PDB File Superimposer

1. Flexible Chain Selection: You can align any chain from the mobile structure to any chain in the reference structure.

2. Kabsch Algorithm: Uses the optimal superposition algorithm for minimizing RMSD.

3. Whole Structure Transformation: All atoms in the mobile PDB file are transformed, not just the alignment chain.

4. Water/HETATM Exclusion: Automatically excludes water molecules from alignment calculations.

Basic usage - align chain A from mobile.pdb to chain A from reference.pdb

python superimpose.py reference.pdb mobile.pdb A A -o aligned.pdb

Use backbone atoms for alignment instead of just C-alpha

python superimpose.py reference.pdb mobile.pdb A B -a backbone -o aligned.pdb

List chains in a PDB file

python superimpose.py --list-chains protein.pdb

Align different chains (e.g., chain B from mobile to chain A from reference)

python superimpose.py reference.pdb mobile.pdb A B -o aligned_AB.pdb

Use all atoms for alignment (more precise but slower)

python superimpose.py reference.pdb mobile.pdb A A -a all -o aligned_all.pdb