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!

--

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

Charles Chen

Research Instructor

University of Pittsburgh School of Medicine

Department of Anesthesiology

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

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

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

... 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 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-...

...

[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 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb [2] Unsubscribe: [email protected]

--

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

Charles Chen

Research Instructor

University of Pittsburgh School of Medicine

Department of Anesthesiology

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

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb [2] Unsubscribe: [email protected]

Links: ------ [1] https://stackoverflow.com/questions/10523415/bash-script-to-execute-command-... [2] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

That's a little more complicated. The below simple Python script should do what you want, assuming all your MolProbity outputs are e.g. xxxx.pdb.log, are all in the same directory, and are the *only* files with the .log extension in the directory. Just copy the script into a file (e.g. mp_parse.py), put it in your working directory and run: python mp_parse.py You should end up with a file called results.csv with the stats tabulated and readable by your favourite spreadsheet program. Cheers, Tristan #!/bin/python import glob from os import path results = {} files = glob.glob('*.log') for file in files: name = path.basename(file).split('.')[0] props = {} results[name] = props with open(file, 'rt') as f: # Bypass details lines = f.read().split('\n') i = 0 for line in lines: i += 1 if 'Summary' in line: break lines = lines[i+1:] for line in lines: #Skip blanks if not line or '=' not in line: continue line = line.strip().split('=') # Throw away whitespace and percent signs props[line[0].strip()] = line[1].strip().split()[0] keys = ( 'Ramachandran outliers', 'favored', 'Rotamer outliers', 'C-beta deviations', 'Clashscore', 'RMS(bonds)', 'RMS(angles)', 'MolProbity score' ) with open('results.csv', 'wt') as out: out.write('Name,') out.write(','.join(keys)+'\n') for name, data in results.items(): out.write(name+',') out.write(','.join([data[key] for key in keys])+'\n') On 2018-06-26 14:42, 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 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-...

...

[2]

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!

--

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

Charles Chen

Research Instructor

University of Pittsburgh School of Medicine

Department of Anesthesiology

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

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb [1] Unsubscribe: [email protected]

--

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

Charles Chen

Research Instructor

University of Pittsburgh School of Medicine

Department of Anesthesiology

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

Links: ------ [1] http://phenix-online.org/mailman/listinfo/phenixbb [2] https://stackoverflow.com/questions/10523415/bash-script-to-execute-command-...

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]