Hi Priyanka, I can't tell which program you are asking about. You sent this question to chimerax-users@cgl.ucsf.edu which is for ChimeraX questions, but you mention Chimera, which has its own different address for questions, chimera-users@cgl.ucsf.edu However, in this case it does not matter, the answer is the same for both programs. The map file does not include rotation information, so you should save the PDB relative to the map. There is more explanation and discussion of this in the bottom section of this Chimera help page: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#afterfittin...> Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Jun 18, 2021, at 4:38 AM, Priyanka Abeyrathne via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi, Could someone assist me to sort out the following? In Chimera, we can save PDB relative to the electron microscopy density map. Can we save the electron microscopy density map relative to the PDB? Any suggestion? Thank you. Priyanka