<div dir="ltr">Hi Wei,<div><br></div><div>Yes, but you would need to open the pickle file that stores the results for the job.</div><div><br></div><div>The pickle file is stored in the same directory as the job parameters. If you select a job and click on "Show details" on the bottom, you'll get a dialog that shows the relative path to the "Config file". The corresponding pickle file is that name, but replace the ".eff" extension with ".pkl". The full path to the file can be constructed by combining the "Directory" field with the "Config file" field. Basically, your project directory has a hidden ".phenix" directory that stores the outputs for each job in the project.</div><div><br></div><div>Once you know where the pickle file is, you can run the following code to print out the list of missing atoms.</div><div><br></div><div><font face="monospace">import sys<br>from libtbx import easy_pickle<br><br>if __name__ == '__main__':<br><br> # for simplicity, assume the first argument is the result pickle<br> assert len(sys.argv) == 2<br> p = easy_pickle.load(sys.argv[1])<br> validation = p.validation<br> missing_atoms = p.validation.missing_atoms<br><br> # print missing atoms<br> # the first column is the chain<br> # the second column is the residue (name and number)<br> # the third column is the altloc<br> # the fourth column is the atom name<br> # the remaining columns are extra information (selection string and location)<br> for missing_atom in missing_atoms:<br> print(missing_atom[:4])</font><br></div><div><br></div><div>So if you save the code in a text file named "extract_missing_atoms.py", you would run the code by typing</div><div><br></div><div><font face="monospace">libtbx.python extract_missing_atoms.py <pickle file></font></div><div><br></div><div>This will work with a validation job (molprobity_<job number>.pkl) as well as a phenix.refine job (refine_<job number>.pkl). Let me know if you run into any issues.</div><div><br></div><div>This is something that we plan on addressing as we work on a new GUI. There are some additions to the Cryo-EM validation GUI where there is an "Export data" button for exporting the data for some of the graphs.</div><div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>--</div><div><span style="font-size:12.8000001907349px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, May 4, 2022 at 2:17 PM Wei Wang <<a href="mailto:ww2283@columbia.edu">ww2283@columbia.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<div>
<div name="messageBodySection">
<div dir="auto">Dear all,<br>
<br>
I would like to get an externally readable list of the <u>missing atoms</u> table in “<u>Summary</u>" session of "<u>Comprehensive validation (X-ray/Neutron)</u>". Currently it seems the information is integrated and clickable only inside the gui window. I want to access the table via sed. Is there a way to extract that table out?<br>
<br>
Best regards,<br>
<br>
Wei</div>
</div>
</div>
_______________________________________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
Unsubscribe: <a href="mailto:phenixbb-leave@phenix-online.org" target="_blank">phenixbb-leave@phenix-online.org</a></blockquote></div>