TEMPy.protein.structure_blurrer
+++++++++++++++++++++++++++++++

All functions used to generate simulated maps from
protein models, and to generate other 3D volumes, such as masks are found in
TEMPy.protein.structure_blurrer.

TEMPy contains multiple methods for generating (or blurring) simulated maps.
Most of these methods generate simulated maps by modelling density around each
atom as a 3D gaussian; a simulated map is generated by summing the guassians
for all atoms in a model. This calculation can be done in fourier space using
:meth:`gaussian_blur <TEMPy.protein.structure_blurrer.StructureBlurrer.gaussian_blur>`
, or in real space using
:meth:`gaussian_blur_real_space <TEMPy.protein.structure_blurrer.StructureBlurrer.gaussian_blur_real_space>`.

Note on real space blurring:
++++++++++++++++++++++++++++++++++++

All real space blurring functions require a :code:`sigma_coeff` argument, that
defines the width of the Gaussian (multiplied by the map resolution) for each
atom. In TEMPy, there are multiple options for the :code:`sigma_coeff` value,
each derived from a specific publication.

Available :code:`sigma_coeff` values:

    * 0.187R corresponding with the Gaussian width of the Fourier
      transform falling to half the maximum at 1/resolution, as
      used in Situs (Wriggers et al, 1999);

    * 0.225R which makes the Fourier transform of the
      distribution fall to 1/e of its maximum value at wavenumber
      1/resolution the default in Chimera (Petterson et al, 2004)

    * 0.356R corresponding to the Gaussian width at 1/e maximum
      height equaling the resolution, an option in Chimera
      (Petterson et al, 2004);

    * 0.425R the fullwidth half maximum being equal to the
      resolution, as used by FlexEM (Topf et al, 2008);

    * 0.5R the distance between the two inflection points being
      the same length as the resolution, an option in Chimera
      (Petterson et al, 2004);

    * 1R where the sigma value simply equal to the resolution,
      as used by NMFF (Tama et al, 2004).

.. automodule:: TEMPy.protein.structure_blurrer
   :members: