Protect - Revision history

Bell: 1 revision

2016-02-08T05:26:50Z

1 revision

Speleo3: make example work with ignore_case=0

2016-01-24T15:26:04Z

make example work with ignore_case=0

Bell: 1 revision

2015-10-19T01:22:11Z

1 revision

OsvaldoMartin: /* SEE ALSO */

2015-08-28T19:44:14Z

Bell: 8 revisions

2014-03-28T03:08:50Z

8 revisions

New page

'''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==
<source lang="python">
cmd.protect(string selection)
</source>

== 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

# 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]]

[[Category:Commands|Protect]]
[[Category:Editing Module|Protect]]

Vinnyrose at 14:47, 20 June 2009

2009-06-20T14:47:03Z

Vinnyrose at 14:18, 20 June 2009

2009-06-20T14:18:49Z

New page

==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==
<source lang="python">
cmd.protect(string selection)
</source>

== 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

# 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]]

[[Category:Commands|Protect]]

Tree at 05:22, 23 February 2005

2005-02-23T05:22:35Z

New page

===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===
<source lang="python">
cmd.protect(string selection)
</source>

===SEE ALSO===
deprotect, mask, unmask, mouse, editing

[[Category:Commands|protect]]

← Older revision		Revision as of 14:47, 20 June 2009
Line 44:		Line 44:

	[[Category:Commands\|Protect]]		[[Category:Commands\|Protect]]
		+	[[Category:Editing Module\|Protect]]

← Older revision	Revision as of 05:26, 8 February 2016
(No difference)

@@ Line 18: / Line 18: @@
 for a in range(2,31): cmd.create("obj","obj",1,a)
 # remove the bond
-unbond 5/c, 6/n
+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)
+protect not ((5/C or 6/N) extend 4)
 # do some quick sculpting
@@ Line 30: / Line 30: @@
 # 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 45: unbond 5/C, 6/N, quiet=1
-mdo 100: bond 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
+orient 5-6/N+CA+C
 mplay
 </source>

← Older revision	Revision as of 01:22, 19 October 2015
(No difference)

@@ Line 41: / Line 41: @@
 ==SEE ALSO==
-[[Deprotect]], [[Mask]], [[Unmask]], [[Mouse]], [[Editing]]
+[[Deprotect]], [[Mask]], [[Unmask]]
 [[Category:Commands|Protect]]
 [[Category:Editing Module|Protect]]