[Cod-bugs] Invalid CIFs for LiNbO3
Antanas Vaitkus
antanas.vaitkus90 at gmail.com
Tue Jul 18 20:30:49 EEST 2017
Dear David Palmer,
thank you for notifying us of this issue. I have updated the symmetry
information in entries 2101175-2101185
(entry 2101175 had the same problem as well). The issue seems to have
originated upstream in the
supplementary material of the original publication. Most likely the files
were ingested into the database in
the early days of the COD before the rigorous automated checks were
implemented. Currently, all newly
added structures are required to have the symmetry operation loop.
There might still be some files that are missing the symmetry operation
information, but these will be located and
tended to once enough resources can be allocated towards this task.
Please let us know if you spot any more inconsistencies in the COD.
Sincerely,
Antanas Vaitkus
2017-07-18 17:43 GMT+03:00 David Palmer <david at crystalmaker.com>:
> Dear Sir/Madam,
>
> The following CIF entries for LiNbO3 are invalid:-
>
> 2101176 - 2101185
>
> These files violate the CIF standard by failing to include any
> general-equivalent positions - as is required in the CIF file
> specification. Instead, the files simply give a vague spacegroup symbol
> (NOTE: there is no agreed syntax for plain-text spacegroup symbols, so
> authors should NEVER rely on a plain-text spacegroup string in a CIF file.)
>
> For reference, the missing general equivalent positions would be as given
> in the following output from CrystalMaker X (*):-
>
> loop_
> _symmetry_equiv_pos_as_xyz
> '+x,+y,+z'
> '-y,+x-y,+z'
> '-x+y,-x,+z'
> '-y,-x,1/2+z'
> '-x+y,+y,1/2+z'
> '+x,+x-y,1/2+z'
> '2/3+x,1/3+y,1/3+z'
> '1/3+x,2/3+y,2/3+z'
> '2/3-y,1/3+x-y,1/3+z'
> '1/3-y,2/3+x-y,2/3+z'
> '2/3-x+y,1/3-x,1/3+z'
> '1/3-x+y,2/3-x,2/3+z'
> '2/3-y,1/3-x,5/6+z'
> '1/3-y,2/3-x,1/6+z'
> '2/3-x+y,1/3+y,5/6+z'
> '1/3-x+y,2/3+y,1/6+z'
> '2/3+x,1/3+x-y,5/6+z'
> '1/3+x,2/3+x-y,1/6+z'
>
> I hope this helps.
>
> Best wishes,
>
> David Palmer
>
>
> (*) CrystalMaker X is a user-funded project to develop the world’s best
> software for crystal and molecular structures. We receive no government
> funding, salaries, research grants or external sponsorship: all our
> software is funded by our users. Pure, transparent, honest. The only viable
> option for long-term development and support.
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--
Antanas Vaitkus,
PhD student at Vilnius University Institute of Biotechnology,
room V325, Saulėtekio al. 7,
LT-10257 Vilnius, Lithuania
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