Hi folks, In Maestro there’s a “minimize” feature where only the selected atoms are allowed to move. It’s very helpful when I make a mutation that I want to locally relax and I want to be sure that the rest of the system won't change. Does ChimeraX support anything like this, or is it on the horizon? Thanks, Daniel
Hi Daniel, Not exactly what you asked, but see the "minimize" mouse mode to jiggle the clicked residue and nearby residues while the assigned button is held down: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html#top> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html#openmm> It's sort of a quick-n-dirty, but consider that this short local molecular dynamics may be more effective in surmounting small energy barriers than minimization. Still, they're both quite limited in exploring conformational space. I hope this helps, 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 May 12, 2026, at 12:57 PM, Daniel David Richman via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi folks,
In Maestro there’s a “minimize” feature where only the selected atoms are allowed to move. It’s very helpful when I make a mutation that I want to locally relax and I want to be sure that the rest of the system won't change. Does ChimeraX support anything like this, or is it on the horizon?
Thanks, Daniel
You can now specify a particular set of atoms to minimize rather than the entire structure. Available in the "minimize" command in today's daily build, and in the Minimize Structure tool in tomorrow's daily build. --Eric Eric Pettersen UCSF Computer Graphics Lab
On May 12, 2026, at 1:49 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Daniel, Not exactly what you asked, but see the "minimize" mouse mode to jiggle the clicked residue and nearby residues while the assigned button is held down: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html#top> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html#openmm>
It's sort of a quick-n-dirty, but consider that this short local molecular dynamics may be more effective in surmounting small energy barriers than minimization. Still, they're both quite limited in exploring conformational space.
I hope this helps, 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 May 12, 2026, at 12:57 PM, Daniel David Richman via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi folks,
In Maestro there’s a “minimize” feature where only the selected atoms are allowed to move. It’s very helpful when I make a mutation that I want to locally relax and I want to be sure that the rest of the system won't change. Does ChimeraX support anything like this, or is it on the horizon?
Thanks, Daniel
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Thank you, this is great! Looking forward to using it. From: Eric Pettersen <pett@cgl.ucsf.edu> Date: Wednesday, May 27, 2026 at 11:55 AM To: Daniel David Richman <ddrichma@stanford.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] regional minimization? You can now specify a particular set of atoms to minimize rather than the entire structure. Available in the "minimize" command in today's daily build, and in the Minimize Structure tool in tomorrow's daily build. --Eric Eric Pettersen UCSF Computer Graphics Lab
On May 12, 2026, at 1:49 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Daniel, Not exactly what you asked, but see the "minimize" mouse mode to jiggle the clicked residue and nearby residues while the assigned button is held down: <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/m... > <https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/tools/m... >
It's sort of a quick-n-dirty, but consider that this short local molecular dynamics may be more effective in surmounting small energy barriers than minimization. Still, they're both quite limited in exploring conformational space.
I hope this helps, 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 May 12, 2026, at 12:57 PM, Daniel David Richman via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi folks,
In Maestro there’s a “minimize” feature where only the selected atoms are allowed to move. It’s very helpful when I make a mutation that I want to locally relax and I want to be sure that the rest of the system won't change. Does ChimeraX support anything like this, or is it on the horizon?
Thanks, Daniel
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://urldefense.com/v3/__https://mail.cgl.ucsf.edu/mailman/archives/list/...
participants (3)
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Daniel David Richman -
Elaine Meng -
Eric Pettersen