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 > > ------------------------------ > > 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/
