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<p class="MsoNormal">It looks like you can create a folder and then have script create the subdirectories in this folder and be one folder out and it works.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks,</p>
<p class="MsoNormal">Ryan Harlich</p>
<p class="MsoNormal"><o:p> </o:p></p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Ryan Harlich<br>
<b>Sent:</b> Tuesday, July 30, 2019 1:21:56 PM<br>
<b>To:</b> Greg Couch <gregc@cgl.ucsf.edu>; chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu>; Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Subject:</b> RE: [Chimera-users] --nogui gets permission denied when fetching pdb id</font>
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<p class="MsoNormal">It looks like it works before I use os.system(‘mkdir … or os.makedirs or os.mkdir. I am not even in that folder as it is a subfolder I am making. Not sure why it is giving me Errno 13. When I delete the folder it works. But I need to create
the folder to save each protein in their folder.</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Ryan Harlich<br>
<b>Sent:</b> Tuesday, July 30, 2019 12:46:44 PM<br>
<b>To:</b> Greg Couch <gregc@cgl.ucsf.edu>; chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu>; Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Subject:</b> RE: [Chimera-users] --nogui gets permission denied when fetching pdb id</font>
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<p class="MsoNormal">I get this.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Opening 1a1x...</p>
<p class="MsoNormal">[Errno 13] Permission denied: '1a1x'</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">It actually worked in a new folder. But then when I ran my python script it did not work. Then I tried doing it via command line instead of python script and I got the permission denied again.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best,</p>
<p class="MsoNormal">Ryan Harlich</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Greg Couch <gregc@cgl.ucsf.edu><br>
<b>Sent:</b> Tuesday, July 30, 2019 12:42:09 PM<br>
<b>To:</b> chimera-users@cgl.ucsf.edu BB <chimera-users@cgl.ucsf.edu>; Eric Pettersen <pett@cgl.ucsf.edu>; Ryan Harlich <ryanharlich@hotmail.com><br>
<b>Subject:</b> Re: [Chimera-users] --nogui gets permission denied when fetching pdb id</font>
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<p>"permission denied" is usually because you don't have write permission for some directory. Run the "system pwd" command to see which directory chimera is running in. You also need permission for a temporary directory and the download directory. As Eric
alluded, the directory that is causing the problem should be obvious from the full error message.</p>
<p> HTH,</p>
<p> Greg<br>
</p>
<div class="moz-cite-prefix">On 7/30/2019 12:31 PM, Eric Pettersen wrote:<br>
</div>
<blockquote type="cite" cite="mid:B4A824D4-E1E2-49BA-849D-23E3C1B5FC0A@cgl.ucsf.edu">
I wouldn’t be able to say without the actual full error output.
<div class=""><br class="">
</div>
<div class="">—Eric<br class="">
<div class="">
<div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);
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<span class="Apple-tab-span" style="white-space: pre;"></span>Eric Pettersen</div>
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<span class="Apple-tab-span" style="white-space: pre;"></span>UCSF Computer Graphics Lab</div>
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<br class="Apple-interchange-newline">
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<blockquote type="cite" class="">
<div class="">On Jul 30, 2019, at 12:01 PM, Ryan Harlich <<a href="mailto:ryanharlich@hotmail.com" class="" moz-do-not-send="true">ryanharlich@hotmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
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<div style="margin: 0in 0in 0.0001pt; font-size: 11pt;
font-family: Calibri, sans-serif;" class="">
Hi Chimera,</div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt;
font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt;
font-family: Calibri, sans-serif;" class="">
I am trying to run a script with the –nogui option and run command “open 1a1x” and I get permission denied. It works with the GUI so I am not sure why it is not working with –nogui.</div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt;
font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt;
font-family: Calibri, sans-serif;" class="">
Best,</div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt;
font-family: Calibri, sans-serif;" class="">
Ryan Harlich</div>
<div style="margin: 0in 0in 0.0001pt; font-size: 11pt;
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<o:p class=""> </o:p></div>
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