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Re: coreCIF.dic-2.4 Discussion List #8

  • To: Distribution list of the IUCr COMCIFS Core Dictionary Maintenance Group <coredmg@iucr.org>
  • Subject: Re: coreCIF.dic-2.4 Discussion List #8
  • From: Howard Flack <crystal@flack.ch>
  • Date: Tue, 27 Jun 2006 11:16:00 +0200
  • In-reply-to: <444921A5.8060409@mcmaster.ca>
  • References: <444921A5.8060409@mcmaster.ca>
Term has finished.

>However, some of the proposals we have been discussing, e.g., adding chemical
>information to identify molecules etc., will be deferred to CIF3,

  I am of the irritating opinion that identification of molecules in CIF is too important to await CIF3.
  As my final fling as chairman of the IUCr Committee on Electronic Publishing (and in order to avoid having my dislocated and fractured shoulder jostled in the poster sessions) in Florence I sat through a good number of the open and closed commission meetings on matters concerned with publication, electronic or otherwise.  Of the utmost relevance concerning the addition of chemical information to CIF were the public and private utterances of various representatives of the CCDC.  As internally (to the database) they have become more and more CIF-oriented over the years, they had reached the point of needing to define their local (private) CIF dictionnary for encoding chemical and molecular information.  I understood that much of the ground work had been done, and the choice of data names and definitions was imminent (in August 2005).  If they have gone ahead with this work, their dictionnary will become the de-facto standard.

> [IDB: COMMENT: There is confusion between the meaning of 'constraint' and
># 'restraint'.  A 'constrained parameter' is one that is not refined.  It may
># be reset between refinements, e.g., to be equal to one of the refined
># parameters, and so may change as the refinement progresses, but it is not a
># variable in the least squares calculation.

There is a confusion in your comment.  A 'constrained parameter' may very well be refined. An atom on a special position such as x, x, x is having the atomic coordinates x, y and z refined by least-squares but constrained such that y = x and z = x. y and z are variable during the least squares and take new values each cycle. From your sentence one could believe that you think for the special position x, x, x that the y and z coordinates take fixed values during a least-squares cycle and are reset to the new value of x at the end of the cycle.

>A 'restraint' is a target value
># for some structure dependent variable (not one that is being
># refined)
  I'm sure that is not quite right either.  For shift-limiting restraints and polar-axis restraints there is no target value. Likewise for similar-molecule restraints.

  Please note that the data items in this section have the same limitation as
  _chemical_absolute_configuration.  They refer to a compound i.e. a collection of molecules, and it is not possible at present to identify molecules in CIF.

># COMMENT: HDF provides the following information
># 24.1 Interdivisional Committee on Terminology, Nomenclature and Symbols of
># the International Union of Pure and Applied Chemistry (IUPAC ICTNS)
># Another proposal concerns the use of the name 'uno', symbol U, for the unit
># one so that dimensionless numbers may be treated in the same way as all
># other SI units.

  You need to ask Andre Authier to keep you updated on this topic.
>This matter should be tracked by the Nomenclature Commission, but we
>recommend that no action be taken before any formal adoption of the uno
>into the SI system - the topic can then be raised again for discussion if
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