This is a read-only mirror of

Practical Pymol for Beginners

From PyMOL Wiki
Jump to navigation Jump to search

Although PyMol has a powerful and flexible command line interface, it can appear daunting to new users. This guide is intended to introduce PyMol basics without leaving the mouse behind.

About the command line

The PyMol command line is a great tool that lets the experienced user change all sorts of options that simply don't appear in the point-and-click graphical interface. It can also be a lot faster. Combined with scripting, it is a powerful option for automating tasks and making intricate changes. Page upon page of PyMol documentation cover these commands, so we're going to ignore them.

Although this guide may include some text commands (like this), they're purely optional and meant to be informative.

Visualize a protein

These instructions cover opening a PDB file and using PyMol as a RasMol replacement. The end result will be a graphic like this:

  1. Obtain a PDB file of your favorite protein. (The Protein Data Bank is a public structure repository containing over 40,000 protein structures in PDB format available for download, not a bad place to look.)
  2. Open the PDB file using File, Open... from the menu bar. The protein's structure will appear, probably rendered as sticks.
  3. On the left side of the PyMol window is the


Saving an image


  • Reinitialize hint