[PyMOL] Determining van der waals radius of a molecule

2010-06-23 Thread Prija Ponnan
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

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

2010-06-23 Thread Jiamu Du
Try probe.

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


On Wed, Jun 23, 2010 at 11:37 AM, Prija Ponnan prija.pon...@gmail.comwrote:

 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.pon...@gmail.comwrote:

 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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 GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
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 http://p.sf.net/sfu/thinkgeek-promo
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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: d...@mskcc.org
Tel: (917) - 292 - 4616
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