Hi Per,
you may check the volume_esp function here:
https://github.com/speleo3/pymol-psico/blob/master/psico/electrostatics.py
As Jason said in that earlier thread, the volume API is work in progress
and will probably change soon.
Cheers,
Thomas
Per Larsson wrote, On 11/21/12 19:01:
Following up myself on this. I did some more digging on Google, and
putting together bits and pieces this is what I have currently.
It works, but does not (yet) allow me to scale the colors according to
eg. the max and min values of my density (which I do not know how to
access).
I guess that means I have a new question about accessing details about
the density-object.
Thanks
/Per
load density.dx, d
cmd.volume(density,d,1.0)
bg_color white
from pmg_tk.skins.normal.ColorRampModel import ColorRamp
r = ColorRamp(nColors=256)
r.addColor(0,(0,0,0,0),0)
r.addColor(2,(0.39,0.67,1,0.01),0)
r.addColor(130,(0,1,0.50,0.25),0)
r.addColor(192,(1,0.0,0.0,0.25),0)
r.addColor(255,(1,0,0,0.25),0)
ramp_colors = r.getRamp()
cmd.volume_color(density,ramp_colors)
21 nov 2012 kl. 17:30 skrev Per Larsson:
Hi pymol-users
I have previously been able to make quite nice visualizations of my
volume object, containing the time-averaged density of atoms from a
MD-simulation.
For making even more improvement, I'd like to be able to use a script
(either python or pml) to control which regions of density gets which
color.
I've found this thread
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10294.html
that suggests it to be possible, but understanding how to use that for
my case is unfortunately (yet) a bit beyond my current pymol-skills.
Ideally I would want to have a solution that allows me to load in my
volume-file (in .dx format), assign colors to different regions of
density systematically (the Volume-GUI is great, but somewhat tricky
to make quick changes with), and display the result on screen.
Is such a thing possible?
Thanks
/Per
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Thomas Holder
PyMOL Developer
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