Strategies for high resolution refinement

[user123]

Hi schow, see Oliver’s post about optimal box size here. You can see it does depend on defocus. You can always test, say going up to 512 if your gpu can handle the refinements.

Cannot align small protein complex particles

Hi Stefan, I would suggest trying using a larger box size - even at 2x the particle size, you will be cutting off a lot of information for a particle so small. The box size to use (in order not to lose information delocalized due to the CTF) is: B=D+(2XLX(dF/D) (from Rosenthal & Henderson JMB 2003) where D is the diameter of the particle, L is the wavelength (~0.02Å at 300kV), dF is the defocus, and D is the target resolution. So at let’s say 1.5um defocus with a target res of 5 Å, you woul…