Hi Yuan, I tried to change the subject line to a description of the topic. Not sure that I understand your question because PDB format is for atomic coordinates and map formats are for maps (quantities at points on a 3D grid), two different types of data. If you mean you want to simulate a density map from atomic coordinates, see the "molmap" command with option "cube true" to make the grid cubic: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.html> Then you can save the newly created map model in MRC format: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#map> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Oct 9, 2025, at 12:23 AM, 张圃源 via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi， I'm a new user of ChimeraX and I'm currently facing a problem. I want to convert a pdb file into an mrc file that can be input into cryoSPARC, and this mrc file should be in the form of a cube volume. I will use ChimeraX to achieve this. How should I proceed? Best Yuan

中山大学 张圃源