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@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*
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