Remove PDB disordered atoms

Problem

You have a PDB with disordered atoms, i.e. different atomic positions with occupancies that add up to 100%. From this PDB you want to create a new one having only one set of the disordered atoms. This can be necessary if you want to perform RMSD calculations or Molecular Dynamics simulations.

Solution

Bio.PDB is proficient in dealing disordered atoms. Each disordered atom has a property indicating its alternative positions: atom.altloc. Usually there are only two alternative positions labelled 'A' and 'B'