[phenixbb] validating ~100 structures

[Pavel Afonine]

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 
> <mailto: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
>
>     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
>     <mailto: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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