Editing Displaying Biochemical Properties (section)

===Display solvent accessible surface===
Using the surface display mode, PyMOL doesn't show the solvent accessible surface, rather it shows the solvent/protein contact surface. The solvent accessible surface area is usually defined as the surface traced out by the center of a water sphere, having a radius of about 1.4 angstroms, rolled over the protein atoms. The contact surface is the surface traced out by the vdw surfaces of the water atoms when in contact with the protein.

PyMOL can show solvent accessible surfaces using the dot or sphere representations:

for dots:
<source lang="python">
show dots
set dot_mode,1
set dot_density,3
</source>

for spheres:
<source lang="python">
alter all,vdw=vdw+1.4
show spheres
</source>

Once the Van der Waals radii for the selection have been altered, the surface representation will also be "probe-inflated" to show a pseudo solvent accessible surface, as detailed above.

for surfaces:
<source lang="python">
alter all,vdw=vdw+1.4
show surface
</source>

[[Image:solvent-accessible_surface.jpg|thumb|Solvent-Accessible Surface Example|left]]


















Note that to display both the molecular surface and the solvent-accessible surface, the object must be duplicated, as is done for [[Surface#Representation-independent Color Control]]. This also applies if the spheres representation is to be used to display "real" atoms.