Positioning of water molecules in a protein
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@stlcop.edu<mailto:jbeale@stlcop.edu>
Hi John, Chimera has many features for examining structural details and interactions among and between sets of atoms. There are so many possibilities I'm at a loss as to how to answer this question. I'll try to touch on a few different things and provide links to where you can learn more. Maybe the "Structure Analysis and Comparison" tutorial would be useful: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> You can examine all the contacts and/or H-bonds made by some set of atoms. There is a "Find Clashes/Contacts" tool and corresponding "findclash" command, <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> and a "FindHBond" tool and corresponding "findhbond" command. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html> Command-line specifications could use specific residue numbers for one or more waters, or "solvent" to mean all waters, or "sel" to mean the current selection. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> You can look at all atoms within a particular cutoff distance of some other set of atoms. Zones can be specified in the command line, or you can select something and then use the menu item "Select... Zone" to also select atoms within a cutoff distance of the initial selection. Example commands: rlabel solvent zr<4.5 (residue-label all residues within 4.5 ang of any solvent atom) color red :453.a za<5 (color red all atoms within 5 ang of residue 453 in chain A) select sel zr<8 (select all residues with any atom within 8 ang of current selection) <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#zones> You can measure distances, angles, ... <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Aug 18, 2010, at 8:19 AM, Beale, John 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
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*
*314-446-8461*
*Cell: 314-315-0409*
*FAX: 314-446-8460*
*jbeale@stlcop.edu*
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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. Cheers, Mike <<< ------------------------------------------------------------------------>>> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125 <>< <>< <>< <>< <>< <>< <>< <>< <>< <>< Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday@caltech.edu <<< ------------------------------------------------------------------------>>> On Aug 19, 2010, at 7:48 AM, Hatuey Hack wrote: 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 314-446-8461 Cell: 314-315-0409 FAX: 314-446-8460 jbeale@stlcop.edu _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
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Beale, John -
Elaine Meng -
Hatuey Hack -
Michael Day