This section provides a quick introduction of model space and camera space cooridinate systems used on PyMol to transform and display molecule structures on the screen.
PyMol uses two coordinate systems to form the viewing model when
the molecule structure is displayed on the screen.
1. Model Space Coordinate System - A 3-dimensional coordinate system
in which molecule atom locations are specified.
For example, the following line in a SDF molecule file
specifies a Carbon atom located at (1.1100, 1.2100, 0.0000)
in the Model Space coordinate system.
1.1100 1.2100 0.0000 C 0 0 0 0 0 0 0 0
2. Camera Space Coordinate System - A 3-dimensional coordinate system
in the display screen and the viewing camera are specified:
X-axis representing the horizontal direction running
from left to right on the screen.
Y-axis representing the vertical direction running
from top to bottom on the screen.
Z-axis representing the viewing direction running
from the viewing camera to the screen.
When you reguest the molecule structure to be displayed
on the screen, PyMol will perform a set of transformation
to map the molecule structure from the model space to the
camera space. This set of transformations is generated
from viewing parameters you sepecified by viewing commands
like "rotate", "move", etc.
The following diagram (source: "A Beginner’s Guide to Molecular Visualization Using PyMOL"
By Nicholas Fitzkee)
shows you the relation of the model space and the camera space
used in PyMol: