Displaying Cryo-EM volumes in ChimeraX

Troubleshooting
1

I am processing Cryo-EM data of a ribosome using CryoSPARC. When I check my volume in the CryoSPARC volume viewer, everything looks fine. However, after downloading the volume, I cannot display it properly in ChimeraX (see attached photo). I am currently using ChimeraX 1.12 and CryoSPARC 4.7.1.

Previously, I worked with ChimeraX 1.9 and CryoSPARC 4.6.2 and did not encounter any problems displaying the volumes.

I al

image
image718Ă—289 91.9 KB

so tested this with an older processed map that I had downloaded a while ago. I can display this volume properly in ChimeraX. However, after uploading it to CryoSPARC (where it is also displayed correctly) and downloading it again, I encounter the same problems when displaying it in ChimeraX .

I am not sure whether this is an issue with CryoSPARC or ChimeraX. I have tried different combinations of the software versions, but so far nothing seems to resolve the problem. I hope you can help me out. I have also contacted the ChimeraX team regarding this issue.

Kind regards,

Paula

2

Welcome @paula to the forum.
Have you compared the sizes and checksums of an mrc file that shows correctly in CryoSPARC, incorrectly in ChimeraX:

  1. on the CryoSPARC computer, inside the project directory (use command
    sha256sum map_file.mrc)
  2. versus on the “local” computer where you run ChimeraX? (sha256 on macOS, command suggestions for MS Windows)

Do the sizes and checksums match?

3

Hi Paula,
It’s difficult to tell from your picture, but is the problem that the volume appears as a flat, 2D plane instead of an expanded, 3D volume?
If that is the case, on the map tab you can play with style→surface, map→show, subregions→full settings (individually or combinations thereof) until the full 3D volume appears.
I’ve noticed this happens sometimes if the file is quite large, but it’s hard to reproduce consistently.

1 Like