[phenixbb] wxu for anisotropic ADP refinement

Pavel Afonine pafonine at lbl.gov
Thu Aug 12 13:26:23 PDT 2010

  Hi Joe,

> If one would like to try different weights for anisotropic ADP 
> refinement (ie fixing wxu) should one be focusing on numbers like 
> - wxu = 199.878301 - instead of the usual low numbers such as - wxu = 
> 0.25 - found during isotropic ADP refinement?

these values may be very different depending on many pretty general 
things such as data resolution, model quality, etc... So it's hard to 
tell what is a good/bad or typical value... I keep eye on X-ray/Geometry 
weight and it appears that the typical value is around 1.-20. or so, but 
it can be drastically different if you switch from ML target to 
something else, like twin LS target.

> While optimize X-ray/ADP weight is useful in phenix, I am still 
> getting anistropic ADP values that are a bit outside what one might 
> expect at 1.5 A compared to the PDB. For the latter, I check things 
> using Parvati (http://skuld.bmsc.washington.edu/parvati/).

Are they nonsensical (physically impossible/wrong) or just different 
from "what is typically observed"? If the latter is the case then, 
provided that everything else is good and makes sense, I wouldn't worry 
about it too much since an outlier does not necessarily means wrong.

If the first is the case then I would set a stricter weight for ADP 
refinement manually (rather than letting it get optimized using 

Let me know if you need any help with this.

Good luck!

More information about the phenixbb mailing list