Hi Eric, Thank you, that’s really helpful! I’ll keep an eye out as steepest descent and conjugate gradient get added, but the Langevin integrator is useful nonetheless—I’ve been having mixed results with the traditional minimization methods, so I’ll see how this works. Really appreciate your kind response. Thanks, Kabir

On Sep 2, 2025, at 3:03 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:

Hi Kabir, The answer is kind of, sort of. We have been working on the minimization functionality for ChimeraX, and there is a "minimize" command in the daily build, but the catch is that it's using an Langevin integrator rather than the steepest descent or conjugate gradient integrators that you are used to from Chimera. So whereas a steepest descent integrator will minimize to the closest local minimum, a Langevin integrator may significantly rearrange the structure in the search for a minimum -- which may or may not be what you want. We intend to add steepest descent and conjugate gradient integrators to the command (and make steepest descent the default), but there are some technical issues we have to overcome with the way OpenMM packages integrators in order to get that to happen, so it could be a few weeks. And then we intend to add a tool version, but that's even further off.

--Eric

Eric Pettersen UCSF Computer Graphics Lab

...

On Aug 30, 2025, at 9:56 AM, Kabir Gupta via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi all,

Does ChimeraX currently have the capability to minimize a structure? The functionality I'm talking about is of the sort available under Tools -> Structure Editing -> Minimize Structure... in the original Chimera. Last I can find is from a mail thread in 2020, at which point this had not yet been implemented in ChimeraX. Is there an acceptable substitute to achieve the same thing now, or do I have to reopen in original Chimera to do minimizations?

Thanks very much, Kabir _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://www.google.com/url?q=https://mail.cgl.ucsf.edu/mailman/archives/list...