I pulled up 1SKT.cif. This is pretty readable. I suggest we implement
this in the CifReader exclusively for now.
I also looked at 5HVP.cif. Are you all SURE that these runs are
independent? That is not at all what is suggested by
http://mmcif.rcsb.org/dictionaries/mmcif_std.dic/Categories/atom_sites_alt.html
or
http://mmcif.pdb.org/mmcif-early/workshop/mmCIF-tutorials/intro/atom.htm
or
http://mmcif.pdb.org/dictionaries/mmcif_std.dic/Categories/atom_sites_alt_ens.html
or
http://www.rcsb.org/pdb/displayFile.do?fileFormat=CIF&structureId=5HVP
Looks to me:
1. you have a set of identifiers 1,2,3, A,B,C, etc.
2. you have a set of ensembles of identifiers -- one per conformation
3. a given "1" for ANY atom corresponds with a given "1" for any other
atom. I don't see this "multiple independent run" business. Again, that
makes no calculational sense to me at all.
4. an atom location with an alt id does not also have a "default"
location, because the only sense to be made from these alternative
locations is that "either 1 or 2"; "either 3 or 4"; etc.
My point is that there are certain reasonable combinations, say "1 with
3" and "2 with 4" that correspond to a given conformation. But "1 with
4" makes no sense, because the calculation only gave two conformations,
not "all possible combinations of alternative locations."
I could be wrong; but if I'm not, it's an easy implementation.
Bob
Bob
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