This tutorial introduces new users to VMD and its
capabilities. It can also be used as a refresher course for the occasional
VMD user wishing to employ this program more productively.
This tutorial has been designed specifically for VMD 1.8.1 and
should take about 3 hours to complete in its entirety.
The tutorial is subdivided into three separate units of increasing
complexity. The first unit covers the basics of molecular graphics
representations and will introduce everything you need to know to generate
nice graphics. The other two units are targeted towards the
scientifically-oriented user
and focus on scripting in VMD. While scripting may be skipped
by the non-technical users, we encourage everyone to give it
a try as it provides some very powerful (and easy to use) tools that
cannot be offered by a simple graphical user interface.
The examples in the tutorial will focus on the study of ubiquitin - a small protein with
interesting properties. Throughout the text, some material will be presented in separate
``boxes". These boxes include complementary information to the tutorial, such as
information about the biological role of ubiquitin, and tips or shortcuts for using VMD.
You can find the ubiquitin files in the files directory that came with this tutorial.
This tutorial assumes that VMD has been correctly installed on the user's computer. For
installation instructions, please refer to the
VMD Installation Guide.
To start VMD, type vmd at a UNIX command-line, or double-click on the VMD application icon.