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<p>Dear Behrouz,</p>
<p>in Xmipp highres (accessible through Scipion) you can say which
is the maximum shift that should be sought. If you have previous
angles from Relion or Cryosparc, you may directly import the
particles in Scipion and refine that alignment.</p>
<p>Kind regards, Carlos Oscar<br>
</p>
<div class="moz-cite-prefix">El 22/08/2022 a las 19:35, Behrouz
Ghazi Esfahani escribió:<br>
</div>
<blockquote type="cite"
cite="mid:F1E2FBB5-89CB-4947-8076-ECD15DE79CB0@fsu.edu">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<span style="color: rgb(29, 28, 29); font-family: Slack-Lato,
Slack-Fractions, appleLogo, sans-serif; font-size: 15px;
font-variant-ligatures: common-ligatures; orphans: 2; widows: 2;
background-color: rgb(248, 248, 248); text-decoration-thickness:
initial;" class="">Hello All,</span><span class="c-mrkdwn__br"
data-stringify-type="paragraph-break" style="box-sizing:
inherit; display: block; height: 8px; color: rgb(29, 28, 29);
font-family: Slack-Lato, Slack-Fractions, appleLogo, sans-serif;
font-size: 15px; font-variant-ligatures: common-ligatures;
orphans: 2; widows: 2; background-color: rgb(248, 248, 248);
text-decoration-thickness: initial;"></span><span
class="c-mrkdwn__br" data-stringify-type="paragraph-break"
style="box-sizing: inherit; display: block; height: 8px; color:
rgb(29, 28, 29); font-family: Slack-Lato, Slack-Fractions,
appleLogo, sans-serif; font-size: 15px; font-variant-ligatures:
common-ligatures; orphans: 2; widows: 2; background-color:
rgb(248, 248, 248); text-decoration-thickness: initial;"><br
class="">
</span><span style="color: rgb(29, 28, 29); font-family:
Slack-Lato, Slack-Fractions, appleLogo, sans-serif; font-size:
15px; font-variant-ligatures: common-ligatures; orphans: 2;
widows: 2; background-color: rgb(248, 248, 248);
text-decoration-thickness: initial;" class="">I want to ask if
there is any way to limit the particle shift while doing
alignment in Relion (or other alternatives?). We have a
multimeric protein that we cannot align as the whole complex. We
are making progress aligning the monomers after picking them
independently. Our problem is that when Cryosparc or Relion
refines and classifies the monomer particles it shifts them
according to the bigger lob of the monomer and centers on that.
We want to see if we can prevent this so the smaller lobe in
part of the alignment. The problem is that when the refinements
center the particle, the smaller lob will touches the mask edge,
but we cannot extract with a larger box size because the
neighboring monomers start to come into view. Thank you!</span>
<div class="">
<div style="orphans: 2; widows: 2;" class=""><font class=""
face="Slack-Lato, Slack-Fractions, appleLogo, sans-serif"
color="#1d1c1d"><span style="caret-color: rgb(29, 28, 29);
background-color: rgb(248, 248, 248); font-size: 15px;"
class=""><br class="">
</span></font></div>
<div class="">
<div><span style="font-size: 15px;" class="">Best<br class="">
Behrouz Ghazi Esfahani<br class="">
PhD Candidate and Graduate Assistant<br class="">
Stroupe Lab - Cellular and Molecular Biology<br class="">
Department of Biological Science<br class="">
Florida State University<br class="">
Phone: (+1) 850-345-7886<br class="">
<a href="mailto:bg19f@my.fsu.edu" class=""
moz-do-not-send="true">Email: bg19f@my.fsu.edu</a></span></div>
</div>
<br class="">
</div>
<br>
<fieldset class="moz-mime-attachment-header"></fieldset>
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