[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.


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 

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 Mayer Ph.D.
Bldg 35, Room 3B 1002 MSC 3712
35 Lincoln Drive
Bethesda MD 20892 3712
Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396
Lab web site: http://snb.nichd.nih.gov/index.htm

Send packages, Fedex and anything requiring a signature to:

Bldg 35, Room 3B 1004
35 Lincoln Drive
Bethesda MD 20892

More information about the phenixbb mailing list