[phenixbb] validating ~100 structures

Oleg Sobolev osobolev at lbl.gov
Mon Jun 25 14:32:07 PDT 2018


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
>
> ******************************************************
>
>
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