Thanks for this, and fixing the problem. For info, this mmCIF is the sort of thing that may be available to an author before the full pdb mmCIF is generated/available, so its great that Jmol can handle such things.
On an unrelated matter, its also great that JSmol can produce animated gifs from such structures (I thought it was only the Java versions that could do this - turns out JSmol will too - understandably a bit slow but nonetheless very impressive!) Thanks again for all your endeavours Cheers Simon Quoting Robert Hanson <hans...@stolaf.edu>: > Nice, simple mmCIF file. This would be a good template for us to use for > writing from Jmol. > > I note that the following three fields in that sample file are ignored by > Jmol: > > _atom_site.label_atom_id > (This data item is a pointer to _chem_comp_atom.atom_id in the > CHEM_COMP_ATOM category.) > > _atom_site.label_comp_id > (This data item is a pointer to _chem_comp.id in the CHEM_COMP category.) > > _atom_site.pdbx_auth_comp_id > (Author's residue name.) > > Instead, Jmol uses: > > _atom_site.auth_atom_id > (An alternative identifier for _atom_site.label_atom_id that may be > provided by an author in order to match the identification used in the > publication that describes the structure.) > > _atom_site.auth_comp_id > (An alternative identifier for _atom_site.label_comp_id that may be > provided by an author in order to match the identification used in the > publication that describes the structure.) > > > I realize that these are listed as "alternative" identifiers; still, this > is what Jmol uses. > > In contrast, Jmol requires these: > > _atom_site.auth_asym_id (chain ID provided by author) > _atom_site.auth_seq_id (residue number provided by author) > > but also reads these for special purposes: > > _atom_site.label_asym_id (chain ID used in BIOMOLECULE definition, in > _pdbx_struct_assembly_gen) > _atom_site.label_seq_id (residue number used in validation and sequence > annotation references) > > > Bob > > On Wed, Feb 25, 2015 at 2:18 PM, Robert Hanson <hans...@stolaf.edu> wrote: > >> http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.12_2015.02.25c.zip >> >> Jmol.___JmolVersion="14.3.12_2015.02.25c" >> >> bug fix: Jmol 14.1.2_2013.12.13 disabled some mmCIF file reading for >> non-wwPDB mmCIF files >> >> >> >> >> On Tue, Feb 24, 2015 at 8:46 AM, <s...@publcif.co.uk> wrote: >> >>> Jmol doesnt appear to be recognizing/calculating secondary structure >>> for some mmcifs - i.e. no cartoons etc. >>> >>> example cif is at >>> http://cif.publcryst.co.uk/cifmoldb/gui/tests/noname.mcf >>> >>> This problem seems to apply to Jmol 14.2 onwards (i.e. works as expected >>> with >>> earlier versions). >>> >>> Any fix/help/workaround would be much appreciated >>> >>> Cheers >>> >>> Simon >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Dive into the World of Parallel Programming The Go Parallel Website, >>> sponsored >>> by Intel and developed in partnership with Slashdot Media, is your hub >>> for all >>> things parallel software development, from weekly thought leadership >>> blogs to >>> news, videos, case studies, tutorials and more. Take a look and join the >>> conversation now. http://goparallel.sourceforge.net/ >>> _______________________________________________ >>> Jmol-users mailing list >>> Jmol-users@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>> >> >> >> >> -- >> Robert M. Hanson >> Larson-Anderson Professor of Chemistry >> Chair, Department of Chemistry >> St. Olaf College >> Northfield, MN >> http://www.stolaf.edu/people/hansonr >> >> >> If nature does not answer first what we want, >> it is better to take what answer we get. >> >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> >> > > > -- > Robert M. Hanson > Larson-Anderson Professor of Chemistry > Chair, Department of Chemistry > St. Olaf College > Northfield, MN > http://www.stolaf.edu/people/hansonr > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > ------------------------------------------------------------------------------ Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
