Latest revision as of 11:02, 15 January 2012

Overview

Type	Python Script
Download	color_by_conservation.py
Author(s)	Jason Vertrees
License	Free
	This code has been put under version control in the project Pymol-script-repo

This script reads an alignment object and colors the protein objects in the alignment by the sequence conservation found in the alignment.

Example Usage

reinitialize
import color_by_conservation
 
# get some kinases
fetch 1opk 3dtc 3p86 2eva 3efw, async=0
 
# turn on the sequence viewer
set seq_view

# align them into the "algn" object
for x in cmd.get_names(): cmd.align(x, "3efw and c. A", object="algn")
 
# color
color_by_conservation aln=algn, as_putty=1

@@ Line 1: / Line 1: @@
+{{Infobox script-repo
+|type      = script
+|filename  = color_by_conservation.py
+|author    = [[User:Inchoate|Jason Vertrees]]
+|license   = Free
+}}
 = Overview =
 This script reads an alignment object and colors the protein objects in the alignment by the sequence conservation found in the alignment.
@@ Line 5: / Line 12: @@
 = Example Usage =
-<source lang="python">
+<syntaxhighlight lang="python">
-# run the script
+reinitialize
+import color_by_conservation
-run show_conserved.py
+# get some kinases
+fetch 1opk 3dtc 3p86 2eva 3efw, async=0
 # turn on the sequence viewer
 set seq_view
-# get some kinases
+# align them into the "algn" object
+for x in cmd.get_names(): cmd.align(x, "3efw and c. A", object="algn")
-fetch 1opk 3dtc 3p86 2eva 3efw, async=0
-# align them into the "aln" object
-for x in cmd.get_names(): cmd.align(x, "3efw and c. A", object="aln")
 # color
+color_by_conservation aln=algn, as_putty=1
-color_by_conservation("aln", as_putty=1)
+</syntaxhighlight>
-</source>
-= The Code =
-<source lang="python">
-def color_by_conservation(aln, names=(), color="rainbow", as_putty=0, _self=cmd):
-    """
-    PARAMETERS
-    aln
-        (string) the alignment object name
-    names
-        (list) a list of object names that are in the alignment;
-               if (), then PyMOL will attempt to glean the names
-               from the alignment object
-    color
-        (string) valid PyMOL spectrum name
-    as_putty
-        (0 or 1) if 0 display is not changed, else participating objects are shown
-                 as cartoon putty, colored by the 'color' field
-    """
-    # PyMOL doesn't yet know about object:alignment
-    # but we need to check that this exists or we might crash
-    if _self.get_type(aln)!="object:":
-        print "Error: Bad or incorrectly specified alignment object."
-        return None
-    r = cmd.get_raw_alignment(aln)
-    if names==():
-        known_objs = []
-        map(known_objs.extend, map(lambda x: map(lambda y: y[0], x), r))
-        known_objs=set(known_objs)
-        # highest number of matches seen
-        M = max(map(len,r)) + 1
-    else:
-        known_objs = set(names)
-        M = len(known_objs) + 1
-    for obj in known_objs:
-        _self.alter(obj, "b=0.0")
-    for af in r:
-        c = float(1.0 + len(af)) / float(M)
-        for y in af:
-            _self.alter("%s and ID %s" % (y[0], y[1]), "b=c", space={'c':c})
-    if as_putty!=0:
-        for obj in known_objs:
-            _self.show_as("cartoon", "%s" % obj)
-            _self.cartoon("putty",  "%s" % obj)
-            _self.spectrum('b', color, obj)
-            _self.sort()
-            _self.rebuild()
-    return None
-</source>
 [[Category:Script_Library]]
 [[Category:Structural_Biology_Scripts]]
+[[Category:Pymol-script-repo]]

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Latest revision as of 11:02, 15 January 2012

Overview

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