Re: [phenixbb] validating ~100 structures

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 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-...

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 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!

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Charles Chen

Research Instructor

University of Pittsburgh School of Medicine

Department of Anesthesiology

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