[Chimera-users] Built-in residue specific annotations in mmCIF?
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"
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.
On 11/11/2015 10:11 AM, Oliver Clarke wrote:
> Hi all,
> As discussed on the ccp4bb
> the mmCIF format incorporates an atom_sites_foornote record
> 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.
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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