Difference between revisions of "Protect"

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==DESCRIPTION==
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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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== Example ==
 
== Example ==
This example makes a very cool little, and fake, molecular movie:
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This example makes a very cool little, and fake, molecular movie.  Copy/paste this into PyMOL:
 
<source lang="python">
 
<source lang="python">
 
load $PYMOL_PATH/test/dat/pept.pdb, obj
 
load $PYMOL_PATH/test/dat/pept.pdb, obj
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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/c, 6/n
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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/c or 6/n) extend 4)
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protect not ((5/C or 6/N) extend 4)
  
 
# do some quick sculpting
 
# do some quick sculpting
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# 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/c, 6/n, quiet=1
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mdo 45: unbond 5/C, 6/N, quiet=1
mdo 100: bond 5/c, 6/n, quiet=1
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mdo 100: bond 5/C, 6/N, quiet=1
  
 
frame 100
 
frame 100
  
 
as sticks
 
as sticks
orient 5-6/n+ca+c
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orient 5-6/N+CA+C
 
mplay
 
mplay
 
</source>
 
</source>
  
 
==SEE ALSO==
 
==SEE ALSO==
[[Deprotect]], [[Mask]], [[Unmask]], [[Mouse]], [[Editing]]
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[[Deprotect]], [[Mask]], [[Unmask]]
  
[[Category:Commands|protect]]
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[[Category:Commands|Protect]]
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[[Category:Editing Module|Protect]]

Latest revision as of 11:26, 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

SEE ALSO

Deprotect, Mask, Unmask