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)
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