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>[]&#39;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">&lt;<a href="mailto:John.Beale@stlcop.edu">John.Beale@stlcop.edu</a>&gt;</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;">
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<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>
<p class="MsoNormal"><span style="font-size: 11pt;"> </span></p><p class="MsoNormal"><span style="font-size: 11pt;">Thanks!</span></p><p class="MsoNormal"><span style="font-size: 11pt;"> </span></p><p class="MsoNormal"><span style="font-size: 11pt;">John</span></p>
<p class="MsoNormal"><span style="font-size: 11pt;"> </span></p><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>
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<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><p class="MsoNormal"><span style="font-size: 11pt;"> </span></p></div></div>
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