[PyMOL] RE: VDW Radii i

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

Michael,

I've cc'd the list with my response.

   "Correct" VDW radii are only in version 0.78 and beyond -- they were
important for the sculpting feature.  Before, PyMOL was using a set that
was about 5% too large (they were originally taken from another popular
graphics program...). =20

Here are the values for key atoms in the current set.

C 1.7
N 1.55
O 1.52
H 1.2
S 1.80
Cl 1.75
Br 1.85
F 1.47
I 1.98
P 1.80

   After loading a molecule, you can use the alter command to provide
your own vdw radii.

   A solvent accessible dot surface (only) can be had with

set dot_mode=3D1
show dots

   Want more dots?  Set dot_density to 3.

   There's no equivalent yet for solid or mesh surfaces.

   Electrostics are in progress -- no public announcements yet.

Warren


--
mailto:wa...@su...
Warren L. DeLano, Ph.D.

> From: michaelw [mailto:mic...@we...]

> I need to confirm that PyMOL is using vanderWaals distances=20
> for generation of=20
> surfaces. Also, has anyone written surface charge or solvent=20
> accessible=20
> surface functions for PyMOL yet?
>=20
> PyMOL is excellent!
>=20
> CHEERS!
>=20
> Michael
>=20