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): http://cci.lbl.gov/~nat/img/phenix/polygon_example.png 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. -Nat ------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]