Getting Started in Jmol
Contributors
This Jmol Training Guide was created with funding from NIH Grant #1 R25 RR022749-01 and NSF-DUE #1323414 and #1725940. Revised 4/2021.

This Jmol Exploration was created using the Jmol Exploration Webpage Creator from the MSOE Center for BioMolecular Modeling.

version 2.0
Exploration Content

Introduction

Physical models of proteins are powerful tools that can be used synergistically with computer visualization tools to explore protein structure and function. Although it is interesting to explore models and visualizations created by others, it is much more engaging to create your own!

A number of molecular visualization programs are on the market; we have selected to use Jmol, which is a free open source molecular visualization program used by students, educators and researchers. These online resources will provide the tools needed to create physical models using 3-D printing technologies, as well as Jmol animations for online Jmol Explorations or electronic posters.

Welcome to the amazing world of proteins – and the fascinating stories that each one can tell!

Jmol

About Jmol

Jmol runs on a Java platform and therefore functions equally well in a PC or Mac environment. Because Jmol is freeware and an open source program, it can be obtained from many locations. For total functionality in designing a structure to be built on a 3-D printer in the CBM, check the website every September to get the current version of Jmol that we will be using for the school year. Note that files created in older versions can be viewed in more recent versions, but files created in more recent versions may not open in older versions of Jmol.

Downloading Jmol

We suggest that you download Jmol directly from the CBM website to ensure you are using the correct version for creating physical models. You may click the link below to download Jmol.

Jmol Version 14.15.3 (Mac or PC) (Single JAR file)

You need to have Java on your computer to run the desktop version of Jmol. Most computers will already have Java installed, but if you do not, you can download it for free from https://java.com/en/download/.

Jmol File Location

Jmol does not need to be 'installed', so once the Jmol file is in place on your computer, the program will be ready to use. Click on the Jmol.jar file to start Jmol on your computer.

You may save the Jmol file you download in any convenient location on your computer. Jmol does not need to be 'installed', so once these files are in place on your computer, the program will be ready to use. Click on the Jmol file to start Jmol on your computer. Files you save in Jmol will be saved in the same file location as the Jmol file.

Protein Data Bank (PDB) Files

Molecular structures can be determined through the use of X-ray Crystallography, Nuclear Magnetic Resonance (NMR), or computer algorithm-based calculations. Once a structure has been determined, each atom in the structure is assigned an (X,Y,Z) coordinate to mark its location in 3-dimensional space. These coordinates are then stored in a file called a Protein Data Bank (PDB) file. Molecular visualization software, such as Jmol, can then use the coordinates stored in a PDB file to create an interactive 3-dimensional visualization of a molecular structure.

Downloading PDB Files

The most common source of free PDB files of macromolecules is the RCSB Protein Data Bank website at https://www.rcsb.org. We will be using Jmol to view the PDB file 1qys.pdb which contains the atomic coordinates for a single molecule of the protein 'Top 7'. To download this file (and all other PDB files) from the Protein Data Bank:


  • Go to the website https://www.rcsb.org.

  • In the top right corner of the website there is a search bar similar to the image below. Type in the four number/letter file name '1qys' and click the 'Search' button.
  • Error:image not available. Check image URL to correct the problem.

  • This should bring you to the page for '1qys.pdb – Top 7'. Just below the search box on the right should be a list of four options similar to the image shown below. Click 'Download Files' and you will see an expanded menu similar to the second image shown below.
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    Error:image not available. Check image URL to correct the problem.

  • Click 'PDB Format' to download the PDB file containing the coordinates for Top 7. This file, named '1qys.pdb', will be saved in the Downloads folder on your computer, but you may move it to another folder if you wish.

Note: It is a good idea to create a new folder for each molecule you explore to organize all PDB files, images, articles and other related work. (See the 'Saving Your Work and Organizing Your Files Training Guide' for more information.)


  • More detailed information about the Protein Data Bank and PDB files will be discussed in the 'Protein Data Bank (PDB) Training Guide'.

If you don't need additional information about the PDB file or don't wish to save a copy of the file on your computer, you can
'call up' the file in Jmol without downloading. See Saving and Opening Files in Jmol for more details.

Setting Up Your Workspace

Launching Jmol

To launch Jmol, click on the 'Jmol.jar'file. Note: it should have an icon similar to one of the images below.

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Jmol icon on PC
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Jmol Icon on Mac

Quick tip: You might wish to create a shortcut to the 'Jmol.jar' file on your desktop and in each of your working folders so you can easily find and launch Jmol.


  • For PC users: right click on the Jmol.jar file and select 'create shortcut'. Copy and paste the shortcut wherever you want to access Jmol quickly.

  • For Mac users: right click on the Jmol.jar file and select make an alias. Copy and paste the alias wherever you want to access Jmol quickly.

Jmol Windows

Once launched, the Jmol Display Window will appear. The Jmol Display Window will show the 3-dimensional structure of the PDB structures you load and design. You can adjust the size of this window by grabbing an edge or corner of the screen with your mouse then clicking and dragging to adjust size. Most people prefer to have this window to occupy half to two-thirds of your screen.

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Jmol Display Window

Console

The Jmol Console is used to input commands. To access the Console, right click anywhere in the Display Window to bring up the Display Window Menu. In this menu, click on the button 'Console' which will open the Jmol Console.

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Accessing the Jmol Console

Because the Console and Display Windows will almost always be used in unison, arrange the windows so that they do not overlap and both fit comfortably on your screen. Most people prefer a larger Display Window.To move the windows, click and drag in the header space.

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Jmol Display and Console windows arranged on desktop

Opening a PDB File

There are two options for opening a PDB file.

Option 1: Open the folder that contains your PDB file. Click and drag your PDB file into the Display Window. Note: you may have to arrange the Jmol window and folder window in such a way that you can see both at the same time in order to click and drag the PDB file.

Option 2: If you have Internet access and don't want to store PDB files on your computer, in the console, enter the command:

load=xxx, where xxxx represents the four character PDB code.

To load Top7 using 1qys.pdb, use the command:

load=1qys

Depending on the PDB file, the structure may appear in one of several formats:


  • Cartoon or Backbone Format: displays the secondary structure of the protein, with sheets in yellow, helices in magenta, and loops and turns in white. Ligands are displayed in ball and stick, and ions and water molecules are in spacefill.

  • Ball and Stick: displays all atoms in the structure (including ions and water molecules) in ball and stick. Atoms are colored in CPK (gray carbon, blue nitrogen, red oxygen). Note that hydrogen atoms are typically not displayed in PDB files.

You'll learn how to change the appearance of the structure in other tutorials.

Moving a Structure in Jmol

Once you have opened your PDB file, the structure should appear in your Jmol Display Window. Click the button below to see what your Jmol Window might look like. (This is a ball and stick rendering.)

Top 7 PDB ID: 1qys

You can now rotate, relocate or zoom in on the molecule in the Display Window.

X-Y Rotation

To rotate the molecule within the X-Y axes on the computer screen,

  • For PC users: place the mouse cursor in the Display Window, hold down the left mouse button, and move the mouse.

  • For Mac users: place the mouse cursor in the Display Window, hold down the mouse button, and move the mouse.

Translation

To move ('translate') the molecule,

  • For PC users: place the mouse cursor in the Display Window, hold the left mouse button along with CTRL and ALT, and move the mouse.

  • For Mac users: place the mouse cursor in the Display window, hold the mouse button down along with CMD, and move the mouse.

Zoom

To zoom in or out,

  • For PC users: place the mouse cursor in the Display Window, hold the left mouse button along with SHIFT, and move the mouse up or down. If the mouse you are using has a center rolling wheel, you can also zoom in and out using this wheel.

  • For Mac users: place the mouse cursor in the Display Window, hold the mouse button down along with SHIFT, and move the mouse up or down.

Z Rotation

To barrel roll (rotate the molecule on the Z axis),


  • For PC users: place the mouse cursor in the Display Window, hold the left mouse button along with SHIFT as if you were going to zoom, but move your mouse left or right instead of up or down.

  • For Mac users: place the mouse cursor in the Display Window, hold the mouse button down along with SHIFT and CMD, and move your mouse left or right.

Jmol