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/[email protected]/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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