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

Greg Couch gregc at cgl.ucsf.edu
Thu Nov 12 16:08:36 PST 2015

Noted.  I've added this to the list of things to do for ChimeraX 
(formerly known as Chimera2).

   -- Greg

On 11/12/2015 02:21 PM, Oliver Clarke wrote:
> 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.
> Oliver.
> On Thu, Nov 12, 2015 at 4:49 PM, Oliver Clarke <olibclarke at gmail.com 
> <mailto: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
>     <mailto: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),
>>         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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