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. > > > > ------------------------------------------------------------------------ > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
