EMAN Wiki

The under-development e3make3d_point.py can be used to produce reconstructions which:

• dramatically improve reconstructions with anisotropic particle distributions
• may fill in some details missing with traditional reconstructions
• naturally denoises reconstructions (without deep learning), and provides better GSFSC resolutions (whether these improvements are real can be debated)

It is very easy to give it a try and see what it produces. While you can run it on any machine with jax set up in your EMAN2 environment, it will run much faster with a GPU. It is more time consuming, but particularly when included in refinement loops, can produce significantly improved structures without any masking.

You can start with an EMAN2, Relion or CryoSparc refinements as a starting point.

• Run a standard e2spa_refine.py on your phase-flipped particle data
• Run exactly the same command with the –pointrecon 500 option added to the command-line, then compare the results of the 2 refinements.
• The main parameter you might want to change with e3make3d_point is the “500”, which is the number of first-stage points to use in the reconstruction. 500 is a good starting point for many single particles. If 500 is too many, you may find more noise than necessary around your particle. If 500 isn't enough, you may find less detail in the structure than expected. If you find 500 doesn't work well, we suggest 125,250,1000 or 2000 depending on which direction you decide you need to move. Nothing magic about these specific values.