Hi all,
I am hoping to get some help with a refinement I am trying to carry out. I have subtracted particles using the RELION 3.1 GUI (with recenter images on mask and new box options enabled – using a smaller box size). I would like to have a tight circular mask applied during the refinement to mask out some density outside the region of interest that can not be effectively subtracted. When I run a refinement with local searches using these subtracted particles I see that the circular mask applied has the overall box diameter (like it is ignoring my input). For clarity my box size = 552 A and value entered in mask diameter = 150 A. I have checked the submission script, job.star, and optimiser.star files and all say the input value "particle_diameter" is 150 A, but when I open the MRC file I see that the circular mask is 552 A. Overall, I believe this explains the significant drop in resolution (3.7 A to 8-9 A), as I see the contaminating density on the periphery of the box being aligned/building up. Consistent with this I have re-boxed with a much smaller diameter that would exclude this peripheral density and the resolution improved (now 7 A) but with this box size I am cropping away some high resolution information.
Hopefully I am missing something very silly!
Cheers,
Jacob
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