[phenixbb] command line molprobity tools

[Engin Özkan]

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

Example:

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

It should say

Example:

   phenix.rotalyze 1ubq.pdb outliers_only=True

Engin

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
>> _______________________________________________
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>> 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