with Cn3D 3.0
Dazzling Graphics with Cn3D 3.0
The newly released Cn3D 3.0 provides dazzling graphics through the use of the OpenGL graphics library. Coupled with the graphics enhancements are several new rendering options and color schemes. The Cn3D sequence window has also been refined to allow easier selection of residues, and better depiction of secondary structural elements, protein domains, and hetero-atoms alongside the sequence.
Cn3D 3.0 depicts solid objects more realistically, taking advantage of highlighting and shadowing. New rendering options include an alpha-carbon backbone worm, or coil representation at three thickness levels. Alpha-helices may now be represented either as blunt-ended cylinders or cylinders with carboxy-terminal caps to indicate the direction of the peptide chain. In addition, ions are depicted as translucent spheres. A new color scheme called Sequence Conservation offers several coloring options when multiple sequences are displayed in the sequence window.
Enhanced Functionality in the Sequence Window
The Cn3D Sequence window operates in either a single or multiple sequence mode. If a single sequence is displayed, then the window is entitled OneD-Viewer and uses a set of options suitable for operations on a single sequence. If more than one sequence is displayed, the window is entitled DDV (DeuxD-Viewer) and a set of options suitable for multiple sequences is active. Columns of a multiple alignment may be colored according to sequence conservation, for example, with these colors mapped to both the sequence and structure windows.
The Sequence window has been given several new abilities in version 3.0. Secondary structural elements are now represented as 3-D-like cartoon images beneath the sequence. NCBI-assigned protein domains are indicated using solid 2-D arrows. Hetero-atoms in the features list are indicated in the sequence display as small triangles positioned near the residues that are closest to them in the 3-D structure. As in earlier versions of Cn3D, additional sequences may be aligned to a structurally anchored sequence by importing FASTA-formatted files or by downloading directly from Entrez over the network.
DDV Viewer Operation
When a sequence alignment is shown in the Sequence window, a different set of options is available. The mouse mode may be changed, using the Options menu, from the default of Select to Query in order to use the mouse to identify residue numbers. A Styles panel, also invoked from the Options menu, allows several sequence-alignment display parameters to be adjusted. These include the use of color and the placement of ruler lines.
The enhanced graphical capabilities of Cn3D 3.0 are illustrated in the views of Human Phenylalanine Hydroxylase (PDB code 1PAH) in Figures 1 and 2. The structure window shows an image of the protein in which the NCBI-defined secondary structural elements, helices and strands, are represented as solid cylinders and planks, respectively, with the pointed ends indicating the amino- to carboxy-terminal direction. An iron atom is seen in the center of the structure, represented as a translucent sphere. Using the Annotation panel, the sites of documented mutations, as taken from Online Mendelian Inheritance in Man (OMIM), are marked by showing these amino acid side-chains in a fat-tube representation.
Figure 2: Cn3D Sequence window view of human phenylalanine hydroxylase (PDB code 1PAH).
The accompanying Sequence window shows these mutable residues in a dark shade (red). Secondary structural elements are shown below the sequence. The single NCBI-derived protein domain for this structure is indicated by the arrow that runs from residue 59 to residue 291. Residues proximal to the iron atom in the structure are marked with an H under the sequence.