The input for RSE are two structures in pdb format and an optional sequence alignment in FASTA format. If the sequence alignment is not provided, the two structures are assumed to be superimposed. If the sequence alignment is provided, the two structures are first superimposed according to the input sequence alignment.
The default output for RSE is the sequence alignment and statistical summary on the screen, similar to SE output. There are also options to generate the optimal transformation matrix and the sequence alignment in FASTA, SHEBA, or GEMM format. There are some other internal options for fine-tuning the program.