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Re: Draft CIF twin dictionary for approval

  • To: coredmg@iucr.org, Regine Herbst-Irmer <rherbst@shelx.uni-ac.gwdg.de>, Tony Linden <alinden@oci.uzh.ch>, Ilia Guzei <iguzei@chem.wisc.edu>, Ton Spek <a.l.spek@uu.nl>, Martin Lutz <m.lutz@uu.nl>, Bill Clegg <bill.clegg@newcastle.ac.uk>
  • Subject: Re: Draft CIF twin dictionary for approval
  • From: "George M. Sheldrick" <gsheldr@shelx.uni-ac.gwdg.de>
  • Date: Mon, 21 Oct 2013 16:17:30 +0200
  • In-Reply-To: <a06240805ce8a98c36d9e@[]>
  • References: <52499D4C.4010106@mcmaster.ca><a06240805ce8a98c36d9e@[]>
Dear Colleagues,

I share Tony's concerns. The SHELX HKLF 5 format for non-merohedral
twins has been well tested for the last 20 years. It can easily be
understood and edited by users, the firms that provide single-crystal
equipment can all generate it and all important refinement programs can
handle it. Since only a single list of reflections is involved, the data
can be processed immediately without the inefficiency of having to store
and look up other lists. The proposed CIF format has none of these

I should also point out that the CIFs writeen by SHELXL_2013 already
embed the HKLF 5 format files, and so with the help of SHREDCIF a
twinned refinement can be reproduced immediately just like the
refinement of an untwinned structure (and repeating the refinement with
e.g. CRYSTALS would also be straightforward). This also makes archiving
the data easy.

I do not intend to read or write the proposed new format in SHELXL, it
would be an enormous leap backwards. That the suggested format is so
clumsy is not the fault of its authors, it is simply the result of a
serious limitation in the CIF syntax.

Best regards,

On 10/21/2013 11:22 AM, Tony Linden wrote:
> Dear David,
> I looked over the twin CIF definition document.  To be honest, at first
> reading the definitions needed and used to handle reflection data seem
> very complicated for general use.  Below are some thoughts. I don't know
> if these are addressed in the current effort or things not yet quite
> resolved.  Maybe they are, but I did not get my head around all this
> sufficiently well to know.
> First, there are some typos I detected.
> "the this" appears in several places and probably "this" has to be deleted.
> In a description, the range 620 - 624 is given followed by 624 - 629.
> Probably the latter starts at 625.
> Would the definitions for reflection data allow the full input
> reflection file to be reconstructed, e.g. for use in CRYSTALS, SHELXL,
> etc.?  I think the answer is yes, but I want to be sure people agree.
> A fully overlapping reflection would have n individual contributors,
> each with its own values of h,k,l, but one cannot know the contribution
> of each to the measured F**2 and sigma (in the input data).  So how is
> that handled in the current definitions; i.e. I cannot see an example
> where there are two entries with different individual_id and h,k,l, but
> the same F_squared_meas and F_squared_sigma.  I am guessing that the
> _twin_contribution_ list in combination with the _twin_reflection_ list
> achieves this.  OK, but then you have two lists which must be given
> together, so things are getting complicated and long.  Furthermore, the
> appearance of all h,k,l assignments in the _twin_contribution_ list is
> then to some extent duplicated (and complicated) by the use of h,k,l
> again, but only from one component in the _twin_reflection_ list. 
> Understanding how these two lists are constructed, indexed and combined
> seems rather complicated and takes quite a bit of digesting of the
> dictionary to come to grips with.  Could it be simpler???
> Compare this with lines in the HKLF5 style input for SHELXL (CRYSTALS is
> similar)...
>    h   k   l  Fo**2     sigma  component (=individual_id)
>   -4   2  -5  440232    6723  -2
>   -4  -1   6  440232    6723   1
>   -3  -1   6  336093    5357   1
>   -2  -1   6 2138204   47562   1
>   -1  -1   6   71870    1617   1
>    0   1  -6 2044486   44513  -2
>    0  -1   6 2044486   44513   1
> The first and last two lines are overlapping refls from both components
> (common F**2 and sigmas), lines 3-5 are non-overlaps from component 1 only.
> I am not trying to suggest we need to follow the SHELXL path always, but
> I am interested in keeping things relatively simple and easy to
> understand for users.  To me, the SHELXL idea seems less complicated
> than two separate _twin_contribution_ and _twin_reflection_ lists.
> Just my thoughts...
> P.S. Following our discussions in Warwick, I was working on a list of
> CIF items that we might think about updating or other new things
> needed.  I will get that to you eventually, but things have been too
> hectic lately for me to devote much time to it (which is why I could not
> accept James Hester's kind invitation to step into your shoes).
> Best wishes,
> Tony
>> Dear Colleagues,
>> After many years of gestation, a draft CIF dictionary of items for
>> describing twinning in crystals is now available.  It is attached to
>> this email which is being circulated to the core CIF Dictionary
>> Management Group for your approval, this being the final step in the
>> formal COMCIFS approval process.  If you are receiving this message
>> you are invited to review the attached draft and either indicate your
>> approval, or draw attention to potential problems, by replying to the
>> core DMG list at <mailto:coredmg@iucr.org>coredmg@iucr.org. When
>> approved the twinning dictionary will become an addendum to the
>> coreCIF dictionary.
>> The draft is open for review for six weeks ending  on 11 November
>> 2013.  If you have not replied by then, it will be assumed that you
>> approve of the attached document as circulated.  If any questions are
>> raised we will try if possible to resolve them within the review period.
>> The dictionary is also available at the URL
>> <https://github.com/jamesrhester/twinning-dic>https://github.com/jamesrhester/twinning-dic
>> I look forward to receiving your response.
>> David Brown
>> Chair of the core CIF Dictionary Management Group
>> Attachment converted: Macintosh HD:cif_twinning_ver0.6.dic (TEXT/R*ch)
>> (0072E233)
>> Attachment converted: Macintosh HD:idbrown.vcf (TEXT/R*ch) (0072E234)
>> _______________________________________________
>> coreDMG mailing list
>> coreDMG@iucr.org
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Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582

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