Editing Displaying Biochemical Properties (section)

===Polar surface area===
For a solvent accessible PSA approximation:
<source lang="python">
set dot_density, 3
remove hydro
remove solvent
show dots
set dot_solvent, on
get_area elem N+O
get_area elem C+S
get_area all
</source>

For molecular PSA approximation
<source lang="python">
set dot_density, 3
remove hydro
remove solvent
set dot_solvent, off
get_area elem N+O
get_area elem C+S
get_area all
</source>

Showing dots isn't mandatory, but it's a good idea to confirm that you're getting the value for the atom dot surface you think you're using.
Please realize that the resulting numbers are only approximate, reflecting the sum of partial surface areas for all the dots you see. To increase accuracy, set dot_density to 4, but be prepared to wait...