.. _config_ref tasks psfgen mods:

``mods``
========

Specifies modifications to the sequence or structure in the PDB file

Single-valued attributes:

  * ``mutations``: Single-residue mutations, expressed as shortcodes (e.g., C:F32A to mutate residue 32 of chain C from PHE to ALA); note that the residue must be present in the PDB source file, and that the mutation will not be made if the residue is not present

    Example:

    .. code-block:: yaml
    
       mutations:
       - C:F32A
       - A:TRP,100,ARG
       - B:K50M

  * ``ssbonds``: additional ssbonds, expressed as shortcodes; e.g., C_154-A_298 to add an ssbond between resids 154 of chain C and 298 of chain A.  Note that the indicated residues must by CYS's.  If they are not, you should include each in a mutation shortcode in the mutations list

    Example:

    .. code-block:: yaml
    
       ssbonds:
       - C_154-A_298
       - A_100-B_200

  * ``ssbondsdelete``: existing ssbonds to break, expressed as shortcodes; e.g., C_154-A_298 will break the existing ssbond between resids 154 of chain C and 298 of chain A so that each is a reduced CYS.

    Example:

    .. code-block:: yaml
    
       ssbondsdelete:
       - C_154-A_298
       - A_100-B_200

  * ``links``: additional generic bonds, expressed as shortcodes; e.g., C_154_N-A_298_M to add a link between atom N of resid 154 of chain C and atom M of resid 298 of chain A.

    Example:

    .. code-block:: yaml
    
       links:
       - C_154_N-A_298_M
       - A_100_CA-B_200_O

  * ``deletions``: residue ranges to delete, expressed as shortcodes; e.g., C:99-101 deletes residues 99 to 101 (inclusive) of chain C

    Example:

    .. code-block:: yaml
    
       deletions:
       - C:99-101
       - A:50-60

  * ``substitutions``: residue ranges to replace with a new sequence; e.g., C:99-101,GG replaces residues 99, 100, and 101 of chain C with two glycines

    Example:

    .. code-block:: yaml
    
       substitutions:
       - C:99-101,GG
       - A:50-60,GGG

  * ``insertions``: sequence of residues to insert C-terminal to a specified residue in a specified chain; e.g., C,123,GRETA inserts the residues Gly123A, Arg123B, Glu123C, Thr123D, and Ala123E immediately C-terminal to residue 123 of chain C; if the resid includes a terminal "+", then inserted resids are incremented as integers

    Example:

    .. code-block:: yaml
    
       insertions:
       - C,123,GRETA
       - A,50,GGG+

  * ``patches``: CHARMM36-style patches to apply to the system

    Example:

    .. code-block:: yaml
    
       patches:
       - ASPP:C:199

  * ``crotations``: dihedral angle rotations

    Example:

    .. code-block:: yaml
    
       crotations:
       - psi,E,661,693,60
       - phi,E,662,693,60
       - alpha,B,33,52
       - alpha,B,144,153
       - alpha,D,32,52
       - alpha,D,144,153

  * ``transrot``: global translations and rotations

  * ``Cfusions``: fuse residues from named residue range of named protein chain of named input PDB coordinate file to C-terminus of named segment of base molecule

  * ``grafts``: graft residues from named residue range of named chain of named input PDB coordinate file onto target residue of base molecule

    Example:

    .. code-block:: yaml
    
       grafts:
       - A_1304:4b7i,C_1-8
       - B_1304:4b7i,C_1-8
       - C_1304:4b7i,C_1-8
       - A_1305:4b7i,C_1-8
       - B_1305:4b7i,C_1-8
       - C_1305:4b7i,C_1-8



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