VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Mon Mar 01 2004 - 02:20:19 CST

On Sun, 29 Feb 2004 11:45:49 -0500 (EST) Satyavani Vemparala wrote:

>
>
> Hello

hello,

>
> Is there a command in VMD to see waters 'inside' a protein? i.e., if there
> is a hydrophobic cavity in a pore, and i want to see the number of waters
> within this cavity, is there a command/script ?
>
> i feel 'within' is too generic.

what if you do something like
'(within y.yy of resid X) and (within y.yy of resid Z) and ...'
for several or all of the cavity residues?

axel.

>
> Thanks
> Vani
> 

--
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Axel Kohlmeyer      e-mail:  axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum                   http://www.theochem.ruhr-uni-bochum.de
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If you make something idiot-proof, the universe creates a better idiot.