Molecular Representations

Several types of molecular representation are available in Chimera, and more than one type can be present in a single display. The default representation is a simple line or wireframe drawing in which atoms are shown as dots and bonds as wires. Further options are stick with "endcap" atoms and stick bonds, ball-and-stick with ball (small sphere) atoms and stick bonds, and sphere with sphere (full VDW radius) atoms and stick bonds. The sphere representation is also called a Corey-Pauling-Koltun (CPK) model. In addition, proteins and nucleic acids can be drawn as a ribbon, and proteins with PDB secondary structure records can be drawn as "pipes and planks."

wire stick ball-and-stick CPK ribbon pipes-and-planks

The bond linewidth in the wire representation is a model attribute; that is, different parts of a single model cannot have different linewidths (although they can be in different, non-wire representation types). Wire, stick, ball-and-stick, and CPK representations are attributes of the individual atoms and bonds (see also draw mode). The secondary structure ribbon is an attribute at the residue level. The pipes-and-planks representation is not an attribute but a separately constructed VRML object. Finally, how pseudobonds are drawn are pseudobond group attributes.

There are several ways to change or add representations:

In Chimera, all of the representation types can be manipulated in real time, unlike the space-filling models created with the commands conic, neon, and ribbonjr.


Molecular surfaces can be created, displayed, and manipulated in real time. A surface is calculated and displayed using the Surface section of the Actions menu or the command surface.

solid surface mesh surface dot surface

The surface representation can be switched among solid, mesh, and dot using:

Note that molecular surfaces produced by Chimera are created with embedded software from the MSMS package by Prof. Michel Sanner, described in:

"Reduced surface: an efficient way to compute molecular surfaces," M.F. Sanner, A. J. Olson, and J.C. Spehner, Biopolymers 38, 305 (1996).

A VDW dot surface can be displayed with the command vdw and its density adjusted with vdwdensity (density=5 in the example below).
vdw surface
The VDW dot size and dot density can also be adjusted in the the molecule model attributes panel.

Finally, isosurfaces (contour surfaces) for three-dimensional numerical data sets can be displayed with Volume Viewer and DelPhiViewer.