Lectura y visualización básicas

• Lee el texto (si necesitas un tamaño de texto mayor, cámbialo en el navegador pulsando las teclas Control y Más (+)) y avanza usando la barra de desplazamiento a la derecha de la pantalla.
• Pulsa en los : Mientras vas leyendo, si encuentras un y pulsas sobre él se mostrará una imagen nueva en el panel 3D integrado con el texto. A veces el panel 3D no está visible en la pantalla y es preciso desplazarse arriba o abajo para verlo. Si quieres visitar enlaces normales, conviene que pulses con el botón derecho para que se abran en otra ventana o pestaña del navegador y así no perder la página de Proteopedia.
• Observa las imágenes 3D: el texto debería explicar lo que muestran. ¿Es una vista general o la ampliación de un detalle? ¿Sabes lo que representa cada color? ¿Hay alguna etiqueta? En las secciones siguientes se explican formas de aprender más sobre la estructura que se muestra. Si encuentras la imagen demasiado pequeña, puedes aumentarla pulsando en el botón [🔍+] situado bajo el panel 3D (esto estrechará la zona del texto) o bien abrir una ventana nueva pulsando el botón "popup" situado también bajo el panel 3D. Ten en cuenta que esta vista ampliada en ventana nueva no se actualizará automáticamente cuando pulses en un nuevo enlace verde en la página.
• Usa el ratón para girar la imagen 3D: Para apreciar realmente la naturaleza tridimensional de las proteínas y otras moléculas deberías arrastrar el puntero del ratón para cambiar el ángulo de visión. Imagina que cuando arrastras con el ratón es como si agarrases los átomos del frente y los desplazases, mientras se mantiene fijo el centro de la molécula. ¡Inténtalo! Tras girar la molécula ¿puedes ver algo que antes estaba oculto? ¿Hace esto más fácil visualizar la forma tridimensional según vas moviendo la molécula?

Más uso del ratón

• Identify 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.
• Press 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).
• Start over: Sometimes, after zooming or rotating, the molecule is gone, or you get lost. To get back to the original view, press the green link again.
• Measure: 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!

Uso del menú de Jmol

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 parts: 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. 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
• Re-center: 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!
• 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. Once you are done, you might want to turn off picking by Set picking->None (the default behavior). Otherwise, you will add labels every time you click on an atom.

Uso de la consola

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.