XPLO2D from the USF-Suite does this:
<snippet from manual>
You feed it a PDB file of the model to which you want to restrain your
refinement model (e.g., that high-resolution native structure you
already have, even though it may be in a different spacegroup or with
different domain orientations). The program generates an X-PLOR include
file which contains DIHEdral statements for the PHI, PSI, CHI-1 and
CHI-2 torsions of the protein. If you protein contains a hinge region,
simply remove or comment-out the relevant PHI and PSI restraints. If you
don't want to impose restraints on CHI-1 and/or CHI-2, set the
corresponding weights to zero (at the top of the X-PLOR include file).
I never tried, but this will be compatible with phenix as well.
Cheers
Eckhard
Phil Evans schrieb:
> 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
--
Eckhard Hofmann <[log in to unmask]>
Ruhr-Uni Bochum
AG Proteinkristallographie, LS Biophysik, ND04/316
44780 Bochum
Tel: +49-(0)234/32-24463, Sekr. -24461, FAX: -14762
|