VMD-L Mailing List

From: Ran Friedman (ran_at_hemi.tau.ac.il)
Date: Thu May 04 2006 - 03:17:24 CDT

Dear Linda,

We used VOLBL to calculate the volume of cavities and represented the
cavity-bordering atoms by their VDW radii, after changing the VDW radii
values to those used in VOLBL. You can have a look at BJ: 85 p. 886-896
(2003).

Ran.

Wei Fu (Linda) wrote:

>Hello,
>
>Is there any way to display the volume of cavity/pocket/channel of a protein in VMD? Do I need to install some plugin program or calculate the volume of cavity by other software, then use VMD to read the map of the volume?
>
>Best,
>
>Linda
>
>2006-05-02
>
> Linda
> Postdoctoral Research Associate
> Department of Biology and Biochemistry
> University of Houston
> 4800 Calhoun Rd. HSC #402C
> Houston, TX 77204-5001 USA
> Phone:713-743-8355(o)
> Fax:713-743-8351
> Email: fuwei_at_adrik.bchs.uh.edu
> http://adrik.bchs.uh.edu/~fuwei/
>
>
>
>
> +++++++++++++++++++++++++++++++++++++++++++
> This Mail Was Scanned By Mail-seCure System
> at the Tel-Aviv University CC.
>
> 

-- 
------------------------------------------------------
Ran Friedman
http://bioinfo.tau.ac.il/~ran
Laser Laboratory for Fast Reactions in Biology
Department of Biochemistry
Faculty of Life Sciences
Tel-Aviv University
Tel. +972-3-6409824
Fax. +972-3-6409875
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