Thank you very much.
I had trouble with Jason's method but the second one worked great! Now I
have beautifull e-static surfaces to show at my talk. Thank you!
> Thanks for the nice writeup, Jason!
> There are two main ways that I know of to visualize two potentials at
> This is one. If you're looking at, e.g., a protein-protein interface, it
> 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
> 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
> 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
> 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
> 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 <
> jason.vertrees@...> wrote:
>> Hi Yarrow,
>> > Does anyone know how to visualize the surface potentials of two
>> > 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
>> -- Jason
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>> (e) Jason.Vertrees@...
>> (o) +1 (603) 374-7120
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> Michael Lerner, Ph.D.
> IRTA Postdoctoral Fellow
> Laboratory of Computational Biology NIH/NHLBI
> 5635 Fishers Lane, Room T909, MSC 9314
> Rockville, MD 20852 (UPS/FedEx/Reality)
> Bethesda MD 20892-9314 (USPS)
Molecular Biology and Biochemistry Dept.
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Natural Sciences I, Rm 2403
Irvine, CA 92697