Hi Nuki, ChimeraX does not have a general minimization tool currently. We hope to have one in the future. There are some related features in ChimeraX to pull parts of the structure to specified coordinates, or to jiggle a sidechain, but these are not a user-friendly general minimization tool. For details see the following and links therein: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/tug.html> So for general minimization, you may need to keep using Chimera currently. Regards, 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 Mar 3, 2025, at 9:50 PM, N.B. Nugroho via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX developers

I a little bit confuse to find the Structure Minimization menu in ChimeraX. In Chimera 1.16 it located in menu Tools>Structure Editing>Minimize Structure. Could you please guide me for this little problem.

Best regards Nuki B Nugroho