Re: [PyMOL] Determining van der waals radius of a molecule

[Jiamu Du <ji...@gm...>]

Try probe.

http://kinemage.biochem.duke.edu/software/probe.php


On Wed, Jun 23, 2010 at 11:37 AM, Prija Ponnan <pri...@gm...>wrote:

> Yes, coumarin is not sperical and so its diificult to calculate the radius
> by determining its volume.
> I am given task to calculate the vdw radius of a diacetoxy coumarin
> molecule and I happen to find that  PYMOL has an option to label vdw radius.
> But the PYMOL could label vdw radius of individual atom. Can anyone suggest
> me how i could determine vdw radius using any software.
>
> Thank you
>
> On Wed, Jun 23, 2010 at 2:58 PM, Prija Ponnan <pri...@gm...>wrote:
>
>> Hello
>>
>> I want to determine van der waals radius of a coumarin molecule.
>> Pymol has an option to calculate van  der waals radius, but it calculate
>> vdw radius of individual atoms.
>> Is it possible to determine vdw radius of the molecule as a whole.
>>
>> Thank you
>>
>> --
>> Prija Ponnan
>>
>
>
>
> --
> Prija Ponnan
>
>
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-- 
Jiamu Du, Ph.D.
Postdoctoral Research Fellow
Laboratory of Structural Biology
Memorial Sloan-Kettering Cancer Center
RRL 269, 430 E 67th Street
New York, NY, 10021
E-mail: du...@ms...
Tel: (917) - 292 - 4616