Open question for the community.
I am currently working on some proteins that have very flexible domains. I have crosslinked them with glutaraldehyde and obtaining maps of various such complexes going up to 4.5 angstroms. However i think this is a gross overestimation of the resolution based on the FSC curve and my previous experience with cryo-EM of crosslinked proteins. Comparable analyses in different software gives results that are atleast an angstrom lower in resolution and seem more realistic. Is there anyway i can highpass filter my particles before refiement to take out all frequencies above 5 or 5.5 angstrom even? Or during the refinement i there any way to cut the resolution at say 5 or 5.5 angstrom? I have tried limiting the alignment resolution but my FSC still goes to >5 ang and looks bad.
A related question is - of the 4 FSC curves Cryosparc publishes, can i take out the corrected and tight mask? the no mask and spherical mask FSC actually correspond really well to my cryo-EM maps and this is exactly the type of resolution i would expect for my maps.