[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.)
-Nat
-------------------
Nathaniel Echols
Lawrence Berkeley Lab
510-486-5136
NEchols at lbl.gov
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