[chimerax-users] AlphaFold best_model.pdb could not visually overlap the input sequence using matchmaker

[Rudy Richardson]

It seems that the problem could be with trying to align each of the entire
complexes. Predictive models of structures with multiple protein chains can
have a difficult time with finding the correct interactions between chains.

Have you tried the 3D alignment with each of the corresponding 3 chains? I
took the A-chain of 7cr5 and did a 3D alignment with the B chain of 4rR0
using Sheba in Yasara and got a Calpha RMSD of 1.094 A over 111 aligned
residues with 100.0% similarity. I have attached a PDB file of the aligned
structures.

Best regards,

R.J. Richardson


On Sun, Mar 26, 2023 at 8:38 AM Cheng Fei Phung via ChimeraX-users <
chimerax-users at 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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