On Tue, Jun 26, 2018 at 10:36 AM Tristan Croll <tic20@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@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@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@phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb [2]
>> Unsubscribe: phenixbb-leave@phenix-online.org
>
> --
>
> ***************************************************
>
> Charles Chen
>
> Research Instructor
>
> University of Pittsburgh School of Medicine
>
> Department of Anesthesiology
>
> ******************************************************
>
> _______________________________________________
> phenixbb mailing list
> phenixbb@phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb [2]
> Unsubscribe: phenixbb-leave@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
>
> _______________________________________________
> phenixbb mailing list
> phenixbb@phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave@phenix-online.org