Reconstructions with hollow centers

Troubleshooting
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#1

Hi,

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!
Thanks,
Rick

#2

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?

#3

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

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

#4