Hi Marcus, Maybe you are looking at instructions for Chimera, which is a different program than ChimeraX. The Chimera menu has "File... Save Mol2" but as you said, the ChimeraX menu just has "File... Save". Assuming that you are actually using ChimeraX, and you have some atomic structure model(s) currently open, then you can just use "File... Save" and then in that dialog, choose Files of type: "Mol2" to save a Mol2 file. 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 6, 2021, at 1:51 PM, Marcus Agyin via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello, I am emailing to get clarification on how I would convert a chimera file into a Mol2 file. If I’m understanding correctly, I would need to click on “File” and in the pop-up menu there would be a “save as Mol2” option, however, all that it is showing the generic “Save” option.

Thanks in advance, Marcus Agyin