Pymol
Pymol is an open-source molecular visualisation program (binaries, full documentation is not freely available, however). Compilation of v1.1 was straightforward (v1.2 is in beta). It is not installed on the clusters. You can find in ~csw34/bin on both clust and mek-quake and run it from there. It is, however, on the SUSE workstations. See the documentation for details.
The advantages Pymol has over VMD come from (a) the quality of the graphics you can produce as it has a built in ray-tracing facility (b) better handling of multiple structures and alignment (c) provides a set of libraries that can be called from python. One can run pymol interactively through scripts and not bother with the GUI. It does have downsides, namely that getting many of these options to work is not as easy as with VMD when you have a simple GUI to work with. It also runs slower as it is more graphics intensive (which is amplified as you're running it over the network) so if you are hoping to visualise a large molecule, VMD might be a better option. The below tutorials will hopefully illuminate some of the most useful options!
Tutorials
- changing the representation of your molecule (lines, sticks, cartoon, ribbon etc)
- handling multiple structures - alignment, display and orientation
- producing sexy ray-traced images
- saving your current setup for future review
- advanced colouring