[phenixbb] Molprobity percentile statistic

Nathaniel Echols NEchols at lbl.gov
Tue Oct 20 11:12:00 PDT 2009

On Oct 19, 2009, at 7:03 PM, hari jayaram wrote:
> And thats the reason I liked the molprobity statistics expressed as
> percentile since it helped me realize how far I have to go relative to
> other structures at the PDB. If its not too difficult can I cast my
> vote to report it inside the phenix GUI. Its just that running the
> full analysis inside of phenix is significantly faster than running it
> on the duke webservers.

It isn't very difficult at all - but we need to discuss the best  
source of these scores.  An additional complication in Phenix is that  
we also incorporate diffraction data into validation (depending on  
which version of the program you're using), which complements the  
geometry analyses.  One side effect is that only PDB entries for which  
structure factors are available are included in the distributions used  
by Polygon.  (This probably improves the distributions, however.)

> Regardless  thanks for the hint about phenix.polygon .
> I just looked at my phenix.polygon report and I am afraid its a little
> asymmetric.

Since the server bounced the original post I've saved the image you  
sent here (since it's a good example):


The colors are a bit confusing (next release will be improved), but  
this is about what I'd expect to see.  What you should look out for is  
values that fall on the extremed ends of the distribution, or very  
lopsided or pointy shapes.  I can't really suggest absolute guidelines  
since these statistics are so different and the PDB won't (and  
shouldn't) have a Gaussian distribution for each one - and keep in  
mind that most models in the PDB would probably benefit from further  
refinement.  I find this type of analysis very informative, but we  
don't want people to fall into the trap of leaving obvious errors in  
the model because they only looked at global scores.

Anyway, I've added some more similar graphs for surveying PDB  
statistics in the GUI - they'll be in the next version.


Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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