Hello.
I am new to Cryo-EM reconstruction and am now trying to learn CryoSPARC. I reconstructed an EMPIAR-10028 density map (first ab initio then homogeneous refinement) using particle images from EMPIAR, and compared my reconstruction with the “groundtruth” one (EMD-2660), but the FSC in Align 3D job could only reach 40.59 angstrom.
My CryoSPARC reconstruction: empiar10028_cryosparc_long.mrc - Google Drive
I wonder is it proper to compare two density maps using Align 3D job, are there more steps I need to do before comparing two density maps?
Best regards.
Have you checked that you can align them manually (e.g. in Chimera)? Perhaps your ab initio converged on the inverted hand solution?
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Hi @qhz991029! As @olibclarke says, when your FSC from the Align 3D job is this bad it typically indicates that the job did not find the proper alignment. If you download and compare the two maps in ChimeraX you will likely see that they’re significantly misaligned.
Improvements to the algorithms used to align volumes are currently in the works.
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Thank you so much for your reply!
The bad result indeed comes from poor alignment. I tried another alignment method and now FSC is much more reasonable.
BTW I wonder what is the standard procedure to compare reconstructions from different methods? Is there anything like a common reference frame? As I am new in Cryo-EM reconstruction, I am even not sure is it reasonable to compare reconstructions from different methods 
Best regards.