[phenixbb] validating ~100 structures

CPMAS Chen cpmasmit at gmail.com
Tue Jun 26 06:42:50 PDT 2018


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
>
> 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
>> Unsubscribe: phenixbb-leave at phenix-online.org
>>
>
>

-- 

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

Charles Chen

Research Instructor

University of Pittsburgh School of Medicine

Department of Anesthesiology

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