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@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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