Building an all hydrogen model
Keywords: manual

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##
Building an all hydrogen model

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.

Example: examples/automodel/model-default-allh.py

      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()