For awhile I have been refining particle clusters that are identified/‘purified’ during 3DVA which has been quite illuminating for my system (GSFSC 0.143 between 2.6 and 2.1A for each cluster refinement). Now, however, with largely the same procedure (the only difference being that I have downsampled my particle box size from 512 to 256 for my input particles) I am being given a clear GSFSC underestimate (see curves). My pixel size is 0.86 A/pxl. The only non-default parameters that I have in the job are:
- C5 symmetry is applied
- Initial lowpass resolution = 10A (it is a high contrast sample with high symmetry)
- Optimize per-particle defocus (ON)
- Optimize per-group CTF params (ON)
- Cache particle images on SSD (OFF)
Any ideas what is going on here?