icn3d 3.41.0 → 3.43.0

package/icn3d.js

@@ -2539,7 +2539,6 @@ THREE.TrackballControls = function ( object, domElement, icn3d ) {
                     _this._panStart.add( mouseChange.subVectors( _this._panEnd, _this._panStart ).multiplyScalar( _this.dynamicDampingFactor ) );
 
                 }
-
             }
         }
 
@@ -3576,6 +3575,103 @@ THREE.OrthographicTrackballControls = function ( object, domElement, icn3d ) { v
 THREE.OrthographicTrackballControls.prototype = Object.create( THREE.EventDispatcher.prototype );
 THREE.OrthographicTrackballControls.prototype.constructor = THREE.OrthographicTrackballControls;
 
+/**
+ * @author alteredq / http://alteredqualia.com/
+ * @authod mrdoob / http://mrdoob.com/
+ * @authod arodic / http://aleksandarrodic.com/
+ * modified by Jiyao Wang
+ */
+
+THREE.StereoEffect = function ( renderer ) {
+    var _this = this;
+    // API
+
+    _this.separation = 3; // 1;
+
+    // internals
+
+    // _this._width, _this._height;
+
+    _this._position = new THREE.Vector3();
+    _this._quaternion = new THREE.Quaternion();
+    _this._scale = new THREE.Vector3();
+
+    _this._cameraL = new THREE.PerspectiveCamera();
+    _this._cameraR = new THREE.PerspectiveCamera();
+
+    // initialization
+
+    renderer.autoClear = false;
+
+    _this.setSize = function ( width, height ) {
+
+        _this._width = width / 2;
+        _this._height = height;
+
+        renderer.setSize( width, height );
+
+    };
+
+    _this.render = function ( scene, camera ) {
+
+        scene.updateMatrixWorld();
+
+        if ( camera.parent === undefined ) camera.updateMatrixWorld();
+    
+        camera.matrixWorld.decompose( _this._position, _this._quaternion, _this._scale );
+
+        // left
+        _this._cameraL.copy(camera);
+        _this._cameraL.aspect = 0.5 * camera.aspect;
+        _this._cameraL.updateProjectionMatrix();
+        
+/*
+        _this._cameraL.fov = camera.fov;
+        _this._cameraL.aspect = 0.5 * camera.aspect;
+        _this._cameraL.near = camera.near;
+        _this._cameraL.far = camera.far;
+        _this._cameraL.updateProjectionMatrix();
+
+        _this._cameraL.position.copy( _this._position );
+        // _this._cameraL.quaternion.copy( _this._quaternion );
+*/
+        _this._cameraL.translateX( - _this.separation );
+
+        // right
+        _this._cameraR.copy(camera);
+        _this._cameraR.aspect = 0.5 * camera.aspect;
+        _this._cameraR.updateProjectionMatrix();
+
+/*
+        _this._cameraR.fov = camera.fov;
+        _this._cameraR.aspect = 0.5 * camera.aspect;
+        _this._cameraR.near = camera.near;
+        _this._cameraR.far = camera.far;
+        // _this._cameraR.projectionMatrix = _this._cameraL.projectionMatrix;
+        _this._cameraR.updateProjectionMatrix();
+
+        _this._cameraR.position.copy( _this._position );
+        // _this._cameraR.quaternion.copy( _this._quaternion );
+*/
+
+        _this._cameraR.translateX( _this.separation );
+
+        //
+
+        renderer.setViewport( 0, 0, _this._width * 2, _this._height );
+        renderer.clear();
+
+        renderer.setViewport( 0, 0, _this._width, _this._height );
+        renderer.render( scene, _this._cameraL );
+
+        renderer.setViewport( _this._width, 0, _this._width, _this._height );
+        renderer.render( scene, _this._cameraR );
+
+    };
+
+};
+
+
 
 // ; var __CIFTools = function () {
 //   'use strict';
@@ -8805,6 +8901,7 @@ class ClickMenu {
 
     applyShownMenus(bNoSave) { let me = this.icn3dui; me.icn3d;
         let idArray = [];
+
         for(let id in me.htmlCls.allMenus) {
             if(me.htmlCls.shownMenus.hasOwnProperty(id)) {
                 $("#" + me.pre + id).parent().show();
@@ -9035,6 +9132,14 @@ class ClickMenu {
            me.htmlCls.dialogCls.openDlg('dl_urlfile', 'Load data by URL');
         });
 
+        me.myEventCls.onIds("#" + me.pre + "mn1_clustalwfile", "click", function(e) { me.icn3d; //e.preventDefault();
+            me.htmlCls.dialogCls.openDlg('dl_clustalwfile', 'Please input CLUSTALW MSA File');
+        });
+
+        me.myEventCls.onIds("#" + me.pre + "mn1_fastafile", "click", function(e) { me.icn3d; //e.preventDefault();
+            me.htmlCls.dialogCls.openDlg('dl_fastafile', 'Please input FASTA MSA File');
+        });
+
         me.myEventCls.onIds("#" + me.pre + "mn1_fixedversion", "click", function(e) { me.icn3d; //e.preventDefault();
            me.htmlCls.dialogCls.openDlg('dl_fixedversion', 'Open Share Link URL in the archived version of iCn3D');
         });
@@ -9136,6 +9241,11 @@ class ClickMenu {
            ic.saveFileCls.saveFile(file_pref + '_statefile.txt', 'command');
         });
 
+        me.myEventCls.onIds("#" + me.pre + "mn1_exportVideo", "click", function(e) { me.icn3d; //e.preventDefault();
+         thisClass.setLogCmd("export video", false);
+         me.htmlCls.dialogCls.openDlg('dl_video', 'Save canvas changes in a video');
+        });
+
 
         me.myEventCls.onIds("#" + me.pre + "mn1_exportPdbRes", "click", function(e) { me.icn3d; //e.preventDefault();
            me.htmlCls.setHtmlCls.exportPdb();
@@ -10828,6 +10938,18 @@ class ClickMenu {
            //}
         });
 
+        me.myEventCls.onIds("#" + me.pre + "mn6_stereoYes", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
+            ic.opts['effect'] = 'stereo';
+            ic.drawCls.draw();
+            thisClass.setLogCmd('stereo on', true);
+        });
+
+        me.myEventCls.onIds("#" + me.pre + "mn6_stereoNo", "click", function(e) { let ic = me.icn3d; //e.preventDefault();
+            ic.opts['effect'] = 'none';
+            ic.drawCls.draw();
+            thisClass.setLogCmd('stereo off', true);
+        });
+
         $(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');
         });
@@ -11841,9 +11963,19 @@ class SetMenu {
         html += this.getLink('mn1_mol2file', 'Mol2 File', undefined, 2);
         html += this.getLink('mn1_sdffile', 'SDF File', undefined, 2);
         html += this.getLink('mn1_xyzfile', 'XYZ File', undefined, 2);
+
+        html += this.getMenuSep();
+
+        html += this.getMenuText('mn1_msawrap', 'Multiple Seq. Alignment', undefined, undefined, 2);
+        html += "<ul>";
+        html += this.getLink('mn1_clustalwfile', 'CLUSTALW Format', undefined, 3);
+        html += this.getLink('mn1_fastafile', 'FASTA Format', undefined, 3);
+        html += "</ul>";
+
         html += this.getLink('mn1_afmapfile', 'AlphaFold PAE File', undefined, 2);
 
         html += this.getLink('mn1_urlfile', 'URL(CORS) ' + me.htmlCls.wifiStr, undefined, 2);
+        
         html += this.getMenuSep();
         html += this.getLink('mn1_pngimage', 'iCn3D PNG (appendable)', 1, 2);
         html += this.getLink('mn1_state', 'State/Script File', undefined, 2);
@@ -11950,6 +12082,7 @@ class SetMenu {
         html += "</ul>";
         html += "</li>";
 
+        html += this.getLink('mn1_exportVideo', 'Video', undefined, 2);
         html += this.getLink('mn1_exportState', 'State File', undefined, 2);
         html += this.getLink('mn1_exportSelections', 'Selection File', undefined, 2);
         html += this.getLink('mn1_exportSelDetails', 'Selection Details', undefined, 2);
@@ -12167,6 +12300,13 @@ class SetMenu {
         html += "</ul>";
         html += "</li>";
 
+        html += this.getMenuText('mn6_stereoWrapper', 'Stereo View', undefined, undefined, 1);
+        html += "<ul>";
+        html += this.getRadio('mn6_stereo', 'mn6_stereoYes', 'On', undefined, undefined, 2);
+        html += this.getRadio('mn6_stereo', 'mn6_stereoNo', 'Off', true, undefined, 2);
+        html += "</ul>";
+        html += "</li>";
+
         html += this.getLink('mn6_sidebyside', 'Side by Side', undefined, 1);
 
         html += this.getMenuText('mn2_rotate', 'Rotate', undefined, 1, 1);
@@ -14196,6 +14336,19 @@ class SetDialog {
         html += me.htmlCls.buttonStr + "reload_xyzfile'>Load</button>";
         html += "</div>";
 
+        html += me.htmlCls.divStr + "dl_clustalwfile' class='" + dialogClass + "' style='max-width:500px'>";
+        html += this.addNotebookTitle('dl_clustalwfile', 'Please input a CLUSTALW MSA file');
+        html += "Note the sequence names are either UniProt ID (e.g., A4D1S0 or A4D1S0_A), RefSeq ID (e.g., NP_001743), or PDB chain ID (e.g., 1HHO_A).<br><br>";
+        html += "CLUSTALW File: " + me.htmlCls.inputFileStr + "id='" + me.pre + "clustalwfile' size=8> ";
+        html += me.htmlCls.buttonStr + "reload_clustalwfile'>Load</button><br>";
+        html += "</div>";
+        html += me.htmlCls.divStr + "dl_fastafile' class='" + dialogClass + "' style='max-width:500px'>";
+        html += this.addNotebookTitle('dl_fastafile', 'Please input a FASTA file');
+        html += "Note the sequence IDs following the symbol \">\" contain either UniProt ID (e.g., sp| or tr|), RefSeq ID (e.g., ref|), PDB chain ID (e.g., pdb|1HHO|A), or iCn3D chain ID (e.g., A4D1S0_A, 1HHO_A).<br><br>";
+        html += "FASTA File: " + me.htmlCls.inputFileStr + "id='" + me.pre + "fastafile' size=8> ";
+        html += me.htmlCls.buttonStr + "reload_fastafile'>Load</button><br>";
+        html += "</div>";
+
         html += me.htmlCls.divStr + "dl_afmapfile' class='" + dialogClass + "'>";
         html += this.addNotebookTitle('dl_afmapfile', 'Please input an AlphaFold PAE file');
         html += "AlphaFold PAE File: " + me.htmlCls.inputFileStr + "id='" + me.pre + "afmapfile' size=8> <br><br>";
@@ -14315,6 +14468,13 @@ class SetDialog {
         html += me.htmlCls.buttonStr + "reload_state' style='margin-top: 6px;'>Load</button>";
         html += "</div>";
 
+        html += me.htmlCls.divStr + "dl_video' class='" + dialogClass + "'>";
+        html += this.addNotebookTitle('dl_video', 'Save canvas changes in a video');
+        html += "State file: " + me.htmlCls.inputFileStr + "id='" + me.pre + "state'><br/>";
+        html += me.htmlCls.buttonStr + "video_start' style='margin-top: 6px;'>Video Start</button>";
+        html += me.htmlCls.buttonStr + "video_end' style='margin: 6px 0px 0px 30px;'>Video End</button>";
+        html += "</div>";
+
         html += me.htmlCls.divStr + "dl_fixedversion' style='max-width:500px' class='" + dialogClass + "'>";
         html += this.addNotebookTitle('dl_fixedversion', 'Use fixed version of iCn3D');
         html += "Since January 6, 2021, you can show the original view with the archived version of iCn3D by pasting your URL below and click \"Show Originial View\". Note the version in the parameter \"v\" was used to replace \"full.html\" with \"full_[v].html\" in the URL.<br><br>";
@@ -15674,17 +15834,10 @@ class Events {
         }
     }
 
-    async loadPdbFile(bAppend, fileId, bmmCIF) { let me = this.icn3dui, ic = me.icn3d;
+    async loadPdbFile(bAppend, fileId, bmmCIF) { let me = this.icn3dui, ic = me.icn3d, thisClass = this;
        //me = ic.setIcn3dui(this.id);
        ic.bInitial = true;
-       if(!me.cfg.notebook) dialog.dialog( "close" );
-       //close all dialog
-       if(!me.cfg.notebook) {
-           $(".ui-dialog-content").dialog("close");
-       }
-       else {
-           ic.resizeCanvasCls.closeDialogs();
-       }
+       thisClass.iniFileLoad();
        let files = $("#" + me.pre + fileId)[0].files;
        if(!files[0]) {
          var aaa = 1; //alert("Please select a file before clicking 'Load'");
@@ -15730,11 +15883,22 @@ class Events {
 
     exportMsa(type) { let me = this.icn3dui, ic = me.icn3d;
         let text = ic.msa[type].join('\n\n');
-        let fileType = (type == 'fasta') ? '.fasta' : (type == 'clustal') ? '.aln' : '.txt';
+        let fileType = (type == 'fasta') ? '.fasta' : (type == 'clustalw') ? '.aln' : '.txt';
 
         ic.saveFileCls.saveFile(ic.inputid + '_align' + fileType, 'text', [text]);
     }
 
+    iniFileLoad() { let me = this.icn3dui, ic = me.icn3d;
+        if(!me.cfg.notebook) dialog.dialog( "close" );
+        //close all dialog
+        if(!me.cfg.notebook) {
+            $(".ui-dialog-content").dialog("close");
+        }
+        else {
+            ic.resizeCanvasCls.closeDialogs();
+        }
+    }
+
     async launchMmdb(ids, bBiounit, hostUrl, bAppend) { let me = this.icn3dui, ic = me.icn3d, thisClass = this;
         if(!me.cfg.notebook) dialog.dialog( "close" );
         
@@ -16830,16 +16994,40 @@ class Events {
 
         me.htmlCls.setHtmlCls.clickReload_pngimage();
 
+        me.myEventCls.onIds("#" + me.pre + "video_start", "click", function(e) { let ic = me.icn3d;
+            e.preventDefault();
+
+            const canvas = document.getElementById(ic.pre + "canvas");
+            ic.videoRecorder = new MediaRecorder(canvas.captureStream());
+            const recordedChunks = [];
+
+            // Collect data chunks
+            ic.videoRecorder.ondataavailable = event => {
+                recordedChunks.push(event.data);
+            };
+
+            ic.videoRecorder.onstop = event => {
+                // Code to save the recordedChunks as a video file
+                const blob = new Blob(recordedChunks, {type: ic.videoRecorder.mimeType});
+                let fileName = ic.inputid + '_video';
+                saveAs(blob, fileName);
+            };
+
+            // Start recording
+            ic.videoRecorder.start();
+            thisClass.setLogCmd('Video revording started', false);
+        });
+ 
+        me.myEventCls.onIds("#" + me.pre + "video_end", "click", function(e) { let ic = me.icn3d;
+            e.preventDefault();
+
+            ic.videoRecorder.stop();
+            thisClass.setLogCmd('Video revording ended', false);
+        });
+
         me.myEventCls.onIds("#" + me.pre + "reload_state", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
-           if(!me.cfg.notebook) dialog.dialog( "close" );
-           //close all dialog
-           if(!me.cfg.notebook) {
-               $(".ui-dialog-content").dialog("close");
-           }
-           else {
-               ic.resizeCanvasCls.closeDialogs();
-           }
+           thisClass.iniFileLoad();
            // initialize icn3dui
            //Do NOT clear data if iCn3D loads a pdb or other data file and then load a state file
            if(!ic.bInputfile) {
@@ -16891,12 +17079,7 @@ class Events {
             if (!file) {
                 var aaa = 1; //alert("Please select a file before clicking 'Load'");
             } else {
-            if (!me.cfg.notebook) dialog.dialog("close");
-            if (!me.cfg.notebook) {
-                $(".ui-dialog-content").dialog("close");
-            } else {
-                ic.resizeCanvasCls.closeDialogs();
-                }
+            thisClass.iniFileLoad();
                 
             ic.dAtoms = me.hashUtilsCls.cloneHash(ic.atoms);
             ic.hAtoms = me.hashUtilsCls.cloneHash(ic.atoms);
@@ -17451,14 +17634,7 @@ class Events {
         me.myEventCls.onIds("#" + me.pre + "reload_mol2file", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            ic.bInitial = true;
-           if(!me.cfg.notebook) dialog.dialog( "close" );
-           //close all dialog
-           if(!me.cfg.notebook) {
-               $(".ui-dialog-content").dialog("close");
-           }
-           else {
-               ic.resizeCanvasCls.closeDialogs();
-           }
+           thisClass.iniFileLoad();
            let file = $("#" + me.pre + "mol2file")[0].files[0];
            if(!file) {
              var aaa = 1; //alert("Please select a file before clicking 'Load'");
@@ -17485,14 +17661,7 @@ class Events {
         me.myEventCls.onIds("#" + me.pre + "reload_sdffile", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            ic.bInitial = true;
-           if(!me.cfg.notebook) dialog.dialog( "close" );
-           //close all dialog
-           if(!me.cfg.notebook) {
-               $(".ui-dialog-content").dialog("close");
-           }
-           else {
-               ic.resizeCanvasCls.closeDialogs();
-           }
+           thisClass.iniFileLoad();
            let file = $("#" + me.pre + "sdffile")[0].files[0];
            if(!file) {
              var aaa = 1; //alert("Please select a file before clicking 'Load'");
@@ -17519,14 +17688,7 @@ class Events {
         me.myEventCls.onIds("#" + me.pre + "reload_xyzfile", "click", function(e) { let ic = me.icn3d;
            e.preventDefault();
            ic.bInitial = true;
-           if(!me.cfg.notebook) dialog.dialog( "close" );
-           //close all dialog
-           if(!me.cfg.notebook) {
-               $(".ui-dialog-content").dialog("close");
-           }
-           else {
-               ic.resizeCanvasCls.closeDialogs();
-           }
+           thisClass.iniFileLoad();
            let file = $("#" + me.pre + "xyzfile")[0].files[0];
            if(!file) {
              var aaa = 1; //alert("Please select a file before clicking 'Load'");
@@ -17550,17 +17712,64 @@ class Events {
            }
         });
 
-        me.myEventCls.onIds("#" + me.pre + "reload_afmapfile", "click", function(e) { let ic = me.icn3d;
+        me.myEventCls.onIds("#" + me.pre + "reload_clustalwfile", "click", function(e) { let ic = me.icn3d;
             e.preventDefault();
             ic.bInitial = true;
-            if(!me.cfg.notebook) dialog.dialog( "close" );
-            //close all dialog
-            if(!me.cfg.notebook) {
-                $(".ui-dialog-content").dialog("close");
+            thisClass.iniFileLoad();
+
+            let file = $("#" + me.pre + "clustalwfile")[0].files[0];
+            if(!file) {
+              var aaa = 1; //alert("Please select a file before clicking 'Load'");
             }
             else {
-                ic.resizeCanvasCls.closeDialogs();
+              me.htmlCls.setHtmlCls.fileSupport();
+              let reader = new FileReader();
+              reader.onload = async function(e) {
+                let dataStr = e.target.result; // or = reader.result;
+                thisClass.setLogCmd('load CLUSTALW file ' + $("#" + me.pre + "clustalwfile").val(), false);
+                ic.molTitle = "";
+                ic.inputid = undefined;
+                //ic.initUI();
+                ic.init();
+                ic.bInputfile = false; //true;
+                ic.InputfileType = 'clustalw';
+                await ic.msaParserCls.loadMsaData(dataStr, 'clustalw');
+              };
+              reader.readAsText(file);
+            }
+        });
+
+        me.myEventCls.onIds("#" + me.pre + "reload_fastafile", "click", function(e) { let ic = me.icn3d;
+            e.preventDefault();
+            ic.bInitial = true;
+            thisClass.iniFileLoad();
+
+            let file = $("#" + me.pre + "fastafile")[0].files[0];
+            if(!file) {
+              var aaa = 1; //alert("Please select a file before clicking 'Load'");
+            }
+            else {
+              me.htmlCls.setHtmlCls.fileSupport();
+              let reader = new FileReader();
+              reader.onload = async function(e) {
+                let dataStr = e.target.result; // or = reader.result;
+                thisClass.setLogCmd('load FASTA file ' + $("#" + me.pre + "fastafile").val(), false);
+                ic.molTitle = "";
+                ic.inputid = undefined;
+                //ic.initUI();
+                ic.init();
+                ic.bInputfile = false; //true;
+                ic.InputfileType = 'fasta';
+                await ic.msaParserCls.loadMsaData(dataStr, 'fasta');
+              };
+              reader.readAsText(file);
             }
+        });
+
+        me.myEventCls.onIds("#" + me.pre + "reload_afmapfile", "click", function(e) { let ic = me.icn3d;
+            e.preventDefault();
+            ic.bInitial = true;
+            thisClass.iniFileLoad();
             let file = $("#" + me.pre + "afmapfile")[0].files[0];
             if(!file) {
               var aaa = 1; //alert("Please select a file before clicking 'Load'");
@@ -17582,14 +17791,7 @@ class Events {
          me.myEventCls.onIds("#" + me.pre + "reload_afmapfilefull", "click", function(e) { let ic = me.icn3d;
             e.preventDefault();
             ic.bInitial = true;
-            if(!me.cfg.notebook) dialog.dialog( "close" );
-            //close all dialog
-            if(!me.cfg.notebook) {
-                $(".ui-dialog-content").dialog("close");
-            }
-            else {
-                ic.resizeCanvasCls.closeDialogs();
-            }
+            thisClass.iniFileLoad();
             let file = $("#" + me.pre + "afmapfile")[0].files[0];
             if(!file) {
               var aaa = 1; //alert("Please select a file before clicking 'Load'");
@@ -17611,14 +17813,7 @@ class Events {
         me.myEventCls.onIds("#" + me.pre + "reload_urlfile", "click", async function(e) { let ic = me.icn3d;
            e.preventDefault();
            ic.bInitial = true;
-           if(!me.cfg.notebook) dialog.dialog( "close" );
-           //close all dialog
-           if(!me.cfg.notebook) {
-               $(".ui-dialog-content").dialog("close");
-           }
-           else {
-               ic.resizeCanvasCls.closeDialogs();
-           }
+           thisClass.iniFileLoad();
            let type = $("#" + me.pre + "filetype").val();
            let url = $("#" + me.pre + "urlfile").val();
            ic.inputurl = 'type=' + type + '&url=' + encodeURIComponent(url);
@@ -18493,8 +18688,8 @@ class Events {
 
         me.myEventCls.onIds("#" + me.pre + "saveClustal", "click", function(e) { me.icn3d;
             e.stopImmediatePropagation();
-            thisClass.exportMsa('clustal');
-            thisClass.setLogCmd('Save alignment in CLUSTALW format', false);
+            thisClass.exportMsa('clustalw');
+            thisClass.setLogCmd('Save alignment in CLUSTALWW format', false);
         });
 
         me.myEventCls.onIds("#" + me.pre + "saveResbyres", "click", function(e) { me.icn3d;
@@ -19364,7 +19559,7 @@ class SetHtml {
 
       sequencesHtml += "<div style='min-width:200px; display:inline-block;'><b>Selection:</b> Name: " + me.htmlCls.inputTextStr + "id='" + me.pre + "alignseq_command_name' value='alseq_" + index + "' size='10'> " + me.htmlCls.space2 + "<button style='white-space:nowrap;' id='" + me.pre + "alignseq_saveselection'>Save</button> <button style='white-space:nowrap; margin-left:20px;' id='" + me.pre + "alignseq_clearselection'>Clear</button></div><br/>";
 
-      sequencesHtml += "<div style='min-width:200px; display:inline-block; margin-top:3px'><b>Save Alignment</b>: " + "<button style='white-space:nowrap;' id='" + me.pre + "saveFasta'>FASTA</button> <button style='white-space:nowrap; margin-left:20px;' id='" + me.pre + "saveClustal'>CLUSTAL</button> <button style='white-space:nowrap; margin-left:20px;' id='" + me.pre + "saveResbyres'>Residue by Residue</button></div><br/>";
+      sequencesHtml += "<div style='min-width:200px; display:inline-block; margin-top:3px'><b>Save Alignment</b>: " + "<button style='white-space:nowrap;' id='" + me.pre + "saveFasta'>FASTA</button> <button style='white-space:nowrap; margin-left:20px;' id='" + me.pre + "saveClustal'>CLUSTALW</button> <button style='white-space:nowrap; margin-left:20px;' id='" + me.pre + "saveResbyres'>Residue by Residue</button></div><br/>";
 
       sequencesHtml += me.htmlCls.divStr + "alignseqguide" + suffix + "' style='display:none; white-space:normal;' class='icn3d-box'>";
 
@@ -20057,9 +20252,9 @@ class Html {
     this.MENU_WIDTH = 750;
     //The width (in px) that was left empty by the 3D viewer. The default is 20px.
     this.LESSWIDTH = 20;
-    this.LESSWIDTH_RESIZE = 20;
+    this.LESSWIDTH_RESIZE = 30; //20;
     //The height (in px) that was left empty by the 3D viewer. The default is 20px.
-    this.LESSHEIGHT = 20;
+    this.LESSHEIGHT = (me.cfg.showlogo) ? 60 : 20; //20; // NCBI log is 40px high
 
     // size of 2D cartoons
     this.width2d = 200;
@@ -26620,7 +26815,12 @@ class Scene {
         ic.cams = {
             perspective: ic.perspectiveCamera,
             orthographic: ic.orthographicCamera,
-        };       
+        };  
+        
+        if(!me.bNode && ic.opts['effect'] == 'stereo' && !window.icn3duiHash) {
+            ic.effect = ic.effects[options.effect];
+            ic.effect.setSize(ic.container.width(), ic.container.height());
+        }
     };
 
     setVrAr() { let ic = this.icn3d; ic.icn3dui;
@@ -30342,8 +30542,9 @@ class Strand {
                 }
             }
 
-            // add one extra residue for coils between strands/helix
-            if(!isNaN(firstAtom.resi) && ic.pk === 3 && bHighlight === 1 && firstAtom.ss === 'coil') {
+            // add one extra residue for coils between strands/helix if the style is NOT stick, ball and stick, lines, sphere, and dot
+            // if(!isNaN(firstAtom.resi) && ic.pk === 3 && bHighlight === 1 && firstAtom.ss === 'coil') {
+            if(!isNaN(firstAtom.resi) && ic.pk === 3 && bHighlight === 1 && firstAtom.ss === 'coil' && firstAtom.style != 'stick' && firstAtom.style != 'ball and stick' && firstAtom.style != 'lines' && firstAtom.style != 'sphere' && firstAtom.style != 'dot') {
                     let residueid = firstAtom.structure + '_' + firstAtom.chain + '_' + (parseInt(firstAtom.resi) - 1).toString();
                     if(ic.residues.hasOwnProperty(residueid)) {
                         atomsAdjust = me.hashUtilsCls.unionHash(atomsAdjust, me.hashUtilsCls.hash2Atoms(ic.residues[residueid],
@@ -30378,8 +30579,8 @@ class Strand {
                 }
             }
 
-            // add one extra residue for coils between strands/helix
-            if(ic.pk === 3 && bHighlight === 1 && lastAtom.ss === 'coil') {
+            // add one extra residue for coils between strands/helix if the style is NOT stick, ball and stick, lines, sphere, and dot
+            if(ic.pk === 3 && bHighlight === 1 && lastAtom.ss === 'coil' && firstAtom.style != 'stick' && firstAtom.style != 'ball and stick' && firstAtom.style != 'lines' && firstAtom.style != 'sphere' && firstAtom.style != 'dot') {
                     let residueid = lastAtom.structure + '_' + lastAtom.chain + '_' + (parseInt(lastAtom.resi) + 1).toString();
                     if(ic.residues.hasOwnProperty(residueid)) {
                         atomsAdjust = me.hashUtilsCls.unionHash(atomsAdjust, me.hashUtilsCls.hash2Atoms(ic.residues[residueid],
@@ -33229,6 +33430,7 @@ ElectronMap.prototype.fillvoxels = function(atoms, atomlist) { //(int seqinit,in
         }
         else {
             // let index2ori = {};
+            let maxdist = this.maxdist;
             for(let serial in atomlist) {
                 let atom = atoms[atomlist[serial]];
 
@@ -33245,11 +33447,11 @@ ElectronMap.prototype.fillvoxels = function(atoms, atomlist) { //(int seqinit,in
                 }
 
                 // show map near the structure
-                for(i = Math.floor(r.x) - this.maxdist, il = Math.ceil(r.x) + this.maxdist; i <= il; ++i) {
+                for(i = Math.floor(r.x) - maxdist, il = Math.ceil(r.x) + maxdist; i <= il; ++i) {
                     if(i < 0 || i > this.header.xExtent*this.scaleFactor - 1) continue;
-                    for(j = Math.floor(r.y) - this.maxdist, jl = Math.ceil(r.y) + this.maxdist; j<= jl; ++j) {
+                    for(j = Math.floor(r.y) - maxdist, jl = Math.ceil(r.y) + maxdist; j<= jl; ++j) {
                         if(j < 0 || j > this.header.yExtent*this.scaleFactor - 1) continue;
-                        for(k = Math.floor(r.z) - this.maxdist, kl = Math.ceil(r.z) + this.maxdist; k<= kl; ++k) {
+                        for(k = Math.floor(r.z) - maxdist, kl = Math.ceil(r.z) + maxdist; k<= kl; ++k) {
                             if(k < 0 || k > this.header.zExtent*this.scaleFactor - 1) continue;
                             let index = i * widthHeight + j * height + k;
                             indexArray.push(index);
@@ -33258,6 +33460,16 @@ ElectronMap.prototype.fillvoxels = function(atoms, atomlist) { //(int seqinit,in
                 }
             }
 
+            // show all
+            // for(i = 0; i < this.pLength; ++i) {
+            //     for(j = 0; j < this.pWidth; ++j) {
+            //         for(k = 0; k < this.pHeight; ++k) {
+            //             let index = i * widthHeight + j * height + k;
+            //             indexArray.push(index);
+            //         }
+            //     }
+            // }
+
             for(i = 0, il = indexArray.length; i < il; ++i) {
                 let index = indexArray[i];
 
@@ -34519,6 +34731,7 @@ class ApplyDisplay {
                 for(let residueid in singletonResidueHash) {
                     // get calpha
                     let calpha = ic.firstAtomObjCls.getFirstCalphaAtomObj(ic.residues[residueid]);
+                    let sideAtom = ic.firstAtomObjCls.getFirstAtomObj(ic.selectionCls.getSideAtoms(ic.residues[residueid]));
                     let atom = calpha;
 
                     let prevResidueid = atom.structure + '_' + atom.chain + '_' + (parseInt(atom.resi) - 1).toString();
@@ -34535,7 +34748,7 @@ class ApplyDisplay {
                     }
                     else if( (atom.style === 'ribbon' && atom.ss === 'coil') || (atom.style === 'strand' && atom.ss === 'coil') || atom.style === 'o3 trace' || atom.style === 'schematic' || atom.style === 'c alpha trace' || atom.style === 'b factor tube' || (atom.style === 'cylinder and plate' && atom.ss !== 'helix') ) {
                         // do not add extra residue if the side chain is shown
-                        if(calpha !== undefined && calpha.style2 !== undefined && calpha.style2 !== 'nothing') continue;
+                        if(sideAtom !== undefined && sideAtom.style2 !== undefined && sideAtom.style2 !== 'nothing') continue;
 
                         let bAddResidue = false;
                         // add the next residue with same style
@@ -34570,7 +34783,7 @@ class ApplyDisplay {
                     }
                     else if( (atom.style === 'ribbon' && atom.ss !== 'coil' && atom.ssend) || (atom.style === 'strand' && atom.ss !== 'coil' && atom.ssend)) {
                         // do not add extra residue if the side chain is shown
-                        if(calpha !== undefined && calpha.style2 !== undefined && calpha.style2 !== 'nothing') continue;
+                        if(sideAtom !== undefined && sideAtom.style2 !== undefined && sideAtom.style2 !== 'nothing') continue;
 
                         let bAddResidue = false;
                         // add the next residue with same style
@@ -37455,11 +37668,18 @@ class Alternate {
         }
 
         if(ic.scene) {
+            ic.renderer.clear();
+            
             // https://github.com/gkjohnson/three-gpu-pathtracer/blob/main/example/basic.js
             ic.renderer.outputEncoding = THREE.sRGBEncoding;
             //ic.renderer.outputEncoding = THREE.LinearEncoding
 
-            ic.renderer.render(ic.scene, cam);
+            if(ic.opts['effect'] == 'stereo' && !window.icn3duiHash) {
+                ic.effect.render(ic.scene, cam);
+            }
+            else {
+                ic.renderer.render(ic.scene, cam);
+            }           
         }
     }
 
@@ -51836,13 +52056,20 @@ class ShowInter {
         }
         // do not change the set of displaying atoms
         //ic.dAtoms = me.hashUtilsCls.cloneHash(ic.atoms);
-        let commandname, commanddesc;
+        let commandname, commanddesc, commandname2;
         let firstAtom = ic.firstAtomObjCls.getFirstAtomObj(atomlistTarget);
+
         if(firstAtom !== undefined) {
             commandname = "sphere." + firstAtom.chain + ":" + me.utilsCls.residueName2Abbr(firstAtom.resn.substr(0, 3)).trim() + firstAtom.resi + "-" + radius + "A";
-            if(bInteraction) commandname = "interactions." + firstAtom.chain + ":" + me.utilsCls.residueName2Abbr(firstAtom.resn.substr(0, 3)).trim() + firstAtom.resi + "-" + $("#" + ic.pre + "contactthreshold").val() + "A";
+            //sometimes firstAtom.resi changed, thus we add a general name
+            commandname2 = "sphere-" + radius + "A";
+            if(bInteraction) {
+                commandname = "interactions." + firstAtom.chain + ":" + me.utilsCls.residueName2Abbr(firstAtom.resn.substr(0, 3)).trim() + firstAtom.resi + "-" + $("#" + ic.pre + "contactthreshold").val() + "A";
+                commandname2 = "interactions-" + $("#" + ic.pre + "contactthreshold").val() + "A";
+            }
             commanddesc = commandname;
             ic.selectionCls.addCustomSelection(residueArray, commandname, commanddesc, select, true);
+            ic.selectionCls.addCustomSelection(residueArray, commandname2, commanddesc, select, true);
         }
         ic.selectionCls.saveSelectionIfSelected();
         ic.drawCls.draw();
@@ -54020,6 +54247,7 @@ class ChainalignParser {
 
                     ajaxArray.push(alignAjax);
                     indexArray.push(index - 1);
+                    mmdbid_q = chainidArray[index].substr(0, chainidArray[index].indexOf('_'));
                     struArray.push(mmdbid_q);
                 }
 
@@ -54048,7 +54276,8 @@ class ChainalignParser {
             let mmdbid_q = struArray[i];
             let index = indexArray[i];
 
-            let bEqualMmdbid = (mmdbid_q == mmdbid_t);
+            // let bEqualMmdbid = (mmdbid_q == mmdbid_t);
+            let bEqualMmdbid = (mmdbid_q.substr(0,4) == mmdbid_t.substr(0,4));
             let bEqualChain = false;
 
             let queryData = {}; // check whether undefined
@@ -54298,7 +54527,7 @@ class ChainalignParser {
 
     transformStructure(mmdbid, index, alignType, bForce) { let ic = this.icn3d, me = ic.icn3dui;
         let chainidArray = ic.structures[mmdbid];
-
+        
         for(let i = 0, il = chainidArray.length; i < il; ++i) {
             for(let serial in ic.chains[chainidArray[i]]) {
                 let atm = ic.atoms[serial];
@@ -54430,6 +54659,26 @@ class ChainalignParser {
         return chainidArray;
     }
 
+    addPostfixForStructureids(structArray) { let ic = this.icn3d; ic.icn3dui;
+        let struct2cnt = {};
+        for(let i = 0, il = structArray.length; i < il; ++i) {
+            let struct = structArray[i].toUpperCase(); 
+
+            if(!struct2cnt.hasOwnProperty(struct)) {
+                struct2cnt[struct] = 1;
+            }
+            else {
+                ++struct2cnt[struct];
+            }
+
+            struct = (struct2cnt[struct] == 1) ? struct : struct + struct2cnt[struct];
+
+            structArray[i] = struct;
+        }
+
+        return structArray;
+    }
+
     async downloadChainalignment(chainalign) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
@@ -54471,6 +54720,7 @@ class ChainalignParser {
 
         ic.afChainIndexHash = {};
         ic.pdbChainIndexHash = {};
+
         for(let index = 1, indexLen = alignArray.length; index < indexLen; ++index) {
             let pos2 = alignArray[index].indexOf('_');
             let mmdbid_q_tmp = alignArray[index].substr(0, pos2).toUpperCase();
@@ -54578,7 +54828,8 @@ class ChainalignParser {
 
             if(queryData !== undefined && JSON.stringify(queryData).indexOf('Oops there was a problem') === -1
                 ) {
-                ic.mmdbidArray.push(mmdbid_q);
+                // ic.mmdbidArray.push(mmdbid_q);
+                ic.mmdbidArray.push(mmdbid_q.substr(0,4));
                 queryDataArray.push(queryData);
             }
             else {
@@ -54617,7 +54868,8 @@ class ChainalignParser {
                     // let align = (me.bNode) ? dataArray[index2 - missedChainCnt] : dataArray[index2 - missedChainCnt].value;//[0];
                     let align = dataArray[index2 - missedChainCnt].value;//[0];
 
-                    let bEqualMmdbid = (mmdbid_q == mmdbid_t);
+                    // let bEqualMmdbid = (mmdbid_q == mmdbid_t);
+                    let bEqualMmdbid = (mmdbid_q.substr(0,4) == mmdbid_t.substr(0,4));
                     let bEqualChain = (chain_q == chain_t);
 
                     me.htmlCls.clickMenuCls.setLogCmd("Align " + mmdbid_t + " with " + mmdbid_q, false);
@@ -54788,15 +55040,14 @@ class ChainalignParser {
 
         let structArray = [];
 
-        for(let i = 0, il = structArrayTmp.length; i < il; ++i) {
-            let id = structArrayTmp[i].toUpperCase();
-            // sometimes we want to load same structure multiple times
-            if(!ic.structures.hasOwnProperty(id) && structArray.indexOf(id) == -1) {
-                structArray.push(structArrayTmp[i]);
-            }
-            else {
-                // only when bNoDuplicate is undefined/false, it's allowed to load multiple copies of the same structure
-                if(!bNoDuplicate) structArray.push(structArrayTmp[i] + me.htmlCls.postfix);
+        // only when bNoDuplicate is undefined/false, it's allowed to load multiple copies of the same structure
+        if(!bNoDuplicate) {
+            structArray =  this.addPostfixForStructureids(structArrayTmp);
+        }
+        else {
+            for(let i = 0, il = structArrayTmp.length; i < il; ++i) {
+                let id = structArrayTmp[i].toUpperCase();
+                if(!ic.structures.hasOwnProperty(id)) structArray.push(structArrayTmp[i]);
             }
         }
         
@@ -58791,6 +59042,283 @@ class XyzParser {
     }
 }
 
+/**
+ * @author Jiyao Wang <wangjiy@ncbi.nlm.nih.gov> / https://github.com/ncbi/icn3d
+ */
+
+class MsaParser {
+    constructor(icn3d) {
+        this.icn3d = icn3d;
+    }
+
+    async loadMsaData(data, type) { let ic = this.icn3d, me = ic.icn3dui;
+        let bResult = await this.loadMsaSeqData(data, type);
+
+        if(me.cfg.align === undefined && Object.keys(ic.structures).length == 1) {
+            $("#" + ic.pre + "alternateWrapper").hide();
+        }
+
+        let typeStr = type.toUpperCase();
+
+        if(!bResult) {
+          var aaa = 1; //alert('The ' + typeStr + ' file has the wrong format...');
+        }
+        else {
+            // retrieve the structures
+            me.cfg.bu = 0; // show all chains
+            await ic.chainalignParserCls.downloadMmdbAf(ic.struArray.join(','));
+            me.htmlCls.clickMenuCls.setLogCmd('load mmdbaf0 ' + ic.struArray.join(','), true);
+
+            // get the position of the first MSA residue in the full sequence
+            let startPosArray = []; 
+            for(let i = 0, il = ic.inputChainidArray.length; i < il; ++i) {
+                let chainid = ic.inputChainidArray[i];
+                let inputSeqNoGap = ic.inputSeqArray[i].replace(/-/g, '');
+
+                // get the full seq
+                let fullSeq = '';
+                for(let j = 0, jl = ic.chainsSeq[chainid].length; j < jl; ++j) {
+                    fullSeq += ic.chainsSeq[chainid][j].name;
+                }
+
+                // find the starting position of "inputSeq" in "fullSeq" 
+                let pos = fullSeq.toUpperCase().indexOf(inputSeqNoGap.substr(0, 20).toUpperCase());
+                if(pos == -1) {
+                    console.log("The sequence of the aligned chain " + chainid + " (" + inputSeqNoGap.toUpperCase() + ") is different from the sequence from the structure (" + fullSeq.toUpperCase() + "), and is thus not aligned correctly...");
+                    pos = 0;
+                }
+                startPosArray.push(pos);
+            }
+
+            // define residue mapping
+            // The format is ": "-separated pairs: "1,5,10-50 | 1,5,10-50: 2,6,11-51 | 1,5,10-50"
+            let predefinedres = '';
+
+            let chainid1 = ic.inputChainidArray[0], inputSeq1 = ic.inputSeqArray[0], pos1 = startPosArray[0];
+            // loop through 2nd and forward
+            for(let i = 1, il = ic.inputChainidArray.length; i < il; ++i) {
+                let chainid2 = ic.inputChainidArray[i];
+                let inputSeq2 = ic.inputSeqArray[i];
+                let pos2 = startPosArray[i];
+
+                let index1 = pos1, index2 = pos2;
+                let resiArray1 = [], resiArray2 = [];
+                for(let j = 0, jl = inputSeq2.length; j < jl; ++j) {
+                    if(inputSeq1[j] != '-' && inputSeq2[j] != '-' && ic.chainsSeq[chainid1][index1] && ic.chainsSeq[chainid2][index2]) {
+                        let resi1 = ic.chainsSeq[chainid1][index1].resi;
+                        let resi2 = ic.chainsSeq[chainid2][index2].resi;
+                        if(ic.residues[chainid1 + '_' + resi1] && ic.residues[chainid2 + '_' + resi2]) {
+                            resiArray1.push(ic.chainsSeq[chainid1][index1].resi);
+                            resiArray2.push(ic.chainsSeq[chainid2][index2].resi);
+                        }
+                    }
+                    
+                    if(inputSeq1[j] != '-') ++index1;
+                    if(inputSeq2[j] != '-') ++index2;
+                }
+                let resiRangeStr1 = ic.resid2specCls.resi2range(resiArray1, true);
+                let resiRangeStr2 = ic.resid2specCls.resi2range(resiArray2, true);
+
+                predefinedres += resiRangeStr1 + ' | ' + resiRangeStr2;
+                if(i < il -1) predefinedres += ': ';
+            }
+
+            // realign based on residue by residue
+            let alignment_final = ic.inputChainidArray.join(',');
+
+            if(predefinedres && (alignment_final.split(',').length - 1) != predefinedres.split(': ').length) {
+                var aaa = 1; //alert("Please make sure the number of chains and the lines of predefined residues are the same...");
+                return;
+            }
+
+            me.cfg.resdef = predefinedres.replace(/:/gi, ';');
+
+            let bRealign = true, bPredefined = true;
+            let chainidArray = alignment_final.split(',');
+            await ic.realignParserCls.realignChainOnSeqAlign(undefined, chainidArray, bRealign, bPredefined);
+ 
+            me.htmlCls.clickMenuCls.setLogCmd("realign predefined " + alignment_final + " " + predefinedres, true);
+
+
+            ic.opts['color'] = 'identity';
+            ic.setColorCls.setColorByOptions(ic.opts, ic.hAtoms);
+            me.htmlCls.clickMenuCls.setLogCmd("color identity", true);
+
+            // show selection
+            ic.selectionCls.showSelection();
+            me.htmlCls.clickMenuCls.setLogCmd("show selection", true);
+        }
+    }
+
+    async loadMsaSeqData(data, type) { let ic = this.icn3d; ic.icn3dui;
+        let lines = data.split(/\r?\n|\r/);
+        if(lines.length < 2) return false;
+
+        ic.init();
+
+        ic.molTitle = "";
+
+        let seqHash = {};
+
+        let bStart = false, bSecBlock = false, chainid = '', seq = '', bFound = false;
+
+        if(type == 'clustalw' && lines[0].substr(0,7) != 'CLUSTAL') { // CLUSTAL W or CLUSTALW
+            return false;
+        }
+
+        let startLineNum = (type == 'clustalw') ? 1 : 0;
+
+        // 1. parse input msa
+        for(let i = startLineNum, il = lines.length; i < il; ++i) {
+            let line = lines[i].trim();
+            if(line === '') {
+                if(bStart) bSecBlock = true;
+                bStart = false;
+                continue;
+            }
+
+            if(!bStart) { // first line
+                if(type == 'fasta' && line.substr(0,1) != '>') {
+                    return false;
+                }
+                bStart = true;
+            }
+
+            if(type == 'clustalw') {
+                if(line.substr(0, 1) != ' ' && line.substr(0, 1) != '\t') {
+                    let chainid_seq = line.split(/\s+/);
+                    let idArray = chainid_seq[0].split('|');
+                    let result = this.getChainid(idArray, bStart && !bSecBlock);
+                    bFound = result.bFound;
+                    chainid = result.chainid;
+
+                    if(bFound) {
+                        if(!seqHash.hasOwnProperty(chainid)) {
+                            seqHash[chainid] = chainid_seq[1];
+                        }
+                        else {
+                            seqHash[chainid] += chainid_seq[1];
+                        }
+                    }
+                }
+            }
+            else if(type == 'fasta') {
+                if(line.substr(0,1) == ">") {
+                    // add the previous seq
+                    if(chainid && seq && bFound) seqHash[chainid] = seq;
+                    chainid = '';
+                    seq = '';
+
+                    let pos = line.indexOf(' ');
+                    let idArray = line.substr(1, pos).split('|');
+                    
+                    if(idArray.length == 1) {
+                        chainid = idArray[0];
+                    }
+                    else {
+                        let result = this.getChainid(idArray, true);
+                        bFound = result.bFound;
+                        chainid = result.chainid;
+                    }
+                }
+                else {
+                    seq += line;
+                }
+            }
+        }
+
+        // add the last seq
+        if(type == 'fasta' && chainid && seq && bFound) seqHash[chainid] = seq;
+
+        // 2. get the PDB ID or RefSeqID or AlphaFold ID
+        ic.inputChainidArray = [];
+        ic.inputSeqArray = [];
+        ic.struArray = [];
+
+        // find the tempate where the first residue is not gap
+        let template = '';
+        for(let chainid in seqHash) {
+            let seq = seqHash[chainid];
+            if(seq.substr(0,1) != '-') {
+                template = chainid;
+                await this.processOneChain(chainid, seqHash);
+                break;
+            }
+        }
+        if(!template) template = Object.keys(seqHash)[0];
+
+        for(let chainid in seqHash) {
+            if(chainid != template) await this.processOneChain(chainid, seqHash);
+        }
+
+        return true;
+    }
+
+    async processOneChain(chainid, seqHash) { let ic = this.icn3d, me = ic.icn3dui;
+        ic.inputSeqArray.push(seqHash[chainid]);
+        // ic.inputSeqArray.push(seqHash[chainid].replace(/-/g, '')); // remove the gaps in seq
+
+        if(chainid.lastIndexOf('_') == 2) { // refseq ID
+            // convert refseq to uniprot id
+            let url = me.htmlCls.baseUrl + "vastdyn/vastdyn.cgi?refseq2uniprot=" + chainid;
+    
+            let data = await me.getAjaxPromise(url, 'jsonp', false, 'The protein accession ' + chainid + ' can not be mapped to AlphaFold UniProt ID...');
+            if(data && data.uniprot) {
+                if(!ic.uniprot2acc) ic.uniprot2acc = {};
+                let uniprot = data.uniprot;
+                ic.uniprot2acc[uniprot] = chainid;
+                ic.struArray.push(uniprot);
+                ic.inputChainidArray.push(uniprot + '_A');
+            }
+            else {
+                console.log('The accession ' + refseqid + ' can not be mapped to AlphaFold UniProt ID. It will be treated as a UniProt ID instead.');
+                ic.struArray.push(chainid);
+                ic.inputChainidArray.push(chainid + '_A');
+            }
+        }
+        else if(chainid.indexOf('_') != -1) { // PDB ID
+            let stru = chainid.substr(0, chainid.indexOf('_')).substr(0, 4);
+            ic.struArray.push(stru);
+            ic.inputChainidArray.push(chainid);
+        }
+        else if(chainid.length > 5) { // UniProt ID
+            ic.struArray.push(chainid);
+            ic.inputChainidArray.push(chainid + '_A');
+        }
+    }
+
+    getChainid(idArray, bWarning) { let ic = this.icn3d; ic.icn3dui;
+        let bFound = false;
+        let chainid = idArray[0];
+
+        for(let j = 0, jl = idArray.length; j < jl; ++j) {
+            if(idArray[j] == 'pdb') {
+                chainid = idArray[j+1] + '_' + idArray[j+2];
+                bFound = true;
+                break;
+            }
+            else if(idArray[j] == 'ref') { // refseq
+                let refseq = idArray[j+1].split('.')[0];
+                chainid = refseq; // + '_A';
+                bFound = true;
+                break;
+            }
+            else if(idArray[j] == 'sp' || idArray[j] == 'tr') { // uniprot
+                let uniprot = idArray[j+1];
+                chainid = uniprot;
+                bFound = true;
+                break;
+            }
+        }
+
+        if(!bFound && bWarning) {
+            var aaa = 1; //alert("The sequence ID " + idArray.join('|') + " does not have the correctly formatted PDB, UniProt or RefSeq ID...");
+        }
+
+        return {chainid: chainid, bFound: bFound};
+    }
+}
+
 /**
  * @author Jiyao Wang <wangjiy@ncbi.nlm.nih.gov> / https://github.com/ncbi/icn3d
  */
@@ -58932,7 +59460,7 @@ class RealignParser {
       // If rmsd from vastsrv is too large, realign the chains
       //if(me.cfg.chainalign && !me.cfg.usepdbnum && me.cfg.resdef && rmsd > 5) {  
       // redo algnment only for VAST serv page 
-      if(!me.cfg.usepdbnum && me.cfg.resdef && rmsd > 5) {    
+      if(!me.cfg.usepdbnum && me.cfg.resdef && rmsd > 5 && me.cfg.chainalign) {    
         console.log("RMSD from VAST is larger than 5. Realign the chains with TM-align."); 
         //let nameArray = me.cfg.chainalign.split(',');
         let nameArray = Object.keys(chainidHash);
@@ -59388,7 +59916,8 @@ let resRangeArray = (me.cfg.resrange) ? decodeURIComponent(me.cfg.resrange).spli
         let predefinedResArray, predefinedResPair;
 
         if(bPredefined) {
-            predefinedResArray = decodeURIComponent(me.cfg.resdef).trim().replace(/\+/gi, ' ').split(': ');
+            // predefinedResArray = decodeURIComponent(me.cfg.resdef).trim().replace(/\+/gi, ' ').split(': ');
+            predefinedResArray = decodeURIComponent(me.cfg.resdef).trim().replace(/\+/gi, ' ').split('; ');
             
             if(predefinedResArray.length != chainidArray.length - 1) {
                var aaa = 1; //alert("Please make sure the number of chains and the lines of predefined residues are the same...");
@@ -59665,7 +60194,7 @@ class DensityCifParser {
        let thisClass = this;
 
        let url;
-       let detail = (me.utilsCls.isMobile() || me.cfg.notebook) ? 2 : 4; //0 : 4;
+       let detail = (me.utilsCls.isMobile() || me.cfg.notebook) ? 0 : 4; // max 6
 
        //https://www.ebi.ac.uk/pdbe/densities/doc.html
        if(type == '2fofc' || type == 'fofc') {
@@ -59676,6 +60205,7 @@ class DensityCifParser {
             url = "https://www.ebi.ac.uk/pdbe/volume-server/x-ray/" + pdbid.toLowerCase() + "/box/" + min_max[0][0] + "," + min_max[0][1] + "," + min_max[0][2] + "/" + min_max[1][0] + "," + min_max[1][1] + "," + min_max[1][2] + "?detail=" + detail;
        }
        else if(type == 'em') {
+           detail = (me.utilsCls.isMobile() || me.cfg.notebook) ? 0: 5; // max 6
            url = "https://www.ebi.ac.uk/pdbe/densities/emd/" + emd.toLowerCase() + "/cell?detail=" + detail;
        }
 
@@ -61035,7 +61565,8 @@ class ParserUtils {
               ic.rmsd_supr = me.rmsdSuprCls.getRmsdSuprCls(coordsFrom, coordsTo, n);
 
               // apply matrix for each atom
-              if(ic.rmsd_supr.rot !== undefined && ic.rmsd_supr.rmsd < 0.1) {
+            //   if(ic.rmsd_supr.rot !== undefined && ic.rmsd_supr.rmsd < 0.1) {
+              if(ic.rmsd_supr.rot !== undefined && ic.rmsd_supr.rmsd < 1) { // 6M17 has some coordinates change and rmsd is 0.3
                   let rot = ic.rmsd_supr.rot;
                   let centerFrom = ic.rmsd_supr.trans1;
                   let centerTo = ic.rmsd_supr.trans2;
@@ -61249,11 +61780,12 @@ class ParserUtils {
       
       // set defined sets before loadScript
       if(ic.bInitial) {
-        if(me.cfg.mobilemenu) {
-            me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.simpleMenus);
-            let bNoSave = true;
-            me.htmlCls.clickMenuCls.applyShownMenus(bNoSave);
-        }
+        // if(me.cfg.mobilemenu) {
+        //     me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.simpleMenus);
+        //     let bNoSave = true;
+        //     me.htmlCls.clickMenuCls.applyShownMenus(bNoSave);
+        // }
+
         // else {
         //     me.htmlCls.shownMenus = me.hashUtilsCls.cloneHash(me.htmlCls.allMenus);
         //     me.htmlCls.clickMenuCls.applyShownMenus();
@@ -61310,6 +61842,10 @@ class ParserUtils {
               if(me.cfg.closepopup || me.cfg.imageonly) {
                   ic.resizeCanvasCls.closeDialogs();
               }
+
+              if(!me.cfg.showlogo) {
+                $("#ncbi_logo").hide();
+              }
           }
           else {
               ic.hlUpdateCls.updateHlAll();
@@ -63725,7 +64261,7 @@ class SetSeqAlign {
 
     setMsaFormat(chainidArray) { let ic = this.icn3d; ic.icn3dui;
         //set MSA
-        let fastaFormat = '', clustalFormat = 'CLUSTALW\n\n', resbyresFormat = '';
+        let fastaFormat = '', clustalwFormat = 'CLUSTALWW\n\n', resbyresFormat = '';
         let chainArrayClustal = [];
         
         let consArray = [], resiArrayTemplate = [];
@@ -63734,8 +64270,8 @@ class SetSeqAlign {
             let chainid = chainidArray[i];
             fastaFormat += '>' + chainid + '\n';
 
-            let clustalArray = [];
-            let clustalLine = chainid.padEnd(20, ' ');
+            let clustalwArray = [];
+            let clustalwLine = chainid.padEnd(20, ' ');
             let consLine = ''.padEnd(20, ' ');
 
             let resiArrayTarget = [], resiArrayQuery = [];
@@ -63744,7 +64280,7 @@ class SetSeqAlign {
             for(let j = 0, jl = ic.alnChainsSeq[chainid].length; j < jl; ++j) {
                 let resn = ic.alnChainsSeq[chainid][j].resn;
                 fastaFormat += resn;
-                clustalLine += resn;
+                clustalwLine += resn;
                 if(i == il - 1) {
                     let alignedClass = ic.alnChainsSeq[chainid][j].class;
                     if(alignedClass == 'icn3d-cons') {
@@ -63763,7 +64299,8 @@ class SetSeqAlign {
                     resiArrayTemplate.push(ic.alnChainsSeq[chainid][j].resi);
                 }
                 else {
-                    if(ic.alnChainsSeq[chainid][j].aligned) {
+                    // if(ic.alnChainsSeq[chainid][j].aligned) {
+                    if(ic.alnChainsSeq[chainid][j].aligned && ic.alnChainsSeq[chainidTemplate][j] && ic.alnChainsSeq[chainid][j]) {
                         resiArrayTarget.push(ic.alnChainsSeq[chainidTemplate][j].resi);
                         resiArrayQuery.push(ic.alnChainsSeq[chainid][j].resi);
                     }
@@ -63773,9 +64310,9 @@ class SetSeqAlign {
 
                 if(cnt % 60 == 0) {
                     fastaFormat += '\n';
-                    clustalLine += ' ' + String(parseInt(cnt / 60) * 60);
-                    clustalArray.push(clustalLine);
-                    clustalLine = chainid.padEnd(20, ' ');
+                    clustalwLine += ' ' + String(parseInt(cnt / 60) * 60);
+                    clustalwArray.push(clustalwLine);
+                    clustalwLine = chainid.padEnd(20, ' ');
 
                     if(i == il - 1) {
                         consArray.push(consLine);
@@ -63786,7 +64323,7 @@ class SetSeqAlign {
 
             // add last line
             if(cnt % 60 != 0) {
-                clustalArray.push(clustalLine);
+                clustalwArray.push(clustalwLine);
                 if(i == il - 1) {
                     consArray.push(consLine);
                 }
@@ -63794,7 +64331,7 @@ class SetSeqAlign {
 
             fastaFormat += '\n';
 
-            chainArrayClustal.push(clustalArray);
+            chainArrayClustal.push(clustalwArray);
             if(i == il - 1) chainArrayClustal.push(consArray);
 
             // residue by residue
@@ -63804,23 +64341,23 @@ class SetSeqAlign {
             if(i > 0) resbyresFormat += resiRangeStr1 + ' | ' + resiRangeStr2 + '\n';
         }
 
-        // CLUSTALW
+        // CLUSTALWW
         for(let j = 0, jl = chainArrayClustal[0].length; j < jl; ++j) {
             for(let i = 0, il = chainArrayClustal.length; i < il; ++i) {
-                clustalFormat += chainArrayClustal[i][j] + '\n';
+                clustalwFormat += chainArrayClustal[i][j] + '\n';
             }
-            clustalFormat += '\n';
+            clustalwFormat += '\n';
         }
         
         // seq MSA
         if(!ic.msa) ic.msa = {};
 
         if(!ic.msa['fasta']) ic.msa['fasta'] = [];
-        if(!ic.msa['clustal']) ic.msa['clustal'] = [];
+        if(!ic.msa['clustalw']) ic.msa['clustalw'] = [];
         if(!ic.msa['resbyres']) ic.msa['resbyres'] = [];
 
         ic.msa['fasta'].push(fastaFormat);
-        ic.msa['clustal'].push(clustalFormat);
+        ic.msa['clustalw'].push(clustalwFormat);
         ic.msa['resbyres'].push(resbyresFormat);
     }
 }
@@ -66576,6 +67113,12 @@ class ApplyCommand {
       else if(command == 'set slab off') {
         ic.opts['slab'] = 'no';
       }
+      else if(command == 'stereo on') {
+        ic.opts['effect'] = 'stereo';
+      }
+      else if(command == 'stereo off') {
+        ic.opts['effect'] = 'none';
+      }
       else if(command == 'set assembly on') {
         ic.bAssembly = true;
       }
@@ -68649,16 +69192,26 @@ class DefinedSets {
        } // outer for
     }
 
-    setHAtomsFromSets(nameArray, type) { let ic = this.icn3d, me = ic.icn3dui;
+    setHAtomsFromSets(nameArray, type) { let ic = this.icn3d; ic.icn3dui;
        for(let i = 0; i < nameArray.length; ++i) {
          let selectedSet = nameArray[i];
 
-         if((ic.defNames2Atoms === undefined || !ic.defNames2Atoms.hasOwnProperty(selectedSet)) &&(ic.defNames2Residues === undefined || !ic.defNames2Residues.hasOwnProperty(selectedSet)) ) continue;
+         this.setHAtomsFromSets_base(selectedSet, type);
 
+         // sometimes the "resi" changed and thus the name changed
+         //"sphere." + firstAtom.chain + ":" + me.utilsCls.residueName2Abbr(firstAtom.resn.substr(0, 3)).trim() + firstAtom.resi + "-" + radius + "A";
+         if(Object.keys(ic.hAtoms).length == 0 && (selectedSet.split('.')[0] == 'sphere' || selectedSet.split('.')[0] == 'interactions')) {
+            let pos = selectedSet.lastIndexOf('-');
+            selectedSet = selectedSet.split('.')[0] + selectedSet.substr(pos);
+            this.setHAtomsFromSets_base(selectedSet, type);
+         }
+       } // outer for
+    }
+
+    setHAtomsFromSets_base(selectedSet, type) { let ic = this.icn3d, me = ic.icn3dui;
          if(ic.defNames2Atoms !== undefined && ic.defNames2Atoms.hasOwnProperty(selectedSet)) {
 
              let atomArray = ic.defNames2Atoms[selectedSet];
-
              if(type === 'or') {
                  for(let j = 0, jl = atomArray.length; j < jl; ++j) {
                      ic.hAtoms[atomArray[j]] = 1;
@@ -68704,7 +69257,6 @@ class DefinedSets {
                  ic.hAtoms = me.hashUtilsCls.exclHash(ic.hAtoms, atomHash);
              }
          }
-       } // outer for
     }
 
     updateAdvancedCommands(nameArray, type) { let ic = this.icn3d; ic.icn3dui;
@@ -68727,6 +69279,7 @@ class DefinedSets {
 
     combineSets(orArray, andArray, notArray, commandname) { let ic = this.icn3d, me = ic.icn3dui;
        ic.hAtoms = {};
+       
        this.setHAtomsFromSets(orArray, 'or');
 
        if(Object.keys(ic.hAtoms).length == 0) {
@@ -70165,6 +70718,10 @@ class LoadScript {
             ic.resizeCanvasCls.resizeCanvas(me.htmlCls.WIDTH, me.htmlCls.HEIGHT, true);
         }
 
+        if(!me.cfg.showlogo) {
+          $("#ncbi_logo").hide();
+        }
+
         // an extra render to remove artifacts in transparent surface
         if(ic.bTransparentSurface && ic.bRender) ic.drawCls.render();
 
@@ -70822,19 +71379,22 @@ class Selection {
     selectSideChains() { let ic = this.icn3d, me = ic.icn3dui;
         let currHAtoms = me.hashUtilsCls.cloneHash(ic.hAtoms);
 
-        //let nuclMainArray = ["C1'", "C1*", "C2'", "C2*", "C3'", "C3*", "C4'", "C4*", "C5'", "C5*", "O3'", "O3*", "O4'", "O4*", "O5'", "O5*", "P", "OP1", "O1P", "OP2", "O2P"];
+        ic.hAtoms = this.getSideAtoms(currHAtoms);
+        ic.hlUpdateCls.showHighlight();
+    }
 
-        ic.hAtoms = {};
-        for(let i in currHAtoms) {
+    getSideAtoms(atoms) { let ic = this.icn3d, me = ic.icn3dui;
+        let sideAtoms = {};
+        for(let i in atoms) {
             if((ic.proteins.hasOwnProperty(i) && ic.atoms[i].name !== "N" && ic.atoms[i].name !== "H" 
               && ic.atoms[i].name !== "C" && ic.atoms[i].name !== "O"
               && !(ic.atoms[i].name === "CA" && ic.atoms[i].elem === "C") && ic.atoms[i].name !== "HA")
               ||(ic.nucleotides.hasOwnProperty(i) && me.parasCls.nuclMainArray.indexOf(ic.atoms[i].name) === -1) ) {
-                ic.hAtoms[i] = 1;
+                sideAtoms[i] = 1;
             }
         }
 
-        ic.hlUpdateCls.showHighlight();
+        return sideAtoms;
     }
 
     selectMainSideChains() { let ic = this.icn3d, me = ic.icn3dui;
@@ -71450,9 +72010,12 @@ class Resid2spec {
     resi2range(resiArray, bString) {var ic = this.icn3d; ic.icn3dui;
         let range = [], rangeStr = '';
     
-        let resiArraySorted = resiArray.sort(function(a, b) {
-           return parseInt(a) - parseInt(b);
-        });
+        // some chains such as 3SN6_R start with residues with high residue numbers, then end with residues with low residue numbers
+        // let resiArraySorted = resiArray.sort(function(a, b) {
+        //    return parseInt(a) - parseInt(b);
+        // });
+
+        let resiArraySorted = resiArray;
         
         let startResi = resiArraySorted[0];
         let prevResi, resi;
@@ -72737,18 +73300,29 @@ class Dssp {
 
                 ic.pdbDataArray = await this.promiseWithFixedJobs(pdbAjaxArray);
 
-                let bNoMoreIg = await thisClass.parseRefPdbData(ic.pdbDataArray, template);
                 let numRound = 0;
+                let bNoMoreIg = await thisClass.parseRefPdbData(ic.pdbDataArray, template, undefined, numRound);
+                 ++numRound;
 
                 //while(!bNoMoreIg) {
                 while(!bNoMoreIg && numRound < 15) {
                     let bRerun = true;
-                    bNoMoreIg = await thisClass.parseRefPdbData(ic.pdbDataArray, template, bRerun);
+                    bNoMoreIg = await thisClass.parseRefPdbData(ic.pdbDataArray, template, bRerun, numRound);
                     ++numRound;
                 }
             }
             else {
-                await thisClass.parseRefPdbData(undefined, template);
+                await thisClass.parseRefPdbData(undefined, template, undefined, numRound);
+            }
+
+            // refnum should be adjusted after all Ig are detected since sometimes the sheet extension may affect another Ig domain
+            if(!ic.chainid2igtrack) ic.chainid2igtrack = {};
+            for(let chainid in ic.chains) {
+                let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.chains[chainid]);
+                if(ic.proteins.hasOwnProperty(atom.serial)) {
+                    let giSeq = ic.showSeqCls.getSeq(chainid);
+                    ic.chainid2igtrack[chainid] = this.ajdustRefnum(giSeq, chainid);
+                }
             }
         // }
         // catch(err) {
@@ -72757,7 +73331,7 @@ class Dssp {
         // }
     }
 
-    async parseRefPdbData(dataArray, template, bRerun) { let ic = this.icn3d, me = ic.icn3dui;
+    async parseRefPdbData(dataArray, template, bRerun, numRound) { let ic = this.icn3d, me = ic.icn3dui;
         let thisClass = this;
 
         let struArray = Object.keys(ic.structures);
@@ -72851,7 +73425,7 @@ class Dssp {
                 dataArray2 = await this.promiseWithFixedJobs(ajaxArray);
 
                 let bRound1 = true;
-                bNoMoreIg = await thisClass.parseAlignData(dataArray2, domainidpairArray, bRound1);
+                bNoMoreIg = await thisClass.parseAlignData(dataArray2, domainidpairArray, bRound1, numRound);
 
                 /// if(ic.deferredRefnum !== undefined) ic.deferredRefnum.resolve();
             }
@@ -72897,7 +73471,7 @@ class Dssp {
 
                 dataArray3 = await this.promiseWithFixedJobs(ajaxArray);
 
-                bNoMoreIg = await thisClass.parseAlignData(dataArray3, domainidpairArray3);
+                bNoMoreIg = await thisClass.parseAlignData(dataArray3, domainidpairArray3, undefined, numRound);
             }
 
             return bNoMoreIg;
@@ -73125,7 +73699,7 @@ class Dssp {
                             delete ic.domainid2refpdbname[domainid];
                             delete ic.domainid2score[domainid];
                         }
-                        continue;  
+                        continue;                          
                   }
                 // }
             }
@@ -73189,7 +73763,7 @@ class Dssp {
         return domainid2segs; // only used in round 2
     }
 
-    async parseAlignData(dataArray, domainidpairArray, bRound1) { let ic = this.icn3d, me = ic.icn3dui;
+    async parseAlignData(dataArray, domainidpairArray, bRound1, numRound) { let ic = this.icn3d, me = ic.icn3dui;
         let bNoMoreIg = false;
 
         let domainid2segs = this.parseAlignData_part1(dataArray, domainidpairArray, bRound1);
@@ -73214,7 +73788,8 @@ class Dssp {
                 //let pdbid = domainid.substr(0, domainid.indexOf('_'));
                 let chainid = domainid.substr(0, domainid.indexOf(','));
 
-                if(ic.refpdbHash.hasOwnProperty(chainid)) {
+                // Adjusted refpdbname in the first try
+                if(ic.refpdbHash.hasOwnProperty(chainid) && numRound == 0) {
                     refpdbnameList = [chainid];
 
                     if(!me.bNode) console.log("Adjusted refpdbname for domainid " + domainid + ": " + chainid);
@@ -73267,7 +73842,7 @@ class Dssp {
 
             dataArray3 = await this.promiseWithFixedJobs(ajaxArray);
 
-            bNoMoreIg = await this.parseAlignData(dataArray3, domainidpairArray3, false);
+            bNoMoreIg = await this.parseAlignData(dataArray3, domainidpairArray3, false, numRound);
 
             // end of round 2
             return bNoMoreIg;
@@ -73512,6 +74087,8 @@ class Dssp {
             }
         }
 
+        // refnum should be adjusted after all Ig are detected since sometimes the sheet extension may affect another Ig domain
+        /*
         if(!ic.chainid2igtrack) ic.chainid2igtrack = {};
         for(let chainid in ic.chains) {
             let atom = ic.firstAtomObjCls.getFirstAtomObj(ic.chains[chainid]);
@@ -73520,6 +74097,7 @@ class Dssp {
                 ic.chainid2igtrack[chainid] = this.ajdustRefnum(giSeq, chainid);
             }
         }
+        */
     }
 
     getStrandFromRefnum(oriRefnum, finalStrand) { let ic = this.icn3d; ic.icn3dui;
@@ -78452,7 +79030,7 @@ 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', 'dl_translate'];
+        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_clustalwfile', 'dl_fastafile', '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];
@@ -79198,9 +79776,10 @@ class SaveFile {
                 ssObj.resn = atom.resn;
                 ssObj.resi = atom.resi;
 
-                if(parseInt(atom.resi) > parseInt(prevResi) + 1) {
-                    ssObj.ss = ' ';
-                    ssArray.push(ssObj);
+                if(parseInt(atom.resi) > parseInt(prevResi) + 1  || atom.ssbegin) {
+                    let ssObj2 = me.hashUtilsCls.cloneHash(ssObj);
+                    ssObj2.ss = ' ';
+                    ssArray.push(ssObj2);
                 }
 
                 if(atom.ss == 'helix') {
@@ -79211,13 +79790,13 @@ class SaveFile {
                     ssObj.ss = 'S';
                     ssArray.push(ssObj);
                 }
-
+/*
                 if(atom.ssend) {
                     let ssObj2 = me.hashUtilsCls.cloneHash(ssObj);
                     ssObj2.ss = ' ';
                     ssArray.push(ssObj2);
                 }
-
+*/
                 prevResi = atom.resi;
             }
 
@@ -79225,9 +79804,9 @@ class SaveFile {
             for(let i = 0, il = ssArray.length; i < il; ++i) {
                 let ssObj = ssArray[i];
 
-                if(ssObj.ss != prevSs || ssObj.ssbegin) {
+                if(ssObj.ss != prevSs) {
                     // print prev
-                    stru2header[stru] += this.printPrevSecondary(bHelix, bSheet, prevRealSsObj, ssCnt);
+                    if(prevSs !== ' ') stru2header[stru] += this.printPrevSecondary(bHelix, bSheet, prevRealSsObj, ssCnt);
 
                     // print current
                     ssCnt = 0;
@@ -79235,7 +79814,7 @@ class SaveFile {
                     bSheet = false;
                     prevRealSsObj = undefined;
 
-                    if(ssObj.ss != ' ') {
+                    if(ssObj.ss !== ' ') {
                         if(ssObj.ss == 'H') {
                             bHelix = true;
                             prevRealSsObj = ssObj;
@@ -79251,7 +79830,7 @@ class SaveFile {
                     }
                 }
 
-                if(ssObj.ss != ' ') {
+                if(ssObj.ss !== ' ') {
                     ++ssCnt;
                     prevRealSsObj = ssObj;
                 }
@@ -79899,7 +80478,7 @@ class ShareLink {
                     let shortName = strArray[strArray.length - 1];
                     ic.saveFileCls.saveFile(inputid + '-' + shortName + '.png', 'png');
                     let text = '<div style="float:left; border: solid 1px #0000ff; padding: 5px; margin: 10px; text-align:center;">';
-                    text += '<a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/share.html?' + shortName + '" target="_blank">';
+                    text += '<a href="https://www.ncbi.nlm.nih.gov/Structure/icn3d/share2.html?' + shortName + '" target="_blank">';
                     text += '<img style="height:300px" src ="' + inputid + '-' + shortName + '.png"><br>\n';
                     text += '<!--Start of your comments==================-->\n';
                     let yournote =(ic.yournote) ? ': ' + ic.yournote.replace(/\n/g, "<br>").replace(/; /g, ", ") : '';
@@ -79914,13 +80493,14 @@ class ShareLink {
             if(bPngHtml && data.shortLink === undefined) {
                 ic.saveFileCls.saveFile(inputid + '_icn3d_loadable.png', 'png');
             }
-
+/*
             //shorturl: https://icn3d.page.link/NvbAh1Vmiwc4bgX87
             let urlArray = shorturl.split('page.link/');
-            //if(urlArray.length == 2) shorturl = me.htmlCls.baseUrl + 'icn3d/share.html?' + urlArray[1];
             // When the baseURL is structure.ncbi.nlm.nih.gov, mmcifparser.cgi has a problem to pass posted data in Mac/iphone
             // So the base URL is still www.ncbi.nlm.nih.gov/Structure,just use short URL here
             if(urlArray.length == 2) shorturl = 'https://www.ncbi.nlm.nih.gov/Structure/icn3d/share.html?' + urlArray[1];
+*/
+            shorturl = 'https://www.ncbi.nlm.nih.gov/Structure/icn3d/share2.html?' + shorturl;
 
             $("#" + ic.pre + "short_url").val(shorturl);
             $("#" + ic.pre + "short_url_title").val(shorturl + '&t=' + ic.yournote);
@@ -79939,6 +80519,7 @@ class ShareLink {
     }
 
     getShareLinkPrms(url, bPngHtml) { let ic = this.icn3d, me = ic.icn3dui;
+        /*
         //https://firebase.google.com/docs/dynamic-links/rest
         //Web API Key: AIzaSyBxl9CgM0dY5lagHL4UOhEpLWE1fuwdnvc
         let fdlUrl = "https://firebasedynamiclinks.googleapis.com/v1/shortLinks?key=AIzaSyBxl9CgM0dY5lagHL4UOhEpLWE1fuwdnvc";
@@ -79962,6 +80543,26 @@ class ShareLink {
                 }
             });
         });
+        */
+
+        let serviceUrl = "https://icn3d.link/?longurl=" + encodeURIComponent(url);
+        return new Promise(function(resolve, reject) {
+            $.ajax({
+                url: serviceUrl,
+                dataType: 'json',
+                cache: true,
+                success: function(data) {
+                    resolve(data);
+                },
+                error : function(xhr, textStatus, errorThrown ) {
+                    let shorturl = 'Problem in getting shortened URL';
+                    $("#" + ic.pre + "ori_url").val(url);
+                    $("#" + ic.pre + "short_url").val(shorturl);
+                    $("#" + ic.pre + "short_url_title").val(shorturl + '&t=' + ic.yournote);
+                    if(!bPngHtml) me.htmlCls.dialogCls.openDlg('dl_copyurl', 'Copy a Share Link URL');
+                }
+            });
+        });
     }
 
     shareLinkUrl(bAllCommands, bOutputCmd, bStatefile) { let ic = this.icn3d, me = ic.icn3dui;
@@ -79988,6 +80589,7 @@ class ShareLink {
                 if(key === 'height' && value === '100%') continue;
 
                 if(key === 'resize' && value === true) continue;
+                if(key === 'showlogo' && value === true) continue;
                 if(key === 'showmenu' && value === true) continue;
                 if(key === 'showtitle' && value === true) continue;
                 if(key === 'showcommand' && value === true) continue;
@@ -81100,8 +81702,10 @@ class Ray {
         this.icn3d = icn3d;
     }
 
-    rayCaster(e, bClick) {
+    rayCaster(e, bClick) { let ic = this.icn3d; ic.icn3dui;
+      if(!ic.opts || ic.opts['effect'] == 'none') {
         this.rayCasterBase(e, bClick);
+      }
     }
 
     rayCasterBase(e, bClick) { let ic = this.icn3d; ic.icn3dui;
@@ -82422,6 +83026,14 @@ class iCn3D {
                 });
             }
 
+            this.effects = {
+                //'anaglyph': new THREE.AnaglyphEffect(this.renderer),
+                //'parallax barrier': new THREE.ParallaxBarrierEffect(this.renderer),
+                //'oculus rift': new THREE.OculusRiftEffect(this.renderer),
+                'stereo': new THREE.StereoEffect(this.renderer),
+                'none': this.renderer
+            };
+
             this.overdraw = 0;
         }
         else {
@@ -82568,14 +83180,6 @@ class iCn3D {
 
     this.bExtrude = true;
 
-    this.effects = {
-        //'anaglyph': new THREE.AnaglyphEffect(this.renderer),
-        //'parallax barrier': new THREE.ParallaxBarrierEffect(this.renderer),
-        //'oculus rift': new THREE.OculusRiftEffect(this.renderer),
-        //'stereo': new THREE.StereoEffect(this.renderer),
-        'none': this.renderer
-    };
-
     this.maxD = 500; // size of the molecule
     this.oriMaxD = this.maxD; // size of the molecule
     //this.cam_z = -150;
@@ -82628,6 +83232,7 @@ class iCn3D {
     //The default display options
     this.optsOri = {};
     this.optsOri['camera']             = 'perspective';        //perspective, orthographic
+    this.optsOri['effect']             = 'none';               //stereo, none
     this.optsOri['background']         = 'black';              //transparent, black, grey, white
     this.optsOri['color']              = 'chain';              //spectrum, secondary structure, charge, hydrophobic, conserved, chain, residue, atom, b factor, red, green, blue, magenta, yellow, cyan, white, grey, custom, ig strand
     this.optsOri['proteins']           = 'ribbon';             //ribbon, strand, cylinder and plate, schematic, c alpha trace, backbone, b factor tube, lines, stick, ball and stick, sphere, nothing
@@ -82821,6 +83426,7 @@ class iCn3D {
     this.pdbParserCls = new PdbParser(this);
     this.sdfParserCls = new SdfParser(this);
     this.xyzParserCls = new XyzParser(this);
+    this.msaParserCls = new MsaParser(this);
     this.realignParserCls = new RealignParser(this);
     this.densityCifParserCls = new DensityCifParser(this);
     this.ParserUtilsCls = new ParserUtils(this);
@@ -83077,7 +83683,7 @@ class iCn3DUI {
     //even when multiple iCn3D viewers are shown together.
     this.pre = this.cfg.divid + "_";
 
-    this.REVISION = '3.41.0';
+    this.REVISION = '3.43.0';
 
     // In nodejs, iCn3D defines "window = {navigator: {}}"
     this.bNode = (Object.keys(window).length < 2) ? true : false;
@@ -83086,6 +83692,7 @@ class iCn3DUI {
     if(this.cfg.width === undefined) this.cfg.width = '100%';
     if(this.cfg.height === undefined) this.cfg.height = '100%';
     if(this.cfg.resize === undefined) this.cfg.resize = true;
+    if(this.cfg.showlogo === undefined) this.cfg.showlogo = true;
     if(this.cfg.showmenu === undefined) this.cfg.showmenu = true;
     if(this.cfg.showtitle === undefined) this.cfg.showtitle = true;
     if(this.cfg.showcommand === undefined) this.cfg.showcommand = true;
@@ -83506,8 +84113,12 @@ iCn3DUI.prototype.show3DStructure = async function(pdbStr) { let me = this;
     }
     else if(me.cfg.align !== undefined) {
         // ic.bNCBI = true;
-
+        if(me.cfg.align.indexOf('185055,') != -1) {
+            me.cfg.align = me.cfg.align.replace('185055,', '199731,'); //the mmdbid of PDB 6M17 was changed from 185055 to 199731
+        }
+ 
         let alignArray = me.cfg.align.split(','); // e.g., 6 IDs: 103701,1,4,68563,1,167 [mmdbid1,biounit,molecule,mmdbid2,biounit,molecule], or 2IDs: 103701,68563 [mmdbid1,mmdbid2]
+        
         if(alignArray.length === 6) {
             ic.inputid = alignArray[0] + "_" + alignArray[3];
         }
@@ -83900,6 +84511,7 @@ exports.MarchingCube = MarchingCube;
 exports.MmcifParser = MmcifParser;
 exports.MmdbParser = MmdbParser;
 exports.Mol2Parser = Mol2Parser;
+exports.MsaParser = MsaParser;
 exports.MyEventCls = MyEventCls;
 exports.OpmParser = OpmParser;
 exports.ParasCls = ParasCls;