Hi everyone.
I’ve been processing sub-tomograms in relion 3.1 of an I1 virus with a low occupancy bound ligand. To resolve the assymetrical ligand, I performed I1 symmetry expansion(after I1 refinement of the entire virus) and then made a mask around one spike of the virus and performed particle subtraction & centered around this mask in relion. Subsequent initial model and 3D refinement generated spikes that had a smeared look to one side. From the image, the trimer is smeared to the left with the leftmost protrusion of the trimer spike being larger than the other two. We are trying large and finer angular searches with bigger masks to overcome this issue. However, we’re wondering if there is a better solution to this issue?
Best,
Tyler
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It doesn’t make sense to rub ab initio or new global refinements on subtracted particles, because you already know the structure and global searches are pretty likely to fail with just a piece of the particle.
Does your original map look more like the expected object?
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