Color by conservation: Difference between revisions

From PyMOLWiki
Jump to navigation Jump to search
m (d'oh)
No edit summary
 
(3 intermediate revisions by one other user not shown)
Line 1: Line 1:
{{Infobox script-repo
|type      = script
|filename  = scripts/color_by_conservation.py
|author    = [[User:Inchoate|Jason Vertrees]]
|license  = Free
}}
= Overview =
= Overview =
This script reads an alignment object and colors the protein objects in the alignment by the sequence conservation found in the alignment.
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 =
= 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
# turn on the sequence viewer
set seq_view
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
 
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 index %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:Script_Library]]
[[Category:Structural_Biology_Scripts]]
[[Category:Structural_Biology_Scripts]]
[[Category:Pymol-script-repo]]

Latest revision as of 20:38, 22 June 2025

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

Overview

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

Cbcon.png

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
Retrieved from "https://pymolwiki.org/index.php?title=Color_by_conservation&oldid=13895"