<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><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="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta charset="UTF-8" class=""><div dir="ltr" lang="en" 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;"><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> <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=""><br class=""></pre><pre style="background-color: rgb(255, 255, 255);" class="">thanks,</pre><pre style="background-color: rgb(255, 255, 255);" class="">amith</pre>
<br class=""></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="">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="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></div></blockquote></div><br class=""></div></div></body></html>