Difference between revisions of "Protect"
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| − | + | ==DESCRIPTION== | |
'''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. | ||
| − | + | ==USAGE== | |
protect (selection) | protect (selection) | ||
| − | + | ==PYMOL API== | |
<source lang="python"> | <source lang="python"> | ||
cmd.protect(string selection) | cmd.protect(string selection) | ||
</source> | </source> | ||
| − | ===SEE ALSO | + | == Example == |
| + | This example makes a very cool little, and fake, molecular movie: | ||
| + | <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 5-6/n+ca+c | ||
| + | mplay | ||
| + | </source> | ||
| + | |||
| + | ==SEE ALSO== | ||
[[Deprotect]], [[Mask]], [[Unmask]], [[Mouse]], [[Editing]] | [[Deprotect]], [[Mask]], [[Unmask]], [[Mouse]], [[Editing]] | ||
[[Category:Commands|protect]] | [[Category:Commands|protect]] | ||
Revision as of 07:50, 30 April 2009
DESCRIPTION
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:
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