[phenixbb] question on bad geometry

Pavel Afonine pafonine at lbl.gov
Wed Sep 1 08:58:26 PDT 2010


On 9/1/10 5:25 AM, Thomas C. Terwilliger wrote:
> Just to emphasize what Ed points out here, an essential step in completing
> a structure is to compare it, one residue, solvent molecule, or ligand at
> a time, with your electron density map, fixing any inconsistencies between
> the model and the map.

there are tools to help with this. "Comprehensive validation" available 
in PHENIX GUI will give you the map correlation computed for each 
residue (or even atom), so you can pinpoint problem residues in no time 
just by sorting the list and displaying only those having map CC less 
than say 0.8.
Combined with the list of geometry outliers (Ramachandran, bad clashes, 
rotamer and Cb-deviation outliers - this is all reported by 
"Comprehensive validation") and the functionality to click on the 
outlier and immediately get it zoomed in Coot, makes addressing the 
problems much easier.


More information about the phenixbb mailing list