Discussion List Archives

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

Re: Draft CIF twin dictionary for approval

  • To: Distribution list of the IUCr COMCIFS Core Dictionary Maintenance Group <coredmg@iucr.org>
  • Subject: Re: Draft CIF twin dictionary for approval
  • From: Tony Linden <alinden@oci.uzh.ch>
  • Date: Mon, 21 Oct 2013 11:22:11 +0200
  • In-Reply-To: <52499D4C.4010106@mcmaster.ca>
  • References: <52499D4C.4010106@mcmaster.ca>
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,

>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 
>The dictionary is also available at the URL 
>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

  Prof. Dr. Anthony Linden
  Editor, Acta Crystallographica Section C
  University of Zurich
  Institute of Organic Chemistry
  Winterthurerstrasse 190
  CH-8057 Zurich, Switzerland

  Phone:  +41 44 635 4228
  Fax:    +41 44 635 6812

  2014: The International Year of Crystallography
  The Zurich School of Crystallography,
  University of Zurich, June 7-20, 2015
coreDMG mailing list

[Send comment to list secretary]
[Reply to list (subscribers only)]