toString() + ' Res</span>';
                     let htmlTmp = '<span class="icn3d-seqLine">';
                     html3 += htmlTmp2 + htmlTmp3 + '<br>';
@@ -34186,8 +34218,9 @@ class AnnoCddSite {
                     let from = parseInt(fromArray[i]), to = parseInt(toArray[i]);
                                        
                     for(let j = from; j <= to; ++j) {
-                        
-                        let resid = chnid + "_" + j;
+                        let resi = ic.ParserUtilsCls.getResi(chnid, j);
+                        //let resid = chnid + "_" + j;
+                        let resid = chnid + "_" + resi;
                         
                         if(ic.residues.hasOwnProperty(resid)) {
                             bCoordinates = true;
@@ -41114,7 +41147,9 @@ class LineGraph {
         nodeArray2 = nodeArrays.nodeArray2;
         ic.lineGraphStr = '{\n';
 
-        let structureArray = ic.resid2specCls.atoms2structureArray(ic.hAtoms);
+        //let structureArray = ic.resid2specCls.atoms2structureArray(ic.hAtoms);
+        let structureArray = Object.keys(ic.structures);
+
         //if(Object.keys(ic.structures).length > 1) {
         if(structureArray.length > 1) {
 
@@ -41882,6 +41917,7 @@ class GetGraph {
 
     updateGraphColor() { let ic = this.icn3d, me = ic.icn3dui;
       // change graph color
+
       if(ic.graphStr !== undefined) {
           let graphJson = JSON.parse(ic.graphStr);
           let resid2color = {};
@@ -44545,7 +44581,8 @@ class ChainalignParser {
         }
     }
 
-    async downloadChainalignmentPart2b(chainresiCalphaHash2, chainidArray, hAtoms, dataArray, indexArray, mmdbid_t, struArray) { let ic = this.icn3d, me = ic.icn3dui;
+    async downloadChainalignmentPart2b(chainresiCalphaHash2, chainidArray, hAtoms, dataArray, 
+        indexArray, mmdbid_t, struArray) { let ic = this.icn3d, me = ic.icn3dui;
         //let bTargetTransformed = (ic.qt_start_end[0]) ? true : false;
 
         // modify the previous trans and rotation matrix
@@ -45076,11 +45113,16 @@ class ChainalignParser {
                 if(ic.afChainIndexHash.hasOwnProperty(index)) {
                     ++missedChainCnt;
 
-                    // need to pass C-alpha coords and get transformation matrix from backend
-                    ic.t_trans_add[index-1] = {"x":0, "y":0, "z":0};
-                    ic.q_trans_sub[index-1] = {"x":0, "y":0, "z":0};
+                    
 
-                    if(me.cfg.aligntool == 'tmalign') ic.q_trans_add[index-1] = {"x":0, "y":0, "z":0};
+                    if(me.cfg.aligntool == 'tmalign') {
+                        ic.q_trans_add[index-1] = {"x":0, "y":0, "z":0};
+                    }
+                    else {
+                        // need to pass C-alpha coords and get transformation matrix from backend
+                        ic.t_trans_add[index-1] = {"x":0, "y":0, "z":0};
+                        ic.q_trans_sub[index-1] = {"x":0, "y":0, "z":0};
+                    }
 
                     ic.q_rotation[index-1] = {"x1":1, "y1":0, "z1":0, "x2":0, "y2":1, "z2":0, "x3":0, "y3":0, "z3":1};
                     ic.qt_start_end[index-1] = undefined;
@@ -45137,10 +45179,14 @@ class ChainalignParser {
                 ic.q_rotation.push(align[0].q_rotation);
                 ic.qt_start_end.push(align[0].segs);
                 */
-                ic.t_trans_add[index] = align[0].t_trans_add;
-                ic.q_trans_sub[index] = align[0].q_trans_sub;
 
-                if(me.cfg.aligntool == 'tmalign') ic.q_trans_add[index] = align[0].q_trans_add;
+                if(me.cfg.aligntool == 'tmalign') {
+                    ic.q_trans_add[index] = align[0].q_trans_add;
+                }
+                else {
+                    ic.t_trans_add[index] = align[0].t_trans_add;
+                    ic.q_trans_sub[index] = align[0].q_trans_sub;
+                }
 
                 ic.q_rotation[index] = align[0].q_rotation;
                 ic.qt_start_end[index] = align[0].segs;
@@ -47911,6 +47957,8 @@ class RealignParser {
         let ajaxArray = [], chainidPairArray = [];
         let urlalign = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi";
         let urltmalign = me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
+
+        //let cnt = 0;
         let structArray = Object.keys(struct2domain);
         for(let s = 0, sl = structArray.length; s < sl; ++s) {
             let struct1 = structArray[s];
@@ -47923,13 +47971,13 @@ class RealignParser {
 
                 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 j = 0, jl = chainidArray2.length; j < jl; ++j) {
                         let chainid2 = chainidArray2[j];
 
                         let alignAjax;
 
                         if(me.cfg.aligntool != 'tmalign') {
-                            let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(struct2domain[struct1][chainid1]);
                             let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(struct2domain[struct2][chainid2]);
                         
                             let dataObj = {'domains1': jsonStr_q, 'domains2': jsonStr_t};
@@ -47947,7 +47995,8 @@ class RealignParser {
                         }
 
                         ajaxArray.push(alignAjax);
-                        chainidPairArray.push(chainid1 + ',' + chainid2); // chainid2 is target
+                        chainidPairArray.push(chainid1 + ',' + chainid2); 
+                        //++cnt;
                     }
                 }
             }
@@ -47964,6 +48013,87 @@ class RealignParser {
         }                   
     }
 
+    async realignOnStructAlignMsa(nameArray) { let ic = this.icn3d, me = ic.icn3dui;
+        // each 3D domain should have at least 3 secondary structures
+        let minSseCnt = 3;
+        let chainid2domain = {};
+
+        for(let i = 0, il = nameArray.length; i < il; ++i) {
+            let chainid = nameArray[i];
+            let atoms = me.hashUtilsCls.intHash(ic.hAtoms, ic.chains[chainid]);               
+            let sseCnt = 0;
+            for(let serial in atoms) {
+                if(ic.atoms[serial].ssbegin) ++sseCnt;
+                if(sseCnt == minSseCnt) {
+                    chainid2domain[chainid] = atoms;
+                    break;
+                }
+            }
+        }
+
+        let ajaxArray = [], indexArray = [], struArray = [];
+        let urlalign = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi";
+        let urltmalign = me.htmlCls.baseUrl + "tmalign/tmalign.cgi";
+
+        let chainid1 = nameArray[0];
+        let struct1 = chainid1.substr(0, chainid1.indexOf('_'));
+        let jsonStr_t = ic.domain3dCls.getDomainJsonForAlign(chainid2domain[chainid1]);
+
+        for(let i = 1, il = nameArray.length; i < il; ++i) {
+            let chainid2 = nameArray[i];
+            let struct2 = chainid2.substr(0, chainid2.indexOf('_'));
+
+            let alignAjax;
+
+            if(me.cfg.aligntool != 'tmalign') {
+                let jsonStr_q = ic.domain3dCls.getDomainJsonForAlign(chainid2domain[chainid2]);
+            
+                let dataObj = {'domains1': jsonStr_q, 'domains2': jsonStr_t};
+                alignAjax = me.getAjaxPostPromise(urlalign, dataObj);
+            }
+            else {
+                // let pdb_target = ic.saveFileCls.getAtomPDB(chainid2domain[chainid1], undefined, undefined, undefined, undefined, struct1);
+                // let pdb_query = ic.saveFileCls.getAtomPDB(chainid2domain[chainid2], undefined, undefined, undefined, undefined, struct2);
+
+                let pdb_target = ic.saveFileCls.getAtomPDB(ic.chains[chainid1], undefined, undefined, undefined, undefined, struct1);
+                let pdb_query = ic.saveFileCls.getAtomPDB(ic.chains[chainid2], undefined, undefined, undefined, undefined, struct2);
+
+                let dataObj = {'pdb_query': pdb_query, 'pdb_target': pdb_target};
+                alignAjax = me.getAjaxPostPromise(urltmalign, dataObj);                    
+            }
+
+            ajaxArray.push(alignAjax);
+            //chainidPairArray.push(chainid1 + ',' + chainid2); 
+
+            indexArray.push(i - 1);
+            struArray.push(struct2);
+
+            //++cnt;
+        }
+
+        let allPromise = Promise.allSettled(ajaxArray);
+        //try {
+            let dataArray = await allPromise;
+            //ic.qt_start_end = []; // reset the alignment
+            //await ic.chainalignParserCls.downloadChainalignmentPart2bRealignMsa(dataArray, chainidPairArray); 
+
+            // set trans and rotation matrix
+            ic.t_trans_add = [];
+            ic.q_trans_sub = [];
+
+            if(me.cfg.aligntool == 'tmalign') ic.q_trans_add = [];
+
+            ic.q_rotation = [];
+            ic.qt_start_end = [];
+
+            await ic.chainalignParserCls.downloadChainalignmentPart2b(undefined, nameArray, undefined, dataArray, 
+                indexArray, struct1, struArray);
+        // }
+        // catch(err) {
+        //     if(ic.bRender) var aaa = 1; //alert("These structures can NOT be aligned to each other...");
+        // }                   
+    }
+
     async realignChainOnSeqAlign(chainresiCalphaHash2, chainidArray, bRealign, bPredefined) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
@@ -53807,6 +53937,12 @@ class ApplyCommand {
       else if(command == 'export pdb') {
          me.htmlCls.setHtmlCls.exportPdb();
       }
+      else if(command == 'export pdb missing atoms') {
+        await ic.scapCls.exportPdbProfix(false);
+      }
+      else if(command == 'export pdb hydrogen') {
+        await ic.scapCls.exportPdbProfix(true);
+      }
       else if(command == 'export secondary structure') {
          me.htmlCls.setHtmlCls.exportSecondary();
       }
@@ -56197,6 +56333,17 @@ class LoadScript {
         await this.execCommandsBase(start, end, steps);
     }
 
+    getNameArray(command) { let ic = this.icn3d; ic.icn3dui;
+        let paraArray = command.split(' | ');
+        let nameArray = [];
+        if(paraArray.length == 2) {
+            nameArray = paraArray[1].split(',');
+            ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
+        }
+
+        return nameArray;
+    }
+
     async execCommandsBase(start, end, steps, bFinalStep) { let ic = this.icn3d, me = ic.icn3dui;
       let thisClass = this;
       let i;
@@ -56338,31 +56485,37 @@ class LoadScript {
             await ic.scapCls.applyCommandScap(command);
           }
           else if(command.indexOf('realign on seq align') == 0) {
-            let paraArray = command.split(' | ');
-            if(paraArray.length == 2) {
-                let nameArray = paraArray[1].split(',');
-                ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
-            }
+            this.getNameArray(command);
 
             await thisClass.applyCommandRealign(command);
           }
+          else if(command.indexOf('realign on structure align msa') == 0) {
+            let nameArray = this.getNameArray(command);
+
+            me.cfg.aligntool = 'vast';
+
+            await ic.realignParserCls.realignOnStructAlignMsa(nameArray);
+          }
           else if(command.indexOf('realign on structure align') == 0) {
-            let paraArray = command.split(' | ');
-            if(paraArray.length == 2) {
-                let nameArray = paraArray[1].split(',');
-                ic.hAtoms = ic.definedSetsCls.getAtomsFromNameArray(nameArray);
-            }
+            this.getNameArray(command);
 
             me.cfg.aligntool = 'vast';
 
-            await thisClass.applyCommandRealignByStruct(command);
+            await ic.realignParserCls.realignOnStructAlign();
+          }
+          else if(command.indexOf('realign on tmalign msa') == 0) {
+            let nameArray = this.getNameArray(command);
+
+            me.cfg.aligntool = 'tmalign';
+
+            await ic.realignParserCls.realignOnStructAlignMsa(nameArray);
           }
           else if(command.indexOf('realign on tmalign') == 0) {
-            thisClass.getHAtoms(ic.commands[i]);
+            this.getNameArray(command);
 
             me.cfg.aligntool = 'tmalign';
 
-            await thisClass.applyCommandRealignByStruct(ic.commands[i]);
+            await ic.realignParserCls.realignOnStructAlign();
           }
           else if(command.indexOf('realign on vastplus') == 0) {
             thisClass.getHAtoms(ic.commands[i]);
@@ -59831,11 +59984,12 @@ console.log("free energy: " + energy + " kcal/mol");
 
           // get the full mutatnt PDB
           let pdbDataMutant = ic.saveFileCls.getAtomPDB(ic.atoms, false, false, false, chainResi2pdb);
+
           ic.hAtoms = {};
           let bMutation = true;
           ic.loadPDBCls.loadPDB(pdbDataMutant, pdbid, false, false, bMutation, bAddition);
           //let allAtoms2 = me.hashUtilsCls.cloneHash(ic.hAtoms);
-          
+
           ic.setStyleCls.setAtomStyleByOptions(ic.opts);
           ic.setColorCls.setColorByOptions(ic.opts, ic.hAtoms);
 
@@ -59890,11 +60044,10 @@ console.log("free energy: " + energy + " kcal/mol");
           }
 
           if(bPdb) {
-              //let pdbStr = '';
-              //pdbStr += ic.saveFileCls.getAtomPDB(ic.hAtoms);
+              // let file_pref =(ic.inputid) ? ic.inputid : "custom";
+              // ic.saveFileCls.saveFile(file_pref + '_' + snpStr + '.pdb', 'text', [pdbDataMutant]);
 
-              let file_pref =(ic.inputid) ? ic.inputid : "custom";
-              ic.saveFileCls.saveFile(file_pref + '_' + snpStr + '.pdb', 'text', [pdbDataMutant]);
+              await thisClass.exportPdbProfix(false, pdbDataMutant, snpStr); 
 
               ic.drawCls.draw();
           }
@@ -59945,7 +60098,40 @@ console.log("free energy: " + energy + " kcal/mol");
 
             /// if(ic.deferredScap !== undefined) ic.deferredScap.resolve();
             return;
-        }    }
+        }
+    }
+
+    async exportPdbProfix(bHydrogen, pdb, snpStr) { let ic = this.icn3d, me = ic.icn3dui;
+      let pdbStr;
+
+      if(pdb) {
+        pdbStr = pdb;
+      }
+      else {
+        let atoms = me.hashUtilsCls.intHash(ic.dAtoms, ic.hAtoms);
+        pdbStr += ic.saveFileCls.getAtomPDB(atoms);
+      }
+
+      let url = me.htmlCls.baseUrl + "scap/scap.cgi";
+      let hydrogenStr = (bHydrogen) ? '1' : '0';
+      let dataObj = {'pdb': pdbStr, 'profix': '1', 'hydrogen': hydrogenStr};
+
+      let data;
+       
+      try {
+        data = await me.getAjaxPostPromise(url, dataObj, undefined, undefined, undefined, undefined, 'text');
+      }
+      catch(err) {
+        var aaa = 1; //alert("There are some problems in adding missing atoms or hydrogens...");
+        return;
+      }
+
+      let file_pref =(ic.inputid) ? ic.inputid : "custom";
+      let postfix = (bHydrogen) ? "add_hydrogen" : "add_missing_atoms";
+      if(snpStr) postfix = snpStr;
+
+      ic.saveFileCls.saveFile(file_pref + '_icn3d_' + postfix + '.pdb', 'text', [data]);
+   }
 }
 
 /**
@@ -63789,10 +63975,11 @@ class SaveFile {
         }
 
 //        if(!bNoSs) {
-            let prevResi, stru;
+            let prevResi, stru, chainid;
             for(let i in calphaHash) {
                 let atom = ic.atoms[i];
                 stru = atom.structure;
+                chainid = atom.structure + '_' + atom.chain;
 
                 if(atom.ssbegin) {
                     if(atom.ss == 'helix') {
@@ -63813,7 +64000,9 @@ class SaveFile {
                 if(atom.ssend) {
                     if(atom.ss == 'helix') {
                         bHelixEnd = true;
-                        let helixLen = ic.resid2ncbi[atom.resi] - ic.resid2ncbi[prevResi];
+                        let residEnd = ic.resid2ncbi[chainid + '_' + atom.resi];
+                        let residStart = ic.resid2ncbi[chainid + '_' + prevResi];
+                        let helixLen = (residEnd && residStart) ? parseInt(residEnd.substr(residEnd.lastIndexOf('_') + 1)) - parseInt(residStart.substr(residStart.lastIndexOf('_') + 1)) : 0;
                         let helixType = 1;
                         if(bHelixBegin) stru2header[stru] += atom.resn.padStart(5, ' ') + atom.chain.replace(/_/gi, '').substr(0, 2).padStart(2, ' ')
                             + atom.resi.toString().padStart(5, ' ') + '  ' + helixType + helixLen.toString().padStart(36, ' ') + '\n';
@@ -63894,7 +64083,7 @@ class SaveFile {
             }
 
             let chainResi = atom.chain + '_' + atom.resi;
-            if(chainResi2pdb && chainResi2pdb.hasOwnProperty(chainResi)) {
+            if(chainResi2pdb && chainResi2pdb.hasOwnProperty(chainResi)) {    
                 if(!addedChainResiHash.hasOwnProperty(chainResi)) {
                     pdbStr += chainResi2pdb[chainResi];
                     addedChainResiHash[chainResi] = 1;
@@ -64059,7 +64248,7 @@ class SaveFile {
         }
 
         pdbStr += connStr;
-
+        
         if(bMulStruc) pdbStr += '\nENDMDL\n';
 
         return pdbStr;
@@ -67451,7 +67640,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.21.3';
+    this.REVISION = '3.22.0';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;