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<div>Ok. Thanks a lot.</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> Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Sent:</b> June 27, 2022 12:57 PM<br>
<b>To:</b> Shubham Devesh Ramgoolam <sdramgoolam@uwaterloo.ca><br>
<b>Cc:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Trajectory computation slowing down overtime</font>
<div> </div>
</div>
<div class="" style="word-wrap:break-word; line-break:after-white-space">Hi Shubham,
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>Both angles are perfectly valid. Since most people would intuitively think of the "angle between the planes" as the smaller (<=90) angle, that's why in the plane-plane angle sample
code I supplied it always returns the <=90 angle:</div>
<div class=""><br class="">
</div>
<div class="">
<div class=""><b class="">Plane-plane angle</b>:</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>from chimerax.geometry import angle</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>a = angle(plane1.normal, plane2.normal)</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>if a > 90:</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>a = 180 - a</div>
<div class=""><br class="">
</div>
<div class="">--Eric</div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Jun 27, 2022, at 12:04 AM, Shubham Devesh Ramgoolam via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
Hi all,</div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
</div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
I have noticed that for some residue, the plane normal displayed in the log, after using define plane command, is antiparallel to the plane normal obtained with low level mathematical primitives.</div>
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</div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
This would cause any angle measurement involving one such plane and another ‘regular’ plane (same plane normal in both cases) to be different when using the angle command than when using the low level mathematical primitives. The angles are supplementary instead
of identical.</div>
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</div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
I have inserted a screenshot of my log and shell showing the plane normal obtained with the define plane command and with the low level mathematical primitives.</div>
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<span id="x_cid:image003.jpg@01D88A15.A10DEBA0"><1041C798FB7B4B68B81CF26A82B04195.jpg></span></div>
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I am not sure if this is a valid question but which value represents the true angle between the planes?</div>
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Regards,</div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
Shubham Ramgoolam</div>
<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
Sent from<span class="x_Apple-converted-space"> </span><a href="https://go.microsoft.com/fwlink/?LinkId=550986" class="" style="color:blue; text-decoration:underline">Mail</a><span class="x_Apple-converted-space"> </span>for Windows</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif; border:none; padding:0in">
<b class="">From:<span class="x_Apple-converted-space"> </span></b><a href="mailto:pett@cgl.ucsf.edu" class="" style="color:blue; text-decoration:underline">Eric Pettersen</a><br class="">
<b class="">Sent:<span class="x_Apple-converted-space"> </span></b>Tuesday, June 14, 2022 3:20<br class="">
<b class="">To:<span class="x_Apple-converted-space"> </span></b><a href="mailto:sdramgoolam@uwaterloo.ca" class="" style="color:blue; text-decoration:underline">Shubham Devesh Ramgoolam</a><br class="">
<b class="">Cc:<span class="x_Apple-converted-space"> </span></b><a href="mailto:chimerax-users@cgl.ucsf.edu" class="" style="color:blue; text-decoration:underline">ChimeraX Users Help</a><br class="">
<b class="">Subject:<span class="x_Apple-converted-space"> </span></b>Re: [chimerax-users] Trajectory computation slowing down overtime</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
Hi Shubham,</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
Looking at your graph, even the initial time is way too slow, 10+ seconds/frame. For this kind of analysis, you should be using low level mathematical primitives rather than the graphical axes/planes/centroids, which are intended for interactive use and have
a lot of additional overhead, like a triangle mesh for the graphical depiction, color information, etc.</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
So the first thing is you will need to get is the atoms that the primitives will based on. Assuming you know how to select the atoms with a command, you can get them with:</div>
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from chimerax.atomic import selected_atoms</div>
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run(session, "sel<span class="x_Apple-converted-space"> </span><i class="">some-atom-spec</i>")</div>
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atoms = selected_atoms(session)</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
So, the low level primitives are:</div>
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<b class="">Centroid</b>: just an xyz point, which you can get with:</div>
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from chimerax.centroid import centroid</div>
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centroid_pt = centroid(atoms.coords)</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
(which is just atoms.coords.mean(0) actually)</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<b class="">Axis</b>: as long as you not measuring<span class="x_Apple-converted-space"> </span><i class="">distances</i> with an axis, all you need is a direction vector, which is also just an xyz value, which you can get with:</div>
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from numpy.linalg import svd</div>
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center = atoms.coords.mean(0)</div>
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_, vals, vecs = sud(atoms.coords - center, full_matrices=False)</div>
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xyz = vecs[vals.argsort()[-1])</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<b class="">Plane</b>: an origin point and a normal vector, encapsulated as a chimera.geometry.Plane object,<span class="x_Apple-converted-space"> </span><i class="">e.g.</i>:</div>
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from chimerax.geometry import Plane</div>
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plane = Plane(atoms.coords)</div>
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Here are example measurements:</div>
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<b class="">Centroid-centroid distance</b>:</div>
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from chimerax.geometry import distance</div>
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d = distance(xyz1, xyz2)</div>
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</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<b class="">Centroid-plane distance</b>:</div>
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d = abs(plane.distance(xyz))</div>
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</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<b class="">Axis-axis</b> angle:</div>
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from chimerax.geometry import angle</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
a = angle(xyz1, xyz2)</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
This returns a value in the range 0-180. To map that into the 0-90 range:</div>
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if a > 90:</div>
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a = 180 - a</div>
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</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<b class="">Plane-plane angle</b>:</div>
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from chimerax.geometry import angle</div>
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a = angle(plane1.normal, plane2.normal)</div>
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if a > 90:</div>
</div>
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a = 180 - a</div>
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</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
--Eric</div>
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On Jun 13, 2022, at 11:38 AM, Shubham Devesh Ramgoolam via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="" style="color:blue; text-decoration:underline">chimerax-users@cgl.ucsf.edu</a>> wrote:</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
Hi Eric,</div>
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No, I did not.</div>
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I tried it now by adding the following code at the end of the first for loop: run(session, ‘close #1.*’)</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
It made the issue worse, the computation took longer than before. I believe it is because it takes time to close these models.</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<i class="">(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.)</i></div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
Is there a quicker to close these models at the end of each frame?</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
Shubham</div>
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Sent from<span class="x_apple-converted-space"> </span><a href="https://go.microsoft.com/fwlink/?LinkId=550986" class="" style="color:blue; text-decoration:underline">Mail</a><span class="x_apple-converted-space"> </span>for Windows</div>
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<b class="">From:<span class="x_apple-converted-space"> </span></b><a href="mailto:pett@cgl.ucsf.edu" class="" style="color:blue; text-decoration:underline">Eric Pettersen</a><br class="">
<b class="">Sent:<span class="x_apple-converted-space"> </span></b>Monday, June 13, 2022 20:43<br class="">
<b class="">To:<span class="x_apple-converted-space"> </span></b><a href="mailto:sdramgoolam@uwaterloo.ca" class="" style="color:blue; text-decoration:underline">Shubham Devesh Ramgoolam</a><br class="">
<b class="">Cc:<span class="x_apple-converted-space"> </span></b><a href="mailto:chimerax-users@cgl.ucsf.edu" class="" style="color:blue; text-decoration:underline">chimerax-users@cgl.ucsf.edu</a><br class="">
<b class="">Subject:<span class="x_apple-converted-space"> </span></b>Re: [chimerax-users] Trajectory computation slowing down overtime</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
Hi Shubham,</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
Defining those geometric objects creates models. Are you closing those models at the end of each frame?</div>
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--Eric</div>
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Eric Pettersen</div>
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UCSF Computer Graphics Lab</div>
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On Jun 11, 2022, at 11:21 PM, Shubham Devesh Ramgoolam via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="" style="color:blue; text-decoration:underline">chimerax-users@cgl.ucsf.edu</a>> wrote:</div>
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<div class="" style="margin:0in; font-size:11pt; font-family:Calibri,sans-serif">
<span class="" style="font-size:9pt; font-family:Helvetica,sans-serif">I just wanted to specify that I am using the nogui mode of chimeraX for the computation.</span></div>
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<span class="" style="font-size:9pt; font-family:Helvetica,sans-serif">Shubham.</span></div>
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<CB8387F6EE204E1BA668D200AE4A00A4.png></div>
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<b class="">From:</b><span class="x_apple-converted-space"> </span>Shubham Devesh Ramgoolam<br class="">
<b class="">Sent:</b><span class="x_apple-converted-space"> </span>June 12, 2022 1:38 AM<br class="">
<b class="">To:</b><span class="x_apple-converted-space"> </span><a href="mailto:chimerax-users@cgl.ucsf.edu" class="" style="color:blue; text-decoration:underline">chimerax-users@cgl.ucsf.edu</a><span class="x_apple-converted-space"> </span><<a href="mailto:chimerax-users@cgl.ucsf.edu" class="" style="color:blue; text-decoration:underline">chimerax-users@cgl.ucsf.edu</a>><br class="">
<b class="">Subject:</b><span class="x_apple-converted-space"> </span>Trajectory computation slowing down overtime</div>
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<span class="" style="font-size:9pt; font-family:Helvetica,sans-serif"> </span></div>
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Hi all,</div>
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I hope you are doing well.</div>
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I have a Python script for analyzing specific residue pairs for every frame in a trajectory.</div>
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It does so, by using 2 for loops:</div>
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For frame in list_frames:</div>
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Set current frame to frame</div>
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For pair in specific_residue_pairs:</div>
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Do computation</div>
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The computation involves defining geometric objects(centroids, axes, planes) and performing calculations with them(distance, angles).</div>
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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>
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<E0E35EA38D4345BE98A480EB08BE8CEC.png></div>
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Is there a way to maintain the same computation time for every frame in the trajectory?</div>
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Regards,</div>
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Shubham Ramgoolam</div>
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