Editing User:Mglerner (section)

=== Method 1: all at once ===

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:

#. Load up PyMOL with one of your structures.
#. Fire up the plugin. Click on "Choose Externally Generated PQR File" and point it at your PQR file.
#. Click on the Temp File Locations tab and change the name of the temporary DX file to something meaningful, e.g. structure1.dx
#. Set grid and Run APBS as normal.
#. Close the plugin.
#. Type "delete all"
#. Load up the second structure.
#. 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.