[phenixbb] command line molprobity tools

Pavel Afonine pafonine at lbl.gov
Wed May 1 12:28:33 PDT 2013

Hi Engin,

that's right, it outputs only global figures... Tools that Nat listed 
output detailed lists.


On 5/1/13 12:26 PM, Engin Özkan wrote:
> 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.
> Engin
> 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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