<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
<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. Â 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">
<div class="">
<meta charset="UTF-8" class="">
<div dir="ltr" class="pfptBanner" style="margin: 16px
0px; padding: 8px 16px; border-radius: 4px; min-width:
200px; background-color: rgb(208, 216, 220);
border-top-width: 4px; border-top-style: solid;
border-top-color: rgb(144, 164, 174); caret-color:
rgb(0, 0, 0); font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant-caps: normal;
font-weight: 400; letter-spacing: normal; text-align:
start; text-indent: 0px; text-transform: none;
white-space: normal; word-spacing: 0px;
-webkit-text-stroke-width: 0px; text-decoration:
none;" lang="en">
<div class="pfptMessageContainer" style="display:
inline-block; margin: 0px 0px 1px; max-width:
600px;">
<div class="pfptBannerTitle" style="line-height:
18px; display: block; font-family: Arial,
sans-serif !important; font-size: 14px !important;
font-weight: bold !important;">This Message Is
From an External Sender</div>
<div class="pfptBannerSubtitle" style="line-height:
18px; margin-top: 2px; display: block;
font-weight: normal !important; font-family:
Arial, sans-serif !important; font-size: 12px
!important;">This message came from outside your
organization.</div>
</div>
</div>
<div class="elementToProof" style="font-style: normal;
font-variant-caps: normal; font-weight: 400;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; text-decoration: none; font-family: Calibri,
Arial, Helvetica, sans-serif; font-size: 12pt;
background-color: rgb(255, 255, 255);">Hello everyone,</div>
<div class="elementToProof" style="font-style: normal;
font-variant-caps: normal; font-weight: 400;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; text-decoration: none; font-family: Calibri,
Arial, Helvetica, sans-serif; font-size: 12pt;
background-color: rgb(255, 255, 255);"><br class="">
</div>
<div class="elementToProof" style="font-style: normal;
font-variant-caps: normal; font-weight: 400;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
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;
font-variant-caps: normal; font-weight: 400;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; text-decoration: none; font-family: Calibri,
Arial, Helvetica, sans-serif; font-size: 12pt;
background-color: rgb(255, 255, 255);"><br class="">
</div>
<div class="elementToProof" style="font-style: normal;
font-variant-caps: normal; font-weight: 400;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; text-decoration: none; font-family: Calibri,
Arial, Helvetica, sans-serif; font-size: 12pt;
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>Â <span style="color: rgb(0, 128, 0);" class="">1.3</span>Â <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>Â pwd
<span style="color: rgb(227, 74, 220);" class="">Executing:</span>Â pwd
Current working directory is<span style="color: rgb(128, 0, 128);" class="">:</span>Â <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>Â 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>Â 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>Â 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>
</div>
<span style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: 400;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; text-decoration: none; float: none; display:
inline !important;" class="">_______________________________________________</span><br
style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: 400;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: 400;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; text-decoration: none; float: none; display:
inline !important;" class="">ChimeraX-users mailing
list</span><br style="caret-color: rgb(0, 0, 0);
font-family: Helvetica; font-size: 12px; font-style:
normal; font-variant-caps: normal; font-weight: 400;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; text-decoration: none;" class="">
<a href="mailto:ChimeraX-users@cgl.ucsf.edu"
style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant-caps: normal;
font-weight: 400; letter-spacing: normal; orphans:
auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows:
auto; word-spacing: 0px; -webkit-text-size-adjust:
auto; -webkit-text-stroke-width: 0px;"
class="moz-txt-link-freetext" moz-do-not-send="true">ChimeraX-users@cgl.ucsf.edu</a><br
style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: 400;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: 400;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; text-decoration: none; float: none; display:
inline !important;" class="">Manage subscription:</span><br
style="caret-color: rgb(0, 0, 0); font-family:
Helvetica; font-size: 12px; font-style: normal;
font-variant-caps: normal; font-weight: 400;
letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; text-decoration: none;" class="">
<a
href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users"
style="font-family: Helvetica; font-size: 12px;
font-style: normal; font-variant-caps: normal;
font-weight: 400; letter-spacing: normal; orphans:
auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows:
auto; word-spacing: 0px; -webkit-text-size-adjust:
auto; -webkit-text-stroke-width: 0px;"
class="moz-txt-link-freetext" moz-do-not-send="true">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></div>
</blockquote>
</div>
<br class="">
</div>
</div>
<br>
<fieldset class="moz-mime-attachment-header"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
ChimeraX-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:ChimeraX-users@cgl.ucsf.edu">ChimeraX-users@cgl.ucsf.edu</a>
Manage subscription:
<a class="moz-txt-link-freetext" href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a>
</pre>
</blockquote>
</body>
</html>