- 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@[192.168.2.100]> 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
> >http://scripts.iucr.org/mailman/listinfo/coredmg
>
>
> --
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> Dowling College, Kramer Science Center, KSC 121
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>
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