The pseudoatom business looks very cool. I'll have to try it out.
In the meantime, I wanted to mention that you certainly can make
transparent CGOs. Here's some code that I wrote to visualize dock
output in our lab. The files it reads in have lines that look like
<junk> x y z r <junk> temp <junk>
Where x,y,z are the coordinates, r is the radius and temp is some
index that we use to look up colors. If you save this in a file,
you'll have a new command, sds, that will read in such a file and show
the output as spheres. Transparency defaults to 0.4, but you can
change it.
-michael
#!/usr/bin/env python
"""
Use PyMOL to show DOCK spheres
"""
from pymol import cmd,cgo
colors = {'1':[.66,.66,.66],#'grey'
'2':[1,0,0],#'red',
'3':[.55,0,0],#'dark red',
'4':[0.65,1,1],#'blue2',
'5':[.25,.88,.82],#'blue7',
'6':[0.004,.55,.55],#'blue8',
'7':[0.004,.55,.55],#'blue8',
'8':[0,1,1],#'blue13',
'9':[0,1,1],#'blue13',
'11':[0.60,.98,.60],#'pale green',
'12':[0.56,.93,.56],#'light green',
'13':[.20,.80,.20],#'lime green',
'14':[.23,.70,.44],#'green8',
'15':[.23,.70,.44],#'sea green',
'16':[.18,.55,.34],#'sea green',
'17':[.18,.55,.34],#'green',
'18':[0,.5,0],#'forest green',
'19':[0,.5,0],#'forest green',
'20':[.13,.55,.13],#'dark green',
'21':[.13,.55,.13],#'dark green',
}
def graph_temp_via_cgo(name,data,transparency=0):
"""
Data should be [x,y,z,r,temp] where
x,y,z are the coordinates,
r is the radius
temp is something like temperature that we
use to look up colors.
"""
obj = []
for x,y,z,r,temp in data:
#transparency = (y/200.0)
obj.extend( [ cgo.ALPHA,1-transparency])
obj.extend( [ cgo.COLOR] + colors[temp])
obj.extend( [ cgo.SPHERE,x,y,z,r] )
cmd.load_cgo(obj,name,1)
return name
def dock_file_to_data(filename):
data = []
f = file(filename)
for line in f:
if not line.strip():
continue
if line.startswith('#'):
continue
junk1,x,y,z,r,junk2,temp,junk3 = line.split()
x,y,z,r = map(float,(x,y,z,r))
data.append([x,y,z,r,temp])
f.close()
return data
def show_dock_spheres(filename,transparency=0.40):
"""
Reads in a DOCK sphere file and graphs the
results as dock spheres. You can pass the
transparency as an additional argument.
"""
transparency = float(transparency)
data = dock_file_to_data(filename)
graph_temp_via_cgo('dock_spheres',data,transparency)
cmd.extend('sds',show_dock_spheres)
On 4/6/07, DeLano Scientific <del...@delsci.info> wrote:
Pre 1.0:
fragment methane, mysph
remove hydro and mysph
alter mysph, vdw=2.0
as spheres, mysph
set sphere_transparency, 0.5, mysph
Post 1.0:
pseudoatom mysph, vdw=2.0
as spheres, mysph
set sphere_transparency, 0.5, mysph
Cheers,
Warren
________________________________
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On
Behalf Of jjv5
Sent: Friday, April 06, 2007 4:55 AM
To: PyMOL-users@lists.sourceforge.net
Subject: [PyMOL] Single transparent sphere
Hi,
Does anyone know of a good way to create a single transparent sphere of
varying size? We've tried using a single atom and changing the vdw, but we
are unable to produce a surface of a single atom. CGO objects work but
cannot be made transparent. What we'd really like is a transparent CGO
sphere. Any ideas?
Thanks,
Jim
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