Zhanglab forum

1) How should I read the standard output lines for -outfmt -1? For easy of parsing, you may use -outfmt 1 or -outfmt 2, which are more compact. 2) Why are there 2 values for RMSD, Aligned length and TMscore (line 5 and 6)? In line 5 which starts with "User-specified initial alignment: TM/Lali/rmsd ...

You may check https://zhanggroup.org/BioLiP/download.html
which contains "BioLiP.txt.gz".

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 ...

If you are aligning monomeric proteins, TM-align and US-align give the same result.

AlphaFold structures of all human proteins can be downloaded via the alphafold database https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000005640_9606_HUMAN_v4.tar You can then perform pairwise TM-align alignments. You probably would want to use the "-fast" option of the TM-align (C++ version ...

To calculate the RMSD, a Kabsch superimposition (a.k.a. RMSD superimposition) is performed on the subset of aligned residue pairs and the RMSD can be calculated by: RMSD = sqrt ( 1/Lali \sum_{i=1}^Lali d_i ^2 ) where Lali is the number of aligned residue pairs, d_i is the distance between the i-th ...

8stw is a homo-hexamer, where each chain binds to one PLP and one HEM. Therefore, the full biological assembly has 6 different PLP and 6 different HEM ligands for the 6 different chains. Therefore, it is not true that the same ligand binds to 6 different chains simultaneously.

I am afraid what you request is not implementable. It is not possible to implement rotation but no translation.

No, US-align cannot consider pLDDT score.

I am not exactly sure what you mean. If you want to extract the alignment based on a pair of superimposed structure, you can use the "se" program from https://github.com/pylelab/USalign