[phenixbb] command line molprobity tools

Engin Özkan eozkan at stanford.edu
Wed May 1 12:26:15 PDT 2013

Thanks Pavel. This does half the job by reporting the overall values, 
but does not list detail. For example, it tells you the Ramachandran 
outlier percentage, but does not list the outlier residues. Or the bond 
and angle outliers. I would like to see those output as well. These are 
all done beautifully in the GUI, but apparently not output as 
human-readable text files.

I looked at full parameter list, but could not see a longer output switch.


On 5/1/13 12:19 PM, Pavel Afonine wrote:
> Hi Engin,
> try:
> phenix.pdbtools model_stat=true model.pdb
> If this doesn't do what you want then please let me know.
> Pavel
> 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
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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

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