From: <sw...@pu...> - 2015-02-27 14:47:53
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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 <ha...@st...>: > 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 <ha...@st...> 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, <sw...@pu...> 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 >>> Jmo...@li... >>> 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 > |