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<div>I just wanted to specify that I am using the nogui mode of chimeraX for the computation.</div>
<div>Shubham.</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Shubham Devesh Ramgoolam<br>
<b>Sent:</b> June 12, 2022 1:38 AM<br>
<b>To:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Trajectory computation slowing down overtime</font>
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<p class="x_MsoNormal">Hi all,</p>
<p class="x_MsoNormal">I hope you are doing well.</p>
<p class="x_MsoNormal"> </p>
<p class="x_MsoNormal">I have a Python script for analyzing specific residue pairs for every frame in a trajectory.</p>
<p class="x_MsoNormal">It does so, by using 2 for loops:</p>
<p class="x_MsoNormal">For frame in list_frames:</p>
<p class="x_MsoNormal"> Set current frame to frame</p>
<p class="x_MsoNormal"> For pair in specific_residue_pairs:</p>
<p class="x_MsoNormal"> Do computation</p>
<p class="x_MsoNormal"> </p>
<p class="x_MsoNormal">The computation involves defining geometric objects(centroids, axes, planes) and performing calculations with them(distance, angles).</p>
<p class="x_MsoNormal">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:</p>
<p class="x_MsoNormal"> </p>
<p class="x_MsoNormal"><img width="667" height="406" id="x_Graphic_x0020_5" style="width:6.95in; height:4.225in" data-outlook-trace="F:1|T:1" src="cid:image003.png@01D87E37.C872FDF0"></p>
<p class="x_MsoNormal"> </p>
<p class="x_MsoNormal">Is there a way to maintain the same computation time for every frame in the trajectory?</p>
<p class="x_MsoNormal"> </p>
<p class="x_MsoNormal">Regards,</p>
<p class="x_MsoNormal">Shubham Ramgoolam</p>
<p class="x_MsoNormal">Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">
Mail</a> for Windows</p>
<p class="x_MsoNormal"> </p>
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