176 COMPUTER HARDWARE, SOFTWARE
CambridgeSoft at http://www.cambridgesoft.com/software/ offers a variety
of tools including the software suite, ChemOffi ce TM. ChemOffi ce consists of
the following: ChemDraw, Chem3D, ChemFinder, and ChemACX for chem-
ists; BioOffi ce, BioAssay, BioViz, and BioDraw for biologists; and Inventory,
E - Notebook, and The Merck Index for all scientists. ChemOffi ce and
BioOffi ce are available for Microsoft Windows. Chem3D provides visualiza-
tion and display of molecular surfaces, orbitals, electrostatic potentials, charge
densities, and spin densities. Chem3D utilizes MOPAC, Gaussian, GAMESS,
and extended H ü ckel to compute molecular properties. Every biology or
chemistry student should be familiar with the chemical structure drawing
program ChemDraw. Many undergraduate organic chemistry texts bundle
ChemOffi ce, as a course resource. The fi gures in this text have been executed
in ChemDraw Ultra 10.0. Some fi gures with colored visualizations have been
rendered from Protein Data Bank (PDB) fi les in Chem3D Ultra 10.0, then
imported into and labeled using ChemDraw.
The Open - Source visualization program, PyMOL TM is available from
DeLano Scientifi c at http://www.delanoscientifi c.com/ and http://pymol.source-
forge.net/. DeLano Scientifi c, a successful Open - Source software company,
continues to create free and affordable software tools, but also provides com-
mercial software services, added convenience, and other benefi ts to paying
customers who sponsor their efforts through monetary support or value -
for - value exchanges. PyMOL is available from Delano Scientifi c under a tra-
ditional Open - Source license without mandatory usage fees. PyMOL will run
on Linux (or any Unix) operating system, Mac OS X and Windows. PyMOL TM
is a molecular graphics system with an embedded Python interpreter designed
for real - time visualization and rapid generation of high - quality molecular
graphics images and animations. It imports and edits PDB fi les. The PyMOL TM
user ’ s and reference manuals can be downloaded as .html or .pdf fi les. Some
fi gures with colored visualizations have been rendered from Protein Data
Bank (PDB) fi les in PyMOL, then imported into and labeled using ChemDraw
Ultra, version 10.0.
Fujitsu offers the CAChe TM software systems at http://www.computers.
us.fujitsu.com/www/products_bioscience.shtml?products/bioscience/cache. A
variety of programs are available, depending on the user ’ s needs and pocket-
book. Model systems can be generated within CAChe TM or imported from the
Protein Data Bank (PDB) and other chemical drawing programs. CAChe TM
provides a wide range of computational models, from molecular mechanics
through ab initio electronic structure techniques. Small organic and inorganic
molecules, polymers, materials systems, and whole proteins may be treated.
Electronic structure methods include Extended H ü ckel (for all elements),
ZINDO (primarily for UV – visible spectra), MOPAC, and Dgauss (density
functional theory). MOPAC2002, a refi ned MOPAC, covers all main group
elements and many metals using many different models including PM5, AM1,^36
PM3,^37 MINDO/3, and MNDO.^38 It includes the COSMO solvent model and
d orbitals for transition elements. MOPAC2002 includes a linear scaling