Jmol for Beginners
Using Jmol to Study Biomolecules from the Protein Data Base (PDB)

A short workshop to get started

Important Links

Obtain the free software Jmol and link to Jmol resources. Find the link to the download page. Jmol is an open-source Java viewer for chemical structures in 3D.

Obtain PDB files. Protein Data Base (PDB) files include structure files for proteins as well as nucleic acids and carbohydrates.

Download "PDB and Jmol Worksheet" as a Microsoft Word (.docx) document. This is the Jmol for Beginners workshop. You may also download a Microsoft Word (.doc) version or a ".pdf" version.

Download "Using Jmol, a quick guide to simple commands" as a Microsoft Word (.docx) document. You may also download a Microsoft Word (.doc) version or a ".pdf" version.


home page for Warren Johnson


The materials available from this site are designed get someone started using Jmol (free software) to generate molecular models and examine their structures. Only minimal experience with computers is needed to get started.

Jmol is easy to "install". Download Jmol and once the folder is decompressed Jmol is ready to use. Start Jmol by double clicking the "Jmol.jar" icon. You may find it handy to make an alias of the "Jmol.jar" icon for easy starting of the program.

To do the PDB and Jmol Workshop down load your prefered version of this document from the links on the left. Open the "PDB and Jmol Worksheet" and begin. It will also be helpful if you download the "Using Jmol, a quick guide to simple commands" to assist in doing the worksheet.

After completion of this workshop you are ready to make models of any of the biomolecules in the PDB database. Have fun exploring their structures. More advanced information is available from the Jmol home page. A helpful book by Angel Herráez, How to use Jmol to study and present mollecular structures, is an excellent resource for beginners. The companion web site for this book is also very helpful.

Your questions and suggestions for how to improve this workshop and aid beginners in using Jmol are greatly appreciated.

Image from 1lcd.pdb