I don't think there is any way for ChimeraX to incorrectly render a map file. It doesn't look like your showing the map at a low contouring threshold down in the noise, but that is the only way I think you can produce a very different appearance. Are the map dimensions (grid size) reported correctly by ChimeraX? How about the voxel size (use menu Tools / Volume Data / Map Coordinates)? If you sent me an example of the bad map, maybe a small cropped region or a binned version to keep the size small and using ChimeraX menu Help / Report a Bug, I might have an idea if I saw the data.

On Oct 1, 2026, at 2:21 AM, Schliebe, Paula via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear CryoSPARC Team,
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 also 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 CryoSPARC team regarding this issue.
Kind regards,
Paula

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