Protect: Difference between revisions
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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. | '''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. | ||
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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> | ||
==SEE ALSO== | ==SEE ALSO== | ||
[[Deprotect]], [[Mask]], [[Unmask | [[Deprotect]], [[Mask]], [[Unmask]] | ||
[[Category:Commands|Protect]] | [[Category:Commands|Protect]] | ||
[[Category:Editing Module|Protect]] | |||
Latest revision as of 10:26, 24 January 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