[phenixbb] command line molprobity tools

Engin Özkan eozkan at stanford.edu
Wed May 1 12:15:56 PDT 2013

Hi everybody,

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"? BTW, the log file produced by the GUI is not comprehensive at 

I could not find a related mmtbx or cctbx function either. Another 
mentioned tool, phenix.validate, does not even exist in my installation 
(dev 1361).


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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