Academic journal article Journal of Geoscience Education

Using the American Mineralogist Crystal Structure Database in the Classroom

Academic journal article Journal of Geoscience Education

Using the American Mineralogist Crystal Structure Database in the Classroom

Article excerpt


The American Mineralogist Crystal Structure Database is a compilation of every crystal structure potentially of mineralogie or geologic interest. The database, seen as an outreach service, is funded and maintained by NSF, the Mineralogical Society of America and the Mineralogical Association of Canada. This database, when linked with visualization software, provides an invaluable resource for instructors, allowing direct access to crystal structures of almost any mineral, and many at various compositions, pressures or temperatures. Associated with the database is a freeware visualization program, XtalDraw with ancillary software modules, Xpow (for visualization of powder diffraction patterns) and SPEEDEN (for visualization of electron density maps). These software modules are user-friendly, allowing students, instructors, and researchers to easily access various crystal structures. Suggestions for using the database and software in an instructional setting are fiven; full lesson plans and instructional guides are eing developed as Internet resources.


One of the most difficult tasks an instructor faces is relating lecture information to real-world applications. In mineralogy and petrology, this is particularly evidenced when, as instructors, we try to convey the nature of crystalline materials and the inter-relationships between crystal structures and physical properties, ranging from hardness and cleavage to stable pressure-temperature regimes. An ideal pedagogical tool is a database of crystal structure information that is freely and easily accessible, combined with interactive software for visualizing and manipulating the structures so that the data can be viewed as crystal structure drawings, and not just as columns of numbers.

The American Mineralogist Crystal Structure Database is being developed to archive data for every crystal structure of interest to the mineralogical and geological communities (Downs and Hall-Wallace, 2003). It includes all crystal structures published in the American Mineralogist and The Canadian Mineralogist. Crystal structures from The European Journal of Mineralogy are currently being added to the database. The editors of Acta Crystallographica and Springer-Verlag have just formalized an agreement to include their mineralogical data and this will be added to the database soon. The database is funded by the National Science Foundation and is being maintained through the efforts of the Mineralogical Society of America and the Mineralogical Association of Canada. The information in this database is easily accessible through the Internet from the society web pages or directly via / AMS/amcsd.php. Structure data is easily downloaded from the database in both CIF and AMC formats; easily opened into most popular crystal visualization software programs.

In this paper, we provide some initial suggestions for using this information in the classroom. We view these ideas merely as ideas or starting points; individual experiences and instructional settings will undoubtedly suggest variations and/or additional uses.


Each crystal structure is archived in its own file, complete with a citation, cell parameters and symmetry, and a list of elements in the structure. This element list contains the atomic coordinates, site occupancies and, if published, thermal parameters for each element. Each dataset is analyzed for accuracy by checking that the cell parameters reproduce the cell volume, and the atomic coordinates reproduce the bond lengths and angles that are tabulated in the original publication. If there are inconsistencies, then they are corrected, and the corrected dataset is archived. This is an invaluable step, as it is estimated that approximately 50% of published data have errors of one sort or another (Downs and Hall-Wallace, 2003). An example of a dataset for phlogopite is given in Table 1. …

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