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

Michael Day mikeday at caltech.edu
Thu Aug 19 09:46:22 PDT 2010

Hi All,

The solvent (read water) associated with a protein can be very highly conserved from one structure to the next particularly in the first shell where water may may two hydrogen bonds to the protein surface. These conserved waters are chemically interesting and are important for molecular dynamics.


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Dr. Michael W. Day
Director - X-ray Crystallography Lab & Molecular Observatory
California Institute of Technology
Mail Code 139-74
Pasadena, CA 91125

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Beckman Institute, Room 116
Phone: (626) 395-2734
Fax: (626) 449-4159
e-mail: mikeday at caltech.edu
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On Aug 19, 2010, at 7:48 AM, Hatuey Hack wrote:


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.



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.



John M. Beale, Jr., Ph.D.

Professor of Medicinal Chemistry and Pharmacognosy

Saint Louis College of Pharmacy

4588 Parkview Place

Saint Louis, Missouri  63110


Cell: 314-315-0409

FAX: 314-446-8460

jbeale at stlcop.edu


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