Dear PyMOL-ers,
Apologies for not thinking about this question a bit more before mailing
the list - I have now written a script (attached) which does the job.
> Is there a simple way to colour each object currently loaded, with a
> different colour (in the same way that you can colour each chain in a
> molecule differently)? This would be really useful in visualising a
> set of superposed structures.
The script is also available at
http://www.ebi.ac.uk/~gareth/misc
Gareth
--
-----------------------------------------------------------------------------
Gareth Stockwell
PhD student, Thornton Group
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
[email protected]
Tel 01223 492548 Personal homepage:
http://www.ebi.ac.uk/~gareth
#####################################################################
#
# Colour by object
#
#####################################################################
def color_obj(rainbow=0):
"""
AUTHOR
Gareth Stockwell
USAGE
color_obj(rainbow=0)
This function colours each object currently in the PyMOL heirarchy
with a different colour. Colours used are either the 22 named
colours used by PyMOL (in which case the 23rd object, if it exists,
gets the same colour as the first), or are the colours of the rainbow
"""
# Process arguments
rainbow = int(rainbow)
# Get names of all PyMOL objects
obj_list = cmd.get_names('models')
if rainbow:
print "\nColouring objects as rainbow\n"
nobj = len(obj_list)
# Create colours starting at blue(240) to red(0), using intervals
# of 240/(nobj-1)
for j in range(nobj):
hsv = (240-j*240/(nobj-1), 1, 1)
# Convert to RGB
rgb = hsv_to_rgb(hsv)
# Define the new colour
cmd.set_color("col" + str(j), rgb)
print obj_list[j], rgb
# Colour the object
cmd.color("col" + str(j), obj_list[j])
else:
print "\nColouring objects using PyMOL defined colours\n"
# List of available colours
colours = ['red', 'green', 'blue', 'yellow', 'violet', 'cyan', \
'salmon', 'lime', 'pink', 'slate', 'magenta', 'orange', 'marine', \
'olive', 'purple', 'teal', 'forest', 'firebrick', 'chocolate', \
'wheat', 'white', 'grey' ]
ncolours = len(colours)
# Loop over objects
i = 0
for obj in obj_list:
print " ", obj, colours[i]
cmd.color(colours[i], obj)
i = i+1
if(i == ncolours):
i = 0
# HSV to RGB routine taken from Robert L. Campbell's color_b.py script
# See http://biophysics.med.jhmi.edu/rlc/work/pymol/
# Original algorithm from: http://www.cs.rit.edu/~ncs/color/t_convert.html
def hsv_to_rgb(hsv):
h = float(hsv[0])
s = float(hsv[1])
v = float(hsv[2])
if( s == 0 ) :
#achromatic (grey)
r = g = b = v
else:
# sector 0 to 5
h = h/60.
i = int(h)
f = h - i # factorial part of h
#print h,i,f
p = v * ( 1 - s )
q = v * ( 1 - s * f )
t = v * ( 1 - s * ( 1 - f ) )
if i == 0:
(r,g,b) = (v,t,p)
elif i == 1:
(r,g,b) = (q,v,p)
elif i == 2:
(r,g,b) = (p,v,t)
elif i == 3:
(r,g,b) = (p,q,v)
elif i == 4:
(r,g,b) = (t,p,v)
elif i == 5:
(r,g,b) = (v,p,q)
else:
(r,g,b) = (v,v,v)
print "error, i not equal 1-5"
return [r,g,b]
# Add color_obj to the PyMOL command list
cmd.extend("color_obj",color_obj)
