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<div class="">Hi,</div>
<div class=""><br class="">
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There has been a paper where they applied this logic to get a ~13Å reconstruction of the HIV Env spikes from intact virus, without imposing symmetry: <span class=""><br class="">
Alsahafi et al (2019) An Asymmetric Opening of HIV-1 Envelope Mediates Antibody-Dependent Cellular Cytotoxicity<br class="">
</span>
<div class=""><a href="https://www.sciencedirect.com/science/article/pii/S1931312819301143?via=ihub#bib6" class="">https://www.sciencedirect.com/science/article/pii/S1931312819301143?via%3Dihub#bib6</a></div>
<div class=""><br class="">
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<div class="">The orientation distribution in the paper supplement shows that it is almost completely composed of side views.</div>
<div class=""><br class="">
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<div class="">All the best </div>
<div class="">Tom<br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 25 Mar 2020, at 16:23, Basil Greber <<a href="mailto:basilgreber@gmx.net" class="">basilgreber@gmx.net</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">I
am also confused by this. Shouldn’t a tomographic series (180 degrees worth of side views) do it for a C1 particle?</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Basil</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
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<blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
Am 25.03.2020 um 00:06 schrieb Philip Köck <<a href="mailto:koeck@kth.se" class="">koeck@kth.se</a>>:<br class="">
<br class="">
Why do you say that the symmetry has to be at least C3?<br class="">
<br class="">
All the best,<br class="">
<br class="">
Philip<br class="">
<br class="">
<br class="">
<br class="">
Från: 3dem <<a href="mailto:3dem-bounces@ncmir.ucsd.edu" class="">3dem-bounces@ncmir.ucsd.edu</a>> för Dmitry Lyumkis <<a href="mailto:dlyumkis@salk.edu" class="">dlyumkis@salk.edu</a>><br class="">
Skickat: den 25 mars 2020 07:07<br class="">
Till: Jacopo Marino<br class="">
Kopia: <a href="mailto:3dem@ncmir.ucsd.edu" class="">3dem@ncmir.ucsd.edu</a><br class="">
Ämne: Re: [3dem] Membrane protein structure: orientation issue<br class="">
<br class="">
Assuming this is a symmetric membrane protein with at least 3-fold rotational symmetry, you don’t need the top and bottom views to fully sample Fourier space and arrive at a high-quality reconstruction. Side-views of a rotationally symmetric particle are sufficient,
and the reconstruction will be complete.<span class="Apple-converted-space"> </span><br class="">
<br class="">
<br class="">
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<br class="">
<br class="">
<br class="">
Dmitry Lyumkis<br class="">
Assistant Professor<br class="">
The Salk Institute for Biological Studies<br class="">
10010 North Torrey Pines Road, La Jolla, CA 92037<br class="">
T: 858-453-4100 x1155<br class="">
E: <a href="mailto:dlyumkis@salk.edu" class="">dlyumkis@salk.edu</a><br class="">
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On Mar 24, 2020, at 10:53 PM, Jacopo Marino <<a href="mailto:jacopo.marino@psi.ch" class="">jacopo.marino@psi.ch</a>> wrote:<br class="">
<br class="">
<br class="">
How much do you really need top and bottom views for 3D reconstruction ? Have you tried ?<br class="">
<br class="">
<br class="">
On 25.03.2020 06:48, Saumya Verma Bajaj wrote:<br class="">
<br class="">
<br class="">
Dear all,<span class="Apple-converted-space"> </span><br class="">
<br class="">
I am trying to solve the structure of a tetrameric membrane protein complex, with the protein embedded in detergent micelle (0.05% GDN) and a soluble accessory protein attached to it. <br class="">
<br class="">
Following 2D classification, while the side views and oblique views are easily visible, and the top/bottom are very few (~1-2%) (please see attached image) and get further diminished in subsequent rounds of 2D classification. <br class="">
<br class="">
While we are trying different grid types to overcome the orientation problem at the sample level, I was wondering if there are certain tweaks we can make to the analysis parameters (particle picking, box size, mask, ctf etc.) to enhance the signal of protein
embedded within a micelle in the current data set. We are using Relion3.1 for SPA.<span class="Apple-converted-space"> </span><br class="">
<br class="">
Any suggestions to salvage this set of data will be very helpful.<span class="Apple-converted-space"> </span><br class="">
<br class="">
Thank you.<br class="">
Best regards,<br class="">
Saumya<span class="Apple-converted-space"> </span><br class="">
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