<html><head><base href="x-msg://11/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi John,<div>I had some suggestions after your similar question earlier this year,</div><div><<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-August/005456.html">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-August/005456.html</a>></div><div><<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-August/005459.html">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2010-August/005459.html</a>></div><div><br></div><div>... those generally provide some analysis of which waters are H-bonding at any given time. </div><div><br></div><div>If you wanted to follow a particular water residue through time, you could select it and then indicate in FindHBond (or using similar options of findhbond command) to restrict the calculation to only H-bonds of that water, then run the same calculation at different time steps.</div><div><br></div><div>The only other idea I have is maybe to use the "occupancy" map calculation capability of MD Movie. This would be more appropriate for tracking probable locations of water oxygens or hydrogens over the whole trajectory than for following one water at a time. That is described here</div><div><<a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#occupancy">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#occupancy</a>></div><div>... and also used in this tutorial</div><div><<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#part2">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembles2.html#part2</a>></div><div><br></div><div>Best</div><div>Elaine</div><div><div><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; 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: 0px; "><div>-----</div><div>Elaine C. Meng, Ph.D. </div><div>UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab</div><div>Department of Pharmaceutical Chemistry</div><div>University of California, San Francisco</div><div><br></div></span></div><div><div>On Oct 26, 2010, at 8:04 AM, Beale, John wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; 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: 0px; font-size: medium; "><div bgcolor="white" background="cid:image001.jpg@01CB74F5.349460E0" lang="EN-US" link="blue" vlink="purple"><div class="WordSection1" style="page: WordSection1; "><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(112, 48, 160); ">I am conducting molecular dynamics simulations on a protein in explicit water. I would like to be able to determine the positions of waters of hydration of the protein at the beginning and then at various points along the MD trajectory. What I need to do is locate the position of a water molecule that is hydrogen bonded to a given amino acid and somehow tabulate the positional data.<o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(112, 48, 160); "><o:p> </o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(112, 48, 160); ">Is there a way to do this in Chimera?<o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(112, 48, 160); "><o:p> </o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(112, 48, 160); ">Thanks!<o:p></o:p></span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(112, 48, 160); "><o:p> </o:p></span></div><div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; "><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: black; ">John M. Beale, Jr., Ph.D.<o:p></o:p></span></b></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; "><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: black; ">Professor of Medicinal Chemistry and Pharmacognosy<o:p></o:p></span></b></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; "><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: black; ">Saint Louis College of Pharmacy<o:p></o:p></span></b></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; "><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: black; ">4588 Parkview Place<o:p></o:p></span></b></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; "><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: black; ">Saint Louis, Missouri 63110<o:p></o:p></span></b></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; "><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: black; ">314-446-8461<o:p></o:p></span></b></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; "><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: black; ">Cell: 314-315-0409<o:p></o:p></span></b></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; "><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: black; ">FAX: 314-446-8460</span></b><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(128, 100, 162); "><o:p></o:p></span></b></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; "><b><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(112, 48, 160); "><a href="mailto:jbeale@stlcop.edu" style="color: blue; text-decoration: underline; ">jbeale@stlcop.edu</a><o:p></o:p></span></b></div></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; "><span style="font-size: 11pt; font-family: Arial, sans-serif; "><o:p> </o:p></span></div></div>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline; ">Chimera-users@cgl.ucsf.edu</a><br><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="color: blue; text-decoration: underline; ">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></div></span></blockquote></div><br></div></body></html>