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COMCIFS Annual Report for 2006

  • To: "Discussion list of the IUCr Committee for the Maintenance of the CIFStandard (COMCIFS)" <comcifs@iucr.org>
  • Subject: COMCIFS Annual Report for 2006
  • From: David Brown <idbrown@mcmaster.ca>
  • Date: Mon, 26 Mar 2007 14:00:36 -0400
COMCIFS report to the IUCr Executive Committee for the year 2006.
Since 2005 was the year of the Florence Congress at which the future of 
CIF was examined in some detail, our report for that year looked back on 
the fifteen years of CIF development and usage, presenting the 
perspective of what COMCIFS had achieved and where it was going in the 
future.  2006 has been mostly a year of consolidation of these decisions. 

The most far-reaching project that COMCIFS is currently pursuing is the 
development of the new Dictionary Definition Language with Methods, DDLm 
(previously referred to as DDL3). Its adoption in principle by COMCIFS 
during the IUCr Congress in Florence opened the way for the development 
of a DDLm dictionary which will shortly be presented to COMCIFS for 
adoption. On adoption it will be used to develop a new suite of CIFm 
dictionaries that incorporate innovative features such as methods 
(computer-readable algebraic algorithms). It is also designed to 
simplify dictionary maintenance and management.  Most importantly, 
programs written to exploit the new features of these dictionaries will 
be able to read all previously written CIFs, both those using coreCIF 
and mmCIF which are currently mutually incompatible. The detailed work 
on DDLm has been undertaken by Nick Spadaccini, Syd Hall and John 
Westbrook, assisted by the visit of John Westbrook to Perth and a 
three-day workshop involving Brian McMahon, Syd Hall and David Brown 
held in Chester during the year, with financial support from the IUCr. 
Following the expected adoption of DDLm to complement the current DDL1 
and DDL2, work will begin on preparing CIFm dictionaries. The approval 
of a coreCIFm dictionary will provide the materials essential for those 
interested in developing software for the new standard.   It is not the 
intention that DDLm will replace the existing dictionaries and software, 
but it will provide enhancements that are not currently available.

Work continues on the evolution of CIF dictionaries.  The coreCIF 
Dictionary Maintenance Group continued working on the coreCIF dictionary 
revisions suggested by over a decade of extensive use, and it is coming 
within sight of the end of this project. Ilia Guzei and David Brown 
started developing a component of the coreCIF dictionary describing the 
constraints and restraints used in structure refinement, and Arie van 
der Lee and his colleagues have started work on a new CIF dictionary for 
reflectivity measurements. 

2006 and early 2007 have been a time of renewed activity for imgCIF. 
Herbert Bernstein and Robert Sweet organized a successful workshop in 
conjunction with the American Crystallographic Association 2006 meeting 
in Hawaii to promote the implementation of the imgCIF dictionary in 
capturing images of diffraction patterns, primarily at synchrotron 
sources.  They have obtained funding for two more imgCIF workshops, one 
at BNL immediately after the the NSLS/CFN meeting in May 2007 and one in 
England in conjunction with BSR 2007 in August 2007.  There has  been 
significant progress in use of imgCIF both at SLS and at Diamond.  
Changes to the imgCIF dictionary to support uses of imgCIF at SLS, 
Diamond and ESRF will be proposed on the imgCIF list shortly and will be 
discussed at the upcoming workshops.

Howard Einspahr worked closely with John Westbrook, of the PDB, and IUCr 
editorial staff to develop streamlined procedures for incorporating 
structural data from PDB deposits in associated publications.  This work 
has involved identifying mmCIF data items relevant to a full literature 
description, and the development of a tool for authors that will create 
experimental tables for inclusion in manuscripts from mmCIF files. 

The IUCr editorial office has released a public version of its publcif 
software. This software may be used to edit CIFs for publication.  It 
combines dictionary-based CIF validation with a sophisticated collection 
of utilities that will assist prospective authors.  These include active 
links to the checkCIF service, the ability to incorporate validation 
report forms (VRFs) generated by checkCIF, data entry wizards, table 
editors, previews of articles formatted in the styles of the different 
IUCr structural journals, citation sorting and checking, private 
databases of authors and citations, and dictionary browsing facilities. 
The software is being further developed to support publication of 
biological macromolecular structures. 

With financial help from the IUCr, Herbert Bernstein and students have 
produced updated versions of standard software libraries and tools (the 
CIFTEST parser test and validation suite, CIFtbx3, cyclops, vcif2, and a 
new utility to fold and unfold long-line CIFs) that are compliant with 
the version 1.1 CIF specification. 

The cif-developers list continues to act as a discussion list and 
opportunity for software developers to advertise their new software. The 
Python package PyCIFRW was described in a CIF applications paper in 
Journal of Applied Crystallography [Hester, J. R. (2006). J. Appl. 
Cryst. 39, 621-625].  

Finally, but by no means least, the IUCr won the 2006 Award for 
Publishing Innovation of the Association of Learned and Professional 
Society Publishers (ALPSP) for its development of the Crystallographic 
Information Framework and the use of checkCIF in data exchange, quality 
assurance and integrated data publication.

David Brown

fn:I.David Brown
org:McMaster University;Brockhouse Institute for Materials Research
adr:;;King St. W;Hamilton;Ontario;L8S 4M1;Canada
title:Professor Emeritus
tel;work:+905 525 9140 x 24710
tel;fax:+905 521 2773

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