Crystal Chuang wrote:
> Hi Coot Users,
>
> I have a question on dealing with gaps in between chains of residues. I had a
> shorter chain of residues that was separated by a gap from a longer chain.
> The gap was due to an area of weak density where I was not able to map
> residues or decide on the correct side chains corresponding to the known
> sequence. After making a few changes and improving the density, I extended
> the shorter chain by adding terminal residues and kept building until it
> reached the longer chain. Even though I'd renumbered the residues so that
> they are now sequential, for some reason, I cannot regularize or real space
> refine the bonds between that of the last residue of the shorter chain with
> the first residue of the longer chain. It is as if COOT sees them as two
> separate, independent chains and will not allow me to connect the two into
> one long continuous strand. Has anyone also come across this problem? Is
> there a way I can try to get around it?
Hi Crystal,
I suspect that you are right, Coot is indeed seeing them as separate
chains. It has been my experience that if they really are in the same
chain, then Coot can connect them.
So, why does Coot think that they are in different chains?
The chain IDs are different?
The short chain is in a different model to the longer chain?
The short and longer chain residues in the pdb file are separated by a
chain that is a different chain?
The residues are in a "strange" order in the pdb file? (say for example
the residues are not in residue number order). A quick bit of cutting
and pasting should put that to rights...
Hope that helps,
Paul.
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