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Example structure: Lysozyme

In this tutorial, we will use lysozyme bound to a as our example structure. In the , the protein is shown in blue ("deep sky blue", to be exact) as a carbon alpha trace, and the carbohydrate is shown in all-bonds, colored using the CPK color scheme. Lysozyme was the first enzyme structure to be solved.

Basic reading and viewing

• Read the text (tell your browser if you need a bigger font by clicking control-plus) and use the scroll bar on the right to navigate.
• Click on : While reading, as you encounter , click on it to get a new figure the the 3D window integrated into the text. Sometimes the 3D window is not visible on the screen, and you have to scroll up or down to find it. If you want to check out regular hyperlinks, try right-clicking it to open the link in a new tab of your browser.
• Look at the 3D figures: The text should explain what you see. Is it an overall view or a zoomed-in detailed view? Do you know what the colors mean? Are there any labels? You can learn more about the depicted structure by using techniques explained in the following sections. If the figure is too small, either make it bigger using the magnifier glass at the bottom of the 3D window (this will squeeze the text, though) or open a new window using the popup control at the bottom of the 3D window (you will have to update this after clicking on green links, though).
• Use the mouse to rotate the 3D figure: To really appreciate the three-dimensional nature of proteins and other molecules, you should drag the molecule to change the view. Imagine that when you drag, you are holding on to the atoms in the foreground, and dragging them while the center of rotation stays put. Try it! After rotating the molecules, can you see any features that were hidden before? Does it become easier to visualize the three-dimensional shape as you move the molecule?

Using the mouse

• Identifying atoms: Make sure the molecule is not spinning on its own (you can turn that off in the 3D browser by clicking the "+/- spin" text on the bottom). Then, hover (i.e. point with the mouse pointer without moving or clicking) over an atom, and a small pop-up text will appear. Try it! Here is an example text: "[ALA]23:A.CA #252" illustrating the format. It shows that the atom hovered over is part of alanine (ALA) residue number 23 of chain A (or subunit A). The atom is an alpha carbon (CA) and has the serial number 252 in the coordinate file.
• Pressing shift: When you press shift while dragging the molecule, the mouse pointer will look differently, and behave differently. Now, dragging up and down will zoom in or out, and dragging left and right will rotate the molecule around the z-axis. Try it! If your screen is touch-sensitive, you can also zoom with the usual two-finger pinch gestures. To move (translate) the molecule, press shift, double-click and drag. If your screen is touch-sensitve, you can also drag with two fingers. Try it! After you moved the molecule, it will still rotate around the old center of rotation (below we'll discuss how you can use the menu to change the center of rotation).
• If you get lost: Sometimes, after zooming or rotating, the molecule is gone, or you loose your bearings. To get back to the original view, press the green link again.
• Measuring: To measure distances, angles and torsion angles, you start by double-clicking an atom. For a distance, you just double-click a second atoms, and the distance appears. Repeating the process will erase the distance measurement. For angles, you need to define three atoms, with a double-click, click, double-click sequences. For torsion angles, ou might have guessed it, you need four atoms (double-click, click, click, double-click). If you clicked on the wrong atom midway, click on an empty space to cancel. Try it!

Using the Jmol menu

The menu is quite extensive, and we will only discuss a small subset here. To open the Jmol menu, press control and click the mouse with the mouse pointer in the 3D window, or right-click the mouse if possible.

• Select menu: The "select" submenu has lots of options to select different parts of the molecule. The number in parenthesis after the word "select" indicates how many atoms are selected at this moment. Before you start playing with the selection menu, check the "Selection halos" box in the submenu. Once checked, selected atoms will be shown with yellow circles around them. Try Select->Protein->By residue name->Ala to select all the alanine residues in the protein. (Notice the clusters of halos corresponding to alanine residues). Then, try something else like selecting all sulfur atoms in the structure. Each new selection will deselect previous selections.
• Change representation: The "style" submenu allows you to change how the selected atoms are represented. Try first selecting all alanine residues, and showing them as ball and stick by clicking Style->Scheme->Ball-and-stick.
• Change colors: The "color" submenu allows you to choose colors for the selected atoms (and the other drawing objects such as secondary structure cartoons associated with those atoms). Try making the alanines violet by using Color->Atoms->Violet
• Center on an atom: If you want to explore a part the depicted structure in detail, it makes sense to change the center of rotation. Use Set picking->Center and then click on an atom in the region of interest. Now, the atom will be the new center of rotation (i.e. not move while you rotate the molecule) and will stay in the picture no matter how far you zoom in. Try it! Once you have defined a new center of rotation, you might want to turn off the centering with Set picking->None (the default behavior). Otherwise, you will recenter every time you click on an atom.
• Add labels: To add labels indicating the residue name and number, use Set picking->Label. Clicking on any atom will add a label, and clicking a second time will delete it again.

Using the console

The console is a way to pass any command to Jmol. As a casual user of Jmol, you only need to know a handful of commands not available through the menu. If you become a frequent user of Jmol, you might stop using the menu and type commands instead once you are familiar with them. To open the console, use the menu item "Console". Try it.

• Finding a residue: If you want to find a specific residue in a structure and you know the residue number, say residue 72, type "center 72" in the console. You can also select it by typing "select 72", and then change how it is represented in the 3D figure by using the menu.
• Selecting multiple parts of the molecule: When using the menu to select, each new selection command cancels the old one. Using the console, you can type something like "selected selected or 33" to add residue 33 to your selection. You can also select multiple parts of the structure in a single command like "select (42, 67, 82) and sidechain and _C", which would select all carbon atoms in the side chain of residues 42, 67 and 82. You can learn common selection command in this tutorial. The complete set of selection commands is explained in the Jmol manual.
• Showing hydrogen bond: Select the entire structure or parts you are interested in (e.g. "select backbone and helix"), then type "hbonds calculate" in the console. This will calculate possible hydrogen bonds and display them.
• Increasing the size of labels shown when hovering: When giving a presentation and projecting a page, the "hover labels" are sometimes too small and too complicated to be appreciated by the viewers. A command like

hover "%n%R %a"; font hover 30

will help.