Hi Ye -

The solvent excluded surface is the default surface representation in PyMOL.  (Solvent accessible surface can also be generated using `set surface_solvent, on`.)  View the surface with:

show surface, myobj

You can modify van der Waals radii like this:

alter myobj, vdw=vdw*1.2
rebuild

You can also a selection or `all` instead of your object name.  

http://pymolwiki.org/index.php/Surface
http://pymolwiki.org/index.php/Surface_solvent
http://pymolwiki.org/index.php/Alter

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Avenue
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/






On Feb 13, 2014, at 11:15 PM, ymei <ymei@itcs.ecnu.edu.cn> wrote:

Hi all,

Can anyone tell me how to generate the solvent exclusive surface with
scaled (e.g. 1.2, 1.4, 1.6, etc) VDW radii for protein?
I want to visualize the electrostatic potential on these surfaces, in
order to get an idea how the potential changes from the protein to its
vicinity.

Thank you in advance.

Ye


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