Thanks for the nice writeup, Jason!

There are two main ways that I know of to visualize two potentials at once. This is one. If you're looking at, e.g., a protein-protein interface, it may be useful to map two different electrostatic potentials to two different PyMOL objects. Here's my overly-cautious recipe for doing that:

1. Load up PyMOL with one of your structures.
2. Fire up the plugin. Click on "Choose Externally Generated PQR File" and point it at your PQR file.
3. Click on the Temp File Locations tab and change the name of the temporary DX file to something meaningful, e.g. structure1.dx
4. Set grid and Run APBS as normal.
5. Close the plugin.
6. Type "delete all"
7. Load up the second structure.
8. Repeat steps 2-4, changing the name to something like structure2.dx this time.

Now you have two correctly generated electrostatics potential maps (note: the reason I had you do things with one structure at a time loaded in PyMOL is so that you wouldn't have to fiddle around with the "Selection to use" section of the Main options tab). Use the load command to load up the other pqr file and the other dx map, then use the visualization panes as normal.



On Tue, Feb 1, 2011 at 9:48 AM, Jason Vertrees <> wrote:
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  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.


-- Jason

Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

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