Crystallography Online

Introduction

This NIST (National Institute of Standards and Technology) workshop arose out of a remark by Dr. Mary L. Good, Under Secretary of Commerce for Science and Technology of the US Government to Dr. John R. Rumble Jr. Director of NIST Standard Reference Data Program concerning the availability of crystallographic databases to scientists (both academia and industry) in the USA. Some 80 scientists mostly from the USA gathered together for the 2-day meeting at the NIST headquarters just outside Washington DC. Most unfortunately Dr. Good could not be present because of some very urgent business in Washington so we did not find out exactly about her concerns for crystallographic databases in the USA. The full proceedings of the workshop will be published in a forthcoming number of the NIST Journal of Research.

Formal Data Activities

G.H. Wood - CRYSTMET - The NRCC Metals Crystallographic Data File

Much time and effort has been spent on CRYSMET to convert its archive files into a relational database using ORACLE. This permits different versions of the database to be generated for different uses according to user demand. In particular an interface is now available over the WWW combining the power of ORACLE with a Netscape-based interface. (As an aside the current market strategy of the ORACLE corporation is turned in the same direction. They have produced their own WWW browser and authoring environment, and now also have pc/windows versions of ORACLE for big pcs.) The ORACLE database is essentially for internal use by the NRCC to create the distributed forms of the CRYSMET. CRYSMET also now produces dynamically accessible structure/property maps according to user requests.

E. Fluck - Inorganic Crystal Structure Database and Standardized Data and Crystal Chemical Characterization of Inorganic Structure Types (TYPIX) - two tools for inorganic chemists and crystallographers

After listening to this speech one could have no doubts about the good intentions of the Gmelin Institute to continue its lasting committment and activity with ICSD and TYPIX.

G. Bergerhoff - Evaluation of Crystallographic Data with the Program DIAMOND

DIAMOND is a pc Windows programme written in C++. It will deal with all of the crystallographic databases and even enables you to build your own. Its database engine is home-written. You can read all about it on URL http://www.rhrz.uni-bonn.de/~unc422/diamond.html

D. Watson - The Cambridge Structural Database (CSD) - Current Activities and Future Plans

At present, the CSD receives approximately 50 new structures per working day.

E. Abola - The Protein Data Bank: Current Status and Future Challenges

The PDB will change name and become the MSD - Macromolecular Structure Database. It will still be located at BNL. Its contents will no longer be limited to proteins. The MSD archives structure factors as well as coordinates. The MSD has plans to archive data in a relational database, to implement an auto-deposition system and to set up international data centres. The OPM (Object Protocol Model), an object view of data layered on SYBASE is receiving attention. For user queries, a WWW form-based request will be converted on the server side into SQL. At the moment it takes between 80 and 120 days to enter a structure into the MSD which is very good in comparison to normal publication times.

H.M. Berman - The Nucleic Acid Database: Its Evolution and Future Plans

At URL http://ndbserver.rutgers.edu

L.C. Andrews - Current Activities of the International Centre for Diffraction Data

In house the ICDD uses a pc-based relational database (PARADOX) to maintain the PDF and achieve low-end compatibility.

A.D. Mighell - NIST Crystal and Electron Diffraction Data Center

NIST maintain their databases in-house as relational databases using ORACLE. The cell dimension data link between the different databases. Cell dimensions are very characteristic of a crystalline substance and provide a very powerful fingerprint.

Scientific Usages

J.A. Kaduk - Conventional and Eccentric Uses of Crystallographic Databases in Practical Materials Identification Problems

Kaduk has extracted data from different databases and then structured them into a personal relational database system. This enables him to crosslink information drawn from different sources - a tremendous problem with existing systems.

S.K. Byram - Using the NIST Crystal Data Identification File within Siemens' Software for Single Crystal and SMART CCD Diffractometers

Hold onto your seats to hear that the Siemens people would like to see the price of database access for non-academic users be reduced considerably. They will continue their practice of bundling hardware and software together as this corresponds to the situation in the academic world where it is difficult to get funds for updates once a large initial investment has been undertaken.

R.P. Goehner - Crystallographic Data Base Design for Phase Analysis in the Scanning Electron Microscope

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G.L. Gilliland - Biological Macromolecule Crystallization Database

This database uses POSTGRES, a public-domain object-oriented database system, and already has a WWW interface.

D.S. Eggleston - Use of Crystallographic Databases in the Drug Discovery Process

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C.P. Brock - Investigations of the Systematics of Crystal Packing using the Cambridge Structural Database

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Data Transfer: Ensuring State-of-the-Art Technology

R.L. Harlow - Troublesome Crystal Structures: Prevention, Detection and Resolution

R.L. Harlow awards an annual prize at the ACA meeting for the worst ORTEP plot of the year. He showed some beauties. A good criterion of a bad structure (and of a good one as well) is a low R value.

I.D. Brown - CIF: A Standard for Crystallographic Data Interchange

As an introduction a terrifying slide of automation at its most efficient was presented. Everybody laughed. The message behind the humour was certainly worth thinking about.

B. McMahon - The Role of Journals in Maintaing Data Integrity: Checking of Crystal Structure Data at Acta Crystallographica

The Acta Crystallographica technical editor's office in Chester undertakes much of the checking of crystal structure data submitted for publication. Data is either submitted as a CIF or transformed into one and then run through the checking mill. CIF files may be submitted by e-mail by intending authors for prechecking. As this system is also used to produce the typeset document for publication, authors receive a postscript file containing a proof document corresponding very closely to the published article. Several participants praised this feature as they had found it difficult to raise travel funds from funding sources on the basis of the plain printout of the corresponding CIF.

J. Spring - Electronic Publishing and the Journals of the American Chemical Society

The ACS is going full-speed ahead to deliver some of their journals in electronic form over the 'net'. The Journal of Physical Chemistry should come out in this form at the beginning of 1996. (The AIP already distributes Applied Physics Letters and Physical Review Letters in this format.)

D.G. Watson - How the Cambridge Crystallographic Data Center Obtains its Information

CSD has implemented a system of depositing unpublished crystal structure data directly by e-mail which has been criticized in some quarters.

H. Behrens - Data Import and Validation in the Inorganic Crystal Structure Database

A detailed description of how the ICSD checks, removes and avoids errors in the ICSD.

H.D. Flack - The World-Wide Web as a Crystallographic Data Resource

On-line crystallographic cyberflak - the full text of the paper is available at http://www.unige.ch/crystal/ahdf/nist.www.html

Discussion - Adequacy of Current Crystallographic Data Activities

• J. Flippen-Anderson proposed that NIST should sponsor the formation of a working group on forming a federation of databases in crystallography. There was not overt enthusiasm for this proposal.
• E. Abola wanted to see work towards producing a common bibliographic database for crystallography.
• J.A. Kaduk wanted to know why NIST had organized the workshop.

The full proceedings of the workshop have been published as a Special Issue of the NIST Journal of Research (Volume 101, Number 3, May-June 1996). Copies may be obtained, free of charge, from the workshop organizer(karen@tiber.nist.gov).

Howard Flack - 16th November 1995