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