[phenixbb] validating ~100 structures

[Tristan Croll]

... or you could just listen to Pavel!

On 2018-06-26 14:55, Pavel Afonine wrote:
> 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.
> 
>  Pavel
> 
> On 6/26/18 06:42, CPMAS Chen wrote:
> 
>> Thanks!
>> 
>> I used the bash scripts you two provided. It works great.
>> 
>> 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.
>> 
>> Appreciate your help!
>> 
>> =================================== Summary
>> ===================================
>> 
>> Ramachandran outliers = 0.38 %
>> favored = 95.27 %
>> Rotamer outliers = 0.00 %
>> C-beta deviations = 10
>> Clashscore = 184.98
>> RMS(bonds) = 0.0193
>> RMS(angles) = 2.77
>> MolProbity score = 3.06
>> 
>> On Mon, Jun 25, 2018 at 5:32 PM Oleg Sobolev <osobolev at lbl.gov>
>> wrote:
>> 
>> Hi Charles,
>> 
>> I would use any scripting language you are familiar with - python,
>> bash, csh. Here is a bash script adapted from
>> 
> https://stackoverflow.com/questions/10523415/bash-script-to-execute-command-on-all-files-in-a-directory
>> [1]
>> 
>> for file in *.pdb
>> do
>> echo $file
>> phenix.molprobity "$file" > "$file"_results.txt
>> done
>> 
>> On mac - make a file mpscript put it in a directory with your .pdb,
>> then run
>> chmod a+x mpscript
>> ./mpscript
>> 
>> Hope it helps.
>> 
>> Best regards,
>> Oleg Sobolev.
>> 
>> On Mon, Jun 25, 2018 at 1:39 PM, CPMAS Chen <cpmasmit at gmail.com>
>> wrote:
>> 
>> Hi, All,
>> 
>> 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?
>> 
>> Thanks!
>> 
>> --
>> 
>> ***************************************************
>> 
>> Charles Chen
>> 
>> Research Instructor
>> 
>> University of Pittsburgh School of Medicine
>> 
>> Department of Anesthesiology
>> 
>> ******************************************************
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> 
>  --
> 
> ***************************************************
> 
> Charles Chen
> 
> Research Instructor
> 
> University of Pittsburgh School of Medicine
> 
> Department of Anesthesiology
> 
> ******************************************************
> 
> _______________________________________________
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> phenixbb at phenix-online.org
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> 
> 
> 
> Links:
> ------
> [1]
> https://stackoverflow.com/questions/10523415/bash-script-to-execute-command-on-all-files-in-a-directory
> [2] http://phenix-online.org/mailman/listinfo/phenixbb
> 
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