Re: [phenixbb] command line molprobity tools

Hi Nat, I saw mmtbx.validation_summary, but it says it extracts header info. That is not running molprobity for a file that came from a different refinement program. I like the individual tools, ramalyze (awesome name construction!) has already replaced my using of procheck commandline. Now I can use the others too. Comprehensive, but not the whole kitchen sink, would be what you see in the GUI reported, but in simple text form. The percentages/numbers of outliers, followed by the identity of those outliers. It would be great if when I hit the button for "View Log File" (or more accurately, a "View Result File"), what would appear is what I see in the GUI, which is concise enough but also detailed at the perfect level. Thanks, 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