<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style><![endif]--><style><!--
/* Font Definitions */
@font-face
{font-family:Helvetica;
panose-1:2 11 5 4 2 2 2 2 2 4;}
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
span.apple-converted-space
{mso-style-name:apple-converted-space;}
p.xmsonormal, li.xmsonormal, div.xmsonormal
{mso-style-name:x_msonormal;
mso-margin-top-alt:auto;
margin-right:0in;
mso-margin-bottom-alt:auto;
margin-left:0in;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
.MsoChpDefault
{mso-style-type:export-only;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style>
</head>
<body lang="EN-US" link="blue" vlink="#954F72" style="word-wrap:break-word">
<div class="WordSection1">
<p class="MsoNormal">Hi Eric,</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">No, I did not.</p>
<p class="MsoNormal">I tried it now by adding the following code at the end of the first for loop: run(session, ‘close #1.*’)</p>
<p class="MsoNormal">It made the issue worse, the computation took longer than before. I believe it is because it takes time to close these models.</p>
<p class="MsoNormal"><i>(Originally, I tried fixing the issue by closing the entire session and starting a new one. However, it took too much time for chimeraX to close a session, after defining lots of geometric objects.)<o:p></o:p></i></p>
<p class="MsoNormal">Is there a quicker to close these models at the end of each frame?</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Shubham</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">
Mail</a> for Windows</p>
<p class="MsoNormal"><o:p> </o:p></p>
<div style="mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal" style="border:none;padding:0in"><b>From: </b><a href="mailto:pett@cgl.ucsf.edu">Eric Pettersen</a><br>
<b>Sent: </b>Monday, June 13, 2022 20:43<br>
<b>To: </b><a href="mailto:sdramgoolam@uwaterloo.ca">Shubham Devesh Ramgoolam</a><br>
<b>Cc: </b><a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a><br>
<b>Subject: </b>Re: [chimerax-users] Trajectory computation slowing down overtime</p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Shubham,<o:p></o:p></p>
<div>
<p class="MsoNormal">Defining those geometric objects creates models. Are you closing those models at the end of each frame?<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<div>
<p class="MsoNormal">--Eric<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Eric Pettersen<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">UCSF Computer Graphics Lab<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On Jun 11, 2022, at 11:21 PM, Shubham Devesh Ramgoolam via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">I just wanted to specify that I am using the nogui mode of chimeraX for the computation.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">Shubham.<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><img border="0" width="512" height="2" style="width:5.3333in;height:.025in" id="Horizontal_x0020_Line_x0020_1" src="cid:image002.png@01D87F76.44ECD5B0"><o:p></o:p></p>
<div id="divRplyFwdMsg">
<p class="MsoNormal"><b>From:</b><span class="apple-converted-space"> </span>Shubham Devesh Ramgoolam<br>
<b>Sent:</b><span class="apple-converted-space"> </span>June 12, 2022 1:38 AM<br>
<b>To:</b><span class="apple-converted-space"> </span><a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a> <<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>><br>
<b>Subject:</b><span class="apple-converted-space"> </span>Trajectory computation slowing down overtime<span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"><o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif"> <o:p></o:p></span></p>
</div>
</div>
<div>
<div>
<div>
<p class="MsoNormal">Hi all,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">I hope you are doing well.<o:p></o:p></p>
</div>
<p class="xmsonormal" style="margin:0in"> </p>
<div>
<p class="MsoNormal">I have a Python script for analyzing specific residue pairs for every frame in a trajectory.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">It does so, by using 2 for loops:<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">For frame in list_frames:<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> Set current frame to frame<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> For pair in specific_residue_pairs:<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> Do computation<o:p></o:p></p>
</div>
<p class="xmsonormal" style="margin:0in"> </p>
<div>
<p class="MsoNormal">The computation involves defining geometric objects(centroids, axes, planes) and performing calculations with them(distance, angles).<o:p></o:p></p>
</div>
<div>
<p class="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:<o:p></o:p></p>
</div>
<p class="xmsonormal" style="margin:0in"> <o:p></o:p></p>
<div>
<p class="MsoNormal"><E0E35EA38D4345BE98A480EB08BE8CEC.png><o:p></o:p></p>
</div>
<p class="xmsonormal" style="margin:0in"> </p>
<div>
<p class="MsoNormal">Is there a way to maintain the same computation time for every frame in the trajectory?<o:p></o:p></p>
</div>
<p class="xmsonormal" style="margin:0in"> </p>
<div>
<p class="MsoNormal">Regards,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Shubham Ramgoolam<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Sent from<span class="apple-converted-space"> </span><a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a><span class="apple-converted-space"> </span>for Windows<o:p></o:p></p>
</div>
<p class="xmsonormal" style="margin:0in"> <o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
ChimeraX-users mailing list<br>
<a href="mailto:ChimeraX-users@cgl.ucsf.edu">ChimeraX-users@cgl.ucsf.edu</a><br>
Manage subscription:<br>
<a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></span><o:p></o:p></p>
</div>
</blockquote>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</body>
</html>