Apologies if you get this answer multiple times. The mailing list was rejecting my response for some unknown reason, and this is my second attempt at sending it: Hi Billy, Hopefully somebody with more knowledge in this area can say more, but my guess is that the issue is with the software that reads the STL files after they are written out rather than with ChimeraX writing them. How I tested: open 7pfx delete protein save dna.stl close open 7pfx delete nucleic-acid save protein.stl close open *.stl <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#local> Regardless of whether I move the structure around between these commands, when I open the saved STL files back in ChimeraX it uses the same coordinates as in the original structure and the two are aligned properly with each other (as well as with the original atomic structure if I open that too). Maybe the printing software tries to center objects automatically, which causes a shift if the two objects are opened from two separate files. However, I really have no idea, or even if that were the case, how you could avoid it. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco