[phenixbb] command line molprobity tools
eozkan at stanford.edu
Wed May 1 12:39:31 PDT 2013
I saw mmtbx.validation_summary, but it says it extracts header info.
That is not running molprobity for a file that came from a different
I like the individual tools, ramalyze (awesome name construction!) has
already replaced my using of procheck commandline. Now I can use the
Comprehensive, but not the whole kitchen sink, would be what you see in
the GUI reported, but in simple text form. The percentages/numbers of
outliers, followed by the identity of those outliers. It would be great
if when I hit the button for "View Log File" (or more accurately, a
"View Result File"), what would appear is what I see in the GUI, which
is concise enough but also detailed at the perfect level.
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"?
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