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
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