This is done by using the allhmodel class rather than automodel. Otherwise, operation is identical. Note that the allhmodel class automatically turns on env.io.hydrogen for you and selects the all-atom topology and radii files.
from modeller import * from modeller.automodel import * log.verbose() env = environ() env.io.atom_files_directory = ['.', '../atom_files'] a = allhmodel(env, alnfile='alignment.ali', knowns='5fd1', sequence='1fdx') a.starting_model = a.ending_model = 4 a.make()