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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[PyMOL] figure of buried surface area

2009-08-08 Thread Jiamu Du
Dear Pymol BBSers,
I want to generate a figure to show the overlap of two binding epitopes.
Both two proteins A and B can interact with protein C, while their binding
epitopes on C are overlapped. So I want to generate a figrue as this: the
surface of protein C is colored as white, the buried surface area of A on C
is colored as red, the buried surface area of B on C is colored as yellow,
and the overlapped region is colored as orange. I tried several time, all
the figures are not so beautiful. Is there anyone who can perform this well?

Thanks and best wishes.


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Jiamu Du, Ph.D.
State Key Laboratory of Molecular Biology
Institute of Biochemistry and Cell Biology
Shanghai Institutes for Biological Sciences
Chinese Academy of Sciences
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Shanghai 200031
P. R. China
Tel: +86-21-5492-1117
E-mail: jiam...@gmail.com
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