To run this practical you will need to use the VMD molecular visualisation program. VMD is a very powerful program, and only a brief description of its use is given here. To get more information, please look at the VMD tutorial.

VMD is a very powerful program that can be used to view 3D models of molecules. VMD can read molecule files in many formats, with the most common format being PDB (Protein Data Bank, used to store protein crystal structures). VMD has a slightly confusing interface, that can take a little getting used to. Here are some instructions that will help you perform common actions;

To start VMD, type vmd in the command-line console.

Opening a file:

Click the VMD menu item File|New Molecule. This will open a new window. In the new window click "Browse" to open a file viewer, and then navigate using this viewer to find the molecule file that you wish to view. Once you have selected the file, click "Load" to load the molecule.

Changing the representation:

Click the menu item Graphics|Representations. This will open a new window. In this new window, change the representation by selecting different representations from the "Drawing Method" drop down box.

Selecting only a subset of atoms:

Click the menu item Graphics|Representations. This will open a new window. In this new window, click in the white text box below "Selected Atoms" (it currently contains the text "All" - meaning all atoms are selected). Change this text by adding in a selection search term, and then hit return to see your new atom selection. Selection search terms in VMD are very powerful, but too complex to go into here. Either use the search terms provided by the practical, or please look at the VMD manual.