Mineralogy Database

jmol Structure

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Crystal Structure

To use the Jmol applet, your browser must have Java and Javascript enabled. The JmolApplet is a web browser applet that can be integrated into web pages and is based on the Jmol/ Rasmol/ Chime scripting language developed for viewing complex organic molecules.

Example Jmol Applet Structure (Graphite)

What's New

Major new addition to Webmineral. View interactive crystal structure diagrams using Jmol Applet.

This capability just recently came available with the publication of the open-source program, Jmol,  written in java and the companion java applet for web use. This program replaces Chime and does not require that the user install a "helper" plugin. The ability to visualize and manipulate crystal structures completes the capabilities of webmineral as a mineral database. Users can also download and run Jmol as a stand-alone application.

The generation of these mineral structure required the following:

  •  Mineral Structures - Thanks to the tireless effort of Dr Robert Downs and his associates at the University of Arizona for their crystal structure database. This database contains every structure ever published in the American Mineralogist, The Canadian Mineralogist, European Journal of Mineralogy and Physics and Chemistry of Minerals as well as other selected journals. These structure files contain over 12,000 entries. It will take me some time go through them all.
  •  Format Conversion - Now that we have all this data, the goal is to convert the Crystallographic Information File (.cif) into a format amenable for web display of mineral structural data. The format conversion process is as follows:
    •  Convert .cif format to Protein Data Bank format (.ent) files. This step has caused the most problems due to the fact that the .ent format is designed primarily for proteins and other large organic structures.  I am still finding the work-a rounds for these problems.
    • During the development phase of adding crystal structures to webmineral, the .ent files are loaded full size. Future enhancements will include the use of .gz compression to lessen the bandwidth. When .gz compression is added, the structure files will be added to the species pages and not as a stand-alone table.
  •  Browser Display - From the jmol.org page : "Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems.
    • The JmolApplet is a web browser applet that can be integrated into web pages.
    • The Jmol application is a standalone Java application that runs on the desktop.
    • The JmolViewer is a development tool kit that can be integrated into other Java applications."

Other References to Mineral Structures

American Mineralogist Crystal Structure Database
Jmol - Java Molecular Structure
IUCr - Crystallographic Information File
RCSB PDB  - Protein Data Bank
CCDC - Cambridge Crystallographic Data Centre

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