protect protects a set of atoms from tranformations performed using the editing features. This is most useful when you are modifying an internal portion of a chain or cycle and do not wish to affect the rest of the molecule.
This example makes a very cool little, and fake, molecular movie. Copy/paste this into PyMOL:
load $PYMOL_PATH/test/dat/pept.pdb, obj # create the fake trajectory (of states) for a in range(2,31): cmd.create("obj","obj",1,a) # remove the bond unbond 5/c, 6/n # This protects everything but all atoms witing 4 # Ang. of residue 5's carbon and residue 6's nitrogen. protect not ((5/c or 6/n) extend 4) # do some quick sculpting sculpt_activate obj, 30 sculpt_iterate obj, 30, 100 smooth obj, 30, 3 # then program a bond-break/re-form movie mset 1 x30 1 -30 30 x30 30 -1 mdo 45: unbond 5/c, 6/n, quiet=1 mdo 100: bond 5/c, 6/n, quiet=1 frame 100 as sticks orient 5-6/n+ca+c mplay