For proteins, this includes checking for: (i) missing amino acids, (ii) missing atoms within sidechains, (iii) missing hydrogens and appropriately protonated systems, and (iv) minimal clashes within crystal packing interfaces. It is also important to consider whether or not to include the crystal waters within your system; some crystal waters may play functional roles in protein system . This can be done using tools such as PDBFixer , or Ensembler .