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This now starts looking like writing a simple python script using
basic CCTBX functionality is most optimal option.. I'm attaching the
script that does it. 'result' object contains all you need. Just
format its content the way you like.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 6/26/18 06:42, CPMAS Chen wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAAU4GKbr4VRurZGaqSaC8YMbcPQAPUEdtHtb65COc_WtjjW3sA@mail.gmail.com">
<div dir="ltr">Thanks!
<div><br>
</div>
<div>I used the bash scripts you two provided. It works great. </div>
<div><br>
</div>
<div>A further question, how do I extract the output summary of
the molprobity results from all 100 files into a single file.
Ideally, I would like to make the data into a table. </div>
<div><br>
</div>
<div>Appreciate your help!</div>
<div><br>
</div>
<div>
<div>=================================== Summary
===================================</div>
<div><br>
</div>
<div> Ramachandran outliers = 0.38 %</div>
<div> favored = 95.27 %</div>
<div> Rotamer outliers = 0.00 %</div>
<div> C-beta deviations = 10</div>
<div> Clashscore = 184.98</div>
<div> RMS(bonds) = 0.0193</div>
<div> RMS(angles) = 2.77</div>
<div> MolProbity score = 3.06</div>
</div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Mon, Jun 25, 2018 at 5:32 PM Oleg Sobolev <<a
href="mailto:osobolev@lbl.gov" moz-do-not-send="true">osobolev@lbl.gov</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Charles,
<div><br>
</div>
<div>I would use any scripting language you are familiar
with - python, bash, csh. Here is a bash script adapted
from</div>
<div><a
href="https://stackoverflow.com/questions/10523415/bash-script-to-execute-command-on-all-files-in-a-directory"
target="_blank" moz-do-not-send="true">https://stackoverflow.com/questions/10523415/bash-script-to-execute-command-on-all-files-in-a-directory</a><br>
</div>
<br>
<div>
<div>for file in *.pdb</div>
<div>do</div>
<div> echo $file</div>
<div> phenix.molprobity "$file" > "$file"_results.txt</div>
<div>done</div>
</div>
<div><br>
</div>
<div>On mac - make a file mpscript put it in a directory
with your .pdb, then run</div>
<div>chmod a+x mpscript</div>
<div>./mpscript</div>
<div><br>
</div>
<div>Hope it helps.</div>
<div><br>
</div>
<div>Best regards,</div>
<div>Oleg Sobolev.</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Mon, Jun 25, 2018 at 1:39 PM,
CPMAS Chen <span dir="ltr"><<a
href="mailto:cpmasmit@gmail.com" target="_blank"
moz-do-not-send="true">cpmasmit@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi, All,
<div><br>
</div>
<div>I have about 100 structures needs be validated
and optimized. what will be a fast way to do so? Can
I somehow put phenix.molprobity in a circle?<br
clear="all">
<div><br>
</div>
<div>Thanks!</div>
<div><br>
</div>
-- <br>
<div dir="ltr"
class="m_7869143088461595327m_674535493315817815gmail_signature"
data-smartmail="gmail_signature">
<div dir="ltr">
<div>
<p>***************************************************</p>
<p>Charles Chen</p>
<p>Research Instructor</p>
<p>University of Pittsburgh School of Medicine</p>
<p>Department of Anesthesiology</p>
<p>******************************************************</p>
</div>
</div>
</div>
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</blockquote>
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<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr" class="gmail_signature"
data-smartmail="gmail_signature">
<div dir="ltr">
<div>
<p>***************************************************</p>
<p>Charles Chen</p>
<p>Research Instructor</p>
<p>University of Pittsburgh School of Medicine</p>
<p>Department of Anesthesiology</p>
<p>******************************************************</p>
</div>
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