Dear Helge, > G533 in chain a > C823 in chain A > G1186 in chain A > C1147 in chain A > A614 in chain a These are actually what I just reported to Paul - the "DNA-SER" link problem, while some of them are DNA-TYR, but the same issue.
Coot tries to make these links when RNA/DNA residues are close to SER or TYR. It is related to the AA-RNA problem: https://pemsley.github.io/coot/blog/2023/06/05/AA-RNA.html > D2T > 3TD > 6MZ In the monomer library, they have been demoted to NON-POLYMER because they do not use the standard atom names. However, it is completely fine to change D2T and 3TD group names to peptide/RNA, as the problematic atom names are those that do not exist in polymers (OXT equivalent for example). Changing 6MZ group name to RNA would be suboptimal, because they use O1P/O2P/O3P names instead of the standard OP1/OP2/OP3, and restraints for these atoms would not be used in the refinement (if you change the group name to RNA). Best regards, Keitaro On Thu, 24 Aug 2023 at 16:03, Helge Paternoga <helge.patern...@uni-hamburg.de> wrote: > > Dear Paul, > > I just had the chance to try out the new Coot version 9.8.91 from CCP4 > and I would like to report that RSR of ribosomes is still broken (albeit > not as severely as before). > > You can have a look at PDB-7K00 for examples: > > https://www.rcsb.org/structure/7K00 > > https://www.ebi.ac.uk/emdb/EMD-22586 > > I went through the model with sphere refine to check for broken areas > and identified many, here are a few: > > G533 in chain a > C823 in chain A > G1186 in chain A > C1147 in chain A > A614 in chain a > > > In addition, there are three modified residues in that model that still > require edited restraints to make them work in Coot: > > D2T > 3TD > 6MZ > > Here, the group name is "NON-POLYMER", I changed that to RNA (3TD+6MZ) > or L-peptide (D2T) which makes it work in Coot. Is that ok to do? > > Many regards, > > Helge > > ######################################################################## > > 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/ ######################################################################## 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/
