Chapter 4. Geometry and Conventions

Table of Contents

Coordinate system
Discretization/digitization/sampling of space
Rotations and views
Origin: Placement of objects
Point group symmetry
Helical symmetry
Crystallographic symmetry

Bsoft deals with real space objects, whether they are densities (encoded in images) or molecular structures. Understanding the conventions adopted in Bsoft is important to doing image and molecular processing effectively.

Coordinate system

  • Orthogonal/Cartesian (exceptions are periodic cases such as crystals or helices, and spherical or cylindrical coordinate systems).

  • Right-handed (implicitly defining a right-handed rotation convention).

  • Default view is down the z-axis (vector {0,0,1}, with z values decreasing with distance from the viewer.

The use of an orthogonal coordinate system may seem obvious, but non-orthogonal systems are used in fields such as crystallography, where certain mathematical operations are simplified by using non-orthogonal coordinate systems. Other alternatives include spherical and cylindrical coordinate systems. In the absence of mathematical utility, the simplest choice is an orthogonal or Cartesian system. The options of right-handed and left-handed coordinate systems are equivalent, with the choice going to the most commonly used one. The right-handed rotation implicit in a right-handed coordinate system is defined as a clockwise rotation around an axis, with the viewer looking in the positive direction of the axis. There are an infinite number of possibilities for the default view. Defining one of the major axes of the coordinate system as the default view direction, and placing the other two axes in vertical and horizontal directions, offers a finite number of possibilities. Two such views are common, both using the z-axis, but in opposite directions, and placing the x-axis horizontally and the y-axis vertically. The first convention views space in the positive z direction, i.e., z values increase with distance from the viewer (up the axis {0,0,1}). This convention is consistent with conventions in text and the arrangement of pixels on a computer monitor, i.e., start in the top-left corner and read row-by-row. The second convention views space in the negative z direction, which is a 180 degree rotation around the x-axis with respect to the first viewing convention (thus down the axis {0,0,1}). The worth of this convention is that it orients the x and y axes in the same way as one would do to plot a curve on a graph. Mathematical operations therefore become easier to understand from the user's point of view.