How to apply subtracted particle orietation to full particles?

Local Refinement
1

Hi, all. I wanted to know how to apply subtracted particle orietation to full particles.
I did a local refinement after particle subtraction. Then, I wanted to apply the orietation of aligned particles to full particles. I wondered the relation between extracted particles and subtarcted particles. I tried to check them in star file by csparc2star.py. But it was difficult to match them. Can anyone help me?

2

Hi @Yuqi, you can do this using the low level results interface. See how to do this here: https://guide.cryosparc.com/processing-data/tutorials-and-case-studies/job-builder-tutorial#fine-tuned-control-over-individual-results

In your case, you would swap the particles blob of the subtracted particles with the one from the original non-subtracted particles, while keeping the alignments 3D blob from the subtracted particles. Does that make sense?

Cheers
Oli

3 Likes
3

Hi @olibclarke

I have the same issue. I have done focussed classification using subtracted particles. Now I would like to reconstruct particles from just one class, but using the original corresponding particles for this subset. I have tried to replace the particles blob with the original one and then reconstruct. However, I get an error
“IndexError: list index out of range”. What is also strange is that I can see in the log

Split A has 3609 particles
Split B has 0 particles

Cheers,
Juha

4

Hmm weird - it works for my data so there must be something specific to your dataset that is causing the issue or triggering a bug. Is the number of particles correct, does it match what you expect? Could it be a symmetry issue - e.g. subtracted particles are after sym expansion, while originals are not?

5

I haven’t done symmetry expansion. The set of particles after subtraction and classification is a subset of original particles.

6

Update: if I use option “force re-do GS split” it works!

1 Like
7

That was the next thing I was going to suggest! I wonder where it is losing the half-set assignments though… if you do reconstruction of the subtracted particles (not replacing with the originals) do you get the same error?