With my latest dataset, when I try to open the output from homogeneous refinement jobs, it opens as a stack of 2D images instead of a 3D model. This doesn’t happen with my older datasets, however they were all done with older versions of cryosparc.
How are you trying to open the output? I suspect this is a Chimera issue/feature, not cryosparc.
How large is your box size? Chimera defaults to opening large volumes as a stack of planes, to save resources.
The files are local on the workstation, so I was using the open feature of chimera. While the box size is large(~650A) it did not have this issue with the unrefined volumes. If it is a chimera issue, how would I open the file such that it would display as a 3D volume? Thanks.
What do you mean by “unrefined volumes”? If you mean from heterogeneous refinement, that is because the box size is by default smaller (128px).
Re chimera, you can change this behavior within the Volume Viewer - I would suggest consulting the help page for the Volume Viewer in Chimera for more details.