[3dem] Relion issue Autopick - 2D classification

[Marino Jacopo (PSI)]

Hi Lucia,
Don’t be desperate. You are in the initial phase of learning how to use Relion and cryosparc, so frustration might be normal.

Preferential orientation is an interesting topic and it might not impede that you reach high resolution density maps.
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.

You can also continue with cryosparc, maybe change the picking parameters to see whether you really don’t have much other 2D classes.

Go to ab-initio with your best 2D-classes. What do you get there ?

Good luck
Jacopo

From: 3dem <3dem-bounces at ncmir.ucsd.edu> On Behalf Of Lucia
Sent: Thursday, 22 April 2021 12:17
To: 3dem at ncmir.ucsd.edu
Subject: [3dem] Relion issue Autopick - 2D classification

Hi all,

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.

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.

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).

I was hoping someone could give me some suggestions that help me to overcome that point because I'm desperate.

Thanks!
Lucia
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20210422/2bacdfab/attachment.html>