Pairwise alignment
The -alignpair command aligns two structures
The first structure is given after ‑alignpair,
the second structure is specified by the ‑input2 option.
If multiple chains are found in one or both of these files, then an all-vs-all comparison
is made to find the highest-scoring pair.
Search output files are supported; only the highest-scoring
alignment will be reported.
The ‑output option specifies a PDB format
file for a rigid rotation of the query chain which optimizes RMSD overlap with the second chain.
You can load the rotated query together with the target chain in a molecure viewer tool such as Pymol
to visualize the superposition.
Example
reseek -alignpair 1abc.pdb -input2 2xyz.pdb -aln 1abc_2xyz.txt \
-output 1abc_rotated.pdb
