Hi Elaine,
I am not sure if this appeared already earlier in the BB, but is there a way to
compute the inner lumen volume of a particle, which has some large openings
(≈40 Å), with ChimeraX? Maybe with some kind of segmentation?
Thanks a lot in advance,
Xavier

On 16/9/25 20:49, Elaine Meng via ChimeraX-users wrote:

Hi Ryssa,
The ChimeraX alphafold tool runs ColabFold, which is based on AlphaFold 2 and does not predict post-translational modifications.
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html>

There is another ChimeraX tool that runs Boltz, which is somewhat based on AlphaFold 3.   Although the Boltz program can predict post-translational modifications, however, it is a current limitation of the ChimeraX interface (tool and command) that there is no way to specify such modifications. Sorry about that.  See
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/boltz.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/boltz.html#limitations>

I hope this clarifies the current situation,
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 Sep 16, 2025, at 11:16 AM, Parks, Ryssa via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hello, I am trying to predict and model a peptide docking to a receptor protein using ChimeraX's AlphaFold interface, and I was wondering if there is any way to specify post-translational modifications in the AlphaFold input function in ChimeraX? Our peptide has an amidated C-terminus, and my searches online have not yielded much success.

Thank you,
Ryssa Parks


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