[phenixbb] Molprobity percentile statistic

Nathaniel Echols NEchols at lbl.gov
Mon Oct 19 16:02:08 PDT 2009

On Oct 19, 2009, at 3:32 PM, hari jayaram wrote:
> Hi i just started using the phenix GUI front-end to Molprobity . Its
> really nice the way it plugs into coot and displays all the statistics
> etc.
> Is there any place that it also reports the percentile clashscore and
> percentile Molprobity score for overall model quality  a la the
> webserver at molprobity.biochem.duke.edu

Currently, no.  I believe we now have most or all of the data  
necessary to calculate the clashscore as a percentile - I'll ask Pavel  
about this.  It probably won't be difficult to add.

We don't report an overall score for validation, mostly because such a  
statistic is potentially misleading and not especially useful.  If  
you're interested in comparisons to existing structures, the program  
phenix.polygon will show where your structure falls in the  
distribution of similar PDB models, but you should consider each  
statistic individually.  (And take into account local measures, like  
real-space fit.)


Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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