Thanks! guess I had it backwards.
eab
On 05/15/2015 03:19 PM, Yong Wang wrote:
Pymol should draw the molecular surface (or Connolly surface) by default. If you want
the solvent accessible surface, turn on the option "solvent accessible" under
Setting/Surface.
Yong
-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Edward A.
Berry
Sent: Friday, May 15, 2015 3:08 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Two kinds of solvent-accessible-surface ?
If I remember correctly, there are two different ways to calculate a surface by
rolling a ball over it, and i think that I want a program to calculate the
non-conventional one.
As I understand, the ASA is defined as the surface traced out by the _center_
of the rolling sphere, i.e. one radius above the vdw surface. The justification
being that an atom (i.e. it's center coordinates) can't get any closer to the
surface than that. The second type of surface is defined by the closest
approach of the _surface_ of the rolling sphere, i.e. it would be the vdw
radius of the (protein) but not descending into cracks between atoms where the
rolling ball won't fit.
For making models of a multisubunit protein, and wanting to be able to assemble
the separately-made subunits so that they make intermolecular vdw contacts, the
second kind of surface would be desirable, as otherwise atoms won't be able to
get their surfaces closer than twice the sphere radius. Is that an option that
can be chosen in pymol or such?
Thanks,
eab