I’m working with a fairly small particle size on the order of 100 kDa, and it seems like both the heterogeneous and homogenous refinement jobs are wanting to align really strongly on the edges of my particles, yielding what is essentially a “hollow” 3D volume. Example below.
Wondering if there are any advanced parameters I’m not aware of that could be helpful for working with this dataset and overcome this issue.
Did you figure out how to solve this problem? I get similar situation when working on 100 kDa protein. Thank you.
Do you think it’s a very floppy particle? Have you tried ab initio to higher max resolution (say 6A) followed by refinement with lower lowpass filter (like 8-10A)?
Thank you for your advice. Yes, for my case the particle is floppy. I have used 6A in Ab-initio, but haven’t tried 8-10 A lowpass filter in refinement. I will try it. Thank you.