Protein Preparation

Since PDB structures often lack hydrogen atoms in water molecules, we need to add them. We can use the addMissingAtoms() function. This function utilizes either Openbabel or PDBFixer. Those are external packages; therefore, they should be installed independently (see Recommended Programs).

If we prefer not to install additional tools, we can alternatively provide a PDB structure with hydrogens already added by other software.

Here, we will fetch a structure of LMW-PTP (PDB: 5KQM) from Protein Data Bank (PDB) in uncompressed form using compressed=False and add missing atoms using addMissingAtoms():

In [1]: pdb = '5kqm'

In [2]: filename = fetchPDB(pdb, compressed=False)

@> Connecting wwPDB FTP server RCSB PDB (USA).
@> 5kqm downloaded (5kqm.pdb)
@> PDB download via FTP completed (1 downloaded, 0 failed).

In [3]: filename2 = addMissingAtoms(filename)

@> Hydrogens were added to the structure.
Structure addH_5kqm.pdb is saved in the local directry.

A new file containing hydrogens is now generated, prefixed with 'addH_'. For protein structures lacking hydrogens, results will also be computed without applying angle criteria.