Contributed by Ramon Crehuet
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.
is proficient in dealing with disordered atoms. Each disordered atom has
a property indicating its alternative positions:
there are only two alternative positions labelled ‘A’ and ‘B’. The key
is to save a PDB with the optional
select argument. This argument
needs to return a
True value for the atoms that have to be saved. In the
following example we save all not-disordered atoms and the ‘A’ positions
of the disordered ones.
from Bio.PDB import * parser = PDBParser() s = parser.get_structure("my_pdb", "my_pdb.pdb") io = PDBIO() class NotDisordered(Select): def accept_atom(self, atom): return not atom.is_disordered() or atom.get_altloc() == "A" io = PDBIO() io.set_structure(s) io.save("ordered.pdb", select=NotDisordered())
Note that the code above does not eliminate the alternate location identifier (‘A’ in the example above). It is the programmer’s responsibility to eliminate the identifier when necessary.
keepAltID = ... class NMROutputSelector2(Select): # Inherit methods from Select class def accept_atom(self, atom): if (not atom.is_disordered()) or atom.get_altloc() == keepAltID: atom.set_altloc(" ") # Eliminate alt location ID before output. return True else: # Alt location was not one to be output. return False # end of accept_atom() # end of NMROutputSelector2()
It is trivial to change that to save ‘B’ altloc positions. One can even
do more complicated selections based on other atom properties. The key
is to generate a class that returns
False for a given atom. One
could also think of deleting atoms with ‘B’ values in
# Will not work! for atom in all_atoms: # all_atoms is a list containg all atoms if atom.altloc == "B": del atom
but that does not work, because it only deletes the local variable and not the PDB structure.