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<p><tt>How much do you really need top and bottom views for 3D
reconstruction ? Have you tried ?</tt><br>
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<div class="moz-cite-prefix">On 25.03.2020 06:48, Saumya Verma Bajaj
wrote:<br>
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cite="mid:CA+_vNvRA9sTiqTN4Pk2wRuROCPJJap9nGQi-_ToFSqAhCTSFpQ@mail.gmail.com">
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<p class="MsoNormal" style="margin:0cm 0cm
0.0001pt;line-height:normal;text-align:justify"><font style=""
face="arial, sans-serif">Dear all,</font></p>
<p class="MsoNormal" style="margin:0cm 0cm
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face="arial, sans-serif"> </font></p>
<p class="MsoNormal" style="margin:0cm 0cm
0.0001pt;line-height:normal;text-align:justify"><font
face="arial, sans-serif">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. </font></p>
<p class="MsoNormal" style="margin:0cm 0cm
0.0001pt;line-height:normal;text-align:justify"><font
face="arial, sans-serif"> </font></p>
<p class="MsoNormal" style="margin:0cm 0cm
0.0001pt;line-height:normal;text-align:justify"><font
face="arial, sans-serif">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. </font></p>
<p class="MsoNormal" style="margin:0cm 0cm
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face="arial, sans-serif"> </font></p>
<p class="MsoNormal" style="margin:0cm 0cm
0.0001pt;line-height:normal;text-align:justify"><font
face="arial, sans-serif">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.</font></p>
<p class="MsoNormal" style="margin:0cm 0cm
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face="arial, sans-serif"> </font></p>
<p class="MsoNormal" style="margin:0cm 0cm
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face="arial, sans-serif">Any suggestions to salvage this set
of data will be very helpful.</font></p>
<p class="MsoNormal" style="margin:0cm 0cm
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face="arial, sans-serif"> </font></p>
<p class="MsoNormal" style="margin:0cm 0cm
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face="arial, sans-serif">Thank you.</font></p>
<p class="MsoNormal" style="margin:0cm 0cm
0.0001pt;line-height:normal;text-align:justify"><font
face="arial, sans-serif">Best regards,</font></p>
<p class="MsoNormal" style="margin:0cm 0cm
0.0001pt;line-height:normal;text-align:justify"><font style=""
face="arial, sans-serif">Saumya</font></p>
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</blockquote>
<pre class="moz-signature" cols="72">--
Dr. Jacopo Marino
Laboratory of Biomolecular Research
Paul Scherrer Institute
OFLB/005
5232 Villigen PSI, Switzerland
tel: +41 56 310 5484 (or +41 56 310 5777)
e-mail: <a class="moz-txt-link-abbreviated" href="mailto:jacopo.marino@psi.ch">jacopo.marino@psi.ch</a>
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