How to import particles from relion

solved

#1

Hi everyone,
I am trying to import particles from relion. But I’m confused about what should the inputs are.


Like-
What should be the source micrographs? Should it be CTF estimated?
What should be the “particle meta” and the “particle data”?

And could anyone also help explain what is the “Ignore raw data” “Length of mic. path suffix to cut” “Length of part. path suffix to cut”

Thanks a lot!


#2

Hi Rui, if you are importing a particle star file from relion, typically you will only need to select it in the “particle meta path” field - no other inputs are necessary.

Cheers
Oli


#3

Hi Oli,

Importing the particles by only specifying the “particle meta path” works for me however, I’m wondering if there is a method to import particles from RELION3 that allows one to link imported particles to their original motion&ctf corrected micrographs in RELION such that one could perform local motion correction in cryoSPARC?

Many thanks,

Christopher


#4

I’m not sure - I don’t think so but perhaps one of the devs can comment? @apunjani @sarulthasan?


#5

Hi @Chris, @olibclarke,

It is possible to do this, though a bit trickier than just the standard particle import.
You must first import the micrographs (this can be before or after CTF estimation). Then import the particles, connecting the imported micrographs as the “Source Micrographs”. Then set the “Length of Mic. path suffix to cut” and “Length of part. path suffix to cut” (you may have to run the job and have it fail a couple times to get it right) so that the particles and micrographs can be corresponded (the matching is based on the remaining path string from the particle and micrograph after the suffix is cut from each). The output of this import job will contain particles that are linked to the imported micrographs/movies, so you can do local motion correction in cryoSPARC.

Hope this helps!


#6

Aha, “Length of part. path suffix to cut”, now I understand what it means. Very cool.