[Chimera-users] Built-in residue specific annotations in mmCIF?

Oliver Clarke olibclarke at gmail.com
Thu Nov 12 13:49:49 PST 2015

I see what you mean Greg... it is not at all clear how to use this now that
I look at it in more detail.

A hack using this entry as a handle for persistent notes would certainly be
useful in the medium term, but in the longer term it would be nice to have
a established syntax, so that notes written in Chimera could be read and
displayed in Coot, for example (see here for discussion:

But I guess this might require some discussion with the PDB - according to
their FAQ old-school PDB files will become obsolete next year and
mmCIF/PDBx will be the only game in town...


On Thu, Nov 12, 2015 at 4:22 PM, Greg Couch <gregc at cgl.ucsf.edu> wrote:

> 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>
> 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.
> _______________________________________________
> Chimera-users mailing listChimera-users at cgl.ucsf.eduhttp://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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