Try probe.

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


On Wed, Jun 23, 2010 at 11:37 AM, Prija Ponnan <prija.ponnan@gmail.com> 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 <prija.ponnan@gmail.com> 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

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net



--
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: duj@mskcc.org
Tel: (917) - 292 - 4616