Dear Vaheh
Usually we do not rename chains as part of the curation procedure.
There are instances when we do, for example when a chain has to be split
into two chains and a new chain has to be defined, but this isn't
typical.
Because of this the wwPDB mmCIF file for each entry will usually contain
the chains as defined by the depositor.
If two letter chain IDs were used by the depositor then this is
incompatible with the PDB format and a best effort PDB file is created.
This will contain remapped chain IDs with a single letter for the
chains.
If you are using this best effort PDB file then I would encourage using
the mmCIF file instead.
If this is not the case, please can you share examples through our
helpdesk ([email protected]) where this has occurred so we can
investigate.
Many thanks
John
On 2021-11-01 15:00, Oganesyan, Vaheh wrote:
Hi All,
This question is mostly for RCSB and PDBe: why are you renaming chains
in the deposited PDB files? Why does it matter what letter is assigned
to the chain? For 1,2 or 3 chain structures it is manageable, but for
more chains and/or many complexes per asu this becomes quite a
challenge. And if chains are similar in shape it is a real pain.
Reading associated manuscripts and looking at those structures is an
additive that feels unnecessary.
Thank you in advance for explaining the logic behind.
Vaheh Oganesyan, Ph.D.
R&D | Biologics Engineering
One Medimmune Way, Gaithersburg, MD 20878
T: 301-398-5851
[email protected]
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John Berrisford
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492529
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