Re: [apbs-users] visualization in PyMol

[Thomas H. <tho...@sc...>]

Hi Wolfram,

Yes that's the correct way of doing it. Just add:

4) set surface_ramp_above_mode

See:
http://pymolwiki.org/index.php/Surface_ramp_above_mode

Cheers,
  Thomas

On 19 Aug 2015, at 11:45, wtempel <wt...@GM...> wrote:

> Hello,
> I would like to compare the the electric surface potentials of releated proteins, without using the PyMOL APBS plugin.
> To this end, I have used pdb2pqr and apbs to to produce “pqr” and “dx” files and loaded the files as objects “pqr” and “dx”, respectively.
> Is it an abuse of the calculations’ results if I
> 1) show surface pqr
> 2) ramp_new ramp, dx, [-10,0,10]
> 3) set surface_color, ramp, pqr
> to show (and compare) surface potentials for inference of binding selectivity toward peptides, nucleotides, etc.?
> Is my method correct, as in: can I expect to see the correct APBS potentials on the PyMOL-generated surface, for that given surface?
> If so, is the PyMOL-generated surface over the pqr coordinates a reasonable choice for my purpose?
> Thank you,
> Wolfram Tempel

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.