Ticket #2675: Error-log-1.html

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1<!DOCTYPE html>
2<html>
3<head>
4<title> ChimeraX Log </title>
5<script type="text/javascript">
6/*
7 * === UCSF ChimeraX Copyright ===
8 * Copyright 2016 Regents of the University of California.
9 * All rights reserved. This software provided pursuant to a
10 * license agreement containing restrictions on its disclosure,
11 * duplication and use. For details see:
12 * http://www.rbvi.ucsf.edu/chimerax/docs/licensing.html
13 * This notice must be embedded in or attached to all copies,
14 * including partial copies, of the software or any revisions
15 * or derivations thereof.
16 * === UCSF ChimeraX Copyright ===
17 */
18
19window.onload = function() {
20 cxlinks_base="http://www.rbvi.ucsf.edu/chimerax/docs/"
21 if(!window.navigator.userAgent.includes("ChimeraX")){
22 window.onclick = function(e){
23 if(e.target.tagName.toLowerCase()!="a")
24 return true;
25 var url=e.target.getAttribute("href").toLowerCase();
26 if(url.startsWith("help:")){
27 window.location.href = cxlinks_base + url.substring(5);
28 return false;
29 }
30 if(url.startsWith("cxcmd:")){
31 alert("This link only works in a ChimeraX browser and would execute a command.");
32 return false;
33 }
34 return true;
35 }
36 var ls=document.links;
37 for(var i=0;i<ls.length;i++){
38 var link=ls[i];
39 var url=link.getAttribute("href").toLowerCase();
40 if(url.startsWith("cxcmd:"))
41 link.style.color="darkred";
42 }
43 }
44};
45</script>
46</head>
47<h1> ChimeraX Log </h1>
48<style>
49
50.cxcmd {
51 display: block;
52 font-weight: bold;
53 margin-top: .5em;
54 background-color: #ddd;
55}
56a.no_underline {
57 text-decoration: none;
58}
59
60.cxcmd_as_doc {
61 display: inline;
62}
63.cxcmd_as_cmd {
64 display: none;
65}
66</style>
67
68<table border=1 cellpadding=4 cellspacing=0>
69 <thead>
70 <tr>
71 <th colspan="2">Startup Messages</th>
72 </tr>
73 </thead>
74 <tbody>
75 <tr>
76 <td><i>warning</i></td> <td style="background-color:#ffb961">&#x27;clip&#x27; is a prefix of an existing command &#x27;clipper&#x27;</td> </tr>
77 </tbody>
78</table><br/>UCSF ChimeraX version: 0.91 (2019-07-07)<br>
79© 2016-2019 Regents of the University of California. All rights reserved.<br>
80<a href="cxcmd:help help:credits.html">How to cite UCSF ChimeraX</a><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;C:\\Users\\khan\\Desktop\\IUCrJ_Revision\\IUCrJ\\1st Revision\\Figures\\Supporting Information\\emd_6716.map&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;C:\\Users\\khan\\Desktop\\IUCrJ_Revision\\IUCrJ\\1st Revision\\Figures\\Supporting Information\\emd_6716.map&quot;">open &quot;C:\\Users\\khan\\Desktop\\IUCrJ_Revision\\IUCrJ\\1st Revision\\Figures\\Supporting Information\\emd_6716.map&quot;</a></div></div>Opened emd_6716.map, grid size 60,60,60, pixel 4.8, shown at level 1.77, step 1, values float32<br>
81<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/set.html">set</a> bgColor white</div><div class="cxcmd_as_cmd"><a href="cxcmd:set bgColor white">set bgColor white</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html#image">save image</a> &quot;C:/Users/khan/Desktop/IUCrJ_Revision/IUCrJ/1st Revision/Figures/Supporting Information/Suzuki_etal04.bmp&quot; width 488 height 516</div><div class="cxcmd_as_cmd"><a href="cxcmd:save image &quot;C:/Users/khan/Desktop/IUCrJ_Revision/IUCrJ/1st Revision/Figures/Supporting Information/Suzuki_etal04.bmp&quot; width 488 height 516">save image &quot;C:/Users/khan/Desktop/IUCrJ_Revision/IUCrJ/1st Revision/Figures/Supporting Information/Suzuki_etal04.bmp&quot; width 488 height 516</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/save.html">save</a> &quot;C:/Users/khan/Desktop/IUCrJ_Revision/IUCrJ/1st Revision/Figures/Supporting Information/Suzuki_etal04.mrc&quot; models #1</div><div class="cxcmd_as_cmd"><a href="cxcmd:save &quot;C:/Users/khan/Desktop/IUCrJ_Revision/IUCrJ/1st Revision/Figures/Supporting Information/Suzuki_etal04.mrc&quot; models #1">save &quot;C:/Users/khan/Desktop/IUCrJ_Revision/IUCrJ/1st Revision/Figures/Supporting Information/Suzuki_etal04.mrc&quot; models #1</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/open.html">open</a> &quot;C:/Users/khan/Desktop/IUCrJ_Revision/IUCrJ/1st Revision/Figures/Supporting Information/EMD-1887.map&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:open &quot;C:/Users/khan/Desktop/IUCrJ_Revision/IUCrJ/1st Revision/Figures/Supporting Information/EMD-1887.map&quot;">open &quot;C:/Users/khan/Desktop/IUCrJ_Revision/IUCrJ/1st Revision/Figures/Supporting Information/EMD-1887.map&quot;</a></div></div>Opened EMD-1887.map, grid size 180,180,120, pixel 2.8, shown at level 320, step 1, values float32<br>
82<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> rightMode select</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode rightMode select">ui mousemode rightMode select</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html">select</a> #2</div><div class="cxcmd_as_cmd"><a href="cxcmd:select #2">select #2</a></div></div>2 models selected<br>
83<div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/set.html">set</a> bgColor black</div><div class="cxcmd_as_cmd"><a href="cxcmd:set bgColor black">set bgColor black</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> rightMode &quot;rotate selected models&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode rightMode &quot;rotate selected models&quot;">ui mousemode rightMode &quot;rotate selected models&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> rightMode &quot;translate selected models&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode rightMode &quot;translate selected models&quot;">ui mousemode rightMode &quot;translate selected models&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> rightMode rotate</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode rightMode rotate">ui mousemode rightMode rotate</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> rightMode &quot;translate selected models&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode rightMode &quot;translate selected models&quot;">ui mousemode rightMode &quot;translate selected models&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> rightMode rotate</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode rightMode rotate">ui mousemode rightMode rotate</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> rightMode &quot;rotate selected models&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode rightMode &quot;rotate selected models&quot;">ui mousemode rightMode &quot;rotate selected models&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> rightMode &quot;translate selected models&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode rightMode &quot;translate selected models&quot;">ui mousemode rightMode &quot;translate selected models&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> rightMode &quot;rotate selected models&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode rightMode &quot;rotate selected models&quot;">ui mousemode rightMode &quot;rotate selected models&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> rightMode rotate</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode rightMode rotate">ui mousemode rightMode rotate</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> rightMode &quot;translate selected models&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode rightMode &quot;translate selected models&quot;">ui mousemode rightMode &quot;translate selected models&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> rightMode rotate</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode rightMode rotate">ui mousemode rightMode rotate</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> rightMode &quot;translate selected models&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode rightMode &quot;translate selected models&quot;">ui mousemode rightMode &quot;translate selected models&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> rightMode rotate</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode rightMode rotate">ui mousemode rightMode rotate</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> rightMode &quot;translate selected models&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode rightMode &quot;translate selected models&quot;">ui mousemode rightMode &quot;translate selected models&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> rightMode rotate</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode rightMode rotate">ui mousemode rightMode rotate</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> rightMode &quot;translate selected models&quot;</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode rightMode &quot;translate selected models&quot;">ui mousemode rightMode &quot;translate selected models&quot;</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> rightMode rotate</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode rightMode rotate">ui mousemode rightMode rotate</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/set.html">set</a> bgColor white</div><div class="cxcmd_as_cmd"><a href="cxcmd:set bgColor white">set bgColor white</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/ui.html#mousemode">ui mousemode</a> rightMode select</div><div class="cxcmd_as_cmd"><a href="cxcmd:ui mousemode rightMode select">ui mousemode rightMode select</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/select.html#clear">select clear</a></div><div class="cxcmd_as_cmd"><a href="cxcmd:select clear">select clear</a></div></div>Traceback (most recent call last):<br>
84&nbsp;&nbsp;File &quot;C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py&quot;, line 855, in &lt;lambda&gt;<br>
85&nbsp;&nbsp;&nbsp;&nbsp;save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess))<br>
86&nbsp;&nbsp;File &quot;C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py&quot;, line 595, in file_save_cb<br>
87&nbsp;&nbsp;&nbsp;&nbsp;self.save_dialog.display(self, session)<br>
88&nbsp;&nbsp;File &quot;C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\save_dialog.py&quot;, line 114, in display<br>
89&nbsp;&nbsp;&nbsp;&nbsp;fmt.update(session, self)<br>
90&nbsp;&nbsp;File &quot;C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\savemap.py&quot;, line 67, in update<br>
91&nbsp;&nbsp;&nbsp;&nbsp;self._map_menu.value = m<br>
92&nbsp;&nbsp;File &quot;C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\item_chooser.py&quot;, line 269, in value<br>
93&nbsp;&nbsp;&nbsp;&nbsp;or (val is not None and self.value == val):<br>
94&nbsp;&nbsp;File &quot;C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\item_chooser.py&quot;, line 246, in value<br>
95&nbsp;&nbsp;&nbsp;&nbsp;self._sleep_check()<br>
96&nbsp;&nbsp;File &quot;C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\item_chooser.py&quot;, line 81, in _sleep_check<br>
97&nbsp;&nbsp;&nbsp;&nbsp;self._items_change()<br>
98&nbsp;&nbsp;File &quot;C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\item_chooser.py&quot;, line 287, in _items_change<br>
99&nbsp;&nbsp;&nbsp;&nbsp;prev_value = self.value<br>
100&nbsp;&nbsp;File &quot;C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\item_chooser.py&quot;, line 255, in value<br>
101&nbsp;&nbsp;&nbsp;&nbsp;return self.item_map[text]<br>
102KeyError: &#x27;emd_6716.map #1&#x27;<br>
103<br/>KeyError: 'emd_6716.map #1'<br><br> File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\item_chooser.py", line 255, in value<br> return self.item_map[text]<br><br><i>See log for complete Python traceback.</i><br><br/><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html#hide">hide</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:hide #!1 models">hide #!1 models</a></div></div><div class="cxcmd"><div class="cxcmd_as_doc"><a href="help:user/commands/show.html">show</a> #!1 models</div><div class="cxcmd_as_cmd"><a href="cxcmd:show #!1 models">show #!1 models</a></div></div>Traceback (most recent call last):<br>
104&nbsp;&nbsp;File &quot;C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py&quot;, line 855, in &lt;lambda&gt;<br>
105&nbsp;&nbsp;&nbsp;&nbsp;save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess))<br>
106&nbsp;&nbsp;File &quot;C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py&quot;, line 595, in file_save_cb<br>
107&nbsp;&nbsp;&nbsp;&nbsp;self.save_dialog.display(self, session)<br>
108&nbsp;&nbsp;File &quot;C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\save_dialog.py&quot;, line 114, in display<br>
109&nbsp;&nbsp;&nbsp;&nbsp;fmt.update(session, self)<br>
110&nbsp;&nbsp;File &quot;C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\savemap.py&quot;, line 67, in update<br>
111&nbsp;&nbsp;&nbsp;&nbsp;self._map_menu.value = m<br>
112&nbsp;&nbsp;File &quot;C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\item_chooser.py&quot;, line 269, in value<br>
113&nbsp;&nbsp;&nbsp;&nbsp;or (val is not None and self.value == val):<br>
114&nbsp;&nbsp;File &quot;C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\item_chooser.py&quot;, line 255, in value<br>
115&nbsp;&nbsp;&nbsp;&nbsp;return self.item_map[text]<br>
116KeyError: &#x27;emd_6716.map #1&#x27;<br>
117<br/>KeyError: 'emd_6716.map #1'<br><br> File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\widgets\item_chooser.py", line 255, in value<br> return self.item_map[text]<br><br><i>See log for complete Python traceback.</i><br><br/></body>
118</html>