Start with a clean PDB of your structure. PyMol can add missing hydrogens and side chains (?), but you can always use a PDB file prepared by psfgen. Then :
- pymol mypdb.pdb
- Plugin → APBS tools
- Select APBS Location. The APBS binary location should already be there (/usr/local/bin/apbs). Add the location of the psize.py file by typping /usr/local/bin/psize.py in the box labeled as such.
- Click 'Set grid' at the bottom of the APBS tools window.
- The unix shell should inform you of the grid size for the calculation.
- Click 'Run APBS' at the bottom of the APBS tools window.
- Select Visualization and click Update. The sub-menus for molecular surface, and the two isosurfaces should appear.
- Click Update in the 'Molecular Surface' sub-menu. You should see it.
- You can also try to plot the isosurfaces (with the 'update' switch in their respective submenus).