John Pak wrote:
Hi all, I was hoping to receive some guidance on the following subject.
I'm refining a structure using REFMAC that shows all the symptoms of
radiation damage. Namely partially broken disulphide bonds and
decarboxylated Asp/Glu residues. I have an idea of how to handle the
partially broken disulphides. I was wondering how people model
decarboxylated Asp/Glu residues. Do you adjust the occupancy of the
carboxylic acid moiety until the negative Fo-Fc density goes away, or
do you losen the side-chain B factor restraint in REFMAC to something
higher, like 30 A^2. I don't know which is more appropriate.
Thanks.
It is difficult because your merged data set will include some
information from complete ASN etc and some from damaged ones..
Prob. all you can do is use the occupancy factor to partially model what
has happened..
Eleanor
