USalign RMSD

[fsin]

I would like to ask how the RMSD between two structures is calculated for USalign

[zcx@umich.edu]

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 aligned residue pair.

Note that the Kabsch superimposition is usually different from the TM-score superimposition, based on which the -o or -rasmol output is generated.