Hi Kirk, Changing subject line and sending to the recommended address for ChimeraX questions chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> (just don't include anything proprietary when using it, since it has a public archive), as I'm not the expert on this topic. Others may be able to answer your question more definitively. However, if I had to guess I would say it doesn't send ligand info anywhere because Boltz runs on your local machine, not on Colab, as per the documentation: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/boltz.html> 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 Mar 4, 2026, at 3:22 PM, Kirk Nelson <knelson@tyra.bio> wrote:
Hello Elaine,
It is super cool that Boltz was added to ChimeraX.
Can you please confirm whether any ligand information is queried against the external database (api.colabfold.com)?
Thank you, Kirk Nelson
From: Elaine Meng <meng@cgl.ucsf.edu> Date: Thursday, December 18, 2025 at 12:35 PM To: chimerax-announce@cgl.ucsf.edu <chimerax-announce@cgl.ucsf.edu> Subject: [chimerax-announce] UCSF ChimeraX 1.11 release
=-=-=-=-=-=-= UCSF ChimeraX version 1.11 has been released!
This will be the last release to support Red Hat Enterprise Linux 8 and its derivatives.
ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/download.html
Updates since version 1.10.1 (July 2024) include:
- 2D Labels and Arrows GUI - Boltz 2 structure prediction of proteins, nucleic acids, and small-molecule ligands, with affinity prediction - Boltz 2 batch ligand-binding predictions (many ligands to same receptor) - General minimization (including ligands) with Minimize Structure tool and "minimize" command - new ViewDock interface (replacing previous ViewDockX) - new types of trajectory plots: H-bonds, RMSD - save trajectory plots to image file - Thermal Ellipsoids GUI - "chirality" command to report stereocenter chirality - save/restore scenes including atomic, ribbon, and volume styles and coloring; more to be added later
For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog
Enjoy! On behalf of the team, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco