<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi All,<div><br></div><div>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.</div><div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Bradley Hand ITC TT'; font-size: 20px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div><div><div><div><div><div><div>Cheers,</div><div>Mike</div><div><br></div><div><<< ------------------------------------------------------------------------>>></div><div>Dr. Michael W. Day</div><div>Director - X-ray Crystallography Lab & Molecular Observatory</div><div>California Institute of Technology</div><div>Mail Code 139-74</div><div>Pasadena, CA 91125</div><div><br></div><div><>< <>< <>< <>< <>< <>< <>< <>< <>< <><</div><div><br></div><div>Beckman Institute, Room 116</div><div>Phone: (626) 395-2734</div><div>Fax: (626) 449-4159</div><div>e-mail: <a href="mailto:mikeday@caltech.edu">mikeday@caltech.edu</a></div><div><<< ------------------------------------------------------------------------>>></div></div></div></div></div></div></div></span>
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<br><div><div>On Aug 19, 2010, at 7:48 AM, Hatuey Hack wrote:</div><br class="Apple-interchange-newline">Hello,<br><br>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.<br clear="all">
<br>[]'s,<br><br>Hatuey<br>
<br><br><div class="gmail_quote">On Wed, Aug 18, 2010 at 12:19 PM, Beale, John <span dir="ltr"><<a href="mailto:John.Beale@stlcop.edu">John.Beale@stlcop.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div bgcolor="white" background="?ui=2&ik=c9e73466a1&view=att&th=12a85c8e342e7d02&attid=0.0.1&disp=emb&zw" link="blue" vlink="purple" lang="EN-US"><img src="x-msg://13/" style="width: 0pt; min-height: 0pt;" height="0" width="0"><div><p class="MsoNormal"><span style="font-size: 11pt;">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.</span></p><div><span style="font-size: 11pt;"> </span><br class="webkit-block-placeholder"></div><p class="MsoNormal"><span style="font-size: 11pt;">Thanks!</span></p><div><span style="font-size: 11pt;"> </span><br class="webkit-block-placeholder"></div><p class="MsoNormal"><span style="font-size: 11pt;">John</span></p><div><span style="font-size: 11pt;"> </span><br class="webkit-block-placeholder"></div><div><p class="MsoNormal"><b><span style="font-size: 11pt; color: rgb(192, 0, 0);">John M. Beale, Jr., Ph.D.</span></b></p><p class="MsoNormal"><b><span style="font-size: 11pt; color: rgb(192, 0, 0);">Professor of Medicinal Chemistry and Pharmacognosy</span></b></p><p class="MsoNormal"><b><span style="font-size: 11pt; color: rgb(192, 0, 0);">Saint Louis College of Pharmacy</span></b></p><p class="MsoNormal"><b><span style="font-size: 11pt; color: rgb(192, 0, 0);">4588 Parkview Place</span></b></p><p class="MsoNormal"><b><span style="font-size: 11pt; color: rgb(192, 0, 0);">Saint Louis, Missouri 63110</span></b></p><p class="MsoNormal"><b><span style="font-size: 11pt; color: rgb(192, 0, 0);">314-446-8461</span></b></p><p class="MsoNormal"><b><span style="font-size: 11pt; color: rgb(192, 0, 0);">Cell: 314-315-0409</span></b></p><p class="MsoNormal"><b><span style="font-size: 11pt; color: rgb(192, 0, 0);">FAX: 314-446-8460</span></b></p><p class="MsoNormal"><b><span style="font-size: 11pt;"><a href="mailto:jbeale@stlcop.edu" target="_blank">jbeale@stlcop.edu</a></span></b></p></div><div><span style="font-size: 11pt;"> </span><br class="webkit-block-placeholder"></div></div></div>
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