Example CommandsΒΆ

The simplest way to run Superposition is by passing in both a reference and a fit input biomolecular structure file:

prompt> superposition -ref 4obd.pdb -fit 1hhp.pdb

Here, Superposition will fit the protein in 1hhp.pdb against the reference protein in 4obd.pdb.

The structural superposition method can be set on the command line with the -method option:

For example:

prompt> superposition -ref 1a29.pdb -fit 1cll.pdb -method ddm

will superpose 1cll.pdb onto the reference file 1a29.pdb using the ddm (difference-distance matrix) method.

To prevent continually over-writing output files, the -prefix flag allows you to give unique names to these files.

prompt> superposition -ref 1a29.pdb -fit 1cll.pdb -prefix FOO_

will write the output structures into a file named FOO_1cll.pdb.