[phenixbb] command line molprobity tools

Nathaniel Echols nechols at lbl.gov
Wed May 1 12:21:11 PDT 2013

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"?


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