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:
<source lang="python">
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 ..→
