I put together a simple perl script to take WHATIF optimal hydrogen
bonds from a known structure and generate refmac or cns restraints. You
can limit it to backbone or all h-bonds.
Refmac:
http://hood.icmb.utexas.edu/~paul/ccp4_hbond
CNS:
http://hood.icmb.utexas.edu/~paul/cns_hbond
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
--
Paul Paukstelis, Ph.D.
Research Associate
Institute for Cellular and Molecular Biology
The University of Texas at Austin
P: 512-471-4778, F: 512-232-3420
[email protected]
