<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=us-ascii">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:PMingLiU;
panose-1:2 2 5 0 0 0 0 0 0 0;}
@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;}
@font-face
{font-family:"\@PMingLiU";
panose-1:2 2 5 0 0 0 0 0 0 0;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
font-size:12.0pt;
font-family:"Calibri",sans-serif;}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-US" link="#0563C1" vlink="#954F72" style="word-wrap:break-word">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt">Hi Justas,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">As far as I know, there is no absolute convention – the two possible icososahedral symmetries are called “I” and “I2”.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">One of them describes an icosahedron where you can “walk” between 5-fold axes thru 3- and 2- fold (5-3-2-5), the other thru 2- then 3-fold (5-2-3-5). Which is referred to as “I” and which as “I2” is, in principle,
irrelevant. The two icosahedra are different structures, they are not mirrors of one hand.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">So just use one of the two option that works in cryosparc. I guess it would be I2…<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> Matthias <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div style="border:none;border-left:solid blue 1.5pt;padding:0in 0in 0in 4.0pt">
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:11.0pt">From:</span></b><span style="font-size:11.0pt"> 3dem
<b>On Behalf Of </b>Rodarte, Justas V<br>
<b>Sent:</b> Thursday, February 4, 2021 7:53 AM<br>
<b>To:</b> 3dem@ncmir.ucsd.edu<br>
<b>Subject:</b> [3dem] Symmetry Matrix Differences Between Cryo-EM Software<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Hi all,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I’m a relative newcomer to the field of Cryo-EM, so my apologies if this question is easy/misplaced/previously answered. I’m working on a VLP with I symmetry that displays 80 spikes. Some programs (Relion,
cisTEM) apply symmetry correctly when moving onto 3D ab-initio, while others (Cryosparc), don’t. I was able to trace this to the fact that these programs use different matrices to apply symmetry, an example is included below. Does anyone know why this is though?
To me it appears to be an oversight that two popular programs apply the same symmetry differently?
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Thank you all for any help or advice you can provide!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Justas Rodarte<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-align:justify">I1 Sym Matrix Relion<o:p></o:p></p>
<table class="MsoNormalTable" border="0" cellpadding="0">
<tbody>
<tr>
<td style="padding:.75pt .75pt .75pt .75pt">
<p class="MsoNormal" style="text-align:justify">rot_axis 2, 1 0 0<o:p></o:p></p>
</td>
</tr>
<tr>
<td style="padding:.75pt .75pt .75pt .75pt"></td>
</tr>
</tbody>
</table>
<p class="MsoNormal" style="text-align:justify"><span style="display:none"><o:p> </o:p></span></p>
<table class="MsoNormalTable" border="0" cellpadding="0">
<tbody>
<tr>
<td style="padding:.75pt .75pt .75pt .75pt">
<p class="MsoNormal" style="text-align:justify">rot_axis 5, 0.85065080702670 0 -0.5257311142635<o:p></o:p></p>
</td>
</tr>
<tr>
<td style="padding:.75pt .75pt .75pt .75pt"></td>
</tr>
</tbody>
</table>
<p class="MsoNormal" style="text-align:justify"><span style="color:black">rot_axis 3, 0.9341723640 0.3568220765 0</span><o:p></o:p></p>
<p class="MsoNormal" style="text-align:justify"><o:p> </o:p></p>
<p class="MsoNormal" style="text-align:justify">I1 Sym Matrix Cryosparc<o:p></o:p></p>
<p class="MsoNormal" style="text-align:justify">rot_axis 2, 0 1 0<o:p></o:p></p>
<p class="MsoNormal" style="text-align:justify">rot_axis 5, -0.85065080702670 0 0.5257311142635<o:p></o:p></p>
<p class="MsoNormal" style="text-align:justify">rot_axis 3, -0.9341723640 0.3568220765<o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
</div>
</body>
</html>