For menu, click on picture with right mouse-button.

Rotation Start and Stop
Display options, including various rendering options
Other options, including Slab Mode, Specular rendering, Stereo (crossed-eye stereo pair)
Coloring options
File options

To rotate about x or y axis, use left mouse-button, move pointer on image.
To rotate about z axis, use Shift and right mouse-button, move pointer horizontally.
To zoom, use Shift and left mouse-button; move down to zoom in, up to zoom out.
To pan, use Ctrl and right mouse-button.
To slice when in Slab Mode, use Ctrl and left mouse-button.

Amino acid Colors

ASP, GLU        bright red
LYS, ARG        blue    
HIS             pale blue
ASN, GLN        green-blue      
PRO             flesh   
CYS, MET        yellow  
SER, THR        orange  
GLY             v.light grey
TRP             purple  
PHE, TYR        dark purple
ALA             light grey
LEU, VAL, ILE   dark green