Discussion List Archives

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

_atom_site_aniso_label is broken

  • Subject: _atom_site_aniso_label is broken
  • From: James Hester <jrh@xxxxxxxxxxxx>
  • Date: Fri, 17 Jun 2005 16:14:16 +0900
In a nutshell:

Both _atom_site_label and _atom_site_aniso_label have the following
lines in their dictionary definitions:

...
_category atom_site
_list_mandatory  yes
...

meaning that they must be included in any list containing items from the
atom_site category.  As an item name can only appear once in any data
block, this means that there can only be one list containing _atom_site
items in a data block (as _atom_site_label and _atom_site_aniso_label
would otherwise appear more than once).  As _atom_site_aniso_label is a
child of _atom_site_label, it must have values drawn from the
_atom_site_label values, so we have a single list, with these two _label
data names taking identical values.

Also, to be valid a CIF must contain *both* these data items in any loop
containing atom_site values.  This is not true for many CIFs out there.

What was intended (as indicated by the comments in the
_atom_site_aniso_label definition) was to allow anisotropic temperature
factors to appear in a separate loop.   This could be accomplished by
setting _list_mandatory to 'no' for both items, and then setting
"_list_reference" to either _atom_site_label or _atom_site_aniso_label
for all items in the atom_site category, or else by creating a separate
_atom_site_aniso category (as was done in the mmCIF).

I'm sure the dictionary developers have been aware of this for at least
10 years, judging by a cursory search in the archives.  What are the
reasons it has been left as-is?  And should we programmers write in a
special exception for these labels?  

James. 
_______________________________________________
cif-developers mailing list
cif-developers@iucr.org
http://scripts.iucr.org/mailman/listinfo/cif-developers

Reply to: [list | sender only]
International Union of Crystallography

Scientific Union Member of the International Science Council (admitted 1947). Member of CODATA, the ISC Committee on Data. Partner with UNESCO, the United Nations Educational, Scientific and Cultural Organization in the International Year of Crystallography 2014.

International Science Council Scientific Freedom Policy

The IUCr observes the basic policy of non-discrimination and affirms the right and freedom of scientists to associate in international scientific activity without regard to such factors as ethnic origin, religion, citizenship, language, political stance, gender, sex or age, in accordance with the Statutes of the International Council for Science.