Animating a Molecular Knot
I read an interesting article in Science about a molecular knot. I decided to download the structure file and play with it in PyMOL. Here's what I did with it.
Displaying a Protein-Protein Interaction Interface
In my cell biology course, we spend significant time on protein-protein interactions because they are so important for practically everything in cells. To show the interacting surface between two proteins I like to create a quick movie using PyMol. Here's how I did it.
Making a Protein Conformation Change Movie
When I teach protein structure in introductory biology, I like to show the dramatic shape changes that can occur when proteins bind ions. My protein of choice for these demonstrations is calmodulin, which undergoes a large conformational change upon binding calcium ions. I recently found the Climber program, which can calculate the structural changes necessary to morph one protein conformation into another using the structure files from the RCSB Protein Data Bank. When combined with PyMOL, the output looks absolutely stunning.
Small Molecule Movies in PyMol
Molecules are inherently three dimensional and 2D representations do not often adequately show the arrangement of atoms, especially for "larger" small molecules. To better show the structure, I made a simple movie where the small molecule rotates around the Y-axis. Here's how I did it.
Displaying Protein NMR States as a Movie
When I teach introductory biology, I like to demonstrate how proteins are not rigid structures. However, I have have no experience conducting molecular dynamics simulations. I found that I could simulate a simulation by morphing between the different states of a protein structure that was determined by NMR. Here is how I did it.