Bell: 3 revisions

2014-03-28T03:06:31Z

3 revisions

Pyadmin: 1 revision

2014-03-28T02:16:16Z

1 revision

Ignat99 at 22:31, 10 May 2013

2013-05-10T22:31:14Z

Speleo3: from pymol import cmd, util

2011-03-03T07:53:55Z

from pymol import cmd, util

New page

[[Image:Highlight ss1.png|right|thumb|300px]]

This script will align and color the paired secondary structures of the two proteins a similar rainbow color.

<source lang="python">
from pymol import cmd, util

def highlight_aligned_ss(obj1,obj2,transform=1,quiet=1):
"""
DESCRIPTION

Aligns two structures and colors their matching
secondary structure elements with a matching
rainbow colorscheme.

USAGE

highlight_aligned_ss obj1, obj2

If transform=0 then the proteins are not
moved after alignment.

EXAMPLES

highlight_aligned_ss 1cll, 1ggz
highlight_aligned_ss 1rlw, 1byn and state 1

SEE ALSO

align

JV 3-2-11
"""

if not cmd.count_atoms(obj1):
print "Error: Object 1 needs at least a few atoms to align."
return None
if not cmd.count_atoms(obj2):
print "Error: Object 2 needs at least a few atoms to align."
return None

# align them
uAln = cmd.get_unused_name("aln")
cmd.align(obj1,obj2,object=uAln,transform=int(transform))
cmd.hide("cgo", uAln)

# select atoms of similar SS
uSimSS = cmd.get_unused_name("similar_ss_")
cmd.select(uSimSS, "((%s or %s) in %s) and (ss 'S' or ss 'H')" %
(obj1,obj2,uAln))

# color by rainbow; these could be
# customized by function parameters
util.rainbow(uSimSS + " and " + obj1)
util.rainbow(uSimSS + " and " + obj2)

# now color everything else grey
cmd.color("grey70", "not (%s)" % uSimSS)

# could also be an option to
# update the representation
# as cartoon

# hide indicators
cmd.select("none")

cmd.extend("highlight_aligned_ss", highlight_aligned_ss)
</source>

[[Category:Scripts_Library]]
[[Category:Structural_Biology_Scripts]]

← Older revision	Revision as of 03:06, 28 March 2014
(No difference)

← Older revision	Revision as of 02:16, 28 March 2014
(No difference)

@@ Line 70: / Line 70: @@
 </source>
-[[Category:Scripts_Library]]
+[[Category:Script_Library]]
 [[Category:Structural_Biology_Scripts]]

HighlightAlignedSS - Revision history

Bell: 3 revisions

Pyadmin: 1 revision

Ignat99 at 22:31, 10 May 2013

Speleo3: from pymol import cmd, util