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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis, Angel Herraez

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 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.
+*'''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
-*'''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
+*'''Recenter''': 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!
-*'''Recenter''': 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. 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.
-*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.