[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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> Chimera-users at cgl.ucsf.edu
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