[phenixbb] command line molprobity tools

Pavel Afonine pafonine at lbl.gov
Wed May 1 12:19:47 PDT 2013

Hi Engin,


phenix.pdbtools model_stat=true model.pdb

If this doesn't do what you want then please let me know.


On 5/1/13 12:15 PM, Engin Özkan wrote:
> 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 all.
> 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).
> Thanks,
> Engin

More information about the phenixbb mailing list