[phenixbb] anisotropic refinement water hydrogens and gui

Pavel Afonine PAfonine at lbl.gov
Tue Mar 9 12:34:33 PST 2010

Hi Christian,

> I did an anisotropic refinement with the gui for a 1.6 Ang. 
> structure I think 
> this is quite O.K. as the R-values seems to be reasonable(14/18.8). 

The R-factors are looking ok indeed.

> But for 
> comparison I want exclude waters and hydrogens explicitly from the 
> anistropic 
> refinement. One could do this in the command line mode via 
> adp.individual.anisotropic ="not water and not element H. I started 
> from the 
> gui and modified the .eff directly by icnluding:
> adp {
>      individual {
>        isotropic = None
>        anisotropic = "not water and not element H"
> In the output pdb all waters have an anisou flag. So I assume 
> phenix refined 
> them anisotropically. How do I have to modify the .eff file to 
> exclude the 
> waters from the anisotropic refinement. 
> I would like to use the gui, because you get this nice summary 
> output with all 
> statistics. 

At 1.6-1.7A resolution you should not refine water with anisotropic ADPs, and H atoms should be refined as riding function. So, I suggested refinement parameters for ADP are:

refinement.refine {
    adp {
      individual {
        isotropic = water or element H
        anisotropic = not (water or element H)

If the Rfree and Rfree-Rwork do do seem to support it, then switch to TLS refinement.


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