Question about energy minimization
Dear Chimera team, Can you please tell me if it’s possible to do energy minimization with Chimera X as I used to in previous Chimera? I looked for it on the Chimera X page and in many tutorials but it looks like this tool was cut out of the software. Thank you very much for your help, Luca
Dear Luca, ChimeraX is developed with a completely new framework, so we are not "cutting" features -- instead we have to re-implement each tool from the ground up to add it to ChimeraX. ChimeraX is actively developed and we are working to add all of the important major features as well as develop many new features that were not available in Chimera. See "ChimeraX vs. Chimera" discussion: <https://www.rbvi.ucsf.edu/chimerax/progress.html> As you can see in that link, a general minimization tool is still one of the missing features. We are working to add in the future, but it is complicated and still requires more time. There are some simplistic minimization-related features in ChimeraX now, although they may not be what you need: mouse modes "minimize" and "tug" <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html#openmm> tug command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/tug.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. I don't know if it applies to you, but I should also mention that Chimera/ChimeraX usage for commercial purposes requires a license: <https://www.rbvi.ucsf.edu/chimera/commercial_license.html>
On Jul 18, 2023, at 3:40 AM, Luca Massaccesi via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera team,
Can you please tell me if it’s possible to do energy minimization with Chimera X as I used to in previous Chimera? I looked for it on the Chimera X page and in many tutorials but it looks like this tool was cut out of the software.
Thank you very much for your help,
Luca
Dear Elaine, Thank you very much for your reply. This new X version is great and I’ll wait for all the new features to be implemented. In the meanwhile I’ll use older build for energy minimization. Best regards, Luca
Il giorno 18 lug 2023, alle ore 17:51, Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Dear Luca, ChimeraX is developed with a completely new framework, so we are not "cutting" features -- instead we have to re-implement each tool from the ground up to add it to ChimeraX. ChimeraX is actively developed and we are working to add all of the important major features as well as develop many new features that were not available in Chimera. See "ChimeraX vs. Chimera" discussion: <https://www.rbvi.ucsf.edu/chimerax/progress.html>
As you can see in that link, a general minimization tool is still one of the missing features. We are working to add in the future, but it is complicated and still requires more time.
There are some simplistic minimization-related features in ChimeraX now, although they may not be what you need:
mouse modes "minimize" and "tug" <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html#openmm>
tug command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/tug.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
P.S. I don't know if it applies to you, but I should also mention that Chimera/ChimeraX usage for commercial purposes requires a license: <https://www.rbvi.ucsf.edu/chimera/commercial_license.html>
On Jul 18, 2023, at 3:40 AM, Luca Massaccesi via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Chimera team,
Can you please tell me if it’s possible to do energy minimization with Chimera X as I used to in previous Chimera? I looked for it on the Chimera X page and in many tutorials but it looks like this tool was cut out of the software.
Thank you very much for your help,
Luca
participants (2)
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Elaine Meng -
Luca Massaccesi