[3dem] Relion issue Autopick - 2D classification

Thu Apr 22 04:29:13 PDT 2021

I agree that it seems you have enough views and maybe the problem is in 
the generation of the initial volume. You may try with methods that work 
with class representatives, rather than raw images, in that way you get 
away from the preferred views. RANSAC and reconstruct significant from 
Xmipp are ones of these methods. You can access them through Scipion.

Kind regards, Carlos Oscar

El 22/04/2021 a las 13:14, Marino Jacopo (PSI) escribió:
>
> To me it does not look like you have  a severe orientation bias (if 
> you have it at all), and you have plenty of particles !
>
> It might be some views are hidden within other classes. How many 
> rounds of 2D-classes and selection you did already ?
>
> For ab-initio, you might play around with parameters (2 classes, zero 
> similarity, higher number of final iterations, etc.) look on the 
> cryosparc forum for similar discussions. Sometimes you need to play 
> with the ab-initio till you get a volume that makes sense, then take 
> the particles that come with it and go to refinement.
>
> If you want help with the parameters for Relion, you need to post a 
> screenshot of your GUI with the parameters. Relion works well too ! 😊
>
> *From:*Lucia <luciatorressanchez3 at gmail.com>
> *Sent:* Thursday, 22 April 2021 12:57
> *To:* Marino Jacopo (PSI) <jacopo.marino at psi.ch>
> *Cc:* 3dem at ncmir.ucsd.edu
> *Subject:* Re: [3dem] Relion issue Autopick - 2D classification
>
> 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):
>
> But then in the 3D, anything makes sense. The "best" AB-initio for the 
> moment looks like...
>
> 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:
>
> 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 <mailto: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
>     <mailto:3dem-bounces at ncmir.ucsd.edu>> *On Behalf Of *Lucia
>     *Sent:* Thursday, 22 April 2021 12:17
>     *To:* 3dem at ncmir.ucsd.edu <mailto: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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