Classification without alignment

open

#1

Is there an option in cryosparc to classify in 2D or 3D but not perform alignment? For example I could take my final refined structure and do a classification to see if there’s any junk that is getting pulled into my class. Sometimes with alignment on it can act like a real particle. If not, then should consider adding in future!


#2

This does not exist to my knowledge, but I agree it would be useful (I frequently use this approach in relion)


#3

is this still not available? would be nice to just check a box or something for ‘skip alignment’


#4

Nope, still not available


#5

Hi Oli, when you export to relion for classification without alignment, how do you get a subset from relion, how do you get the same subset in cryosparc for refinement again?


#6

Hi,

You can either use the subset selection tool in relion to select a particular class (or classes) from the _model.star, or you grab the desired lines from the _data.star at the end of classification (using awk or whatever). You can the import the resulting star file back into cryosparc and continue with refinement. Does that answer your question, or did I misunderstand?

Cheers
Oli


#7

Actually, you are right. My bad. I always thought that Relion cannot use the particles boxed out from cryosparc. In this case, if I export to Relion for classification but using the exactly the same particles, then when I import back the subset star file, cryosparc can recorgnize the particle data already.