Electrostatics in PyMOL

Some  work has been done to add display of electrostatic potential surfaces to PyMOL. Michael Lerner at the University of Michigan has written some PyMOL add-ins that allow PyMOL to interface with the electrostatic calculation program APBS. One can set up an APBS calculation from within PyMOL, then display the resulting positive and negative isosurfaces.

To use this special version of Pymol in the Core on a Linux workstation, simply type:

setup pymol-electro

An basic outline of how to proceed:

• Use the website at the San Diego Supercomputing Center to convert a PDB file into the PQR format needed for APBS.
• Start PyMOL and select "APBS Tools" from the "Wizard" menu
• At the PyMOL command line, use "load_pqr [file].pqr" to read in the PQR created above.
• Left click and hold on the "APBS Tools" button on the right of the screen to display a pop-up submenu. Select "Configure" to enter the configuration for an APBS job. You might want to examine the APBS online documentation.
• Left click and hold on "APBS Tools" to select "Calculate." Click the "Calculate" button, and wait a while, depending on the size of your molecule.
• Once APBS has finished, an apbs_map will have been loaded that contains the results. If you have already run APBS on a model and have a .dx file, you can skip the calculation step. After loading the APBS Tools wizard, load the existing map via:

  load_dx [file].dx

• Select "Electrostatics" from the "Wizard" menu
• From the Electrostatics wizard, you can select different levels of positive and negative potentials. You can also turn on a neutral surface for the entire molecule using the Vdw Buffer. If you want to display an isosurface level that isn't in the popup list, use the following commands:

  cmd.get_wizard().isosurf([Level],"iso_pos")
  
  cmd.get_wizard().isosurf(-[Level],"iso_neg")

  where [Level] represents the absolute value of the desired level.
• To make the surfaces transparent, use the transparency command: e.g.,

  set transparency=0.5

  To change the transparency to different values for different isosurfaces, use the name of the surface: e.g.,

  set transparency=0.6, iso_pos

Disclaimer

Note that these tools are the result of someone's personal customizations of an obsolete version of PyMOL, tweaked to work in the Core. Note also that the APBS program is currently at release 0.3.1. All of this means that these tools are a rough work in progress. If it doesn't seem to be doing something right, it probably can't do it right. The Core staff cannot provide detailed help with these tools.

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