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Official Release PyMOL v2.5 has been released on May 10, 2021.
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Protect

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

  1. create the fake trajectory (of states)

for a in range(2,31): cmd.create("obj","obj",1,a)

  1. remove the bond

unbond 5/C, 6/N

  1. This protects everything but all atoms witing 4
  2. Ang. of residue 5's carbon and residue 6's nitrogen.

protect not ((5/C or 6/N) extend 4)

  1. do some quick sculpting

sculpt_activate obj, 30 sculpt_iterate obj, 30, 100 smooth obj, 30, 3

  1. 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 ..→

A Random PyMOL-generated Cover. See Covers.