[phenixbb] command line molprobity tools

Engin Özkan eozkan at stanford.edu
Wed May 1 12:54:27 PDT 2013

Just figured it out. The problem is with the usage text. It says:


   phenix.rotalyze pdb=1ubq.pdb outliers_only=True

It should say


   phenix.rotalyze 1ubq.pdb outliers_only=True


On 5/1/13 12:48 PM, Engin Özkan wrote:
> I tried to run phenix.ramalyze and rotalyze with the 
> outliers_only=True flags. I get the following errors
> Usage: phenix.ramalyze mypdb.pdb
> Usage: phenix.rotalyze mypdb.pdb
> I thought ramalyze used to work with --outliers_only=True as 
> arguments, but that seems to fail, too. Is this a bug, or am I 
> misreading the usage text?
> Engin
> On 5/1/13 12:21 PM, Nathaniel Echols wrote:
>> 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"?
>> -Nat
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb

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

More information about the phenixbb mailing list