VMD-L Mailing List

From: Justin Gullingsrud (jgulling_at_mccammon.ucsd.edu)
Date: Mon Mar 01 2004 - 03:35:20 CST

One could also select according to distance from some point in space,
e.g.:

    same residue as (sqr(x) + sqr(y) + sqr(z) < sqr(20))

to get residues containing an atom within 20 A of the origin.

Cheers,
Justin

On Mar 1, 2004, at 12:20 AM, Axel Kohlmeyer wrote:

> 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
>>
>
> --
>
> =======================================================================
> 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
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
> 

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