<div dir="ltr">Thank you all!<div><br></div><div>Both bash scripts work, both python scripts work!</div></div><br><div class="gmail_quote"><div dir="ltr">On Tue, Jun 26, 2018 at 10:36 AM Tristan Croll <<a href="mailto:tic20@cam.ac.uk">tic20@cam.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">... or you could just listen to Pavel!<br>
<br>
On 2018-06-26 14:55, Pavel Afonine wrote:<br>
> This now starts looking like writing a simple python script using<br>
> basic CCTBX functionality is most optimal option.. I'm attaching the<br>
> script that does it. 'result' object contains all you need. Just<br>
> format its content the way you like.<br>
> <br>
> Pavel<br>
> <br>
> On 6/26/18 06:42, CPMAS Chen wrote:<br>
> <br>
>> Thanks!<br>
>> <br>
>> I used the bash scripts you two provided. It works great.<br>
>> <br>
>> A further question, how do I extract the output summary of the<br>
>> molprobity results from all 100 files into a single file. Ideally, I<br>
>> would like to make the data into a table.<br>
>> <br>
>> Appreciate your help!<br>
>> <br>
>> =================================== Summary<br>
>> ===================================<br>
>> <br>
>> Ramachandran outliers = 0.38 %<br>
>> favored = 95.27 %<br>
>> Rotamer outliers = 0.00 %<br>
>> C-beta deviations = 10<br>
>> Clashscore = 184.98<br>
>> RMS(bonds) = 0.0193<br>
>> RMS(angles) = 2.77<br>
>> MolProbity score = 3.06<br>
>> <br>
>> On Mon, Jun 25, 2018 at 5:32 PM Oleg Sobolev <<a href="mailto:osobolev@lbl.gov" target="_blank">osobolev@lbl.gov</a>><br>
>> wrote:<br>
>> <br>
>> Hi Charles,<br>
>> <br>
>> I would use any scripting language you are familiar with - python,<br>
>> bash, csh. Here is a bash script adapted from<br>
>> <br>
> <a href="https://stackoverflow.com/questions/10523415/bash-script-to-execute-command-on-all-files-in-a-directory" rel="noreferrer" target="_blank">https://stackoverflow.com/questions/10523415/bash-script-to-execute-command-on-all-files-in-a-directory</a><br>
>> [1]<br>
>> <br>
>> for file in *.pdb<br>
>> do<br>
>> echo $file<br>
>> phenix.molprobity "$file" > "$file"_results.txt<br>
>> done<br>
>> <br>
>> On mac - make a file mpscript put it in a directory with your .pdb,<br>
>> then run<br>
>> chmod a+x mpscript<br>
>> ./mpscript<br>
>> <br>
>> Hope it helps.<br>
>> <br>
>> Best regards,<br>
>> Oleg Sobolev.<br>
>> <br>
>> On Mon, Jun 25, 2018 at 1:39 PM, CPMAS Chen <<a href="mailto:cpmasmit@gmail.com" target="_blank">cpmasmit@gmail.com</a>><br>
>> wrote:<br>
>> <br>
>> Hi, All,<br>
>> <br>
>> I have about 100 structures needs be validated and optimized. what<br>
>> will be a fast way to do so? Can I somehow put phenix.molprobity in<br>
>> a circle?<br>
>> <br>
>> Thanks!<br>
>> <br>
>> --<br>
>> <br>
>> ***************************************************<br>
>> <br>
>> Charles Chen<br>
>> <br>
>> Research Instructor<br>
>> <br>
>> University of Pittsburgh School of Medicine<br>
>> <br>
>> Department of Anesthesiology<br>
>> <br>
>> ******************************************************<br>
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> <br>
> --<br>
> <br>
> ***************************************************<br>
> <br>
> Charles Chen<br>
> <br>
> Research Instructor<br>
> <br>
> University of Pittsburgh School of Medicine<br>
> <br>
> Department of Anesthesiology<br>
> <br>
> ******************************************************<br>
> <br>
> _______________________________________________<br>
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> <a href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a> [2]<br>
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> <br>
> <br>
> <br>
> Links:<br>
> ------<br>
> [1]<br>
> <a href="https://stackoverflow.com/questions/10523415/bash-script-to-execute-command-on-all-files-in-a-directory" rel="noreferrer" target="_blank">https://stackoverflow.com/questions/10523415/bash-script-to-execute-command-on-all-files-in-a-directory</a><br>
> [2] <a href="http://phenix-online.org/mailman/listinfo/phenixbb" rel="noreferrer" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
> <br>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div>
<p></p><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><p></p></div></div></div>