Sub-particle extraction and localized recon

Local Refinement
21

Hello,

I am trying to do something similar using an icosahedral virus bound by Fab fragments. The issue I am encountering is fragments bound too closely to symmetry axes, they end up with multiple binding modes and blur together. I’ve followed along the protocol described here, but I am wondering if it is possible to re-align the subparticles? Essentially I end up with slightly improved resolution at the contact surface, but the positioning of the fabs remained blurred together. I am fairly novice at this, so any help would be appreciated.

Best,
J

22

Completely lost track of this, sorry! Had cause to re-examine recently with a new dataset.

Priors on with 2std range and recentre pose/shift don’t drift off. 3 or 4std still does a little and map looks a little disturbed as a result. Lowpass has almost no effect on whether or not assignments drift. For sample in question, 0.05 degrees needed to be used to match alignment convergence in RELION. Still working on dataset, but on hold briefly as the server has had to go for service due to CPU/IMC failing.

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