Dear cryoSPARC community,
Hope you all are doing well. We are facing issues with refinement of one of our filament data sets (Protomer size=46kDa). The ab-initio reconstruction is pretty decent, and features have started to appear. The problem arises when we try to refine the structure to high resolution with helical refinement. The refined map appears to have a spiky appearance. Please refer to the parameters for helical refinement in the attachment.
Parameters for ab-initio:
Max resolution = 4A,
Initial mini-batch size=1000,
Final mini-batch size=3000
Parameters for helical refinement:
Symmetry alignment= False,
Resolution to search helical symmetry=10,
Twist grid size=256,
Rise and grid size=10,
FSC split resolution=12,
High resolution noise substitution=True
We are using version 4.02. It would be of great help if you can suggest any change in parameters that might improve the refinement.
Thanks and Regards