PyMol GUI and CLI

Molecule Tutorials - Herong's Tutorial Examples

∟PyMol GUI and CLI

This chapter provides quick introductions about PyMol GUI (Graphical User Interface) and CLI (Command Line Interface).

PyMol Screen Layout

Load Molecule from File into PyMol

Virtual Trackball Rotation on PyMol

Zoom In and Out on PyMol

PyMol Command Line Interface

"load" and "delete" Commands on PyMol

"log_open" and "log_close" Commands on PyMol

Model Space and Camera Space on PyMol

"get_view" and "set_view" on PyMol

View Parameters Auto Adjusted on PyMol

Zoom In/Out by Moving Camera

Rotation with Transformation Matrix

Rotation with "turn" Command

Difference of "turn" and "rotate" Commands

Difference of "move" and "translate" Commands

"center", "zoom" and "reset" Commands

Model-to-Camera Space Coordinates Mapping

Camera-to-Model Space Coordinates Mapping

Turn Structure around Camera

"show lines" Presentation Command

"show sticks" Presentation Command

"show spheres" Presentation Command

"show surface" Presentation Command

"show mesh" Presentation Command

Takeaways:

PyMol allows you to load a molecule from a SDF file.
PyMol allows you rotate the molecule in 3-dimensions by clicking and dragging a virtual trackball on the screen.
PyMol allows you zoom in on the molecule by spreading two fingers on the touchpad.
PyMol provides a command line interface to control all visualization functionalities.
PyMol "load" and "delete" commands load and remove molecules.
PyMol maps the molecule from the atom location model space to the camera (screen representation) space with a set of viewing parameters.
PyMol "turn" and "move" commands rotate and move the camera location to change the viewing angle and size of the molecule.
PyMol "rotate" and "translate" commands rotate and translate atom locations in the model space.
PyMol supports multiple representations: lines, sticks, spheres, surface, and mesh.