[phenixbb] command line molprobity tools
pafonine at lbl.gov
Wed May 1 12:28:33 PDT 2013
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
> On 5/1/13 12:19 PM, Pavel Afonine wrote:
>> 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).
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