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COMCIFS Annual Report for 2004

  • To: "Discussion list of the IUCr Committee for the Maintenance of the CIFStandard (COMCIFS)" <comcifs@iucr.org>
  • Subject: COMCIFS Annual Report for 2004
  • From: David Brown <idbrown@mcmaster.ca>
  • Date: Mon, 31 Jan 2005 14:00:21 -0500
Please find below for your information the Annual Report for 2004 which 
has been submitted to the Executive Committee of the IUCr.  This, unlike 
the draft distributed a few days ago, is the final version.

David Brown

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Annual Report of COMCIFS to the IUCr Executive Committee for 2004

COMCIFS is a committee appointed by the Executive Committee of
the IUCr.  It is charged with the supervision of the Union's
Crystallographic Information File (CIF) project.  The current
members of COMCIFS are:

     David Brown (chair)
     Helen Berman
     Herbert Bernstein
     Ralf Grosse-Kunstleve
     Syd Hall
     Gotzon Madariaga
     Brian McMahon
     John Westbrook

Except for meetings held during the IUCr General Assemblies, it
conducts all its business by email.

This year COMCIFS has put considerable energy into the
publication of International Tables for Crystallography Vol G,
the volume that will contain a comprehensive account of the CIF
project.  The deadline for the receipt of copy was at the end of
2003.  Since then the editors and the Chester Office have been
working hard to ensure uniformity of presentation, and the
authors have been checking the proofs in time for publication in
2005.  Checking the proofs has led to the discovery of minor
changes that are needed in some of the CIF dictionaries.  A
revised version of the image-CIF dictionary used for recording
two dimensional diffraction images is expected to be approved
during the coming year.

The IUCr editorial office has, with advice from Brian Toby, been
developing a new set of web pages offering guidelines and powder
CIF (pdCIF) template files for authors who submit powder
diffraction data and Rietveld refinement results as part of an
article for an IUCr journal, with the aim of encouraging authors
to provide data in pdCIF format and to include as much
information as possible in their pdCIFs. Mike Hoyland of the IUCr
office has modified checkcif to run tests appropriate to powder
data. 

The IUCr is also planning to make the series 'International
Tables for Crystallography' available online and is planning to
add features that may include the ability to access and download
symmetry data in CIF format.  This is likely to result in (or
require) the development of a new and enlarged version of the
symmetry CIF dictionary.

As mentioned in last year's report, after fifteen years the
coreCIF dictionary is in the process of a major revision.  A
number of the simpler changes were approved at the end of 2003 as
version 2.3, but during 2004 the Core Dictionary Maintenance
Group has been struggling with the challenge of encoding
descriptions of molecules, extended scattering density and
twinning.  Exploring the different ways in which the chemical and
crystallographic descriptions of a molecule can be linked has
raised some fundamental questions about the methods of linking
information that can only be resolved when we know the direction
in which CIF will develop in the future.  Information technology
has seen major changes since the Union adopted CIF in 1990 and
COMCIFS now needs to plan carefully for the rational development
of CIF over the next decade.

One of COMCIFS goals is to discourage the formation of CIF
dialects, but technical necessities have forced the development
of two somewhat divergent Dictionary Definition Languages (DDL),
DDL1 being used for  the small-cell coreCIF dictionary and DDL2
being used for the large-cell mmCIF dictionary.  Some software
developed for manipulating mmCIFs cannot read those written with
the coreCIF dictionary and vice versa.  It is, however, feasible
to create software that works with both DDL1 and DDL2 (vis.
CIFtbx and the CBFlib-derived parser in RasMol).  Since the
interface between the small- and large-cell structures is
becoming an increasingly important area of study, COMCIFS needs
to explore how these two standards can be made to converge. 

Another problem of concern to COMCIFS is the lack of open-source
CIF software tools, particularly as the wide range of available
XML tools makes XML an attractive alternative.  The IUCr is
making some effort to promote the development of standards-based
open-source utilities and each year sees a few more independently
developed applications added to the collection.  Work is under
way by Herbert Bernstein at Dowling College under contract to the
IUCr to upgrade some of the software used by the IUCr in its
publication process to be compatible with the CIF 1.1
specification and with both DDL1 and DDL2.  This software will be
discussed at the Florence IUCr Congress and will be made
available as open-source software to encourage other software
developers to make their software able to deal with both DDL1 and
DDL2.  The year has also seen the publication of other programs
such as pdCIFplot, written by Brian Toby, designed for refereeing
Rietveld refinements, but also useful as a graphical browser of
powder diffraction data stored on pdCIFs.  Two CIF browser-
editors have also been released: enCIFer by the Cambridge
Crystallographic Data Centre and CIFEDIT by Brian Toby.   These
applications read in the version of the dictionary that was used
to create the CIF, putting the user just a mouse-click away from
all the dictionary information about any item in the CIF.
Further, CIFEDIT is able to handle dictionaries written in both
DDL1 and DDL2.  These browser-editors not only makes it easier to
create and manipulate CIFs, but by reading in the appropriate
dictionary, they do not have to be modified every time a new
version of a dictionary appears.  Many of the frustrations of
maintaining software would disappear if all applications made use
of the machine-readability of CIF dictionaries.

While the CIF standard is now widely adopted by the
crystallographic community, extending it and keeping it up to
date requires considerable effort.  COMCIFS is much indebted to
the many volunteers who contribute to this work and who help to
chart the future course of CIF.

Respectfully submitted by I.David Brown, Chair of COMCIFS



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