In principle in refmac you can resrtraint any torsion angle you want.
If this torsion angle has definition in the dictionary. It includes
phi/psi also.
See
http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_news.html
For example for phi you can do (phi is the proeprty of link between
amino acids)
restraint link TRANS name phi value <value> sigma <sigma> period
<period>
Similarly for links CIS, PTRANS and PCIS
But I cannot guarantee good results. If anybody is interested in
playing around with these restraints I would be interested what would
happen if
you would use these restraints.
Garib
On 9 Nov 2007, at 20:55, Michael S. Chapman wrote:
Echoing some previous comments, restraints on backbone torsion
angles can give substantial improvements in low resolution
refinements. I've seen it in several virus structure refinements
3.25A to 3.75A. Just have to make sure that you then don't use phi/
psi angles as a validation.
There is a very easy / transparent way to restrain backbone torsion
angles in the refinement program TNT by Dale Tronrud & colleagues.
Restraints are available, but given zero weight by default. The
restraint on each torsion angle is specified as a periodic set of
equal optima, such as {0, 180} or {60, 180, 240} just like many
molecular mechanics programs. From decade-old memory, the defaults
for phi & psi are both {60, 180,.240} which can be modified in the
topology files to better target the known optima of a Ramachandran
plot.
A very similar restraint / potential is also available in X-Plor,
and I'm guessing is available in CNS and Phenix, but it might be a
little more work to invoke.
Different design criteria have been used in writing different
refinement programs. There isn't much call for backbone torsion
restraints in typical Shellx or Refmac refinements. If you are
working at unusually low resolution, other programs might be more
suitable.
Michael S. Chapman, R.T. Jones Professor of Structural Biology
Dept. Biochemistry & Molecular Biology; School of Medicine, Mail
Code L224
Oregon Health & Science University
3181 Sam Jackson Park Road; Portland, OR 97239-3098
[EMAIL PROTECTED] / (503) 494-1025; http://xtal.ohsu.edu/
