• Removing hydrogens, renaming HIP to HIS, and renumbering atoms, for all PDBs from a folder to a new folder:

  mkdir folder_new
  for i in folder/*pdb; do pdb_delelem -H $i | pdb_rplresname -HIP:HIS | pdb_reatom -1 | pdb_tidy > folder_new/$(basename $i); done