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)
Major new addition to Webmineral. View interactive
crystal structure diagrams using
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
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
- 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
Crystal Structure Database
Jmol - Java Molecular Structure
IUCr - Crystallographic
RCSB PDB - Protein Data Bank
CCDC - Cambridge
Crystallographic Data Centre
Search the Mineralogy Database
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