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'