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

Oliver Clarke olibclarke at gmail.com
Thu Nov 12 14:21:06 PST 2015

Relating to this, I wonder whether it is possible to find a home for
attributes calculated in Chimera 2 in one of the mmCIF fields?

I mean that's the advantage of mmCIF in theory right, that it is extensible
and can support attributes beyond just position and B-factor?

This would make transferring custom defined or calculated attributes
between different chimera sessions much easier I think, if they were
inherent to the file containing the coordinates, and again would at least
allow for the possibility of data exchange with other programs.


On Thu, Nov 12, 2015 at 4:49 PM, Oliver Clarke <olibclarke at gmail.com> wrote:

> 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:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=coot;8213db52.1511).
> 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...
> Cheers,
> Oliver.
> 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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