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<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Hi Lucia,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Don’t be desperate. You are in the initial phase of learning how to use Relion and cryosparc, so frustration might be normal.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Preferential orientation is an interesting topic and it might not impede that you reach high resolution density maps.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">The suggestion of using Relion to circumvent orientation bias is funny. In Relion you might need to play around with the parameters to pick particles, better you do it with a small set
of micrographs.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">You can also continue with cryosparc, maybe change the picking parameters to see whether you really don’t have much other 2D classes.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Go to ab-initio with your best 2D-classes. What do you get there ?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Good luck<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US">Jacopo<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="en-CH" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span lang="EN-US"> 3dem <3dem-bounces@ncmir.ucsd.edu>
<b>On Behalf Of </b>Lucia<br>
<b>Sent:</b> Thursday, 22 April 2021 12:17<br>
<b>To:</b> 3dem@ncmir.ucsd.edu<br>
<b>Subject:</b> [3dem] Relion issue Autopick - 2D classification<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi all,<br>
<br>
Sorry for bother and thanks for your patience/help. I’m trying to use Relion to Autopick (Laplacian) a set of elongated particles that are around 150A long. I managed to get a nice set of 2D classes in Cryosparc but, since I have preferential orientation, people
recommend me to use Relion to redo my dataset analysis.<o:p></o:p></p>
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<p class="MsoNormal"><br>
But... I'm really stuck, I have no experience with Relion and I don't manage to get any good autopicking that lead me to a 2D classification (even a preliminar one to re do the picking after), I just get black images or nonsense in the 2D classification, even
when I check the images after the autopicking and they don't look bad.<br>
<br>
Honestly idk what to put here about the parameters that I'm using because I tried a bunch but blindly (since I have no idea neither experience).<br>
<br>
I was hoping someone could give me some suggestions that help me to overcome that point because I'm desperate.<br>
<br>
Thanks!<br>
Lucia<o:p></o:p></p>
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