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
--
Thomas Holder
PyMOL Developer
Schrödinger Contractor
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