Q: How can I reduce the box size in a project without starting completely from scratch

A: You don't need to redo particle picking, and you can use 3D maps generated at the original size as initial models for the new size. You need to:

• return to the “generate output step” in particle picking and rerun this with the new box size
• rerun automatic CTF correction
• you should not need to rerun 2-D class averaging or initial model generation as long as you got a reasonable initial model at the old size
• run new refinements with the newly reboxed particles