[phenixbb] getting started with anisotropic refinement
pafonine at lbl.gov
Wed Apr 18 17:37:57 PDT 2012
> I need some help advice regarding anisotropic refinement, which I've
> never done before. My current Rfactors are R-work = 0.1587, R-free =
> 0.1726, resolution 1.26 Å.
two things I would do right away without thinking long:
- add H atoms;
- refine all macromolecular atoms with anisotropic ADPs (probably,
except alternative conformations), and solvent with isotropic ADPs;
Also, please make sure to use recent Phenix version. That may have
impact in your case, since latest phenix.refine have improved handling
of hydrogen atoms (*), and a new bulk-solvent and anisotropic scaling
If you still want to define by hand which atoms to refine
isotropically/anisotropically, then a parameter file like this should
allow to do this:
isotropic = (chain A and resseq 1:100) or (chain X and resseq
300:900) or water
anisotropic = (chain Z and resseq 123 and name CG1) or (element Au)
Make sure you cover all atoms with
isotropic = ...
anisotropic = ...
selections, because the default behavior is that if you change these
parameters then phenix.refine assumes you know what you do. If you do
not select all atoms with these selections, then B-factors of atoms that
are not selected will not be refined. I don't like this and I will
change this once I get a chance.
For your specific example:
isotropic = not (chain A and (resseq 7:44 or resseq 61:149 or
resseq 173:182 or resseq 202:254 or resseq 263:290))
anisotropic = chain A and (resseq 7:44 or resseq 61:149 or
resseq 173:182 or resseq 202:254 or resseq 263:290)
I've never tried but this might work too:
aniso_sel = chain A and (resseq 7:44 or resseq 61:149 or resseq
173:182 or resseq 202:254 or resseq 263:290)
isotropic = not $aniso_sel
anisotropic = $aniso_sel
Phil experts may comment on this more.
Let me know if you have any questions or need any help with this!
(*) "On contribution of hydrogen atoms to X-ray scattering"
> I have TLS groups, and know I need to exclude these from individual
> anisotropic refinement.
> 1) how to decide my atom selection for anisotropic refinement. I've
> identified segments with MC B below 20, but what to do for surface
> residues which have well ordered MC but B factors for side chains
> increase (e.g. along a well ordered Lys side chain) - should (can?) I
> a) refine only MC anisotropically,
> b) refine whole residue anisotropically,
> c) refine isotropic
> 2) How to write a a parameter file for phenix.refine defining the atom
> The residues I'd like to use for anisotropic refinement are: A7-A44
> A61-A149 A173-A182 A202-A254 A263-A290 all in chain A
> I found following on phenix.refine online docs, but am not sure to to
> extend this for a more complex selection needed above, which Ideally
> I'd put into a file to be read in when I start refinement. Could yo
> show me how to do for A7-A44 and A61-A149, and I'll follow example for
> the rest.
> adp.individual.anisotropic="resid 1:2 and not element H"
> adp.individual.isotropic="not (resid 1:2 and not element H)
> Thanks for help.
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