Model Space and Camera Space on PyMol

Molecule Tutorials - Herong's Tutorial Examples

∟Model Space and Camera Space on PyMol

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 request 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 specified 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: