[Chimera-users] Positioning of water molecules in a protein

[Hatuey Hack]

Hello,

What is the meaning to know were a particular water molecule is? After all,
in each protein crystallization process the number/position of water
molecules (solvent in general) will be different. Also: the protein will
always be surrounded by water molecules in a highly dynamical way. This is
without account for the fact that the molecular dynamics simulations will
affected directly by the model used to simulate the water presence.

[]'s,

Hatuey


On Wed, Aug 18, 2010 at 12:19 PM, Beale, John <John.Beale at stlcop.edu> wrote:

> Is there a way to use Chimera to determine what atoms/groups in a protein
> are closest to a particular water molecule? I have an x-ray structure that
> is solvated. I would like to determine the positions of the water molecules
> in the x-ray structure and compare these to the water molecule positions
> after molecular dynamics.
>
>
>
> Thanks!
>
>
>
> John
>
>
>
> *John M. Beale, Jr., Ph.D.*
>
> *Professor of Medicinal Chemistry and Pharmacognosy*
>
> *Saint Louis College of Pharmacy*
>
> *4588 Parkview Place*
>
> *Saint Louis, Missouri  63110*
>
> *314-446-8461*
>
> *Cell: 314-315-0409*
>
> *FAX: 314-446-8460*
>
> *jbeale at stlcop.edu*
>
>
>
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