You can use the Bio.PDB module in Biopython to align PDB files. This is how I did it. The code should be pretty much self-explanatory.
In this example I align the crystal structure of Ubiquitin (PDB code: 1UBQ) to the first structure of a corresponding NMR ensemble (PDB code: 1D3Z, see picture below).
In this example I align the crystal structure of Ubiquitin (PDB code: 1UBQ) to the first structure of a corresponding NMR ensemble (PDB code: 1D3Z, see picture below).
