Tuesday, August 27, 2013

Aligning PDB structures with Biopython

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).


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