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This chapter discusses various advanced topics in Cn3D:
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Animation controls
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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.
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Visualizing crystallographic disorder
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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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Pattern searching
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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.
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Importing user PDB files
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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.
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Stereo views
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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).
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