The PyMOL molecular graphics software package provides support for both the execution of APBS and the visualization of the resulting electrostatic potentials. We will provide a basic demonstration of how go from a PDB entry to a plot of structure & potential in PyMOL using APBS.
Note: This tutorial was written using PyMOLX11Hybrid 0.99 on a Mac.
We'll perform this example with fasciculin-2 (PDB ID 1FAS), a snake neurotoxin which binds the negatively-charged acetylcholinesterase. Please generate the PQR file using the steps outlined in the How do I get my structures ready for electrostatics calculations? section.
Load the PQR file you created into PyMOL (
Go to the P
Note that 0.150 M concentrations for the +1 and −1 ion species are often useful to ensure that electrostatic properties are not overly exaggerated.
Before proceeding with the remaining steps, you must load the electrostatic potential data into PyMOL. Under the "Visualization" tab of the PyMOL APBS Tools window, hit the Update button.
PyMOL makes this step very easy: adjust the positive and negative "Contour" fields to the desired values (usually ±1, ±5, or ±10 kT/e) and hit the Positive Isosurface and Negative Isosurface and Show buttons.
At this point, you probably have a figure that looks something like:
±1 kT/e electrostatic potential isocontours of FAS2 in PyMOL
If the colors are not as you expect, you can change the colors of the objects
If you haven't already, hide the isocontours by hitting Positive Isosurface and Negative Isosurface and Hide buttons.
The surface potential is also straightforward to visualize. Set the "Low" and "High" values to the desired values (usually ±1, ±5, or ±10 kT/e) at which the surface colors are clamped at red (-) or blue (+). Check the "Solvent accessible surface" and "Color by potential on sol. acc. surf." buttons to plot the potential on the solvent-accessible (probe-inflated or Lee-Richards) surface. Hit the "Molecular Surface" Show button to load the surface potential.
±5 kT/e electrostatic potential of FAS2 in PyMOL plotted on the solvent-accessible surface.
In my opinion, the solvent-accessible surface tends to reveal more global features of the surface potential. Tighter surfaces (e.g., van der Waals and molecular or Connolly surfaces) provides more information about the shape of the biomolecule but otherwise tend to simply map atomic surface charges onto the biomolecular surface. Thankfully, PyMOL provides an excellent solution to the conflicting need to obtain geometric information from the molecular surface together with useful electrostatic potential information from the solvent-accessible surface. To visualize the molecule in this way, simply uncheck the "Solvent accessible surface" box and check the "Color by potential on sol. acc. surf." box on the "Visualization tab".
There is a new (developmental) version of the PyMOL-APBS plugin called APBS Tools 2, developed by Michael Lerner. Following is a list of new features of APBS Tools2 over APBS Tools plugin of PyMOL:
You can download this plugin from http://pymolapbsplugin.svn.sourceforge.net/viewvc/pymolapbsplugin/trunk/src/apbsplugin.py
That should give you a file called apbsplugin.py
Once you have the plugin, you can install it via PyMOL's plugin installer:
Note that the plugin will be installed as "APBS Tools2" so that you can continue to use your old version.
Then, follow the same visualization steps above to visualize your biomolecule.
(PyMOL APBS Tools2 works with PyMOL 1.2 and/or newer versions.)