RE: [PyMOL] help with surface parameters

[DeLano, W. <wa...@su...>]

Scott,

> From: Scott Classen [mailto:cl...@uc...]
>=20
> Hello fellow PyMOLers,
> 	Is the surface in PyMOL a solvent accessible surface or=20
> a molecular=20
> surface? It looks like a solvent accessible surface to me. Is=20
> there any=20
> way to change the radius of the water probe that is used to=20
> create the=20
> surface?

PyMOL's default surface is a water contact surface (approximates a =
Connolly surface).

>I noticed that there are a few surface settings, but I can't=20
> figure out what effects they are having on the displayed surface. Can=20
> anybody shed light on these commands? What are their default=20
> settings?=20

You can use the settings editor to get the default (except if you're =
using the native OSX version on a mac).

> What are the high and low values they can take?
>=20
> surface_best
> surface_normal
> surface_proximity
> surface_quality

These settings haven't yet been documented, but they will be in an =
upcoming version of the manual. =20

>   I would like to create a fairly tight molecular surface and I just=20
> can't figure it out. ANy help would be appreciated.

show surface
set surface_quality=3D1
set solvent_radius=3D0.8
rebuild

WARNING: PyMOL may crash if solvent_radius is too low.  If it does, try =
incrementing it by 0.1 until it stabilizes.

Cheers,
Warren