Question about minimization error with af3-produced protein–RNA complex in ChimeraX
Hi, I am trying to minimize an AF3-generated protein–RNA complex [1, attached] in ChimeraX [2,3] , but the minimization fails with the following error: `KeyError: 'RNA-o'` The traceback points to OpenMM while creating the system (`forcefield.createSystem()`). I assume AF3 uses standard nomenclature for atoms and residues, so I was wondering whether this is a known issue with the force field used by ChimeraX for minimization, or if there is a way to work around it. I am aware of the limitations of ChimeraX minimization and am only using it as a quick check before (eventually) proceeding with more rigorous refinement. Thank you for any suggestions. Best regards, -- Bruno Hay Mele, PhD https://github.com/bhym/ [1] metrics (pae/plddt/iptm) are very good [2] just plain minimize #1 [3] Daily build of couple days ago (UCSF ChimeraX version: 1.13.dev202607062345 (2026-07-06) )
Hi Bruno, I can reproduce this problem, and it happens for any RNA. I have created a ticket (#20600 (Minimization of RNA fails)) <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/20600> with you as a recipient so that you will be notified when a fix is made. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jul 9, 2026, at 8:05 AM, Bruno Hay Mele via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I am trying to minimize an AF3-generated protein–RNA complex [1, attached] in ChimeraX [2,3] , but the minimization fails with the following error:
`KeyError: 'RNA-o'`
The traceback points to OpenMM while creating the system (`forcefield.createSystem()`).
I assume AF3 uses standard nomenclature for atoms and residues, so I was wondering whether this is a known issue with the force field used by ChimeraX for minimization, or if there is a way to work around it.
I am aware of the limitations of ChimeraX minimization and am only using it as a quick check before (eventually) proceeding with more rigorous refinement.
Thank you for any suggestions.
Best regards, -- Bruno Hay Mele, PhD https://github.com/bhym/
[1] metrics (pae/plddt/iptm) are very good [2] just plain minimize #1 [3] Daily build of couple days ago (UCSF ChimeraX version: 1.13.dev202607062345 (2026-07-06) ) <fold_s209a_model_0.cif>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Many thanks! Cheers, Il 09/07/2026 19:47, Eric Pettersen via ChimeraX-users ha scritto:
Hi Bruno, I can reproduce this problem, and it happens for any RNA. I have created a ticket (#20600 (Minimization of RNA fails)) <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/20600> with you as a recipient so that you will be notified when a fix is made.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jul 9, 2026, at 8:05 AM, Bruno Hay Mele via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I am trying to minimize an AF3-generated protein–RNA complex [1, attached] in ChimeraX [2,3] , but the minimization fails with the following error:
`KeyError: 'RNA-o'`
The traceback points to OpenMM while creating the system (`forcefield.createSystem()`).
I assume AF3 uses standard nomenclature for atoms and residues, so I was wondering whether this is a known issue with the force field used by ChimeraX for minimization, or if there is a way to work around it.
I am aware of the limitations of ChimeraX minimization and am only using it as a quick check before (eventually) proceeding with more rigorous refinement.
Thank you for any suggestions.
Best regards, -- Bruno Hay Mele, PhD https://github.com/bhym/
[1] metrics (pae/plddt/iptm) are very good [2] just plain minimize #1 [3] Daily build of couple days ago (UCSF ChimeraX version: 1.13.dev202607062345 (2026-07-06) ) <fold_s209a_model_0.cif>_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list --chimerax-users@cgl.ucsf.edu To unsubscribe send an email tochimerax-users-leave@cgl.ucsf.edu Archives:https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
-- Bruno Hay Mele, PhD https://github.com/bhym/
participants (2)
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Bruno Hay Mele -
Eric Pettersen