Hi Kaan, Google has not released AlphaFold 3 source code or executables so you can only run it through their server. They say they will try to release the code in 6 months. This was discussed a few days ago in the ChimeraX mailing list. https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/... https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/... I have updated the current ChimeraX daily build and ChimeraX 1.8 release candidate so that it can read the predicted aligned error files from AlphaFold 3 which are different from AlphaFold 2 because they contain PAE values for individual atoms for ligands, ions and modified residues. Tom

On May 17, 2024, at 7:51 AM, Kaan Okay - HI via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

I use Alphafold through UCSF ChimeraX. It is a very nice tool, I believe its developers have done a good job. As you know, AlphaFold 3 is a new model that allows us to predict DNA modification and protein interactions (https://www.nature.com/articles/s41586-024-07487-w). What I wonder is when this model will be transferred to UCSF ChimeraX and whether we can predict protein interactions and DNA modifications (e.g., 5mC modification on cytosine bases in DNA).

I'm looking forward to hearing from you.

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