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<p>The problem was that Amith was using a chimerax that was an alias
that runs chimerax inside a singularity container. A singularity
container is used so all of the runtime libraries that ChimeraX
needs are guaranteed to be there.<br>
<br>
So the fix was to modify the alias to bind the scratch directories
to the singularity container, ie.,<br>
<br>
alias chimerax='singularity run --bind
/wynton/scratch,/scratch PATH-TO-CHIMERAX_SIF.sif'<br>
<br>
instead of just:<br>
<br>
alias chimerax='singularity run PATH-TO-CHIMERAX_SIF.sif'<br>
<br>
-- Greg<br>
</p>
<div class="moz-cite-prefix">On 4/6/2022 6:46 PM, Tom Goddard via
ChimeraX-users wrote:<br>
</div>
<blockquote type="cite"
cite="mid:3322EFBC-2C7A-40AE-A38B-B5DD7EC97266@sonic.net">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<div class="">Hi Amith,</div>
<div class=""><br class="">
</div>
That rather cryptic error message just means that the directory
you listed in the cd command either does not exist or you do not
have permission to read it. You could try
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>cd /wynton/scratch</div>
<div class=""><br class="">
</div>
<div class="">then if that works try</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>cd /wynton/scratch/avranga1008</div>
<div class=""><br class="">
</div>
<div class="">and just keep going until you find the directory
that is causing the problem.<br class="">
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Apr 6, 2022, at 6:30 PM, Rangarajan,
Amith via ChimeraX-users <<a
href="mailto:chimerax-users@cgl.ucsf.edu"
class="moz-txt-link-freetext" moz-do-not-send="true">chimerax-users@cgl.ucsf.edu</a>>
wrote:</div>
<br class="Apple-interchange-newline">
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<div class="elementToProof" style="font-style: normal;
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background-color: rgb(255, 255, 255);">Hello everyone,</div>
<div class="elementToProof" style="font-style: normal;
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background-color: rgb(255, 255, 255);"><br class="">
</div>
<div class="elementToProof" style="font-style: normal;
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0px; text-decoration: none; font-family: Calibri,
Arial, Helvetica, sans-serif; font-size: 12pt;
background-color: rgb(255, 255, 255);">i am new to
using chimerax in --no gui mode</div>
<div class="elementToProof" style="font-style: normal;
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background-color: rgb(255, 255, 255);">
<pre style="background-color: rgb(255, 255, 255);" class=""><pre style="background-color: rgb(255, 255, 255);" class="">$ chimerax <span style="color: rgb(128, 128, 48);" class="">-</span><span style="color: rgb(128, 128, 48);" class="">-</span>nogui
UCSF ChimeraX version<span style="color: rgb(128, 0, 128);" class="">:</span> <span style="color: rgb(0, 128, 0);" class="">1.3</span> <span style="color: rgb(128, 128, 48);" class="">(</span><span style="color: rgb(0, 140, 0);" class="">2021</span><span style="color: rgb(128, 128, 48);" class="">-</span><span style="color: rgb(0, 140, 0);" class="">12</span><span style="color: rgb(128, 128, 48);" class="">-</span><span style="color: rgb(0, 140, 0);" class="">08</span><span style="color: rgb(128, 128, 48);" class="">)</span>
© <span style="color: rgb(0, 140, 0);" class="">2016</span><span style="color: rgb(128, 128, 48);" class="">-</span><span style="color: rgb(0, 140, 0);" class="">2021</span> Regents of the University of California<span style="color: rgb(128, 128, 48);" class="">.</span> All rights reserved<span style="color: rgb(128, 128, 48);" class="">.</span>
cmd<span style="color: rgb(128, 128, 48);" class="">></span> pwd
<span style="color: rgb(227, 74, 220);" class="">Executing:</span> pwd
Current working directory is<span style="color: rgb(128, 0, 128);" class="">:</span> <span style="color: rgb(128, 128, 48);" class="">/</span>wynton<span style="color: rgb(128, 128, 48);" class="">/</span>home<span style="color: rgb(128, 128, 48);" class="">/</span>jacobson<span style="color: rgb(128, 128, 48);" class="">/</span>avranga1008
cmd<span style="color: rgb(128, 128, 48);" class="">></span> cd <span style="color: rgb(128, 128, 48);" class="">/</span>wynton<span style="color: rgb(128, 128, 48);" class="">/</span>scratch<span style="color: rgb(128, 128, 48);" class="">/</span>avranga1008<span style="color: rgb(128, 128, 48);" class="">/</span><span style="color: rgb(0, 140, 0);" class="">0</span><span style="color: rgb(128, 128, 48);" class="">-</span>binana<span style="color: rgb(128, 128, 48);" class="">/</span><span style="color: rgb(0, 140, 0);" class="">0</span><span style="color: rgb(128, 128, 48);" class="">-</span>docked<span style="color: rgb(128, 128, 48);" class="">-</span>poses
cd <span style="color: rgb(128, 128, 48);" class="">/</span>wynton<span style="color: rgb(128, 128, 48);" class="">/</span>scratch<span style="color: rgb(128, 128, 48);" class="">/</span>avranga1008<span style="color: rgb(128, 128, 48);" class="">/</span><span style="color: rgb(0, 140, 0);" class="">0</span><span style="color: rgb(128, 128, 48);" class="">-</span>binana<span style="color: rgb(128, 128, 48);" class="">/</span><span style="color: rgb(0, 140, 0);" class="">0</span><span style="color: rgb(128, 128, 48);" class="">-</span>docked<span style="color: rgb(128, 128, 48);" class="">-</span>poses
<span style="color: rgb(128, 128, 48);" class="">.</span><span style="color: rgb(128, 128, 48);" class="">.</span><span style="color: rgb(128, 128, 48);" class="">.</span><span style="color: rgb(128, 128, 48);" class="">^</span>
Expected name of a folder to open<span style="color: rgb(128, 128, 48);" class="">/</span>read<span style="color: rgb(128, 0, 128);" class="">;</span> a name of <span style="color: rgb(255, 255, 255); background-color: rgb(221, 0, 0); font-weight: bold; font-style: italic;" class="">'browse'</span> will bring up a file browser or a keyword
</pre><pre style="background-color: rgb(255, 255, 255);" class="">please share your thoughts on how to change dir in the no gui mode.</pre><pre style="background-color: rgb(255, 255, 255);" class="">
</pre><pre style="background-color: rgb(255, 255, 255);" class="">thanks,</pre><pre style="background-color: rgb(255, 255, 255);" class="">amith</pre>
</pre>
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<pre class="moz-quote-pre" wrap="">_______________________________________________
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