[Chimera-users] Built-in residue specific annotations in mmCIF?
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).
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.
> 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:
> 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
> <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"
> 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
>> 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 <mailto:Chimera-users at cgl.ucsf.edu>
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