[3dem] Particles.star file in Tomo Relion

[PABLO CONESA MINGO]

Dear Manon, all!

Let me suggest you use Scipion. Although we haven't made any public  
official announcements I think it is fair to say that Scipion with all  
its tomography plugins are in a very nice, stable, "out-of-beta"  
shape. Most of the nice software for cryoem tomography is already  
integrated. You can go from Tilt series motion correction to  
subtomogram averaging mixing the best software out there like: IMOD,  
Aretomo, gctf, ctffind, Dynamo, crYOLO, Relion4, Eman2, tomo3d,  
membrain, deepfinder, pyseg, ISONet, NOvaCTF, cryoCARE, xmipp and many  
more.

And without the need of editing files or programming scripts, moving  
files around, as a plus you have full traceability of your work,  
cloning, repeating jobs, scheduling, planning night executions... "SPA  
leap" -> Jump to SPA 2d realm from tomograms or subtomograms to use  
SPA 2D classification to prune your data, ...



Here you can find out more about this:

Tomography  
intro->https://urldefense.com/v3/__https://scipion-em.github.io/docs/release-3.0.0/docs/user/tutorials/tomo/tomography-intro.html*tomography-intro__;Iw!!Mih3wA!DWOtS7qOtRjHaGUmMwkDR8yySqhdRKPj25z1whTFMmlrDS98uWojGgLF3RifQDOGJd2Uw7BVj7OJcBRo2lqdKA$ 


Tomography tutorials:  
https://urldefense.com/v3/__https://scipion-em.github.io/docs/release-3.0.0/docs/user/tomography-tutorials.html__;!!Mih3wA!DWOtS7qOtRjHaGUmMwkDR8yySqhdRKPj25z1whTFMmlrDS98uWojGgLF3RifQDOGJd2Uw7BVj7OJcBQIMTTL6w$ 

In particular, this one for doing Relion4 tomography tutorial inside  
Scipion:  
https://urldefense.com/v3/__https://docs.google.com/document/d/1QOi3xbDKM6hGs6XtwxgYRwDKjMbKIBTYgBBmbHnmk2k/edit*heading=h.ngy40hkbs85v__;Iw!!Mih3wA!DWOtS7qOtRjHaGUmMwkDR8yySqhdRKPj25z1whTFMmlrDS98uWojGgLF3RifQDOGJd2Uw7BVj7OJcBQchDUPLA$ 

How to install Scipion  
->https://urldefense.com/v3/__https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/how-to-install.html__;!!Mih3wA!DWOtS7qOtRjHaGUmMwkDR8yySqhdRKPj25z1whTFMmlrDS98uWojGgLF3RifQDOGJd2Uw7BVj7OJcBTF9LPOaw$ 
Linking existing software ->  
https://urldefense.com/v3/__https://scipion-em.github.io/docs/release-3.0.0/docs/scipion-modes/linking-existing-software.html?highlight=linking*software__;Kw!!Mih3wA!DWOtS7qOtRjHaGUmMwkDR8yySqhdRKPj25z1whTFMmlrDS98uWojGgLF3RifQDOGJd2Uw7BVj7OJcBT-46gu3w$ 



Manon, rest, I'm part of Scipion team, so might have an impartial view  
of this, but I'm sure there are users (Scipion users) that may give  
you their view about this.

You and everyone is welcome to join our Discord workspace  
(https://urldefense.com/v3/__https://discord.gg/TzS5VTKQbY__;!!Mih3wA!DWOtS7qOtRjHaGUmMwkDR8yySqhdRKPj25z1whTFMmlrDS98uWojGgLF3RifQDOGJd2Uw7BVj7OJcBT8e1jhiw$ ) where you can directly contact us for  
any question, but also other developers of the methods integrated, and  
users


Happy  EM Tomo Processing.


Mirgaux Manon <manon.mirgaux at ulb.be> escribió:

> Dear all,
>
> Trying to process cryo-tomography data for the first time to do  
> sub-tomogram averaging, I have trouble when importing. Indeed, after  
> having done the Relion tutorial without any trouble and having  
> aligned my micrographs on etomo, I noticed that I need an order_list  
> file and a particles.star file. Although I can write the order file  
> myself, I can't figure out how to generate the particles.star file.  
> I'd be very grateful if someone could help me to clarify this  
> procedure.
>
> Best regards,
>
> Manon Mirgaux
>
>
> Manon Mirgaux, PhD
>
> Expert Scientist in Electron Microscopy (Cryo-EM, TEM, SEM)
>
>
>
> Center for Microscopy and Molecular Imaging (CMMI)
>
>
>
> [cid:d77b1a8d-0967-41a6-8c66-1eee1e2c19ff]
>
> Rue Adrienne Bolland 8 B-6041 Gosselies, Belgium
>
> Tel : +32(0)26509931 GSM: +32(0)470692523
>
> Website:  
> https://urldefense.com/v3/__http://www.cmmi.be__;!!Mih3wA!Hp7U9mg_2CpY8OXI3YOf8ohfIGh47ZVkE_VNbVRGGzrQpHk6fXk0RcC53pdeQ6qm5d0R4MZFdioazz_crHQYM0Sg4Q$ <https://urldefense.com/v3/__http://www.cmmi.be__;!!Mih3wA!Hp7U9mg_2CpY8OXI3YOf8ohfIGh47ZVkE_VNbVRGGzrQpHk6fXk0RcC53pdeQ6qm5d0R4MZFdioazz_crHQYM0Sg4Q$  
> >
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> En télétravail le vendredi - joignable par email, par Teams ou par  
> téléphone (GSM)
>
> [cid:e12ca72e-4eb6-4e1e-8f00-a77de3314aa4]