Thank you both! ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Wednesday, March 4, 2026 4:21:48 PM To: Kirk Nelson <knelson@tyra.bio> Cc: chimerax-users <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] what information goes out from Boltz calculations Hi Kirk, Elaine is correct that no ligand information in Boltz predictions is sent off of your computer. The protein sequences are sent to the public Colabfold multiple sequence alignment https://api.colabfold.com<https://url.avanan.click/v2/r01/___https://api.colabfold.com___.YXAzOnR5cmExOmE6bzpiMzdkYzJkM2M3ODAxOGJlY2FlN2ZkMDc5YjkwMDU1NTo3OmE3Mzc6ZTA2ZDAyODAxMTQ3ZTk0NmYyYjYwMTEwYTlhOGYzNTM3MjgxNjMyMjg2NGRlNWQxNTViZDcyZDg4YjY5ZmU0NjpoOlQ6Rg> run by Martin Steinegger's lab. I don't know if they have a privacy policy -- I suspect the delete all sequence info sent to them. You may also be interested in OpenFold 3 in ChimeraX daily builds (menu Tools / Structure Prediction). It also installs and runs on your local computer and does not send ligand info, only protein sequences to the MSA server. Boltz has ligand affinity prediction. OpenFold 3 has an implementation of the same ligand affinity prediction but it is not yet in ChimeraX. You may also be interested in some tests that show ligand prediction in Boltz 2, OpenFold 3 and AlphaFold 3 half the time produces wrong ligand chemistry and chiralities. https://www.rbvi.ucsf.edu/chimerax/data/ligchem-feb2026/badchem.html<https://url.avanan.click/v2/r01/___https://www.rbvi.ucsf.edu/chimerax/data/ligchem-feb2026/badchem.html___.YXAzOnR5cmExOmE6bzpiMzdkYzJkM2M3ODAxOGJlY2FlN2ZkMDc5YjkwMDU1NTo3OjJiOTE6N2RmYTQwODdmMjYyZGQyOWQxZDkwZDZjMDUwYzI0MmQwZTA0YmU4YTllZWI3MDA0OTNkNDQ0NWE0OGI2ZDE3YTpoOlQ6Rg> Tom On Mar 4, 2026, at 4:09 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: 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://url.avanan.click/v2/r01/___https://rbvi.ucsf.edu/chimerax/docs/user/tools/boltz.html>___.YXAzOnR5cmExOmE6bzpiMzdkYzJkM2M3ODAxOGJlY2FlN2ZkMDc5YjkwMDU1NTo3OjBkOWY6MGUzYmU3ZWQwZGZmMTE2ZWQ5ZDVmNTIzYzYzYWEzNzJlOTQ4MTg3OWZhNTJjYjgyYzNlYjJjNjUyNjhkNTU0Njp0OlQ6Rg; 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://url.avanan.click/v2/r01/___https://www.rbvi.ucsf.edu/chimerax/downlo... 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://url.avanan.click/v2/r01/___https://www.rbvi.ucsf.edu/trac/ChimeraX/w... 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 _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://url.avanan.click/v2/r01/___https://mail.cgl.ucsf.edu/mailman/archive... This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying, or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently delete the original and any copies of this email and any attachments thereto.