[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
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>>
>
>
--
***************************************************
Charles Chen
Research Instructor
University of Pittsburgh School of Medicine
Department of Anesthesiology
******************************************************
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