Re: [PyMOL] generate solvent exclusive surface with scaled VDW radii

[Thomas H. <tho...@sc...>]

Hi Ye and Jared,

there is also the "solvent_radius" setting:

PyMOL> set solvent_radius, 1.4

Cheers,
 Thomas

On 14 Feb 2014, at 15:00, Sampson, Jared <Jar...@ny...> wrote:
> 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 <ym...@it...> 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

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.