Hi Bashir,
In Pymol:
1. Show-------Surface (will generate surface around the protein)
2. Setting-----Surface-------Cavities & Pockets Only. (will show only Cavities inside)
3. Use cavity_cull command to set the filter for cavities.
(eg. set cavity_cull, 40)
Manish
--
Manish Chandra Pathak, Ph.D.
Department of Biochemistry
Emory University School of Medicine
1510 Clifton Road, NE, Room G235
Atlanta, GA 30322 USA
Tel: +1-404-727-2563 Fax: +1-404-727-2738
----- Original Message ----
> From: Muhammed bashir Khan <[log in to unmask]>
> To: [log in to unmask]
> Sent: Wed, April 7, 2010 9:58:20 AM
> Subject: [ccp4bb] Solvent accessible regions of the channel (Pore)
>
> Dear all;
Can anybody help me how I can make the solvent accessible
> surface(inside)
of the channel(pore)by pymol, or by any other
> programme.
Thanks in Advance
--
Muhammad Bashir
> Khan
Department for Biomolecular Structural Chemistry
Max F. Perutz
> Laboratories
University of Vienna
Campus Vienna Biocenter 5
A-1030
> Vienna
Austria
Phone: +43(1)427752224
Fax: +43(1)42779522
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