<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Shubham,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Defining those geometric objects creates models. Are you closing those models at the end of each frame?</div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><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=""><blockquote type="cite" class=""><div class="">On Jun 11, 2022, at 11:21 PM, Shubham Devesh Ramgoolam via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">I just wanted to specify that I am using the nogui mode of chimeraX for the computation.</div><div style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">Shubham.</div><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><hr tabindex="-1" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; display: inline-block; width: 511.546875px;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class=""></span><div id="divRplyFwdMsg" dir="ltr" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Shubham Devesh Ramgoolam<br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>June 12, 2022 1:38 AM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span><a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a> <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Trajectory computation slowing down overtime</font><div class=""> </div></div><div lang="EN-US" link="blue" vlink="#954F72" style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word;" class=""><div class="x_WordSection1"><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi all,</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I hope you are doing well.</div><p class="x_MsoNormal" style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I have a Python script for analyzing specific residue pairs for every frame in a trajectory.</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">It does so, by using 2 for loops:</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">For frame in list_frames:</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> Set current frame to frame</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> For pair in specific_residue_pairs:</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> Do computation</div><p class="x_MsoNormal" style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">The computation involves defining geometric objects(centroids, axes, planes) and performing calculations with them(distance, angles).</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">The issue here is that as we move further in list_frames, the computation takes longer and longer. There is a somewhat linear increase in computation time, as illustrated below:</div><p class="x_MsoNormal" style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span id="cid:image003.png@01D87E37.C872FDF0"><E0E35EA38D4345BE98A480EB08BE8CEC.png></span></div><p class="x_MsoNormal" style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Is there a way to maintain the same computation time for every frame in the trajectory?</div><p class="x_MsoNormal" style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;"> </p><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Regards,</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Shubham Ramgoolam</div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Sent from<span class="Apple-converted-space"> </span><a href="https://go.microsoft.com/fwlink/?LinkId=550986" style="color: blue; 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