Dear Marcin,
Thank you for your feedback. We will improve mmCIF documentation for
this recommendation.
Most of the wwPDB remediation do not require change of chain id or
residue numbering. For new data representation such as carbohydrates and
previous remediation of peptide-like inhibitors, it is unpreventable to
change original chain id and/or numbering. In this case, wwPDB provides
a mapping category to retain original chain id or residue numbering.
Regards,
Jasmine
===========================================================
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087
Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===========================================================
On 12/11/20 8:11 AM, Marcin Wojdyr wrote:
Dear Jasmine,
I fully agree with this recommendation:
To use the wwPDB-assigned chain ID in publications,
_atom_site.auth_seq_id _atom_site.auth_comp_id, and
_atom_site.auth_asym_id can be used for the residue number, residue ID,
and chain ID, respectively.
It would help a lot if the same was recommended in the mmCIF documentation.
Currently, these IDs are described as non-mandatory, alternative IDs,
which suggests (to those few software developers that read the
documentation) that they shouldn't be relied upon.
It'd also be good if the IDs that are recommended for use in
publications weren't changed afterwards as it happened in this
remediation.
Carbohydrate remediation was indeed consulted with the community over
a long time, but perhaps this particular change wasn't made clear. I
always assumed that only the primary (wwPDB internal) IDs are to be
changed, not the ones that were used in publications.
Best regards,
Marcin
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