Convert particles back to relion after subtraction and local refinement

Troubleshooting
1

This is probably aimed at @DanielAsarnow

I am trying to convert back to Relion after doing refinement, particle subtraction and local refinement in csparc to use the original un-subtracted particles for alignment-free classification in Relion. I am using csparc for the local refinement, as the non-uniform refinement option is very useful for my particles.

I have run my particles.cs file through csparc2star. The problem is that the subtraction program in csparc makes a smaller number of new stack files called ‘subtracted_particles_batch_#A/B.mrcs’. The resulting half-map split of particles also leaves the order of the particles different from the original with all of the ‘A’ particles in the first half of the .star file and the B after so I can’t simply copy the relevant columns from the original .star used for the csparc import.

Can you think of a way around this?

I am happy to subtract elsewhere i.e. relion but csparc doesn’t seem to import alignment parameters from the star file to use for the local alignment.

I’m also not sure about the need for the subtraction from half-maps.

Thanks a lot.

2

In order to match up the particles to a .star file, you need some piece of information that’s shared across files and uniquely specifies a particle. Then you can use the merging features in star.py - it won’t matter if the particle order is changed or some are missing.

For example, can you get a file with the micrograph coordinates (X, Y & name)? Maybe there are some other fields that can be used in a passthrough file? If you want, you can send me the last iteration metadata files from one of your subtraction jobs and I’ll take a look.