<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" style="display:none;"> P {margin-top:0;margin-bottom:0;} </style>
</head>
<body dir="ltr">
<div class="elementToProof" style="margin-top: 1em; margin-bottom: 1em; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Dear all,</div>
<div class="elementToProof" style="margin-top: 1em; margin-bottom: 1em; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
I am trying to use Dynamight in Relion 5, but it takes ages for every step. The sample is a membrane protein. It's a dimer, and each monomer has 588 amino acids. I have a ~4Å resolution map in cryoSPARC and took the particles (700,000) to Relion to use Dynamight.
The box size is 300 and I used 2400 Gaussians.</div>
<div class="elementToProof" style="margin-top: 1em; margin-bottom: 1em; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
To ensure everything was fine, I ran a refinement in Relion and used the particles from this refinement as input for the Dynamight job. However, it took more than two weeks to reach Epoch 61 for deformation estimation. I terminated this job and used a subset
of particles (200,000). It took around two weeks to perform the first step for this subset, and then I couldn't visualize the results in Napari. Although Napari eventually opened, it was frozen.</div>
<div style="margin-top: 1em; margin-bottom: 1em; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Am I doing something wrong? Is there any way to speed up the process?</div>
<div class="elementToProof" style="margin-top: 1em; margin-bottom: 1em; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
I appreciate any help you can provide.</div>
<div class="elementToProof" style="margin-top: 1em; margin-bottom: 1em; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Bests,</div>
<div class="elementToProof" style="margin-top: 1em; margin-bottom: 1em; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Sepideh</div>
<div id="Signature">
<p style="margin: 0cm; font-family: Calibri, sans-serif; font-size: 11pt;"><span style="font-size: 10pt; color: rgb(0, 32, 96);"><b>Sepideh Valimehr | PhD</b></span></p>
<p style="margin: 0cm; font-family: Calibri, sans-serif; font-size: 11pt;"><span style="font-size: 10pt; color: rgb(0, 32, 96);"><b>Research Fellow</b></span></p>
<p style="margin: 0cm; font-family: Calibri, sans-serif; font-size: 11pt;"><span style="font-size: 10pt; color: rgb(47, 84, 150); background-color: rgba(0, 0, 0, 0);"><i>Ian Holmes Imaging Center | Bio21 Molecular Science & Biotechnology Institute |The University
of Melbourne</i></span></p>
<p style="margin: 0cm; font-family: Calibri, sans-serif; font-size: 11pt;"><span style="font-size: 10pt; color: rgb(47, 84, 150);"><i>ARC
</i></span><span style="font-size: 10pt; color: rgb(47, 84, 150); background-color: white;"><i>Centre for Cryo-electron Microscopy of Membrane Proteins (CCeMMP)</i></span></p>
<p style="margin: 0cm; font-family: Calibri, sans-serif; font-size: 11pt;"><span style="font-size: 10pt; color: rgb(0, 32, 96);">30 Flemington Road, Parkville Victoria 3052</span></p>
<p style="margin: 0cm; font-family: Calibri, sans-serif; font-size: 11pt;"><span style="font-size: 10pt; color: rgb(0, 32, 96);"><b>T:
</b>+61 3 8344 5589<b> E: </b></span><span style="font-size: 10pt; color: blue;"><u><a href="mailto:s.valimehr@unimelb.edu.au" style="color: blue; margin-top: 0px; margin-bottom: 0px;">s.valimehr@unimelb.edu.au</a></u></span></p>
<p style="margin: 0cm; font-family: Calibri, sans-serif; font-size: 11pt;"><span style="font-size: 10pt; color: rgb(0, 32, 96);"><i>I acknowledge the Traditional Owners of the land on which I work, and pay my respects to the Elders, past and present.</i></span></p>
<p style="margin: 0cm; font-family: Calibri, sans-serif; font-size: 11pt;"><span><img width="404" height="149" style="width: 404px; height: 149px; margin-top: 0px; margin-bottom: 0px;" data-outlook-trace="F:1|T:1" src="cid:560157fd-ad3b-4eab-b900-5e32088e16d9"></span><span style="color: rgb(0, 0, 0);"><img style="max-width: 800px; margin-top: 0px; margin-bottom: 0px;" data-outlook-trace="F:1|T:1" src="cid:8c455fc8-a303-4597-bbf6-94a90686a38c"></span></p>
<p style="margin: 0cm; font-family: Calibri, sans-serif; font-size: 11pt;"> </p>
</div>
</body>
</html>