PyMOL>load dat/il2.pdb
 CmdLoad: "dat/il2.pdb" loaded as "il2".
PyMOL>load dat/pept.pdb
 CmdLoad: "dat/pept.pdb" loaded as "pept".
PyMOL>load dat/3al1.pdb
HEADER    STRUCTURAL PROTEIN                      26-OCT-98   3AL1
TITLE     DESIGNED PEPTIDE ALPHA-1, RACEMIC P1BAR FORM
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: D, L-ALPHA-1;
COMPND   3 CHAIN: A, B;
COMPND   4 ENGINEERED: YES;
COMPND   5 OTHER_DETAILS: N TERMINI ARE ACETYLATED
 ObjectMolecule: Read secondary structure assignments.
 ObjectMolecule: Read crystal symmetry information.
 Symmetry: Found 2 symmetry operators.
 CmdLoad: "dat/3al1.pdb" loaded as "3al1".
PyMOL>util.ss
 util.ss: WARNING: This is not a "correct" secondary structure
 util.ss: assignment algorithm!  Please use only as a last resort.
 util.ss: initiating secondary structure assignment on 163 residues.
 util.ss: extracting sequence and relationships...
 util.ss: analyzing phi/psi angles (slow)...
 util.ss: finding hydrogen bonds...
 util.ss: verifying beta sheets...
 util.ss: assignment complete.
PyMOL>util.cbac
 Executive: Colored 1948 atoms.
 Executive: Colored 922 atoms.
PyMOL>util.cbay
 Executive: Colored 1948 atoms.
 Executive: Colored 922 atoms.
PyMOL>util.cbaw
 Executive: Colored 1948 atoms.
 Executive: Colored 922 atoms.
PyMOL>util.cbas
 Executive: Colored 1948 atoms.
 Executive: Colored 922 atoms.
PyMOL>util.cbc
 util.cbc: color 26,(chain A)
 Executive: Colored 279 atoms.
 util.cbc: color 5,(chain B)
 Executive: Colored 310 atoms.
 util.cbc: color 154,(chain E)
 Executive: Colored 107 atoms.
 util.cbc: color 6,(chain '')
 Executive: Colored 2174 atoms.
PyMOL>hide
PyMOL>show car
PyMOL>zoom
PyMOL>set ray_default_renderer=2
 Setting: ray_default_renderer set to 2.
PyMOL>ray
 RayRenderTest: obtained 19492 graphics primitives.
PyMOL>util.rainbow("pept")
