RasMol is the program I used to make these pages on homeodomains. It is a program that allows a user to view Brookhaven .PDB files (among others). The program is available on many platforms.
Some commands that are very useful in viewing the homeodomain structures have to do with what is known as mixed rendering. Mixed rendering is the ability to view different parts of the same structures as different types of models. For example, I used a backbone structure for the overall protein, cpk for the relevent amino acids , and ball and stick for the DNA. This helps clear up an otherwise impossibly complicated picture.
The commands for accomplishing this fall into two categories: selection of the groups of atoms, and selection of the type of view. Since the selcection of the type of view is easily done via the menus, I will not go into that here. Selection of groups of atoms is slightly more complicated.
Luckily Rasmol is very knowledgeable about biology and chemistry. It knows what part of the structures is protein, DNA or RNA. To choose on of these groups we just have to type SELECT PROTEIN (for example.) That is not too difficult, then. Often we want to choose a specific amino acid or base, and to do that we also use the select command. SELECT R43, for example, will select the arginine which is residue 43 (as numbered in the PDB file.) Bases can be chosen similarly.
Once you have selected part of the structure, you can choose a view or color sytem from the menu. To go back to manipulating the whole structure type SELECT ALL.