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Re: coreCIF.dic-2.4 Discussion List #8

  • To: coredmg@iucr.org
  • Subject: Re: coreCIF.dic-2.4 Discussion List #8
  • From: spea@chem.uu.nl (a.l.spek)
  • Date: Thu, 29 Jun 2006 14:03:28 +0200 (CEST)
  • In-Reply-To: <a06230900c0c96710feb4@[]> from "Herbert J.Bernstein" at Jun 29, 6 07:51:55 am
Essentially, the inclusion of the shelxl.res as 'detail section' in the
CIF has been suggested at several occasions ans settings, including the
Acta editorial board.

Unfortunately, no follow-up was given to this up-to-now.

The only thing that would help is an update of the SHELXL software in
this respect.

Best wishes

Ton Spek
> Dear Colleagues,
>    As an outside observer of the core discussions, may I suggest that
> that you may be considering a false trichotomy:
>    1.  Deferring detailed restraint and constraint information until CIF3; or
>    2.  Incorporating the restraint and constraint information now; or
>    3.  Sidestepping by incorporating the .res information from
> SHELX or similar parsable-but-not-yet-CIF-parsed information
> from other refinement programs.
> Why not do all three?
>    Certainly, the features of CIF3, allowing methods will facilitate the
> presentation of complex constraints, and, when CIF3 is available, this would
> be an area in which to use methods effectively.  However, there is no
> reason not to include as much as can be included now under fully parsed
> CIF tokens, _and_ to carry the "raw" constraint information in, say, a
> "...details" tags immediately.
>    We are facing a similar problem in the imgCIF dictionary.  Images come
> from the vendors with wonderfully detailed headers containing essential
> information.  We have tags to carry much of the same information, but
> things evolve and things are missed.  So we have proposed to add a new
> tag to our dictionary (in this case _diffrn_data_frame.details, described
> as "A description of special aspects of each frame of data.
>      This is an appropriate location in which to record
>      information from vendor headers as presented in those
>      headers, but it should never be used as a substitute
>      for providing the fully parsed information within
>      the appropriate imgCIF/CBF categories.")
>    This is being done in response from a vendor to carry the "raw"
> header information in a comment.  Giving it a tag preserves the
> information in a form that allows it to be examined both by
> users and by software and which encourages the use of existing
> tags for the detailed information and encourages the creation of
> the necessary new tags to carry what has not been handled yet.
>    While this may lead to the same information being presented in
> more than one place, that is just what we already do with various
> "...details" tags, and having information in multiple places in
> a CIF is a lot better than having the information lost.
>    Therefore, I suggest that you:
>    3a.  Immediately add a "...details" tag to carry detailed
> refinement program settings and values in as close to "raw" form
> as possible and in particular to carry the .res information
> from SHELX; and
>    2a.  As time permits that you add and update CIF tags for
> constraints and restraints to whatever extent you can achieve
> agreement, but without removing information from the "...details"
> tag; and
>    1a.  When we have CIF3, that you use its powerful features to
> carry even more of the constraint/restrain information in detailed
> parsable and executable form.
> Perhaps you might consider using, say, _atom_sites_refinement_details
> for item 3a, as
>      "A description of special aspects of the refinement.
>      This is an appropriate location in which to record
>      information from refinement programs as presented in
>      .res files, etc, but it should never be used as a substitute
>      for providing the fully parsed information within
>      the appropriate CIF categories."
> Alternatively, you could use _atom_sites_special_details,
> which already exists, but which does not seem to have a clear
> purpose in life.  This would give it such a purpose.
>    Regards,
>      Herbert
> At 12:28 PM +0200 6/29/06, George M. Sheldrick wrote:
> >My term doesn't finish until July 21st, but since restraints and 
> >constraints have come up again I cannot resist commenting. The main 
> >reason why it is not possible to reproduce a crystal structure 
> >refinement from the data in CIF file is that most of the information 
> >about the restraints and constraints that were applied in the 
> >refinement has been lost or degraded. It is no secret that the 
> >majority of small molecule structures are refined with a program 
> >called SHELX. The last time a change was made to the definitions of 
> >the restraints and constraints used by that program was 1993. In 
> >fact many of them date back to the 1976 version. Surely we have had 
> >enough time to find a way of incorporating this information properly 
> >into a CIF file? Otherwise I may feel obliged in the next version of 
> >SHELX (if there is one) to embed the .res file - which contains all 
> >this information in a concise and unambiguous form - into the CIF 
> >file, as many users have requested.
> >
> >George
> >
> >Howard Flack wrote:
> >>Term has finished.
> >>
> >
> >--
> >Prof. George M. Sheldrick FRS
> >Dept. Structural Chemistry,
> >University of Goettingen,
> >Tammannstr. 4,
> >D37077 Goettingen, Germany
> >Tel. +49-551-39-3021 or -3068
> >Fax. +49-551-39-2582
> >
> >_______________________________________________
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> >coreDMG@iucr.org
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> -- 
> =====================================================
>   Herbert J. Bernstein, Professor of Computer Science
>     Dowling College, Kramer Science Center, KSC 121
>          Idle Hour Blvd, Oakdale, NY, 11769
>                Office:  +1-631-244-3035
>             Lab (KSC 020): +1-631-244-3451
>                   yaya@dowling.edu
> =====================================================
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# Prof. Dr. A.L.Spek, Laboratory of Crystal and Structural Chemistry       #
# Bijvoet Center for Biomolecular Research, Utrecht University.            #
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