Reconstructions with hollow centers


I have been trying to build an ab initio model using Cryoparc, but all of the reconstructions are essentially hollow spheres or similar shapes lacking a central density.

This data set has gone through several rounds of 2D classification in Relion and gives very nice 2D class averages.

A few notes:

  • this is phase-shifted data
  • the particles are small (~200 kDa)
  • the particles are quite densely packed, with multiple neighboring particles visible.

I’ve tried playing around with the mask dimensions, but with no luck.

Any suggestions would be helpful!

No useful suggestions really, except to say that I have used cryosparc to generate an initial model for a small (180kDa) and closely packed set, with no problems - so maybe the phase shift is the issue?

Just realized the I used the wrong flag for black vs white particles. Oops!

It seems to be making protein-like maps right now.