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Scattering factor parameters¤

Modeling the electron scattering amplitudes of individual atoms is an important component of modeling cryo-EM images, as these are typically used to approximate the electrostatic potential. Typically, the scattering factor for each individual atom is numerically approximated with a fixed functional form but varying parameters for different atoms. These parameters are stored in lookup tables in the literature. This documentation provides these lookup tables so that they may be used to compute electrostatic potentials in cryoJAX.

Extracting parameters from a lookup table¤

cryojax.constants.get_tabulated_scattering_factor_parameters(atom_identities: Int[Array, ' n_atoms'] | Int[np.ndarray, ' n_atoms'], scattering_factor_parameter_table: Optional[Float[Array, 'n_params n_elements n_scattering_factors'] | Float[np.ndarray, 'n_params n_elements n_scattering_factors']] = None) -> Float[Array, 'n_params n_atoms n_scattering_factors'] ¤

Gets the parameters for the scattering factor for each atom in atom_identities.

Arguments:

  • atom_identitites: Array containing the index of the one-hot encoded atom names. By default, Hydrogen is "1", Carbon is "6", Nitrogen is "7", etc.
  • scattering_factor_parameter_table: Array containing the table of scattering factors. By default, this is the tabulation from "Robust Parameterization of Elastic and Absorptive Electron Atomic Scattering Factors" by Peng et al. (1996), given by load_peng_element_scattering_factor_parameter_table.

Returns:

The particular scattering factor parameters stored in scattering_factor_parameter_table for atom_identities.

Lookup tables¤

cryojax.constants.read_peng_element_scattering_factor_parameter_table() -> Float[np.ndarray, '2 n_elements 5'] ¤

Function to load the atomic scattering factor parameter table from "Robust Parameterization of Elastic and Absorptive Electron Atomic Scattering Factors" by Peng et al. (1996).

Returns:

The parameter table for parameters \(\{a_i\}_{i = 1}^5\) and \(\{b_i\}_{i = 1}^5\) for each atom, described in the above reference.