From: Tristan Croll <tcroll@altoslabs.com>
Sent: Monday, March 27, 2023 1:10 AM
To: Cheng Fei Phung <feiphung@hotmail.com>
Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] AlphaFold best_model.pdb could not visually overlap the input sequence using matchmaker

... huh. Looking at it again, it seems to me that AlphaFold has predicted the antibody heavy chain in the light chain conformation and vice versa. If you force it to align (predicted heavy) to (experimental light) with "match #2/D to #1/H" then all four antibody domains align reasonably well. Seems like a failure on AlphaFold's part (and one I haven't seen before).

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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