HighlightAlignedSS: Difference between revisions
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(Created page with "This script will align and color the paired secondary structures of the two proteins a similar rainbow color. <source lang="python"> import pymol def highlight_aligned_ss(obj1,...") |
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[[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. | This script will align and color the paired secondary structures of the two proteins a similar rainbow color. | ||
<source lang="python"> | <source lang="python"> | ||
import | from pymol import cmd, util | ||
def highlight_aligned_ss(obj1,obj2,transform=1,quiet=1): | def highlight_aligned_ss(obj1,obj2,transform=1,quiet=1): | ||
| Line 67: | Line 70: | ||
</source> | </source> | ||
[[Category: | [[Category:Script_Library]] | ||
[[Category:Structural_Biology_Scripts]] | [[Category:Structural_Biology_Scripts]] | ||
Latest revision as of 17:31, 10 May 2013
This script will align and color the paired secondary structures of the two proteins a similar rainbow color.
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)