Warning: Most
visualization programs for the PC or Mac use a piece of software called
Chime. The most recent version of Chime is 2.0. Chime is intended to run
with either Microsoft's Internet Explorer or the Netscape Communicator
browser. However, recently introduced, supposedly upgraded, versions of
these two browsers do not work with Chime. More specificially, when
Chime is used with Internet Explorer the version number must be 5.5 SP
1 or lower. When used with Netscape Communicator, the version number must
be 4.76 or lower. The Netscape website offers a means to download older
versions of Netscape.
The most basic approach to visualizing PDB files is by use of the Chime plug-in for the Netscape Navigator browser. All of the needed modules are available without charge via the Internet. You must have NetScape Navigator later running as your browser. The Chime plug-in is available from MDL Information Systems. Chime may already be installed on the computer you are using. To check on this, click Help (on the top line) then About Plug-Ins.
Tutorials for using Chime are available at several web sites. Try this one from Cabrillo Jr. College or this one from Carnegie-Mellon.
After Chime has been installed, all you need to do to view and manipulate a molecule is click on the PDB file that contains the coordinates of the molecule.
Chime can display many properties of a molecule (electric field, lipophilicity,
acidic and basics groups, and so forth) but getting some of the displays
may be a little tedious.
If you have your own computer and are willing to do some additional downloading and installing, more powerful and flexible visualization programs can be used. Many professionals in the field have one or more of these programs routinely available on their desktop and laptop computers.
RasMol
RasMol is a powerful, yet quick running visualization program that
runs on virtually all computer platforms. The program can be downloaded
from the RasMol web page. There are instruction for using the program there,
lots of examples, and a page that gives references to RasMol
tutorials developed around the world. A tutorial not listed there that
is worth a look is from Carnegie-Mellon.
RasMol
can produce output files in a variety of formats that can be used to incorporate
images into other programs. You will have to download and store PDB files
and then open them separately to use this program.
WebLab
ViewerLite
This freeware package is available from Molecular Simulations, Inc.
It has the advantages of being able to display more properties of a molecule,
including its exterior electric field and of being able to write the displayed
image into a files using several formats. Some of these files can be imported
into word processing programs. You may have to download and store PDB files
and then open them separately using this program.
WebMol
Viewer
WebMol was designed to display and analyze structural information contained
in the Protein Data Bank (PDB). It offers more sophisticated graphics than
many packages and has the ability to make Ramachandran and distance plots.
It can be run as an applet or as a stand-alone application.
VMD (Visual Molecular
Dynamics)
VMD is a molecular visualization program for displaying and animating
large biomolecular systems. VMD supports computers running Unix or Windows,
is distributed free of charge, and includes source code.
AAMP
AMMP is a modern, full-featured molecular mechanics, dynamics and modeling
program for biological molecules. It is available in Windows, Linux and
UNIX versions.
"Real world" molecular modeling and simulations of biological molecules tend to use UNIX workstations or high-end personal computers. An account to enable your use of the Silicon Graphics workstations in Rm 1153 of the Chemistry Bldg. can be established. You are welcome to use these machines anytime the room is unlocked and they are not being used for a formal course. You will have to have some familiarity with UNIX to use these workstations.
It is recommended that you start with the program SYBYL although there
are several commercial molecular modeling and simulation packages available
in the department besides SYBYL, including INSIGHT/DISCOVER and MacroModel.
There is more information about SYBYL and some tutorials here.