<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Shriyash,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Chimera can read Maestro files, but not as a trajectory — I believe you will get a very large number of separate models.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Using VMD as an intermediary looks like if would work. You can write a DCD file as per:</div><div class=""><br class=""></div><div class=""><a href="http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/12717.html" class="">http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/12717.html</a></div><div class=""><br class=""></div><div class="">You can also write the corresponding PSF with Extensions <img align="BOTTOM" border="0" alt="$\rightarrow$" apple-inline="yes" id="051B71FD-DB8B-4400-96A3-024D57B38246" src="cid:F3B79204-39BB-4A2C-B7DD-204CEF63ED78@cgl.ucsf.edu" class=""> Modeling <img align="BOTTOM" border="0" alt="$\rightarrow$" apple-inline="yes" id="BF1FBFCB-ACF6-4E5F-B3FF-34D02972ECAB" src="cid:F3B79204-39BB-4A2C-B7DD-204CEF63ED78@cgl.ucsf.edu" class=""> Automatic PSF Builder, though you <i class="">might</i> need to have started from a PDB file — i’m not sure. There’s a tutorial here:</div><div class=""><br class=""></div><div class=""><a href="http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-html/node6.html" class="">Generating a Protein Structure File (PSF)</a></div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""></div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div><br class="Apple-interchange-newline"><br class="Apple-interchange-newline">
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<br class=""><div><blockquote type="cite" class=""><div class="">On Jul 27, 2017, at 9:46 AM, Shriyash Upadhyay <<a href="mailto:shriyash.upadhyay@gmail.com" class="">shriyash.upadhyay@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hello,<div class=""><br class=""></div><div class=""><div style="font-size:12.8px" class="">I am a researcher using DESMOND to run molecular dynamics simulations of protein-DNA interactions. However, I and others in my lab are most comfortable viewing trajectories and creating images in UCSF chimera. Is there a way to export DESMOND trajectories in a format that Chimera can open, either from maestro or some intermediate program like VMD?</div></div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Shriyash Upadhyay</div></div>
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