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.
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