the two TM-scores from US-align show a large discrepancy

[evans]

I am encountering an issue while using US-align to compare multimeric protein structures. The command I used is:
USalign 1ha0. cif 1hgd. cif -ter 0 -mm 1 -outfmt 2

However, I observed that the two TM-scores are quite different, and it seems that only one chain from structure 1 is being compared to all chains in structure 2. This resulted in the following discrepancies:
TM-score = 0.64138 (normalized by the length of Structure_1: L=494, d0=7.90)
TM-score = 0.21099 (normalized by the length of Structure_2: L=1509, d0=12.38)
I am not sure why the comparison is not being made between all chains of both structures.

For additional context: 1ha0 is a trimer composed of three identical monomers, while 1hgd is a hexamer composed of three identical units, each unit resembling a monomer from 1ha0, and each made of two chains.

Could you please advise on how to ensure that the correct chains are being compared in such cases? I have attached the relevant files for your reference. Thank you very much for your time and assistance.

[zcx@umich.edu]

This is not a problem of US-align.

You are using the incorrect file for 1ha0. While it is true that 1ha0 is a homotrimer, each asymmetric unit of 1ha0 only contain one chain.
1ha0.cif.gz is the asymmetric file, which contains and only contains one chain. You can check this by any molecular graphic system such as PyMOL.
If you want the trimer structure, download the biological assembly file.

[evans]

Thank you for your response. I hadn't noticed this issue before, and that was my oversight. I really appreciate your help.

[loraleednelson]

Thanks for sharing this detailed explanation. It really helps clarify how US-align handles multimeric structures. I had similar confusion with TM-score discrepancies before and didn’t realize normalization could cause such differences. Your example with 1ha0 and 1hgd makes it clearer. I’ll try specifying chains manually next time to get more consistent results. Appreciate the helpful post!