Hi, there,
Here are some features about my data: 180K particles; ~4 angstrom map; cFAR, 0.42; SCF, 0.89. According to Job: Orientation Diagnostics | CryoSPARC Guide, it seems that I should discard more junk or contaminants. However, I have already run heterogenous refinements using three junk models and one good model for more than ten rounds that led to only ~5K junk particles left. Also, I have already tried local refinment using diffrent parameter settings, i.e. Gaussian prior or not, different rotation or shift search extents, which didn’t improve map quality with reslution around 4 angstroms at all. Can anyone give some hints for what I should do next, or should I go to modify protein samples for new round of data collection? I would appreciate your response.
Best,
Lau