Yes please.

Paul.

On 31/03/2022 20:20, Eleanor Dodson wrote:
> Could Andrew T please send an example of a data set that fails for
> testing?
>
> Eleanor
>
> On Wed, 30 Mar 2022 at 22:24, Paul Emsley <pems...@mrc-lmb.cam.ac.uk
> <mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:
>
>
>     On 29/03/2022 22:26, DeLaitsch, Andrew T. wrote:
>>
>>
>>     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.
>>
>
>     Why is it that so many correspondents on this list don't mention
>     the version of Coot that they are using, where the got it from or
>     how I (or anyone) might reproduce the problem?
>
>     Hmm.
>
>
>     Paul.
>
>
>
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