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
