Crystallographic Information File (CIF) Call for Review

Phil Bourne system at CUHHCA.HHMI.COLUMBIA.EDU
Thu Apr 14 18:42:25 EST 1994


          Macromolecular Crystallographic Information File (mmCIF)
                            Call for Review

As many of you know the Crystallographic Information File (CIF) format has been
in use in small molecule crystallography for a couple of years.  CIF provides a
mechanism for archiving and exchanging data. The International Union of 
Crystallography established a committee (chaired by Paula Fitzgerald) to 
establish an extension CIF dictionary to addresses the additional experimental
and structural requirements of biological macromolecules.  A draft of this 
dictionary is now available and your input is sought. The dictionary will be 
put before an IUCr Committee for final approval following an appropriate review
period that is intended to end following the American Crystallographic Associa-
tion meeting in late June.  Following IUCr approval the standard will be pub-
lished in Acta Crystallographica.

The macromolecular CIF dictionary is an extension to the core CIF dictionary, 
and the two must be used together to describe macromolecular structures.
The current draft of the macromolecular dictionary as well as an updated ver-
sion of the core dictionary are available electronically as described below.
Please note that the macromolecular dictionary is still very much a draft -
there are data items missing and some of the definitions of data items are in-
complete.  The input that we seek at this time concerns the general 
structure of the data items, their completenes, and the clarity of the 
definitions and examples provided in the dictionary. 

The PDB will adopt mmCIF as their new data definition, so these issues
would seem important.
  
A Note of Software for mmCIF
----------------------------
Not surprisingly the macromolecular dictionary is complex and wide use of mmCIF
will require modifications to existing software to produce mmCIF files, and new
software to manage mmCIF files. Developing this software was the focus of an 
NSF funded workshop held in Tarrytown NY last October. Proceedings of this 
workshop are available via anonymous ftp from cuhhca.hhmi.columbia.edu as 
pub/doc/CIF/Tarrytown.tar.Z

A lively debate continues over the content of the dictionary and the Data
Definition Language (DDL) used to define the types of items the dictionary 
contains. Details of this discussion are best reviewed via gopher on
cuhhca.hhmi.columbia.edu (Port 70).

Comments/Questions 
------------------
Should be addressed as follows:

Contents of the dictionary to Paula Fitzgerald (bean at merck.com)
DDL to Phil Bourne (system at cuhhca.hhmi.columbia.edu)
How the PDB will use mmCIF to Dave Stampf (stampf at bnl.gov)

How To Get The Dictionaries Etc.?
---------------------------------

### From Columbia:

via anonymous ftp from:

cuhhca.hhmi.columbia.edu (128.59.98.1) in pub/doc/CIF/??

via gopher from:
        cuhhca.hhmi.columbia.edu (Port 70)

### From the International Union of Crystallography:

by e-mail - send to sendcif at iucr.ac.uk a message of the form
                send cifdic.C94
                send cifdic.M94

by ftp    - anonymous ftp to ftp.iucr.ac.uk (192.70.242.1), directory pub
            OR directory cifdics

by gopher - gopher.iucr.ac.uk, port 70

by WWW    - URL http://www.iucr.ac.uk/welcome.html

The machine names are all synonyms for diamond.iucr.ac.uk, and are
interchangeable.

They bear the following statements at the head of each file. For the Core:
##############################################################################
#  NOTE: This version of the CIF Core Dictionary is a draft of the           #
#        revised version being considered for approval by the IUCr           #
#        Committee for the Maintenance of the CIF Standard. It is            #
#        hereby released to the general community for comment and            #
#        criticism. Production software should not rely on the new           #
#        features within this draft being available in the future.           #
#                                                                            #
#        Please direct any comments on the definitions in this version       #
#        to the Coordinating Secretary of COMCIFS, Brian McMahon, at         #
#        IUCr, 5 Abbey Square, Chester CH1 2HU, England (bm at iucr.ac.uk).     #
##############################################################################

and for the mm file:
##############################################################################
#  NOTE: This version of the mmCIF Dictionary is a draft of the              #
#        version being considered for approval by the IUCr Committee         #
#        for the Maintenance of the CIF Standard. It is hereby released      #
#        to the general community for comment and criticism. Production      #
#        software should not rely on all the features within this draft      #
#        being available. In particular, the Dictionary Definition           #
#        Language (DDL) employed to state the formal elements of the         #
#        definitions will change in accordance with the final published      #
#        DDL description (A. P. F. Cook & S. R. Hall, manuscript             #
#        submitted for publication in J. Chem. Inform. Comput. Sci. 1994).   #
#                                                                            #
#        Please direct any comments on the definitions in this version       #
#        to Paula Fitzgerald, Merck Research Laboratories, PO Box 2000,      #
#        Ry50-105, Rahway, NJ 07065, USA (paula_fitzgerald at merck.com), or    #
#        to the Coordinating Secretary of COMCIFS, Brian McMahon, at         #
#        IUCr, 5 Abbey Square, Chester CH1 2HU, England (bm at iucr.ac.uk).     #
##############################################################################

Please feel free to distribute these through other relevant ftp sites; but
please ensure that the preliminary nature of these documents is made known to
any prospective taker.

             /Phil Bourne

===========================================================================
Philip E. Bourne
Howard Hughes Medical Institute
Department of Biochemistry and Molecular Biophysics
Columbia University
630 W. 168th Street New York NY 10032 USA

Telephone: (212) 305-3657
FAX:       (212) 305-7379

Internet: system at cuhhca.hhmi.columbia.edu (128.59.98.1)
===========================================================================






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