Working with Jmol

Follow the links on the Jmol Home Page to download the program.

PC Users simply click the green button. Jmol downloads as a compressed (zipped) file. To extract the program:

Mac users running OS X or higher should download the version ending: binary.tar.gz, which can be unpacked/uncompressed in a shell window.

The above procedure works for all zipped files. With Jmol, the second option is easier because Jmol comes as numerous files. Go to the folder where you put Jmol and make a desktop shortcut to the file called "Jmol.jar".

Double click the shortcut to start Jmol. You should see:

Now open a PDB file. Use File --> Open:

and navigate to where you put your PDB files. (I recommend a separate folder in which you keep PDB files, with a subfolder for sequences.) Click on your choice and click OPEN.

The display of all atoms (carbon=gray, nitrogen=blue, oxygen=red) is not particularly informative. Right click in the Jmol window and choose Style --> Scheme --> Cartoon.

This should get you:

You can right click and choose Color --> Structures and explore the various options.

Parts of the structure can be selected for alternative coloring or display style; right click and choose Select:

I used the above sequence of menus to select the coppers that are the catalytic centers of this enzyme.

Jmol is based on the code for Rasmol, and has a command window like that of Rasmol. From the RightClick menu, choose Console, which opens the command window:

Jmol19 (62K)

All of Rasmol's commands, such as the "Select Within" or "Select His93" (for selecting individual residues in a protein will work.

Place the cursor in the command window:

Some .pdb files may list water of crystallization among the "hetero" set. If a bazillion water molecules (single dots) appear when you "select hetero", enter "select water" and then chose a display mode that doesn't apply to water, such as 'cartoon', and the waters will vanish.

Alternatively, try "select ligand" instead of "select hetero". Even better, inspect the pdb file with a text editor and locate the name that has been assigned to any ligands present. Then type "select ligand name" in the console window.

If you know which amino acids are in the binding site for your ligand, you can now repeat the selection process for each in turn. Type, for example, "select Tyr100", then change the display mode and color, and repeat for each identified residue.

If you are not sure about the groups around your ligand, you can use the "within" modifier to the select command:

select within (distance, target)

In this command, "distance" is a distance in Angstroms, corresponding to the radius of a bubble around the target. Anything within this distance is selected.

For example

select within (4.0, Ca)

selects all atoms within 4.0 A of the calcium ion in a protein

You can then manipulate the display as above to visualize the residues.

You can limit the display to those items selected by typing "restrict selected" in the command window. All of the protein except the selected elements will disappear.

Ligand on Cu 1503 in Laccase

To identify the species now displayed, use the label command:

label %n%r

The "%n" calls for the residue name, and the "%r" gives the residue number. Alternatively, click on the species in the display window, and the command window will identify it. Label colors can be changed by using "color label colorname".

If the portion of the molecule you want to examine is somewhat buried, the "slab" command may be helpful.

Jmol keeps track of the commands you issue, and will write them to a file, called a script, that you can use to reproduce any display. When you are satisfied with the display you have created, type in the console window:

write script 'filename.scr'

where 'filename' is the name you choose for the script file. To load the structure display again, just type:

script 'filename.scr'

The script will run, and the display will appear.

If you have the Adobe Acrobat Reader on your computer, you can download here a Quick Reference Card that summarizes Rasmol commands. If you don't have Acrobat, click the icon below to download a FREE copy.


The best thing to do is to download some proteins or nucleic acids, and explore what the various right click options allow you to do to change the display. Finally, when you have an image that you like, you can save it as a graphic. Select File -> Export -> Export Image, and you can save the graphic as a jpeg file.

Jpeg and png graphics both are easily incorporated into Word documents using Insert --> Picture --> From File. The camera button on the Jmol toolbar also allows saving images, and includes several more file formats.

Finally, there is a very extensive help application built into Jmol.

This page last modified 2:28 PM on Monday January 3rd, 2011.
Webmaster, Department of Chemistry, University of Maine, Orono, ME 04469