Example Commands

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 output will list the RMSD of the superposed result, the order in which the ref and fit chains were superposed, and the sequence alignment score, if the method is sequence based. The command should generate a PDB file called superposed_1hhp.pdb that contains the superposed protein and the following message in the log file:

Superposition - RMSD: 1.16, Ref: ABCDEF, Fit: A, SeqScore: 492

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. The command should generate a PDB file called superposed_1cll.pdb that contains the superposed protein and the following message in the log file:

Superposition - RMSD: 0.60, Ref: A, Fit: A, SeqScore: 642

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 -method sse -prefix FOO

will write the output structures into a file named FOO_1cll.pdb and following message to the log file:

Superposition - Tanimoto: 0.31, Ref: A, Fit: A