Conventions

This page collects conventions used throughout pytme. 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 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 analyzer merge method. The file can be read using load_pickle.

For the default analyzer 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.