[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.

Oliver.

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
>>
>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20151112/a50c7dc0/attachment-0001.html>


More information about the Chimera-users mailing list