[phenixbb] validating ~100 structures

CPMAS Chen cpmasmit at gmail.com
Tue Jun 26 10:32:46 PDT 2018


Thank you all!

Both bash scripts work, both python scripts work!

On Tue, Jun 26, 2018 at 10:36 AM Tristan Croll <tic20 at cam.ac.uk> wrote:

> ... 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
> >>
> >> ******************************************************
> >> _______________________________________________
> >> phenixbb mailing list
> >> phenixbb at phenix-online.org
> >> http://phenix-online.org/mailman/listinfo/phenixbb [2]
> >> Unsubscribe: phenixbb-leave at phenix-online.org
> >
> >  --
> >
> > ***************************************************
> >
> > Charles Chen
> >
> > Research Instructor
> >
> > University of Pittsburgh School of Medicine
> >
> > Department of Anesthesiology
> >
> > ******************************************************
> >
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb [2]
> > Unsubscribe: phenixbb-leave at phenix-online.org
> >
> >
> >
> > 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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> > phenixbb at phenix-online.org
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>
>

-- 

***************************************************

Charles Chen

Research Instructor

University of Pittsburgh School of Medicine

Department of Anesthesiology

******************************************************
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