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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