Protect
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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.
USAGE
protect (selection)
PYMOL API
cmd.protect(string selection)
Example
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