Defining symmetry

Symmetry can be defined in "symmetry" blocks at the top level of the JSON configuration file in lists of "sym_tr3ds".

Multiple symmetries can be defined and used simultaneously.

Using a symmetry axis information

{
    "symmetry": {
        "sym_tr3ds": [

            {
                "name": "2fold",
                "axis": "vector of the symmetry axis",
                "center": "symmetry point (through which the above symmetry axis is passing through)",
                "type": "cyclic symmetry type like C2, C3, C8 and so on"

            }

        ]
    }
}

For example:

{
    "symmetry": {
        "sym_tr3ds": [

            {
                "name": "2fold",
                "axis": [0, 0, -1],
                "center": [246.39112398, 246.41114644, 248.600000],
                "type": "C2"

            }

        ]
    }
}

How to get this transformation information? Follow Calculating symmetry instruction how to do it based on an EM map.

Using transformation matrix

{
    "symmetry": {
        "sym_tr3ds": [

            {
                "name": "a unique custom name",
                "rot": "list of 9 values for rotation, 3 for each row of the symmetry matrix",
                "trans": "list of 3 values for translation"
            }

        ]
    }
}

For example:

{
    "symmetry": {
        "sym_tr3ds": [

            {
                "name": "2-fold",
                "rot": [0.70712087, 0.70709269, 0.00003928, -0.70709269, 0.70712087, 0.00000394, 0.00003057, -0.00002499, 1.00000000],
                "trans": [-411.56570152, 993.5285317, 0.09136987]
            }

        ]
    }
}

How to get this transformation matrices? Follow Calculating symmetry instruction how to do it based on an EM map.