[phenixbb] command line molprobity tools

Engin Özkan eozkan at stanford.edu
Wed May 1 12:39:31 PDT 2013

Hi Nat,

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 
refinement program.

I like the individual tools, ramalyze (awesome name construction!) has 
already replaced my using of procheck commandline. Now I can use the 
others too.

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"?
> -Nat
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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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