Joe Smith wrote:
Hello,
I have been building a protein model (resolution 2.2A) which has one
small loop of 6 residues having poor density. I cannot see any side
chain in this region but I can see relatively poor main-chain density
which at least clearly indicate the loop conformation. I am trying my
best to build polyAla chain in this region. But 3-4 residues end up
coming in disallowed region of Ramachandran plot. I think the problem
is - in this region i can not even build the main chain atoms with
high confidence.
Can I build polyGly in this region? or should I just leave this
region? I just don't feel like leaving this region empty.
Any suggestions in this regards is highly appreciated!
regards
Joe
You could try using coot real space refinement with ramachandran
restraints on..
Eleanor
