icn3d 3.31.2 → 3.31.4

package/icn3d.module.js

@@ -3570,20 +3570,20 @@ THREE.OrthographicTrackballControls.prototype = Object.create( THREE.EventDispat
 THREE.OrthographicTrackballControls.prototype.constructor = THREE.OrthographicTrackballControls;
 
 
-; var __CIFTools = function () {
-  'use strict';
+// ; var __CIFTools = function () {
+//   'use strict';
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
 var CIFTools;
 (function (CIFTools) {
     CIFTools.VERSION = { number: "1.1.7", date: "Oct 30 2018" };
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
+// var CIFTools;
+// (function (CIFTools) {
     var Utils;
     (function (Utils) {
         var ChunkedArray;
@@ -3721,7 +3721,7 @@ var CIFTools;
             ChunkedArray.create = create;
         })(ChunkedArray = Utils.ChunkedArray || (Utils.ChunkedArray = {}));
     })(Utils = CIFTools.Utils || (CIFTools.Utils = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
@@ -3731,9 +3731,9 @@ var CIFTools;
  * For the purposes of parsing numbers from the mmCIF data representations,
  * up to 4 times faster than JS parseInt/parseFloat.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Utils;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Utils;
     (function (Utils) {
         var FastNumberParsers;
         (function (FastNumberParsers) {
@@ -3813,13 +3813,13 @@ var CIFTools;
             FastNumberParsers.parseFloat = parseFloat;
         })(FastNumberParsers = Utils.FastNumberParsers || (Utils.FastNumberParsers = {}));
     })(Utils = CIFTools.Utils || (CIFTools.Utils = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Utils;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Utils;
     (function (Utils) {
         var __paddingSpaces = [];
         (function () {
@@ -3962,13 +3962,13 @@ var CIFTools;
             StringWriter.writeFloatPadRight = writeFloatPadRight;
         })(StringWriter = Utils.StringWriter || (Utils.StringWriter = {}));
     })(Utils = CIFTools.Utils || (CIFTools.Utils = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    "use strict";
+// var CIFTools;
+// (function (CIFTools) {
+//     "use strict";
     /**
      * Represents a column that is not present.
      */
@@ -4028,13 +4028,13 @@ var CIFTools;
         }
         Category.getVector = getVector;
     })(Category = CIFTools.Category || (CIFTools.Category = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    "use strict";
+// var CIFTools;
+// (function (CIFTools) {
+//     "use strict";
     var ParserResult;
     (function (ParserResult) {
         function error(message, line) {
@@ -4072,7 +4072,7 @@ var CIFTools;
         return ParserSuccess;
     }());
     CIFTools.ParserSuccess = ParserSuccess;
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
@@ -4116,8 +4116,8 @@ var CIFTools;
     in memory that is very efficient, fast and introduces a very minimal overhead.
 
  */
-var CIFTools;
-(function (CIFTools) {
+// var CIFTools;
+// (function (CIFTools) {
     var Text;
     (function (Text) {
         "use strict";
@@ -4341,13 +4341,13 @@ var CIFTools;
         }());
         Text.Column = Column;
     })(Text = CIFTools.Text || (CIFTools.Text = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Text;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Text;
     (function (Text) {
         "use strict";
         var TokenIndexBuilder;
@@ -4861,13 +4861,13 @@ var CIFTools;
         }
         Text.parse = parse;
     })(Text = CIFTools.Text || (CIFTools.Text = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Text;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Text;
     (function (Text) {
         "use strict";
         var StringWriter = CIFTools.Utils.StringWriter;
@@ -5107,12 +5107,12 @@ var CIFTools;
             }
         }
     })(Text = CIFTools.Text || (CIFTools.Text = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
+// var CIFTools;
+// (function (CIFTools) {
     var Binary;
     (function (Binary) {
         var MessagePack;
@@ -5328,13 +5328,13 @@ var CIFTools;
             MessagePack.decode = decode;
         })(MessagePack = Binary.MessagePack || (Binary.MessagePack = {}));
     })(Binary = CIFTools.Binary || (CIFTools.Binary = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Binary;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Binary;
     (function (Binary) {
         var MessagePack;
         (function (MessagePack) {
@@ -5622,13 +5622,13 @@ var CIFTools;
             }
         })(MessagePack = Binary.MessagePack || (Binary.MessagePack = {}));
     })(Binary = CIFTools.Binary || (CIFTools.Binary = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Binary;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Binary;
     (function (Binary) {
         var MessagePack;
         (function (MessagePack) {
@@ -5748,13 +5748,13 @@ var CIFTools;
             MessagePack.utf8ByteCount = utf8ByteCount;
         })(MessagePack = Binary.MessagePack || (Binary.MessagePack = {}));
     })(Binary = CIFTools.Binary || (CIFTools.Binary = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Binary;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Binary;
     (function (Binary) {
         "use strict";
         /**
@@ -5956,13 +5956,13 @@ var CIFTools;
             }
         })(Decoder || (Decoder = {}));
     })(Binary = CIFTools.Binary || (CIFTools.Binary = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Binary;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Binary;
     (function (Binary) {
         "use strict";
         var File = /** @class */ (function () {
@@ -6120,13 +6120,13 @@ var CIFTools;
             return MaskedStringColumn;
         }());
     })(Binary = CIFTools.Binary || (CIFTools.Binary = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Binary;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Binary;
     (function (Binary) {
         "use strict";
         /**
@@ -6486,13 +6486,13 @@ var CIFTools;
             Encoder.stringArray = stringArray;
         })(Encoder = Binary.Encoder || (Binary.Encoder = {}));
     })(Binary = CIFTools.Binary || (CIFTools.Binary = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Binary;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Binary;
     (function (Binary) {
         "use strict";
         Binary.VERSION = '0.3.0';
@@ -6527,13 +6527,13 @@ var CIFTools;
             Encoding.isSignedIntegerDataType = isSignedIntegerDataType;
         })(Encoding = Binary.Encoding || (Binary.Encoding = {}));
     })(Binary = CIFTools.Binary || (CIFTools.Binary = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Binary;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Binary;
     (function (Binary) {
         "use strict";
         function checkVersions(min, current) {
@@ -6560,13 +6560,13 @@ var CIFTools;
         }
         Binary.parse = parse;
     })(Binary = CIFTools.Binary || (CIFTools.Binary = {}));
-})(CIFTools || (CIFTools = {}));
+// })(CIFTools || (CIFTools = {}));
 /*
  * Copyright (c) 2016 - now David Sehnal, licensed under MIT License, See LICENSE file for more info.
  */
-var CIFTools;
-(function (CIFTools) {
-    var Binary;
+// var CIFTools;
+// (function (CIFTools) {
+//     var Binary;
     (function (Binary) {
         "use strict";
         function encodeField(field, data, totalCount) {
@@ -6669,17 +6669,17 @@ var CIFTools;
         }());
         Binary.Writer = Writer;
     })(Binary = CIFTools.Binary || (CIFTools.Binary = {}));
-})(CIFTools || (CIFTools = {}));
-  return CIFTools;
-}
-if (typeof module === 'object' && typeof module.exports === 'object') {
-  module.exports = __CIFTools();
-} else if (typeof define === 'function' && define.amd) {
-  define(['require'], function(require) { return __CIFTools(); })
-} else {
-  var __target = !!window ? window : this;
-  __target.CIFTools = __CIFTools();
-}
+ })(CIFTools || (CIFTools = {}));
+//   return CIFTools;
+// }
+// if (typeof module === 'object' && typeof module.exports === 'object') {
+//   module.exports = __CIFTools();
+// } else if (typeof define === 'function' && define.amd) {
+//   define(['require'], function(require) { return __CIFTools(); })
+// } else {
+//   var __target = !!window ? window : this;
+//   __target.CIFTools = __CIFTools();
+// }
 
 
 /*
@@ -17826,7 +17826,6 @@ class Events {
                 thisClass.setLogCmd('load mmcif file ' + $("#" + me.pre + "mmciffile").val(), false);
                 ic.molTitle = "";
 
-                /*
                 // let url = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi";
                 // //ic.bCid = undefined;
 
@@ -17844,19 +17843,6 @@ class Events {
                 ic.InputfileType = 'mmcif';
                 // await ic.mmcifParserCls.loadMmcifData(data); 
                 await ic.opmParserCls.loadOpmData(dataStr, undefined, undefined, 'mmcif', undefined, bText);
-                */
-
-                let url = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi";
-
-                let dataObj = {'mmciffile': dataStr};
-                let data = await me.getAjaxPostPromise(url, dataObj, true);
-
-                //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); 
              };
              reader.readAsText(file);
            }
@@ -42086,7 +42072,7 @@ class AnnoIg {
 
             let igType = (parseFloat(tmscore) < ic.refnumCls.TMThreshold ) ? 'Ig' : ic.ref2igtype[info.refpdbname];
             titleArray.push(igType + ' (TM:' + parseFloat(tmscore).toFixed(2) + ')');
-            fullTitleArray.push(igType + ' (TM:' + parseFloat(tmscore).toFixed(2) + '), template: ' + info.refpdbname + ', type: ' + ic.ref2igtype[info.refpdbname] + ' Seq. identity: ' + parseFloat(info.seqid).toFixed(2) + ', aligned residues: ' + info.nresAlign);
+            fullTitleArray.push(igType + ' (TM:' + parseFloat(tmscore).toFixed(2) + '), template: ' + info.refpdbname + ', type: ' + ic.ref2igtype[info.refpdbname] + ', Seq. identity: ' + parseFloat(info.seqid).toFixed(2) + ', aligned residues: ' + info.nresAlign);
 
             domainArray.push(igType);
 
@@ -55383,7 +55369,6 @@ class MmcifParser {
         let url = "https://files.rcsb.org/download/" + mmcifid + ".cif";
         let data = await me.getAjaxPromise(url, 'text', true);
 
-        /*
         // url = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi";
         // let dataObj = {'mmciffile': data};
         // let data2 = await me.getAjaxPostPromise(url, dataObj, true);
@@ -55396,13 +55381,6 @@ class MmcifParser {
 
         // await this.loadMmcifData(bcifJson, mmcifid);
         await ic.opmParserCls.loadOpmData(data, mmcifid, undefined, 'mmcif', undefined, bText);
-        */
-
-        url = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi";
-        let dataObj = {'mmciffile': data};
-        let data2 = await me.getAjaxPostPromise(url, dataObj, true);
-
-        await this.loadMmcifData(data2, mmcifid);
     }
 
     async downloadMmcifSymmetry(mmcifid, type) { let ic = this.icn3d, me = ic.icn3dui;
@@ -56097,8 +56075,6 @@ class BcifParser {
         await ic.opmParserCls.loadOpmData(bcifArrayBuffer, bcifid, undefined, 'bcif', undefined, bText);
     }
 
-    // For text mmCIF file, CIFTools library does not support atom_site.getColumn("Cartn_x").data,
-    // but just support atom_site.getColumn("Cartn_x").getFloat(i). So do not use "bText = true" for now.
     getBcifJson(bcifData, bcifid, bText, bNoCoord) { let ic = this.icn3d, me = ic.icn3dui;
         let text = "";
 
@@ -56161,25 +56137,25 @@ class BcifParser {
             // 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").data;
+            let conf_type_idArray = struct_conf.getColumn("conf_type_id");
 
-            let chain1Array = struct_conf.getColumn("beg_auth_asym_id").data;
-            let resi1Array = struct_conf.getColumn("beg_label_seq_id").data;
+            let chain1Array = struct_conf.getColumn("beg_auth_asym_id");
+            let resi1Array = struct_conf.getColumn("beg_label_seq_id");
 
-            let chain2Array = struct_conf.getColumn("end_auth_asym_id").data;
-            let resi2Array = struct_conf.getColumn("end_label_seq_id").data;
+            let chain2Array = struct_conf.getColumn("end_auth_asym_id");
+            let resi2Array = struct_conf.getColumn("end_label_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[i];
+                let conf_type_id = conf_type_idArray.getString(i);
 
-                let chain1 = chain1Array[i];
-                let resi1 = resi1Array[i];
+                let chain1 = chain1Array.getString(i);
+                let resi1 = resi1Array.getString(i);
                 let id1 = chain1 + "_" + resi1;
 
-                let chain2 = chain2Array[i];
-                let resi2 = resi2Array[i];
+                let chain2 = chain2Array.getString(i);
+                let resi2 = resi2Array.getString(i);
                 let id2 = chain2 + "_" + resi2;
 
                 let ss;
@@ -56211,23 +56187,23 @@ class BcifParser {
             // 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").data;
-            let resi1Array = struct_sheet_range.getColumn("beg_label_seq_id").data;
+            let chain1Array = struct_sheet_range.getColumn("beg_auth_asym_id");
+            let resi1Array = struct_sheet_range.getColumn("beg_label_seq_id");
 
-            let chain2Array = struct_sheet_range.getColumn("end_auth_asym_id").data;
-            let resi2Array = struct_sheet_range.getColumn("end_label_seq_id").data;
+            let chain2Array = struct_sheet_range.getColumn("end_auth_asym_id");
+            let resi2Array = struct_sheet_range.getColumn("end_label_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 chain1 = chain1Array[i];
-                let resi1 = resi1Array[i];
+                let chain1 = chain1Array.getString(i);
+                let resi1 = resi1Array.getString(i);
                 let id1 = chain1 + "_" + resi1;
 
                 sSSBegin[id1] = 1;
 
-                let chain2 = chain2Array[i];
-                let resi2 = resi2Array[i];
+                let chain2 = chain2Array.getString(i);
+                let resi2 = resi2Array.getString(i);
                 let id2 = chain2 + "_" + resi2;
 
                 sSSEnd[id2] = 1;
@@ -56252,28 +56228,28 @@ class BcifParser {
             // 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").data;
+            let conn_type_idArray = struct_conn.getColumn("conn_type_id");
 
-            let chain1Array = struct_conn.getColumn("ptnr1_auth_asym_id").data;
-            let name1Array = struct_conn.getColumn("ptnr1_label_atom_id").data;
-            let resi1Array = struct_conn.getColumn("ptnr1_label_seq_id").data;
+            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").data;
-            let name2Array = struct_conn.getColumn("ptnr2_label_atom_id").data;
-            let resi2Array = struct_conn.getColumn("ptnr2_label_seq_id").data;
+            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[i];
+                let conn_type_id = conn_type_idArray.getString(i);
 
-                let chain1 = chain1Array[i];
-                let name1 = name1Array[i];
-                let resi1 = resi1Array[i];
+                let chain1 = chain1Array.getString(i);
+                let name1 = name1Array.getString(i);
+                let resi1 = resi1Array.getString(i);
                 let id1 = chain1 + "_" + resi1 + "_" + name1;
 
-                let chain2 = chain2Array[i];
-                let name2 = name2Array[i];
-                let resi2 = resi2Array[i];
+                let chain2 = chain2Array.getString(i);
+                let name2 = name2Array.getString(i);
+                let resi2 = resi2Array.getString(i);
                 let id2 = chain2 + "_" + resi2 + "_" + name2;
 
                 // Verify that the linkage is covalent, as indicated by the conn_type_id attribute2
@@ -56314,40 +56290,40 @@ class BcifParser {
         let atom_hetatmArray, resnArray, elemArray, nameArray, chainArray, resiArray, resiOriArray, altArray, bArray, xArray, yArray, zArray, autochainArray = [];
 
         if(!bNoCoord) {
-            atom_hetatmArray = atom_site.getColumn("group_PDB").data;
-            resnArray = atom_site.getColumn("label_comp_id").data;
-            elemArray = atom_site.getColumn("type_symbol").data;
-            nameArray = atom_site.getColumn("label_atom_id").data;
+            atom_hetatmArray = atom_site.getColumn("group_PDB");
+            resnArray = atom_site.getColumn("label_comp_id");
+            elemArray = atom_site.getColumn("type_symbol");
+            nameArray = atom_site.getColumn("label_atom_id");
 
-            chainArray = atom_site.getColumn("auth_asym_id").data;
+            chainArray = atom_site.getColumn("auth_asym_id");
             
-            resiArray = atom_site.getColumn("label_seq_id").data;
-            resiOriArray = atom_site.getColumn("auth_seq_id").data;
-            altArray = atom_site.getColumn("label_alt_id").data;
+            resiArray = atom_site.getColumn("label_seq_id");
+            resiOriArray = atom_site.getColumn("auth_seq_id");
+            altArray = atom_site.getColumn("label_alt_id");
 
-            bArray = atom_site.getColumn("B_iso_or_equiv").data;
+            bArray = atom_site.getColumn("B_iso_or_equiv");
 
-            xArray = atom_site.getColumn("Cartn_x").data;
-            yArray = atom_site.getColumn("Cartn_y").data;
-            zArray = atom_site.getColumn("Cartn_z").data;
+            xArray = atom_site.getColumn("Cartn_x");
+            yArray = atom_site.getColumn("Cartn_y");
+            zArray = atom_site.getColumn("Cartn_z");
 
-            autochainArray = atom_site.getColumn("label_asym_id").data;
+            autochainArray = atom_site.getColumn("label_asym_id");
 
             // get the bond info
             let ligSeqHash = {}, prevAutochain = '';
             for (let i = 0; i < atomSize; ++i) {
-                let atom_hetatm = atom_hetatmArray[i];
-                let resn = resnArray[i];
-                let elem = elemArray[i];
-                let name = nameArray[i];
+                let atom_hetatm = atom_hetatmArray.getString(i);
+                let resn = resnArray.getString(i);
+                let elem = elemArray.getString(i);
+                let name = nameArray.getString(i);
         // use the chain name from author, and use seq id from standardized seq id
                 //let chain = atom_site.getColumn("label_asym_id").getString(i);
-                let chain = chainArray[i];
-                let resi = resiArray[i];
-                let oriResi = resiOriArray[i]; 
-                let alt = altArray[i];
+                let chain = chainArray.getString(i);
+                let resi = resiArray.getString(i);
+                let oriResi = resiOriArray.getString(i); 
+                let alt = altArray.getString(i);
 
-                let autochain = autochainArray[i];
+                let autochain = autochainArray.getString(i);
 
                 resi = oriResi;
 
@@ -56418,9 +56394,9 @@ class BcifParser {
                     }
                 }
 
-                let x = xArray[i];
-                let y = yArray[i];
-                let z = zArray[i];
+                let x = xArray.getFloat(i);
+                let y = yArray.getFloat(i);
+                let z = zArray.getFloat(i);
 
                 let id = serial.toString();
 
@@ -56516,18 +56492,18 @@ class BcifParser {
             }
 
             for (let i = 0; i < atomSize; ++i) {
-                let atom_hetatm = atom_hetatmArray[i];
-                let resn = resnArray[i];
-                let elem = elemArray[i];
-                let name = nameArray[i];
+                let atom_hetatm = atom_hetatmArray.getString(i);
+                let resn = resnArray.getString(i);
+                let elem = elemArray.getString(i);
+                let name = nameArray.getString(i);
         // use the chain name from author, and use seq id from standardized seq id
                 //let chain = atom_site.getColumn("label_asym_id").getString(i);
-                let chain = chainArray[i];
-                let resi = resiArray[i];
-                let oriResi = resiOriArray[i]; 
-                let alt = altArray[i];
+                let chain = chainArray.getString(i);
+                let resi = resiArray.getString(i);
+                let oriResi = resiOriArray.getString(i); 
+                let alt = altArray.getString(i);
 
-                let autochain = autochainArray[i];
+                let autochain = autochainArray.getString(i);
 
                 resi = oriResi;
 
@@ -56575,11 +56551,11 @@ class BcifParser {
                     // }
                 }
 
-                let b = bArray[i];
+                let b = bArray.getString(i);
 
-                let x = xArray[i];
-                let y = yArray[i];
-                let z = zArray[i];
+                let x = xArray.getFloat(i);
+                let y = yArray.getFloat(i);
+                let z = zArray.getFloat(i);
                 //int serial = parseInt(atom_site(i, "id"));
 
                 //let id = chain + "_" + resi + "_" + name;
@@ -56667,19 +56643,19 @@ class BcifParser {
         if(block.getCategory("_pdbx_poly_seq_scheme")) {
             let poly_seq_scheme = block.getCategory("_pdbx_poly_seq_scheme");
 
-            let resiArray = poly_seq_scheme.getColumn("seq_id").data;
-            let oriResiArray = poly_seq_scheme.getColumn("pdb_seq_num").data;
-            let resnArray = poly_seq_scheme.getColumn("mon_id").data;
-            let chainArray = poly_seq_scheme.getColumn("pdb_strand_id").data;
+            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 seqSize = poly_seq_scheme.rowCount;
             let prevChain = "";
             let seq = "";
             for (let i = 0; i < seqSize; ++i) {
-                resiArray[i];
-                let oriResi = oriResiArray[i];
-                let resn = resnArray[i];
-                let chain = chainArray[i];
+                resiArray.getString(i);
+                let oriResi = oriResiArray.getString(i);
+                let resn = resnArray.getString(i);
+                let chain = chainArray.getString(i);
 
                 if(chain != prevChain) {
                     if(i == 0) {
@@ -57108,19 +57084,16 @@ class OpmParser {
         if(type === 'mmtf') {
             await ic.bcifParserCls.parseBcifData(data, pdbid, bFull);
         }
-        else if(type === 'bcif') {
-            await ic.bcifParserCls.parseBcifData(data, pdbid, bFull);
-        }
         else 
         */
 
         if(type === 'mmcif' || type === 'bcif') {
-            if(type === 'mmcif') {
-                ic.loadAtomDataCls.loadAtomDataIn(data, data.mmcif, 'mmcifid', undefined, undefined);
-            }
-            else if(type === 'bcif') {
+            // if(type === 'mmcif') {
+            //     ic.loadAtomDataCls.loadAtomDataIn(data, data.mmcif, 'mmcifid', undefined, undefined);
+            // }
+            // else if(type === 'bcif') {
                 ic.loadCIFCls.loadCIF(data, pdbid, bText);
-            }
+            // }
 
             if(ic.emd !== undefined) {
               $("#" + ic.pre + "mapWrapper1").hide();
@@ -57136,7 +57109,7 @@ class OpmParser {
             if(Object.keys(ic.structures).length == 1) {
                 $("#" + ic.pre + "alternateWrapper").hide();
             }
-    
+/*    
             // load assembly info
             if(type === 'mmcif') {
                 let assembly =(data.assembly !== undefined) ? data.assembly : [];
@@ -57148,7 +57121,7 @@ class OpmParser {
                     }
                 }
             }
-        
+*/        
             if(ic.biomtMatrices !== undefined && ic.biomtMatrices.length > 1) {
                 $("#" + ic.pre + "assemblyWrapper").show();
     
@@ -57270,7 +57243,6 @@ class PdbParser {
             await this.loadPdbData(data, id, undefined, bAppend);
         }
         else if(type === 'mmcif') {
-            /*
             // let url = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi";
             // let dataObj = {'mmciffile': data};
             // let data2 = await me.getAjaxPostPromise(url, dataObj, true);
@@ -57282,12 +57254,6 @@ class PdbParser {
 
             // await ic.mmcifParserCls.loadMmcifData(bcifJson, undefined);
             await ic.opmParserCls.loadOpmData(data, undefined, undefined, 'mmcif', undefined, bText);
-            */
-
-            let url = me.htmlCls.baseUrl + "mmcifparser/mmcifparser.cgi";
-            let dataObj = {'mmciffile': data};
-            let data2 = await me.getAjaxPostPromise(url, dataObj, true);
-            await ic.mmcifParserCls.loadMmcifData(data2, undefined);
         }
         else if(type === 'mol2') {
             await ic.mol2ParserCls.loadMol2Data(data);
@@ -63634,8 +63600,6 @@ class LoadCIF {
         this.icn3d = icn3d;
     }
 
-    // For text mmCIF file, CIFTools library does not support atom_site.getColumn("Cartn_x").data,
-    // but just support atom_site.getColumn("Cartn_x").getFloat(i). So do not use "bText = true" for now.
     loadCIF(bcifData, bcifid, bText, bAppend) { let ic = this.icn3d, me = ic.icn3dui;
         let hAtoms = {};
 
@@ -63742,22 +63706,22 @@ class LoadCIF {
             // 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").data;
+            let conf_type_idArray = struct_conf.getColumn("conf_type_id");
         
-            let chain1Array = struct_conf.getColumn("beg_auth_asym_id").data;
-            let resi1Array = struct_conf.getColumn("beg_label_seq_id").data;
+            let chain1Array = struct_conf.getColumn("beg_auth_asym_id");
+            let resi1Array = struct_conf.getColumn("beg_label_seq_id");
         
-            struct_conf.getColumn("end_auth_asym_id").data;
-            let resi2Array = struct_conf.getColumn("end_label_seq_id").data;
+            struct_conf.getColumn("end_auth_asym_id");
+            let resi2Array = struct_conf.getColumn("end_label_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[i];
+                let conf_type_id = conf_type_idArray.getString(i);
             
-                let startChain = chain1Array[i];
-                let startResi = parseInt(resi1Array[i]);
-                let endResi = parseInt(resi2Array[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) {
@@ -63786,18 +63750,18 @@ class LoadCIF {
             // 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").data;
-            let resi1Array = struct_sheet_range.getColumn("beg_label_seq_id").data;
+            let chain1Array = struct_sheet_range.getColumn("beg_auth_asym_id");
+            let resi1Array = struct_sheet_range.getColumn("beg_label_seq_id");
         
-            struct_sheet_range.getColumn("end_auth_asym_id").data;
-            let resi2Array = struct_sheet_range.getColumn("end_label_seq_id").data;
+            struct_sheet_range.getColumn("end_auth_asym_id");
+            let resi2Array = struct_sheet_range.getColumn("end_label_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[i];
-                let startResi = parseInt(resi1Array[i]);
-                let endResi = parseInt(resi2Array[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;
@@ -63817,28 +63781,28 @@ class LoadCIF {
             // 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").data;
+            let conn_type_idArray = struct_conn.getColumn("conn_type_id");
         
-            let chain1Array = struct_conn.getColumn("ptnr1_auth_asym_id").data;
-            let name1Array = struct_conn.getColumn("ptnr1_label_atom_id").data;
-            let resi1Array = struct_conn.getColumn("ptnr1_label_seq_id").data;
+            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").data;
-            let name2Array = struct_conn.getColumn("ptnr2_label_atom_id").data;
-            let resi2Array = struct_conn.getColumn("ptnr2_label_seq_id").data;
+            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[i];
+                let conn_type_id = conn_type_idArray.getString(i);
             
-                let chain1 = chain1Array[i];
-                name1Array[i];
-                let resi1 = resi1Array[i];
+                let chain1 = chain1Array.getString(i);
+                name1Array.getString(i);
+                let resi1 = resi1Array.getString(i);
                 let id1 = structure + '_' + chain1 + "_" + resi1;
             
-                let chain2 = chain2Array[i];
-                name2Array[i];
-                let resi2 = resi2Array[i];
+                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
@@ -63870,31 +63834,31 @@ class LoadCIF {
             // 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").data;
-            let m11Array = struct_oper_list.getColumn("matrix[1][1]").data;
-            let m12Array = struct_oper_list.getColumn("matrix[1][2]").data;
-            let m13Array = struct_oper_list.getColumn("matrix[1][3]").data;
-            let m14Array = struct_oper_list.getColumn("vector[1]").data;
+            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]").data;
-            let m22Array = struct_oper_list.getColumn("matrix[2][2]").data;
-            let m23Array = struct_oper_list.getColumn("matrix[2][3]").data;
-            let m24Array = struct_oper_list.getColumn("vector[2]").data;
+            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]").data;
-            let m32Array = struct_oper_list.getColumn("matrix[3][2]").data;
-            let m33Array = struct_oper_list.getColumn("matrix[3][3]").data;
-            let m34Array = struct_oper_list.getColumn("vector[3]").data;
+            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[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[i], m12Array[i], m13Array[i], m14Array[i], 
-                    m21Array[i], m22Array[i], m23Array[i], m24Array[i], 
-                    m31Array[i], m32Array[i], m33Array[i], m34Array[i], 
+                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);
             }
         
@@ -63937,41 +63901,42 @@ class LoadCIF {
             ic.opts['nucleotides'] = 'o3 trace'; //nucleotide cartoon, o3 trace, schematic, lines, stick,
         }
 
-        let atom_hetatmArray = atom_site.getColumn("group_PDB").data;
-        let resnArray = atom_site.getColumn("label_comp_id").data;
-        let elemArray = atom_site.getColumn("type_symbol").data;
-        let nameArray = atom_site.getColumn("label_atom_id").data;
-    
-        let chainArray = atom_site.getColumn("auth_asym_id").data;
-    
-        let resiArray = atom_site.getColumn("label_seq_id").data;
-        let resiOriArray = atom_site.getColumn("auth_seq_id").data;
-        let altArray = atom_site.getColumn("label_alt_id").data;
-    
-        let bArray = atom_site.getColumn("B_iso_or_equiv").data;
-    
-        let xArray = atom_site.getColumn("Cartn_x").data;
-        let yArray = atom_site.getColumn("Cartn_y").data;
-        let zArray = atom_site.getColumn("Cartn_z").data;
-    
-        let autochainArray = atom_site.getColumn("label_asym_id").data;
+        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 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 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");
 
         // get the bond info
         let ligSeqHash = {}, prevAutochain = '';
         let prevResn;
         let sChain = {};
         for (let i = 0; i < atomSize; ++i) {
-            let atom_hetatm = atom_hetatmArray[i];
-            let resn = resnArray[i];
-            let elem = elemArray[i];
-            let atom = nameArray[i];
-            let chain = chainArray[i];
-            let resi = resiArray[i];
-            let oriResi = resiOriArray[i]; 
-            let alt = altArray[i];
-            let bFactor = bArray[i];
-
-            let autochain = autochainArray[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);
+
 
             resi = oriResi;
 
@@ -64074,9 +64039,9 @@ class LoadCIF {
 
             //let chain_resi = chain + "_" + resi;
 
-            let x = xArray[i];
-            let y = yArray[i];
-            let z = zArray[i];
+            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 = {
@@ -64236,19 +64201,19 @@ class LoadCIF {
         if(block.getCategory("_pdbx_poly_seq_scheme")) {
             let poly_seq_scheme = block.getCategory("_pdbx_poly_seq_scheme");
 
-            let resiArray = poly_seq_scheme.getColumn("seq_id").data;
-            let oriResiArray = poly_seq_scheme.getColumn("pdb_seq_num").data;
-            let resnArray = poly_seq_scheme.getColumn("mon_id").data;
-            let chainArray = poly_seq_scheme.getColumn("pdb_strand_id").data;
+            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 seqSize = poly_seq_scheme.rowCount;
             let prevChain = "";
             let seqArray = [];
             for (let i = 0; i < seqSize; ++i) {
-                resiArray[i];
-                let oriResi = oriResiArray[i];
-                let resn = resnArray[i];
-                let chain = chainArray[i];
+                resiArray.getString(i);
+                let oriResi = oriResiArray.getString(i);
+                let resn = resnArray.getString(i);
+                let chain = chainArray.getString(i);
 
                 if(chain != prevChain && i > 0) {
                     mChainSeq[prevChain] = seqArray;
@@ -71830,7 +71795,7 @@ class Dssp {
                             delete ic.domainid2refpdbname[domainid];
                             delete ic.domainid2score[domainid];
                         }
-                        // continue;
+                        continue;
                     }
                 // }
 
@@ -72051,10 +72016,12 @@ class Dssp {
 
             if(refpdbname) {
                 let message = "The reference PDB for domain " + domainid + " is " + refpdbname + ". The TM-score is " + score  + ". The sequence identity is " + seqid  + ". The number of aligned residues is " + nresAlign + ".";
+
                 if(!me.bNode) {
                     console.log(message);
                     me.htmlCls.clickMenuCls.setLogCmd(message, false, true);
                 }
+
                 // ic.refPdbList.push(message);
                 ic.domainid2info[domainid] = {'refpdbname': refpdbname, 'score': score, 'seqid': seqid, 'nresAlign': nresAlign};
             }
@@ -72258,7 +72225,7 @@ class Dssp {
         // loops may have numbers such as 1310, 1410
 
         let strand;
-
+/*
         if(refnum < 1000) strand = undefined;
         else if(refnum >= 1200 && refnum < 1290) strand = "A---";
         else if(refnum >= 1320 && refnum < 1390) strand = "A--";
@@ -72281,6 +72248,34 @@ class Dssp {
         else if(refnum >= 9720 && refnum < 9790) strand = "G++";
         else if(refnum > 9900) strand = undefined;
         else strand = " ";
+*/
+
+        // cover all ranges
+        if(refnum < 1000) strand = undefined;
+        else if(refnum >= 1200 && refnum < 1320) strand = "A---";
+        else if(refnum >= 1320 && refnum < 1420) strand = "A--";
+        else if(refnum >= 1420 && refnum < 1520) strand = "A-";
+        else if(refnum >= 1520 && refnum < 1620) strand = "A";
+        else if(refnum >= 1620 && refnum < 1720) strand = "A+";
+        else if(refnum >= 1720 && refnum < 1820) strand = "A++";
+        else if(refnum >= 1820 && refnum < 2000) strand = "A'";
+        else if(refnum >= 2000 && refnum < 3000) strand = "B";
+        else if(refnum >= 3000 && refnum < 3420) strand = "C--";
+        else if(refnum >= 3420 && refnum < 3520) strand = "C-";
+        else if(refnum >= 3520 && refnum < 4000) strand = "C";
+        else if(refnum >= 4000 && refnum < 5000) strand = "C'";
+        else if(refnum >= 5000 && refnum < 6000) strand = "C''";
+        else if(refnum >= 6000 && refnum < 7000) strand = "D";
+        else if(refnum >= 7000 && refnum < 7620) strand = "E";
+        else if(refnum >= 7620 && refnum < 8000) strand = "E+";
+        else if(refnum >= 8000 && refnum < 9000) strand = "F";
+        else if(refnum >= 9000 && refnum < 9620) strand = "G";
+        else if(refnum >= 9620 && refnum < 9720) strand = "G+";
+        else if(refnum >= 9720 && refnum < 9820) strand = "G++";
+        else if(refnum >= 9820 && refnum < 9900) strand = "G+++";
+        else if(refnum > 9900) strand = undefined;
+        else strand = " ";
+
         if(prevStrand) strand = prevStrand;
 
         return strand
@@ -72602,7 +72597,7 @@ class Dssp {
                 refnum3c = (refnum - parseInt(refnum/1000) * 1000).toString();
                 refnum2c = (refnum - parseInt(refnum/100) * 100).toString();
 
-                // for extended strands, since A is 1550 and A+ is 1650, then the AA+ loop will be 1591, 1592, ... 1610, 1611, etc
+                // for extended strands, since A is 1550 and A+ is 1650, then the AA+ loop will be 1591, 1592, ... 1618, 1619, etc
                 bSecThird9 = refnum3c.substr(0,1) == '9' || refnum2c.substr(0,1) == '9' || refnum2c.substr(0,1) == '0' || refnum2c.substr(0,1) == '1';
                 if(bSecThird9) ic.residIgLoop[residueid] = 1;
 
@@ -72748,6 +72743,7 @@ class Dssp {
                     let domainid = ic.resid2domainid[currResid];
                     if(currAtom.ssbegin) { // find the start of the sheet
                         // update the following: startResi,startRefnum,endResi,endRefnum,loopResCnt,resCntBfAnchor,resCntAtAnchor
+                        let oriStartRefnum = strandArray[i].startRefnum;
                         strandArray[i].startResi = currResi;
                         strandArray[i].startRefnum -= j;
                         strandArray[i].loopResCnt -= j;
@@ -72760,6 +72756,8 @@ class Dssp {
                             currResi = ic.ParserUtilsCls.getResi(chnid, currPos);
                             let currResid = chnid + '_' + currResi;
                             delete ic.residIgLoop[currResid];
+                            ic.resid2refnum[currResid] = strandArray[i].strand + (oriStartRefnum - k).toString();
+
                             ic.resid2domainid[currResid] = domainid;
                             ic.resid2refnum_ori[currResid] = 1; // a hash to check which residues were assigned
                         }
@@ -72780,6 +72778,7 @@ class Dssp {
                     let domainid = ic.resid2domainid[currResid];
                     if(currAtom.ssend) { // find the end of the sheet
                         // update the following: startResi,startRefnum,endResi,endRefnum,loopResCnt,resCntBfAnchor,resCntAtAnchor
+                        let oriEndRefnum = strandArray[i].endRefnum;
                         strandArray[i].endResi = currResi;
                         strandArray[i].endRefnum += j;
                         if(i < il - 1) {
@@ -72794,6 +72793,8 @@ class Dssp {
                             currResi = ic.ParserUtilsCls.getResi(chnid, currPos);
                             let currResid = chnid + '_' + currResi;
                             delete ic.residIgLoop[currResid];
+                            ic.resid2refnum[currResid] = strandArray[i].strand + (oriEndRefnum + k).toString();
+
                             ic.resid2domainid[currResid] = domainid;
                             ic.resid2refnum_ori[currResid] = 1; // a hash to check which residues were assigned
                         }
@@ -81194,7 +81195,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.31.0';
+    this.REVISION = '3.31.1';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;