I'm afraid I'm still having some problems: If I add 13 blank lines after the start of a data block, Jmol seems to not handle the secondary structure again, e.g.
data_UNNAMED # loop_ _atom_site.group_PDB ... Furthermore, its not just blank lines, e.g. data_xxxx _atom_sites.entry_id xxxx _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 0.022659 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.001692 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.013535 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.011458 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # ... causes the same problem (I'm guessing there are 13+ items that aren't triggering some parsing switch?) In both examples removing the 'blank/unrecognized' lines fixes the problem. I'm guessing this is a bug? 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
