Visualizing Results

There are several programs available for visualizing your results. If you have used the web server for your calculations, the java jmol plugin may be the easiest method, described directly below. However, if you need more options, there are several external programs, such as pymol, for you to use.

The web server:

The most straightforward way to visualize results is through the web server. If you’ve used the web server to get your structures ready and calculate the electrostatics, you will see a link to “click here to visualize your results.”

The web site uses a java plugin to run jmol in the web browser. If you have trouble using the viewer on OSX, make sure to check your java security settings.

Standalone applications:

PyMOL

The PyMol molecular graphics software package can both run APBS and visualize resulting electrostatic potentials. We will provide a basic demonstration of how to visualize a potential in PyMOL from APBS. To calculate electrostatics in PyMol see the calculate electrostatics page.

Visualize the electrostatic potential

Before proceeding, you must load the electrostatic potential data into PyMOL. Under the “Visualization” tab of the PyMOL APBS Tools window, hit the Update button.

Electrostatic isocontours

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 iso_neg and iso_pos in the main menu. By convention (for electrostatics in chemistry), red is negative (think oxygen atoms in carboxyl groups) and blue positive (think nitrogen atoms in amines).

Surface potentials

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.

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 can simultaneously provide geometric information (from the molecular surface) and 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.