Re: [phenixbb] command line molprobity tools

Just figured it out. The problem is with the usage text. It says: Example: phenix.rotalyze pdb=1ubq.pdb outliers_only=True It should say Example: phenix.rotalyze 1ubq.pdb outliers_only=True Engin On 5/1/13 12:48 PM, Engin Özkan wrote:

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 text?

Engin On 5/1/13 12:21 PM, Nathaniel Echols wrote:

...

On Wed, May 1, 2013 at 12:15 PM, Engin Özkan 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"?

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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