[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.


-- 
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
320 Yue-Yang Road
Shanghai 200031
P. R. China
Tel: +86-21-5492-1117
E-mail: jiam...@gmail.com
--
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Re: [PyMOL] figure of buried surface area

2009-08-08 Thread Shiven Shandilya
Hi Jiamu,

Have you looked at VASCo :

http://genome.tugraz.at/VASCo/

I have found it to be very useful and very capable. Contact
interfaces, electrostatics (with Delphi) and many other features are
available. And best of all, it works extremely well with PyMOL.

Do read the manual carefully and you should be able to get very high
quality surface images with a little tweaking.

Best,
Shiven



On Sat, Aug 8, 2009 at 11:09 PM, Jiamu Dujiam...@gmail.com wrote:
 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.


 --
 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
 320 Yue-Yang Road
 Shanghai 200031
 P. R. China
 Tel: +86-21-5492-1117
 E-mail: jiam...@gmail.com

 --
 Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
 trial. Simplify your report design, integration and deployment - and focus
 on
 what you do best, core application coding. Discover what's new with
 Crystal Reports now.  http://p.sf.net/sfu/bobj-july
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