Qutemol image of Hemoglobin (PDB ID: 2HBB)

Hemoglobin (PDB ID: 2HBB)

Molecular Graphics


PyMOL is a very popular molecular graphics software available on all types of computers (Mac/Windows/Linux) for displaying and saving beautiful molecular graphics. PyMOL is used for 3D visualization of proteins, small molecules, density, surfaces, and trajectories. PyMOL also includes molecular editing, ray tracing, and movies. In addition, PyMOL capabilities can be extended through python scripts.

Quoting from the web site: UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.

ChimeraX is a next-generation molecular visualization program with an all-in-one window interface that provides several advantages relative to Chimera. Here are 3 examples from a longer list found on the home page:

  • High-performance manipulation and rendering of large numbers of atoms
  • Interactive ambient occlusion
  • Toolbars with icons
  • Built-in HTML browser

Sybyl-X 2.1 is a commercial software that has now been released under a free license as it is no longer updated since 2013. However, this is an “industrial strength” powerful software used in Pharmacy for Drug Design high throughput screening. Sybyl-X 2.1 is modular and after this release virtually all modules are now available.

  1. Dickerson, R.E.; Geis, I. (1969). The structure and action of proteins. Menlo Park, CA: W.A. Benjamin.