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for a in range(2,31): cmd.create("obj","obj",1,a) | for a in range(2,31): cmd.create("obj","obj",1,a) | ||
# remove the bond | # remove the bond | ||
| − | unbond 5/ | + | unbond 5/C, 6/N |
# This protects everything but all atoms witing 4 | # This protects everything but all atoms witing 4 | ||
# Ang. of residue 5's carbon and residue 6's nitrogen. | # Ang. of residue 5's carbon and residue 6's nitrogen. | ||
| − | protect not ((5/ | + | protect not ((5/C or 6/N) extend 4) |
# do some quick sculpting | # do some quick sculpting | ||
| Line 30: | Line 30: | ||
# then program a bond-break/re-form movie | # then program a bond-break/re-form movie | ||
mset 1 x30 1 -30 30 x30 30 -1 | mset 1 x30 1 -30 30 x30 30 -1 | ||
| − | mdo 45: unbond 5/ | + | mdo 45: unbond 5/C, 6/N, quiet=1 |
| − | mdo 100: bond 5/ | + | mdo 100: bond 5/C, 6/N, quiet=1 |
frame 100 | frame 100 | ||
as sticks | as sticks | ||
| − | orient 5-6/ | + | orient 5-6/N+CA+C |
mplay | mplay | ||
</source> | </source> | ||
Latest revision as of 05:26, 8 February 2016
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