[3dem] Relion issue Autopick - 2D classification

[Lucia]

Hi Jacopo,

I try but relion is my nightmare. I feel so useless with it.

In cryosparc I get nice 2D classes (or that what people say because of
course I'm far far from have basic knowledge):
[image: Screenshot 2021-04-22 at 12.50.05.png]
But then in the 3D, anything makes sense. The "best" AB-initio for the
moment looks like...
[image: Screenshot 2021-04-22 at 12.56.00.png]


So I moved to relion and I set different combinations of parameters, but
when I try to do the 2D classes (independently of my parameters in the
autopick) I get that:
[image: Screenshot 2021-04-22 at 12.53.48.png]

It's obvious even for me that I'm doing something AWFULLY wrong, but I
swear I tried and I don't understand what I'm doing wrong neither how to
overcome it.

Thanks!!!!
Lucia

El jue, 22 abr 2021 a las 12:43, Marino Jacopo (PSI) (<jacopo.marino at psi.ch>)
escribió:

> 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
>
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