Hi Dario,

Pretty much all of the current tools use MMSeqs2 to do the multiple sequence alignment, and by default reach out to their server to do the job. As I understand it, it caches all alignment results for efficiency (so it can instantly return the cached result for any query identical to one it's seen before). While you can set up your own local server, the requirements are pretty steep - ideally hundreds of GB RAM and a few TB of storage.

Best,

Tristan

On Wed, Jul 2, 2025 at 5:54 PM Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Maybe experts can give more detail, but as I understand it, using ChimeraX "boltz" installs boltz-1 locally on your own machine:

<https://rbvi.ucsf.edu/chimerax/docs/user/tools/boltz.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/boltz.html>
<https://www.rbvi.ucsf.edu/chimerax/data/boltz-apr2025/boltz_help.html>

However, running boltz-1 will use Colabfold server for generating the deep multiple sequence alignment, and we do not have control over how/whether data is stored by that server.

Other than that, I don't see anything in the help about data going in/out from your own computer.

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 Jul 1, 2025, at 8:38 PM, Dario Passos via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Dear ChimeraX team,
>
> I have a question regarding data privacy when using the Boltz-1 structure prediction tool within ChimeraX. Is the input or output data temporarily or permanently stored, logged, or shared in any way by UCSF, ColabFold, or any third-party services? Is there an option to ensure that all data remains strictly local and is not stored externally?
>
> Thank you,
> Dario

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