On 24/11/10 14:12, Paul Emsley wrote:
On 24/11/10 00:14, jy wrote:
Dear Coot and CCP4 users,
I need to add a glycosylated Asn in my protein. To do it, I copied from
an existing PDB file where it has 2 NAG and 1 BMA, and modeled it to the
density in Coot. Then I wrote out the PDB.
WHen I refined the structure again with refmac, an error occured,
"Error: atom: NAG 1 CC is absent in the library"
Im not sure where I should look, but tried to edit the cif file on the
bonding, but just could not get it to work.
The way that I read this that in your PDB file you have a atom named "
CC " in the NAG. However the Refmac dictionary does not have an atom of
that name in the dictionary (not should it, for clarity).
You do not need to edit cif files, just do it the standard way:
Get Monomer
Merge Molecules
{nudge and rotate}
sphere refine.
Oh, and you'll have to delete the bridging O and its H - Coot doesn't do
that yet.
Paul.
