[phenixbb] getting started with anisotropic refinement
Dr. Mark Mayer
mayerm at mail.nih.gov
Wed Apr 18 13:41:57 PDT 2012
Hi Pavel
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. I have TLS groups, and
know I need to exclude these from individual
anisotropic refinement.
Questions:
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 selections.
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.
Mark
.
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