Phil,
I have a student who has been working on a python script that will allow
the user to manually define hydrogen bonds in pymol (i.e. click on the
nitrogen and oxygen atoms that you want to restrain). It then outputs a
restraints definition file for refinement in phenix. It can be tedious
to define the restraints for a large structure (we are working on a low
resolution refinement of a large structure right now), but I haven't
been able to find a better alternative.
If you would like to play with our scripts, let me know.
Sean Johnson
Phil Evans wrote:
Does anyone have a good way of imposing secondary structure restraints
in a low resolution refinement?
I've done this in the past as hydrogen bond distance restraints within
helices, input to refmac as "LINK"s , with the list generated with a
little program and certain amount of pain
refmac now accepts an explicit list of external restraints, as does
phenix.refine, but I'm looking for a way of generating these lists for
quite a large structure without too much hackery, perhaps from a
hydrogen-bond or secondary structure assignment program. Helices are
reasonably straightforward (I can see how to do them from eg DSSP),
but sheets are more complicated.
Any suggestions? I'm sure that someone must have done this
Phil
--
Sean Johnson, PhD
R. Gaurth Hansen Assistant Professor
Utah State University
Department of Chemistry and Biochemistry
0300 Old Main Hill
Logan, UT 84322-0300
(435) 797-2089
(435) 797-3390 (fax)
sean.john...@usu.edu
