Rasmol

A brilliant open source program for molecular visualization written by a computer scientist (Roger Sayle). Although there are many, many, such programs around, few can rival RasMol for its ease of use and subtle power. Although it cannot do as much as Sybyl or Quanta or O - it is 10 times simpler and can do quite a lot for its size. A simple tutorial follows:

1. Find a PDB file to look at, preferably a small protein or DNA (try the PDB).
2. Open it and select Display > Cartoon
3. Try zooming around:
   • Left Mouse(Held Down) : Rotate.
   • Right Mouse(Held Down) : Translate X/Y.
   • Left + Shift : ZOOM!
   • Right + Shift : Rotate Z.
4. Select Colours > Structure. Pink = Helix, Gold = Sheet, Blue = Turn.

Now try the command line:

• Enter select hetero
• Now type spacefill : the ligand(s) or water should be shown as spheres.
• Colour them with colour cpk this colours: N, blue; O, red; C, grey and S, yellow.
• Select nearby sidechains thus: select within(5.0,hetero) and sidechain.
• Colour the selected sidechain atoms: colour red.

Groups of atoms are selected or deselected separately and can be ANDed and ORed like sets. For example:

Select the interface between two chains

Select (*A AND within(5.0, *B)) OR (*B AND within(5.0, *A))
Obviously, the range parameter in the within() function can be altered.