.. _config_ref tasks psfgen source:

``source``
==========

Specifies the processing and interpretation of the initial source coordinate file

Single-valued attributes:

  * ``biological_assembly``: integer index of the biological assembly to construct; default is 0, signifying that the asymmetric unit is to be used (default: 0)

  * ``transform_reserves``: dictionary keyed by chain IDs in the asymmetric unit with values that are lists of chain ID's for symmetry-related chains in other units of the biological assembly

  * ``remap_chainIDs``: dictionary mapping of chainIDs in structure input to new chainIDs

  * ``reserialize``: If true, resets the serial numbers of all atoms based on their order in the input structure file -- use with caution!! (default: False)

  * ``model``: model number to use if there are multiple models in the file

  * ``cif_residue_map_file``: name of output file to write a mapping of CIF chain-residue number to author chain-residue number-insertion

  * ``include``: Logical expressions involving atom attributess used in series to specify those atoms to be included

    Example:

    .. code-block:: yaml
    
       - chainID == 'A'
       - resname == 'GLY'
       - chainID in ['A', 'B']

  * ``exclude``: List of logical expressions involving atom attributes used in parallel to specify those atoms to be excluded



Subattribute:

.. toctree::
   :maxdepth: 1

   source/sequence


.. raw:: html

   <div class="autogen-footer">
     <p>This page was generated by ycleptic v2.0.6 on 2026-05-28.</p>
   </div>