[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.
Pavel.
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