You might be interested in this ChimeraX Python code that was used to assemble large AlphaFold models from many predicted pieces.

https://rbvi.github.io/chimerax-recipes/big_alphafold/bigalpha.html

  Tom


On May 7, 2024, at 11:52 AM, Martin Gordon via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi everyone,

I'm hoping to get some assistance from the community for visualizing structures from multiple AF runs with overlapping subsequences.

We have been using AlphaFold monomer to try to identify structure and domains of a large (+3000aa) human protein. Our AF runs fail to model the full structure (possibly insufficient resources), so we have tried 'breaking' up the protein into overlapping subsequences. 

I was wondering if there is a sensible way to combine these substructures based on their overlapping regions? I have tried matchmaker, which I believe constructs a MSA and attempts to align the structures, but it seems a significant region of the overlap is not aligning correctly (img below with the overlapping subsequences highlighted).

Any guidance is greatly appreciated. 

Thank you,
Martin
<image.png>

Thank you,
Martin
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