[phenixbb] command line molprobity tools

Engin Özkan eozkan at stanford.edu
Wed May 1 12:48:49 PDT 2013

I tried to run phenix.ramalyze and rotalyze with the outliers_only=True 
flags. I get the following errors
Usage: phenix.ramalyze mypdb.pdb
Usage: phenix.rotalyze mypdb.pdb

I thought ramalyze used to work with --outliers_only=True as arguments, 
but that seems to fail, too. Is this a bug, or am I misreading the usage 

On 5/1/13 12:21 PM, Nathaniel Echols wrote:
> On Wed, May 1, 2013 at 12:15 PM, Engin Özkan <eozkan at stanford.edu> wrote:
>> I want to create a comprehensive, human-readable log file by running
>> validation using molprobity tools within phenix command-line. I do not have
>> structure factors/maps. Apparently, the GUI runs validation through
>> phenix.model_vs_data (according to the .eff file), but in command-line, I
>> cannot get phenix.model_vs_data to run without an mtz/hkl. I guess I could
>> provide it a fake data file, and then set the comprehensive flag to "True"?
> You can run these tools:
> phenix.ramalyze model.pdb
> phenix.rotalyze model.pdb
> phenix.cbetadev model.pdb
> phenix.clashscore model.pdb
> phenix.pdb_interpretation model.pdb restraints.cif write_geo_file=True
> Or for the really impatient and easily distracted, like me:
> mmtbx.validation_summary model.pdb
>> BTW, the log file produced by the GUI is not comprehensive at all.
> Define "comprehensive"?
> -Nat
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Engin Özkan
Post-doctoral Scholar
Laboratory of K. Christopher Garcia
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
w ph: (650)-498-7111
cell: (650)-862-8563

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