I would guess that it would be easier to restrain a helix by hydrogen
bond lengths rather than by phi/psi torsion angles, and that could
work for sheets as well.
Phil
On 8 Jan 2009, at 19:05, Garib Murshudov wrote:
If top/par file could be converted to the following type of
instructions then you do not need to define everything in cif file
(these are for torsion angles, all other restraints can be defined
similarly)
General torsion angle restraints for any quartet of atoms:
external torsion first chain [ch] residue [res] insertion [ins]
atom [n] [altecode [a]] next chain [ch] residue [res] insertion
[ins] atom [n] [altecode [a] ] [symm y/n] next chain [ch] residue
[res] insertion [ins] atom [n] [altecode [a] ] next chain [ch]
residue [res] insertion [ins] atom [n] [altecode [a] ]
[symm y/n] value <v> sigma <s> period> <p>
Exampl
external torsion first chain A residue 220 atom C next chain A
residue 220 atom CA next chain A residue 220 atom C next chain A
residue 221 atom N value -60 sigma 10 period 1
regards
Garib
On 8 Jan 2009, at 18:14, Eckhard Hofmann wrote:
Hi Phil,
sorry, haven't read you question properly. No idea how to get
easily from top/par to cif for refmac.....
Probably would need a little scripting, but that's been exactly
your question ...
Eckhard
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 <eckhard.hofm...@bph.ruhr-uni-bochum.de>
Ruhr-Uni Bochum
AG Proteinkristallographie, LS Biophysik, ND04/316
44780 Bochum
Tel: +49-(0)234/32-24463, Sekr. -24461, FAX: -14762
