This chapter discusses various advanced topics in Cn3D:

• Animation controls
• Visualizing crystallographic disorder
• Pattern searching
• Importing user PDB files
• Stereo views

Cn3D provides animation controls to either manually or automatically flip through a set of models. This is a convenient way to see individual molecules out of a set that can come from a VAST alignment of several proteins, an NMR structure that has multiple models, or multiple alternate conformers from a disordered crystal structure (see the next section for more on disorder).

For example, the figure below is the MMDB structure 1ZNF. This is a zinc finger NMR structure that contains 37 models, each of which has a zinc ion bound by two cysteines and two histidines. In order to see all models of an NMR structure, when downloading multiple structures from MMDB make sure the "All Models" option is specified.

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

The animation controls are in the View:Animation submenu. Use Play Frames to flip through all the models; the speed of the animation is controlled with Set Delay - the smaller the number (in milliseconds) the faster the animation. Stop will halt the animation.

You can also do View:Animation:Spin to automatically rotate the view.

Some X-ray crystal structures deal with disordered groups by depositing multiple coordinates for the disordered atoms. These alternate conformers can be viewed with Cn3D, and when run in an animation, provide a quick way to simultaneously visualize all the disordered groups in a structure.

For example, try loading into Cn3D the MMDB entry for 3LZT, the structure of chicken lysozyme. In order to see all alternate conformers, the option "All Models" must be selected in the MMDB structure summary page before downloading the data.

This structure has three sets of alternate coordinates for a variety of residues around the surface of the protein. One can loop through these sets with the same animation controls discussed above. It is probably easiest to see the disordered atoms - mainly sidechains - when using a Style:Rendering Shortcuts:Wire display.

The PDB format does not distinguish between correlated and uncorrelated disorder. Cn3D displays all disorder as if it were correlated. In some cases, a set of alternate conformers is incomplete, as in the case of 3LZT, where for some groups, the authors provide two sets of coordinates, and for others, three. Cn3D will select an arbitrary set of coordinates to fill in an incomplete ensemble, meaning that if ensemble number three is selected for display, and some groups have only two sets, then the coordinates of another set are "borrowed" to fill in the third set for those groups. Otherwise some atoms would seem to "disappear" when viewing a set beyond the number of alternates provided for those atoms.

Cn3D 4.0 includes a pattern search engine, so that you can find and highlight groups of residues in particular order. This is done through the View:Find Pattern menu items in both the alignment and import windows. Simply fill in a pattern specification (in ProSite syntax) in the dialog, and all non-overlapping matches in all sequences in the window will be highlighted.

Some users may wish to view their own, custom PDB files in Cn3D. Cn3D doesn't import PDB files directly, but it is possible to convert PDB files into ASN1 data with a service provided through NCBI's website. Note that this is not guaranteed to work with PDB files that do not conform very closely to the standard; those exported from modeling or other chemical software are often substandard, especially when non-natural residues are present. Use this at your own risk!

Through the VAST search page one can upload a structure (confidentially) to NCBI, where it will be converted to ASN1 data. The intended purpose of this page is actually to allow one to do a structure comparison search against MMDB. The resulting data and alignments can then be downloaded as ASN1 data and viewed in Cn3D.

Stereo views are available in Cn3D as of version 4.3 and can be turned on using the "View | Stereo" menu option. They show a structure in side-by-side stereo, as in the example below of the Tumor Suppressor P53 Complexed With Dna (1TUP).

...click here to launch the structure in Cn3D, then select the "View | Stereo" menu option to replicate the view shown here.

You can control the specifics of the stereo display using the "Preferences" panel, "Advanced" tab:

Eye separation controls the depth of the perceived stereo: By default, the structures are displayed with an eye separation of 5 degrees. A typical range of eye separation is 3 to 6 degrees; at less than 3 degrees, the stereo effect goes away and it's difficult to see depth.

A Proximal toggle switch changes the direction in which the second copy of the structure is rotated. The default setting is distal (uncrossed) stereo, and the toggle switch can be used to change the display to proximal (cross-eyed).