Dear Jason,
you will have to include the planarity either by introducing torsion
restraints for the specified bonds, or by using the plane definition.
Pls. be aware that in the current refmac versions the plane definitions
will be used with a fixed sigma, i.e. the value of the dictionary is not
used.
For the torsion restraints you will have to include them explicitly in
the input, check the earlier posting on torsion restraints.
Garib kindly made an experimental version of refmac which allows easier
inclusion of torsions from the dictionary AND the inclusion of the
sigmas for the plane definitions (One sigma for each plane group, taken
from the first atom in the group in the dictionary).
see for linux binaries:
http://www.ysbl.york.ac.uk/refmac/data/refmac5.4_linintel.tar
http://www.ysbl.york.ac.uk/refmac/data/refmac_news.html
Hope that helps,
Eckhard
Jason Greenwald schrieb:
Dear all,
How does one tell Refmac that the bond between two non-amino-acid
monomers should be planar (in the case that this bond is an amide)?
My ligand has amino-acid and non-animo-acid constituents that are
connected via amides. I have made library definitions for all of the
non-standard parts and Refmac accepts these and makes the bonds between
the various monomers in the ligand.... but treats them as single bonds
and therefore fully rotatable.
Cheers.
Jason
--
Eckhard Hofmann <[EMAIL PROTECTED]>
Ruhr-Uni Bochum
AG Proteinkristallographie, LS Biophysik, ND04/316
44780 Bochum
Tel: +49-(0)234/32-24463, Sekr. -24461, FAX: -14762
