DeepView (all platforms)
DeepView, also known as Swiss-PDBViewer
can be obtained from http://www.expasy.ch/spdbv/mainpage.htm
and following the links and prompts. The most recent version is 3.7
beta2. An excellent tutorial and user manual for DeepView is also
available from Gale Rhodes' homepage at the University of Southern Maine:
http://www.usm.maine.edu/~rhodes/SPVTut/index.html
RasMol (all platforms)
A number of different versions
of RasMol can be found on the web. Of most utility are RasMol 2.7
which can be found at http://www.bernstein-plus-sons.com/software/RasMol_2.7.1/
run by Herbert J. Bernstein. You can retrieve RasMol for several
different computer operating system including Windows Mac, Linux and others.
You may also get compressed files (g-zipped) or uncompressed. S lipghtly
older version (2.6 b2a) is also available at: http://www.umass.edu/microbio/rasmol/getras.htm
along with documentation.
Protein Explorer (Windows and Mac)
Protein Explorer is provided
by Dr. Eric Martz at the University of Massachusetts. This more advanced
form of RasMol incorporates many of the same command instructions and visual
tools plus much more. It can be run off the web at http://molvis.sdsc.edu/protexpl/frntdoor.htm
You can also download a version for use on your own computer at: http://www.umass.edu/microbio/chime/regisfrm/
. You must register to download the appropriate files. Follow the
instructions carefully!
You may also want wish to retrieve software called Kinemage. It is produced by the journal Protein Science and has been made publicly accessible. The main program is a viewer called Mage which, like RasWin, allows one to visualize, rotate, resize in real time, protein x-ray crystal structures that have been deposited in the Protein Databank (these are commonly known as "pdb" files). Furthermore, some of the more useful structures have already been edited for clarity and have been deposited in the journal's archive. These are also available to us over the Web. It is very simple to use and is available in both Mac and PC/Windows versions. We will only be using it to look at structures, but companion software called PreKin can also be used to construct your own images from pdb files.
The Kinemage software is obtainable at: http://kinemage.biochem.duke.edu/
Many files are available for viewing different types of proteins and substructures, and even some DNA structures. The Kinemage supplement to the textbook Protein Structure by Branden and Tooze is available on the Web at: ftp://kinemage.biochem.duke.edu/pub/kinfiles/BT2kins/ and the older version at http://www.chem.uwec.edu/Chem406/B&TSupp.html
Also available are some Kinemage "tours"
of protein structure. These are "ProTour#.kin" files where # is 1
to 8. These can be found at: http://kinemage.biochem.duke.edu/kinemage/kinlist.php#tour.