Re: [PyMOL] Displaying an electrostatic potential on msms

[Peter A. M. <pa...@co...>]

Hi Anna,
I generally run apbs seperately (due to difficulties with Alphas), but use
the plugin  to display with pymol.  apbs will produce two output files,
acc.dx and pot.dx.  acc.dx is the electrostatic potential mapped to the
solvent accessible surface; pot.dx is the electrostatic potential over the
grid.  What I generally do is to load acc.dx into pymol, and they use the
plugin->apbs->display to show the surface (not sure of the exact sequence;
pymol's doing a ray-tracing job for me at the moment so I can't check).

Hope this helps...I've never tried the iso_sliders plugin.  I believe the
author of the apbs plugin is on this list, and will probably give you
clearer answers.

Pete

> Dear All,
>
> I have a 0.98 PyMol version with APBS and Iso_Sliders plugins. However,
my aim is not just visualize isosurfaces of electrostatic potential at
certain values, but to display/map it on molecular surface.
>
> Would you be so kind to share your knowledge with me on this subject?
>
> I'd appreciate any help or advice of yours!
>
> Thanks,
>
> Anna.
>
>
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Pete Meyer
Fu Lab
BMCB grad student
Cornell University