[Chimera-users] Built-in residue specific annotations in mmCIF?
Greg Couch
gregc at cgl.ucsf.edu
Thu Nov 12 13:22:43 PST 2015
That is an excellent suggestion. Currently the mmCIF files from the PDB
provide the free-form text for the footnote, but do not provide the data
that is supposed to be in the associated conformer_family_coord_set
category. And without that data, it will be difficult to figure out and
show exactly which atoms/residues are associated with the footnote. It
looks like that part of the mmCIF specification is unused because it is
not well thought out. The conformer_family_coord_set data category
makes references to CIF save frames, but currently " mmCIF does not
support references to save frames or the use of save frames for purposes
other than for encapsulating dictionary definitions"
[http://mmcif.wwpdb.org/docs/tutorials/mechanics/pdbx-mmcif-syntax.html]. And
since there are no examples, so it is unclear how the mmCIF committee
was expecting this to work.
So until atom_sites_footnote's are "fixed", is getting access to the
text okay? We could probably extract the relevant residues from the
free-form text most of the time, but it would be a hack.
-- Greg
On 11/11/2015 10:11 AM, Oliver Clarke wrote:
> Hi all,
>
> As discussed on the ccp4bb
> (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;2223469c.1511),
> the mmCIF format incorporates an atom_sites_foornote record
> (http://mmcif.wwpdb.org/dictionaries/mmcif_nmr-star.dic/Categories/atom_sites_footnote.html)
> which allows for the direct association of specific
> comments/annotations with particular atoms/residues.
>
> As part of expanding mmCIF support in Chimera2, would it be possible
> to consider incorporating the capacity to read, write, and display
> these records as labels or notes? This could be a great way of
> incorporating built-in-annotations in a structure pertaining to
> specific features that could potentially be readable by other software
> such as Coot and pymol.
>
> Cheers,
> Oliver.
>
>
>
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