Dear Wang Zheyun, That is true, Chimera and ChimeraX are two different programs, and ChimeraX does not have a Minimize Structure tool currently. General minimization is listed in the "missing features" page: <https://www.rbvi.ucsf.edu/chimerax/progress.html> ...however, we are working on adding this capability, in progress, as described in this recent post: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> Best, 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 Sep 22, 2025, at 11:37 PM, Zheyun Wang (MED,124090655) via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX developers:
I am Wang Zheyun, a student in Chinese University of Hong Kong, Shenzhen. In my computational biology course, our professor demonstrated to us that the molecular structure (a file containing several water molecules) can be changed to an energy-minimizing structure using "Minimizing structure" function in Chimera. However, I cannot find this function in ChimeraX(1.10.1), and professor told me that these two are completely different softwares. Is this function available in ChimeraX? If so, may I know where it is? If not, will this be added to ChimeraX or is it deliberately deleted? Looking forward to your reply!
Sincerely, Wang Zheyun