The PopUp Menu
Right-clicking within the Jmol viewer will open the popup menu, which affords many options for changing the appearance of the model. The best way to learn about the ways in which Jmol can project a model is to 'play around' with these options. The following is a very brief guide to using the Select, Render and Color submenus.
Selecting part of the molecule
A particular appearance can be applied to the whole molecular model or some specific component, as selected under the 'Select' submenu. Here, you can select structural components of protein, nucleic acids, hetero structures that are neither protein nor nucleic acid, specific element types, etc.
Rendering Atoms and Bonds
Once a structure has been selected, the atoms and bonds can be drawn (rendered) in several styles. Most commonly, atoms are presented as spheres, which may be sized relative to electron cloud radius of each atom (CPK), or by arbitrary values selected under 'Atoms'. Bonds are typically shown stick-like with diameters sizable under 'Bonds'. 'Wireframe' reduces the molecule to a thin line between the positions of the atoms.
Rendering Structures
The molecular model can also highlight various structural components. 'Backbone' accentuates the peptide bonds of proteins and sugar-PO4 linkages of nucleic acids; 'Trace' does likewise, but as a smooth line interpolated along the path of the backbone; as does ''Ribbons', but as a flat ribbon. 'Cartoon' is a particularly informative by differentially rendering secondary structure of protein (alpha helices and beta sheets); and for nucleic acids, shadowing ring-structures of the nitrogenous bases.
Coloring Structure
Molecular structures can be colored as desired. Specific colors can be assigned to atoms and bonds, or a coloring scheme can be applied. A unique color will be assigned to each element by 'CPK', to each amino acid by 'Amino', to different secondary structures, or each peptide chain. These schemes can be applied to atoms, bonds or structure renderings.
This page gives a brief overview of some of the ways in which the Jmol image can be manipulated, by rotating or moving the image in the Jmol window, or by using the popup menu can be used to change the rendering of molecule. It is not intended to be complete. Further information about rendering options can be found at the Jmol Script Reference site.
Rotating the image
To rotate the image:
Along the X-axis: Hold down the Right mouse button and drag left/right
Along the Y-axis: Hold down the Right mouse button and drag up/down to rotate
Along the Z-axis: Hold down the Shift-key and Left mouse button: and drag left/right
To change the size (zoom) of the image:
Hold down the Shift-key and Right mouse button and drag up and down
To slide the image across the window :
Along the X-axis: Hold down the Control-key and Left mouse button and drag left and right
Along the Y-axis: Hold down the Control-key and Left mouse button and drag up and down