.. include:: ../substitutions.rst .. _coordinate-system: =========== Conventions =========== This page collects conventions used throughout |project|. It covers the coordinate system, the Euler-angle convention, and the layout of pickle files emitted by ``pytme match``. Coordinate System ----------------- Our convention follows the schematics outlined in [1]_. We use a right-handed coordinate system with orthogonal X, Y, and Z axes. Euler angles are expressed using the intrinsic ZYZ convention, with the first rotation around the Z axis, the second around the new Y axis, and the third around the new Z axis (see :py:meth:`euler_to_rotationmatrix `). The default orientation is the z-unit vector (0, 0, 1). Pickle File Layout ------------------ The output of ``pytme match`` is a `pickle `_ file containing a tuple. All but the last element correspond to the return value of a given :doc:`analyzer ` merge method. The file can be read using :py:meth:`load_pickle `. For the default analyzer :py:class:`MaxScoreOverRotations ` the pickle file contains - **Scores**: score for each position in the target. - **Offset**: coordinate system shift. - **Rotations**: optimal rotation index for each translation. - **Rotation Dictionary**: mapping from rotation indices to rotation matrices. - **Sum of Squares**: sum of squares of scores for statistics. - **Metadata**: coordinate system information and parameters for reproducibility. When the ``-p`` flag is passed to ``pytme match`` the output structure differs - **Translations**: peak position. - **Rotations**: rotation matrix describing template orientation at peak. - **Scores**: score at peak. - **Details**: additional properties of the peak. - **Metadata**: coordinate system information and parameters for reproducibility. References ---------- .. [1] Heymann, J.B.; Chagoyen, M.; Belnap, D.M. Common conventions for interchange and archiving of three-dimensional electron microscopy information in structural biology. J Struct Biol 2005, 151, 196-207.