Hi Yarrow,

> Does anyone know how to visualize the surface potentials of two molecules
> simoutaneously using the APBS Tools2.1 plugin?  Thanks.

As Michael wrote the APBS plugin, he might have more to offer, but
here's how I'd do it.  I used this technique to look at two similar
proteins side-by-side in PyMOL (see the 2nd image on
http://www.pymolwiki.org/index.php/APBS).  The trick is to (1) use
grid_mode and grid_slots; and (2) rename the maps as appropriate.
It's not hard, but will take a couple minutes.  Here's how:

# get two proteins; use whatever you like
fetch 1rx1 1rx2, async=0

# put them in the same frame of reference for grid mode
align 1rx1, 1rx2

# run APBS on protein #1, 1rx1
Plugin > APBS Tools2 > ...
Under "selection to use" type "(polymer) and 1rx1"

# rename the map
set_name pymol-generated, 1rx1_map

# run APBS on protein 2, 1rx2; remove the waters
Plugin > APBS Tools2
Under "selection to use" type "(polymer) and 1rx2"

# rename the map
set_name pymol-generated, 1rx2_map

# Now, using APBS show the surfaces make sure you choose
# 1rx1_map for 1rx1 and 1rx2_map for 1rx2; click "Update" if those
# map names are not present.
...

# turn on grid mode
set grid_mode

# assign grid slots just to be sure the right maps
# and proteins are in the right places
set grid_slot, 1, 1rx1
set grid_slot, 1, 1rx1_map
set grid_slot, 1, e_lvl_0_1

set grid_slot, 2, 1rx2
set grid_slot, 2, 1rx2_map
set grid_slot, 2, e_lvl_1_1


Now, you should be set and have an image like that I posted on the PyMOLWiki.

Cheers,

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

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