Hi,

There are two main issues I see here. Regarding the overlay: if you look closely you'll see that the variable domains of the antibody (the two domains directly contacting the antigen) actually overlay really well. The other two domains don't, but that's not particularly unusual - if you compare lots of experimental antibody structures you'll see that these naturally "rock" quite a bit relative to the variable domains, so there's no single "true" conformation here.

The second, bigger, issue: AlphaFold (including its variants like ColabFold) is not suitable for predicting antibody/antigen complexes (or, for that matter, any complexes where all the components didn't evolve in the same organism). It relies deeply on the use of multiple sequence alignments to glean information on the co-evolution of interacting partners over tens to hundreds of millions of years, and can only correctly make this analysis when all the sequences involved are present in the genomes of each individual organism. Antibody/antigen complexes don't meet either of these criteria, so in almost all cases you can expect its predictions for the antibody/antigen interface to be rubbish.

Best,
Tristan

On Sun, Mar 26, 2023 at 1:37 PM Cheng Fei Phung via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,

I am trying do "matchmaker #2 to #1" between colab output ( best_model.pdb which is pasted here at http://ix.io/4rRO ) and https://www.rcsb.org/structure/7CR5
 
However, as seen in https://i.imgur.com/gHL8to3.png , there is not really much visual overlapping since the structures are not rotated properly to match each other.

The log for doing matchmaker command is available here at https://i.imgur.com/78h5CLq.png

The colab notebook is also saved as a screenshot here at https://i.imgur.com/LSTdyZe.png

Manually doing "turn z 1 270 model #1 center #1" or similar rotations commands also do not help.
Please advise.

Regards,
Phung Cheng Fei
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