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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