Hi Mitch, The issue is that the STL file describes a surface, whereas .mrc is a map format (values on a grid), and .pdb is for atomic coordinates. You would have to create a map from the surface in order to save it as a .mrc file. See the command "volume onesmask" to create a map with values of 1 inside the surface and 0 outside the surface: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#onesmask> For example, if your surface is open as model #1, this would create map model #2 and save it as mrc: volumes onesmask #1 save mickey.mrc models #2 However, you really should look at the help link for "volume onesmask" because there are several options and you might prefer to use some of them. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 15, 2025, at 2:09 PM, Mitchell Gulkis via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello everyone,
For instructional purposes, I am trying to generate simulated cryo-EM micrographs from a .stl file, in this case Mickey Mouse. This way, students can hold the 3D printed Mickey up to the micrograph to better understand projection images and angular assignment.
I am able to open the .stl file in ChimeraX, but I can not figure out how to convert it to a format that is accepted by micrograph simulation programs, either .mrc or .pdb. Has anyone else figured out how to do this?
Thanks!
Sincerely,
Mitch