This chapter uses as its example the 1D5R PDB structure; see the previous chapter for instructions on how to retrieve the data for it.

While not intended as a comprehensive reference for Cn3D's user interface, this section provides a basic overview of the program's controls, and illustrates techniques for visualizing different scientific aspects of the data:

• the structure window main menu
• the style panel
• some examples using custom settings
• Cn3D's sequence viewer

For additional information about all the program's features, there is a built-in help document that explains Cn3D's user interface and features in detail. To access it, launch the Cn3D program, then select the menu option for Help:Commands.

The File menu controls the input of data into Cn3D, and output to a variety of data and image file types; these are fairly self-explanatory. In particular, the File:Save action saves the structure along with the current view, drawing settings, and any user annotations, so that work can be saved and retrieved. The File:Export PNG item saves the contents of the structure drawing area to a PNG format image file for use in web pages or publications (like this tutorial!).

The View menu contains items that control how the structure as a whole is displayed. The whole structure can be made larger or smaller with View:Zoom In and View:Zoom Out, and the view returned to its original size and orientation as stored in the data file with View:Restore. View:Reset will fit the entire structure into the window. If there is more than one structure being viewed (e.g. a VAST alignment), or if the structure contains multiple models (e.g. an NMR structure, downloaded with all models), then each structure will be assigned its own "frame." The various View:Frame items control which frame is currently displayed. View:Animation is discussed in a later chapter.

The Show/Hide menu contains operations that allow certain substructures to be shown or hidden. The Show/Hide:Pick Structures dialog lets you choose which individual structures, chains, and domains are turned on or off. The other items in the Show/Hide menu are more relevant to alignment views.

The choices in the Style menu affect the shape and color of the different parts of the structure. For example, the default display for single structures is a combination of Style:Rendering Shortcuts:Worms and Style:Coloring Shortcuts:Secondary Structure which shows a worm backbone, no side chains, and solid objects - arrows and cylinders - to represent strands and helices. The colors are green for helices, strands orange, and coil blue.  (The location and extent of these secondary structure elements is determined by NCBI, and does not represent the helix and strand notations in the original PDB file.) Note that the arrows on the strands (and optionally on helix cylinders) always point in the N-to-C direction. The best way to learn what the other different styles are is simply to try them out!

Cn3D intentionally keeps color separate from drawing style. The Style:Coloring Shortcuts menu choices determine what properties are used to map different parts of the structure to different colors. Using these options, one can easily visualize a structure's NCBI-determined domain composition (Domain), or crystallographic temperatures (Temperature) from the PDB data, etc. The Style:Rendering Shortcuts choices determine the shape of the various parts of the structures, like Worms or Ball and Stick.

The style panel (Style:Edit Global Style) contains detailed controls for all drawing styles, colors, and labels, and is where much of Cn3D's flexibility is contained. In fact, all of the options in the Style:Rendering Shortcuts and Style:Coloring Shortcuts menus are simply convenient shortcuts to different combinations of options in the style panel.

The style panel's Settings tab has four columns of settings for the various structure elements identified on the left; these settings are applied globally to all structures. "On/Off" controls whether the elements are displayed (as well as what type of backbones are used), "Rendering" controls the geometry used to render the elements, and "Color Scheme" controls the elements' colors. Most of these can be set independently, with the exception that worm style can only be used for virtual backbones. The rightmost "User Color" column can be used to set colors for structural elements when the "User Selection" color scheme is chosen. The overall background color is also set this way.

The style panel's Label tab controls labeling of backbones, chain termini, and ions. (The actual fonts used are set from the File:Set Fonts controls in the structure window.)

The style panel's Details tab allows specific control of some geometric properties of the rendering. For example, the Details:Worm tube radius setting controls how thick the worm backbone is when a worm display is chosen.

The Style:Annotate panel is discussed separately in the annotation chapter, but briefly, allows one to set different styles and labeling for specific user-selected residues, to set them apart from the rest of the structure.

Lastly, the File:Preferences:Quality tab controls the "quality" of the OpenGL rendering. All seemingly smooth and rounded objects in OpenGL are actually constructed out of many small flat polygons. The controls on this panel determine how fine a mesh of smaller polygons is used to construct the larger objects. The popup menus give detailed settings, while the three buttons on the right are a convenience to adjust the menus to predetermined settings. There is a tradeoff between the apparent smoothness of the objects and the speed at which they are rendered: more and smaller polygons give an object a nicer rounded appearance, but take longer to draw. Thus on an older computer, a lower quality setting may be necessary for Cn3D to respond quickly enough to be useful interactively. Conversely, on a fast computer, or for saving a prettier picture as a PNG image where speed is not an issue, a high quality setting may be preferable. You can also choose between orthographic and perspective projections.

Some examples using custom settings:

Here is an image saved by File:Export PNG. This is PDB entry 1D5R, showing a close-up of the inhibitor in the active site, with element-colored wireframe sidechains, temperature-colored worm backbone, secondary structure-colored 3-d objects, and PDB-numbered labels every 5 residues. These are all set up in the Style:Edit Global Style panel.

To the right of the image is a link to a datafile of the same structure saved by File:Save. Clicking on this link will bring the structure up in Cn3D, with the initial view the same as the static image file. So for example, the user can zoom out (View:Zoom Out or View:Reset) to see how the surface of the protein has a higher temperature (more motion in the crystal) than the tightly packed core region. This demonstrates how Cn3D can be used to create and view interactive figures in a digital publication; see the annotation chapter for more on this topic.

... and click here to launch this figure in Cn3D

Here is another view of the same protein, with a wireframe backbone colored by secondary structure, 3-d objects colored by domain, and (partially transparent) solvent.

... and click here to launch this figure in Cn3D

When a single structure is loaded into Cn3D, the sequence viewer shows the sequences of all protein and nucleic acid chains in the structure. The color of each residue is coordinated between the structure and sequence windows: each letter of the sequence represents a residue in the structure, and always adopts the color of the backbone's alpha carbon (or phosphorus, for nucleotides), even if side chains are colored differently from backbone in the structure window.

The most powerful application of the sequence window in Cn3D is to allow easy correlation of residues in the sequence with atoms in the structure. This is accomplished by highlighting - just as with a text editor, click-dragging the mouse across a region in the sequence window will cause the letters to "light up", and will apply the same highlight color to the corresponding atoms in the structure window. And the converse is true as well: double-clicking a residue in the structure window will cause it and the corresponding letter in the sequence window to light up.

Thus, the user can quickly locate and highlight interesting parts of the protein from the sequence window, like a cluster of active site residues. For example, here is 1D5R after highlighting some of the key catalytic and binding residues (as identified in Lee et al., 1999):

Note that there are two numbers - sequence location and PDB-assigned - shown for the residues when the mouse is moved over the sequence. This is because the crystallized protein is partially truncated, and other highly disordered residues are left out of the refined structure; these missing regions are not displayed in the sequence (e.g. by gap characters or some other graphic device), but are accounted for in the PDB's numbering scheme. See the alignment chapter, though, for a clever way to get around this problem!