Hi Jiamu,
CASTp is a good tool for examining tunnels (http://sts-fw.bioengr.uic.edu/castp/
). The UCSF program Chimera (http://www.cgl.ucsf.edu/chimera/) can
download from the database and the latest snapshot can open your own
CASTp calculations.
Best,
Wally
On Aug 28, 2008, at 4:50 AM, Jiamu Du wrote:
Dear all,
I want to prepare a figure to present the surface of a channel
inside of a protein as shown in the attached figure.
I have used the program PASS and PYMOL (with CAVER) to make this
figure. Both the programs fail to find the channel. But the channel
is large enough in fact.
Is there any other program can be used for preparing these figures?
Thanks.
--
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: [EMAIL PROTECTED]
<Shell01.jpg>
Walter R.P. Novak, Ph.D.
Postdoctoral Fellow
Rosenstiel Basic Medical Research Center
Brandeis University
415 South St. MS 029
Waltham, MA 02454-9110
Phone: (781) 736-4944
Fax: (781) 736-2405
