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
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
>
>
>
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