Hi,
I'm not sure if that is what you are looking for, but if you want to use
the "real space refine zone" function in coot with sugars that is possible.
For a monosaccharide you will need a cif dictionary with the restraint
definitions - in some cases present in the refmac monomer database, but
be careful not all cif files there are correct. If none is present or if
your monomer is disrupted during refinement you can look at the small
molecule databases (Hic-Up etc) or calculate one with PRODRG
(http://davapc1.bioch.dundee.ac.uk/prodrg/). Load it with "File" "Import
CIF dictionary and real space refinement should work.
If you try to refine a polysaccharide it's a bit more difficult since
coot will ignore any glycosidic bond restraints - if two sugars are
close by and one has well defined density and the other one not it might
even place them on top of each other.
I like to use the anchor tool on the bonding atoms in those cases.
The other option for a polysaccharide is to use PRODRG to generate a
single "monomer" out of your polysaccharide.
In any case at the end you have to inspect the geometry manually since
the restraint definitions are often incomplete.
Greetings
Dirk
Am 22.11.11 01:16, schrieb Jan van Agthoven:
Hi everyone!
Does anyone know if there is a way of auto-refining a sugar in Coot?
Jan
