Jmol console commands: a brief introduction

BIMS/Biochemistry 503
David Auble

Access the menu and open the console (a menu option) by placing the cursor over the Jmol window and control-clicking on a Mac (or right-click on a PC). Using the menu options you can spin, zoom, select molecules or parts of molecules and alter their color, presentation, etc. To enter your own commands is easy: in the menu select console -> open. In the console command window, type "select" followed by the feature whose presentation you would like to manipulate. Follow this with a semicolon, a single space, and then type how you would like the feature to be displayed. When using either the menu or the Jmol console, it is possible to alter the presentation of a macromolecule in many ways (by for instance, changing the color of a selected feature). If you find that the display has been changed in a way that you don't like and don't know how to reverse, it is simplest to reload the page, thereby "erasing" the changes you have made. On some pages there is a reset button that does the same thing. It is important to remember that if a molecule is loaded in the window, it works best to turn off the display feature that you want to change (e.g. get rid of a spacefilling model using the command "spacefill off"), then redefine it using another command (see the second and fourth examples below). If you don't do that, the different types of displays will be superimposed on one another and it will probably be hard to see what is going on. I find that spacefilling and cartoons displays are most informative for protein; wireframe and cartoons are usually most informative for DNA. Notice how displaying the molecules in different ways provides different types of information. Here are examples of some of the more common console commands:

select protein; cartoons; color red
select nucleic; spacefill off; wireframe; color purple
select all; spacefill
select protein; spacefill off; backbone
select 138; color green
select 138:a; color blue
select :a; color yellow

In the examples above, "138" refers to amino acid residue 138 and "a" is chain a. Thus, "138:a" selects residue 138 in chain a. In a particular display, to determine which chain is which or what a particular residue or atom is, hover the cursor over the region of interest and a label will appear. Alternatively, if you click on an atom, a label will appear at the bottom of the browser window. One can also select hetero (heterogeneous atoms including water, ions and ligands), select helix or select sheet to highlight secondary structure, or select backbone or select sidechain. Particular kinds of amino acids can be selected by typing the three letter amino acid abbreviation (e.g. select arg). To select multiple residues, separate the residue numbers by a comma and a space. If you'd like to select a number of consecutive residues, select the first and last residue number separated by a hyphen. Display options such as wireframe, spacefill and backbone often have a default thickness which can be altered by adding a number value after the command. To obtain a more robust wireframe image, for example, type:

wireframe 50

"Restrict" is useful for restricting the display to only those parts of the structure specified in the command. For instance, typing:

restrict protein

will limit the display to only protein.

In some instances, the molecule or feature that you're trying to see will be inappropriately sized in the window. In that case use the zoom command. Typing "zoom 200", for instance, will double the size while "zoom 50" will halve the image size. To reset the image size, type "zoom 100".

Features of interest can also be labeled using the label command. To label a particular residue, it is best to choose a single atom in the residue to append the label, otherwise each residue atom will bear a label. Choose a particular atom number by hovering over an atom in the residue of interest. For example, the command:

select atomno=4803; label Lys15

will add the label "Lys15" adjacent to atom #4803

Additional scripting resources. For detailed information on scripting commands and many additional examples, see this terrific tutorial.
You can also display molecules in Jmol by simply clicking the link in an RCSB page. This means that you can customize the view of any structure in the RCSB Protein Data Bank in the same way. Here is additional info about how to do this.

Saving and printing images. Unfortunately, while one can export images from the Jmol application, there is no export option for the Jmol applet. However, on a Mac running OS X, you can obtain a reasonable image for subsequent use by saving a screenshot. (I have little familiarity with PCs, but it should be possible to obtain a copy of the image using the Print Screen key.) To obtain a screenshot on a Mac, try one of the following combinations of commands. If you save the shot on the clipboard you can then paste it into the desired application for editing. If you save it as a file, you may need to hunt for it on your hard disk.

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