VMD-L Mailing List

From: Deepangi Pandit (deepangi.pandit_at_gmail.com)
Date: Fri Nov 21 2008 - 16:09:12 CST

Hi Ghaleb:
Try downloading the script on the page below and please be sure to
readme.txt for details.

Usage

source _sasa_res.tcl
getAllResSASA "protein" <radius> <framestart fameend>

http://lubos.vrbka.net/?s=sasa

http://www.lubos.vrbka.net/download/vmd/_sasa_res.txt

THX
DP

On Fri, Nov 21, 2008 at 3:44 PM, Ghaleb El Masri <ghaleb.elmasri_at_utoronto.ca
> wrote:

> Dear Colleagues,
>
> I am currently looking at the solvent accessible surface of a protein using
> different solvent radii. I am using a large range of radii, up to 30nm. To
> do this, I am using the solvent drawing method in VMD. I was wondering if
> there was a way to calculate the new enclosed volume of each of my
> representations based on the solvent accessible surface. Is there some sort
> of option or command that will do this? I am fairly new to VMD so perhaps I
> have overlooked an existing feature.
>
> Your help in this matter would be greatly appreciated.
>
> Thank you,
>
> Ghaleb El Masri
> University of Toronto
>
>