Hi,

Add something like this in the header:
LINKR            ALA A  74                     VAL A  84                gap

With regards,

Henriette Rozeboom

Biotechnology

Faculty of Science and Engineering, University of Groningen

9747 AG Groningen, The Netherlands

+31(0)50 363 3904


On Tue, Mar 29, 2022 at 11:37 PM DeLaitsch, Andrew T. <delait...@caltech.edu>
wrote:

> Hi,
>
> I am working on refining antibody-HIV-Env structures in COOT. The problem
> I have is that both antibodies and HIV-Env have standardized numbering
> systems (e.g. Kabat for antibodies and HXB2 for HIV-Env) which result in
> sequential residues in the protein's primary structure not having
> sequential numbering (e.g., residues numbered 143 and 152 should be
> connected by a peptide bond). When doing refinements in COOT, this
> non-sequential numbering causes problems, as the peptide bond is not formed
> and the residues get 'forced' apart from one another as the program thinks
> there should be more residues in-between the two. Is there a simple way to
> go about fixing this? Currently, my workaround is to renumber residues so
> that they are sequentially numbered, and then after the final refinement go
> into the PDB and change the numbering. However, this workaround is
> less-than-ideal as there are a many segments to renumber, and also I rely
> on the HXB2 numbering while doing the refinement to know which residues are
> which in my structure.
>
> Thanks,
> Andy
>
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