Paul,
The same problem is caused by isoaspartate
modifications, which I wrote to you about a few months ago.
There, you have ----RNH--CO--CH2--CHR--NH-----
a linker with a CH2 group inserted into the chain. Apparently quite a few
proteins undergo this sort of isomerisation, but people usually assume
the electron density is disordered...
I still do not know how to model it for one
of my structures in COOT.
See residue IAS101 in 1at6, for example...
Tadeusz
On Tue, 2007-05-15 at 17:06 +0800, Charlie Bond wrote:
>
> > Coot uses the _chem_comp.group to determine the link type.
> > It needs to be either L-peptide or D-peptide to be linked as
an amino
> > acidic chain.
>
> How about non-peptide links, of which my molecule contains a number
(15
> or so, see PDB 1E9W for an example)?
1E9W: Yikes! I think I'll use that as a torture test for the
forthcoming LINK code.
I can't help at the moment, sorry. This will be fixed along with
glycosylation and branching carbohydrates.
Paul.
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