[phenixbb] command line molprobity tools

Engin Özkan eozkan at stanford.edu
Wed May 1 12:56:12 PDT 2013

Thanks, Nat. That's very useful!


On 5/1/13 12:51 PM, Nathaniel Echols wrote:
> On Wed, May 1, 2013 at 12:39 PM, Engin Özkan <eozkan at stanford.edu> wrote:
>> I saw mmtbx.validation_summary, but it says it extracts header info.
> Only R-factors and bond and angle RMSDs (and the latter only for files
> from phenix.refine).  The actual MolProbity stuff is calculated fresh.
>   It's not a very sophisticated tool, I just use it to benchmark
> massive sets of test refinements (where I always run Phenix at the end
> with a null strategy, to control for differences in bulk solvent and
> hydrogen handling).
>> That is
>> not running molprobity for a file that came from a different refinement
>> program.
> Why would you ever want to run one of those? :)
>> 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.
> We have discussed making a unified program ("phenix.molprobity") that
> would do something like this.  There aren't any technical obstacles;
> the only reason it hasn't happened is that this really needs to happen
> as a part of a more comprehensive refactoring of both the validation
> tools in the Phenix GUI, and of the MolProbity server itself.
> Otherwise we will inevitably end up with another jumbled mess with
> lots of code duplication.
> However, in the absence of that, I will add a --verbose flag to
> mmtbx.validation_summary which will dump the output of the individual
> programs sequentially.  It won't be especially pretty, but it's only a
> handful of lines of code.
> -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
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