Using your own initial model
Keywords: manual

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Using your own initial model

Normally, `automodel` generates an initial model by transferring coordinates from the templates. However, if you have a prepared PDB file containing an initial model, you can have `automodel` use this instead with the `inifile` keyword, as in the example below. (This automatically sets automodel.generate_method to `generate.read_xyz` for you, which is necessary for this to work.)

Example: examples/automodel/model-myini.py

      # Modeling using a provided initial structure file (inifile)
      from modeller import *
      from modeller.automodel import *    # Load the automodel class

      log.verbose()
      env = environ()

      # directories for input atom files
      env.io.atom_files_directory = './:../atom_files'

      a = automodel(env,
                    alnfile  = 'alignment.ali',     # alignment filename
                    knowns   = '5fd1',              # codes of the templates
                    sequence = '1fdx',              # code of the target
                    inifile  = 'my-initial.pdb')    # use 'my' initial structure
      a.starting_model= 1                 # index of the first model
      a.ending_model  = 1                 # index of the last model
                                          # (determines how many models to calculate)
      a.make()                            # do homology modeling