Annotating a structure
This chapter describes the features of Cn3D that are used to annotate a
structure with labels and drawing
styles, to create static image files, and to save
work to Cn3D-style (ASN1) data files to reload in another session or
to use as interactive figures in an electronic publication.
Backbone and termini labels
The controls on the style panel's Labels tab (see Style:Edit
Global Style) let
one place text labels automatically at various points along the amino
acid or nucleotide chain. The Spacing dictate
the interval between labels - e.g. on every fifth residue, every twentieth,
etc. Type says whether to use one or three letter residue
abbreviations, and Numbering lets one choose sequential numbers
(1..N along the sequence), PDB-assigned residue numbers, or none. Labels will be in
a color that's visible against the background if Contrast with backbone
is checked, otherwise will assume the color of the residue's backbone.
Labels on chain Termini and Metal Ions can be controlled
here as well.
While automatic labeling is convenient, especially for large structures,
there are many cases where one might want to label and highlight individual,
user-selected residues. This is the subject of the next section.
Suppose Cn3D is being used to create a figure depicting the active site
of a protein. The user might wish to highlight specific amino acids known
to participate in binding and catalysis, using labels and contrasting
drawing styles to distinguish those residues clearly against the rest
of the structure.
This type of specialized annotation is accomplished via the
Style:Annotate dialog. This allows the user
to apply labeling and drawing settings - different from the global settings
- to residues that have been selected (highlighted) in either the sequence
or structure window.
Let's return again to the human PTEN crystal structure. Cn3D can be used
to create a figure that looks somewhat like Figure 2D from Lee
et al., 1999, showing the active site side chains around the inhibitor:
... or click here to launch this
figure in Cn3D
The procedure to create a special annotation style is:
- Highlight the appropriate residues by selecting them in the sequence
window or double-clicking on them in the structure window.
- Go to the Style:Annotate dialog, and hit New. Fill in a name
and a description for this feature. Hit Edit Style to bring up
the style panel, which will now apply only to the selected residues. Set drawing and labeling styles
as desired, probably something that contrasts with the global style
(the style applied to everything not in a specific annotation). Changes
will be immediately shown in the structure window.
- Hit "Done" in the style panel, then "OK" to create
and display the annotation.
The annotation sample above shows how the Annotate dialog was
used to create a binding pocket annotation to label and render those
specific residues. Also included is a second annotation that colors
the catalytic cysteine (C124) yellow.
The drawing and labeling settings for an annotation can be changed by
selecting a feature in the list on the left and hitting Edit and
then Edit Style to bring up the style panel for that
annotation; make the desired changes then hit "Done" to save
and show the new settings. Delete will
remove an annotation, and Move will move the annotation settings
instead to any residues highlighted at the time it is pressed.
Individual annotations can be hidden by selecting them in the list on right
and hitting Turn Off, then shown again by selecting in the list on
the left and hitting Turn On.
Saving structures and images
There are two types of file output from Cn3D: static images and data
files. Each has its advantages and disadvantages, as discussed below.
These features were used to create many of the images and interactive
figures in this document.
The File:Export PNG command saves the current contents of the
structure drawing area to a PNG
format image file, which by default has the same pixel dimensions as the original,
but can be saved to a much larger high-resolution file, e.g. for hardcopy.
These files can be viewed by most modern web browsers and word processors,
and because of their good data compression and full color support, are
ideal for inclusion in electronic publications.
The File:Save command saves the current view to an ASN1 data file,
which is the type of data Cn3D reads. The resulting file contains all
the structure and sequence information present in the original data, along
with the current model orientation (rotation/zoom), any additional sequences
imported, global drawing and labeling settings, and user-defined annotations
(as discussed above). This serves two purposes: first, it lets one save
one's work to a file, as with word processors or other editing software,
to store for retrieval in a later session. Second, and perhaps more importantly,
it lets one use a saved Cn3D session as an interactive figure, which is
the subject of the next section.
Using Cn3D for interactive figures
Throughout this tutorial there appear examples of "interactive figures:"
images with links to downloadable data, that when loaded into Cn3D, reproduce
the image within the interactive environment of Cn3D's interface. Thus
one can prepare a static image that can be used as a traditional illustration
in a digital publication, with the advantage that the user can further
explore the structure(s) and sequence(s) by loading the data into Cn3D.
Then when the program is launched with this data, the initial view will
be the same as in the static image, giving the user a good starting point
to interactively investigate the information being presented.
This is very easy to do: use File:Export PNG and File:Save
to create the static image and data file, respectively, without changing
the structure between these operations. Then link the data file to the
image in some context with the ability launch Cn3D with the name of the
data file as the command line argument.
In a web page, simply use the usual anchor link mechanism to attach the
data to the image. Using the example from above, click on the image to
load the same figure and view into Cn3D:
The more complicated part is setting up the web server to send the data
with the correct mime type, so that the user's browser knows to launch
Cn3D on the downloaded data. NCBI currently uses Apache,
which is controlled by a .htaccess file with the line:
AddType chemical/ncbi-asn1-binary .cn3
This tells Apache to send files with the .cn3 ending as the mime type
a web browser uses to launch Cn3D. Other web servers may have different
mechanisms to do the same thing; consult the server's documentation for