hi all, looking for any input on how to get local motion to work better. Every time I try to use it my map ends up looking worse, which makes no sense to me.
Movies aligned in cryosaprc, CTF estimation done, extract, do refinement and end up with a ~4A structure which looks pretty good. I then set up local motion (with parameters below) using as input the particles from the 4A reconstruction and the output from the full motion frame alignment. Then I clone the job that gave the 4A reconstruction, except now I use the particles output from the local motion job and I end up with a 7A reconstruction that is noticeably uglier. I’m clearly doing something wrong because this makes no sense.
notes on the job setup:
- this is a filament protein. The box is ~550A diameter. I initially extract 1024px while binning to 512px.
- local motion box size is set to 1024px and then I downsample to 512px before doing the recon again.
- local motion multi w/ 2 gpus, all settings are default.
- tried with smaller box size (640 downsample to 320) to get a shorter filament segment but it also failed.
- this has happened with multiple datasets and proteins, so I must really be doing something wrong because I can’t ever get local motion to improve the map.
any help appreciated. thanks!