Molecular Representations

Several kinds of molecular representations are available in Chimera:

wire stick ball-and-stick CPK

The draw mode is an attribute of individual atoms and bonds, whereas wire linewidth is a model attribute. Thus, different parts of a single model cannot have different linewidths, although they can be in different representations.

Proteins and nucleic acids can be drawn as a ribbon. Protein secondary structure can also be shown with PipesAndPlanks, and special representations of the base and sugar components of nucleic acids (combined with sticks in the figure) can be generated with the Nucleotides tool.

ribbon pipes-and-planks VRML nucleotides VRML

Ribbon display is an attribute at the residue level. The pipes-and-planks and special nucleotide representations are VRML objects and can only be displayed/undisplayed as a whole.

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

Molecular surfaces can be created, displayed, and manipulated in real time. A molecular surface can be generated with the Surface section of the Actions menu or the command surface.

solid surface mesh surface dot surface

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

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

M.F. Sanner, A.J. Olson, and J.C. Spehner, "Reduced surface: an efficient way to compute molecular surfaces" Biopolymers 38:305 (1996).
A molecular surface consists of probe contact plus reentrant surface; this is different from the surface traced out by the probe center (often called the solvent-accessible surface). The probe radius and density of vertices can be adjusted in the surface attributes panel.

Dot molecular surfaces in MS/DMS format (calculated and written out by a separate program) can also be displayed in Chimera.

Other Surfaces

vdw surface
A van der Waals (VDW) surface differs from a molecular surface in that fine crevices are not smoothed. A VDW dot surface can be displayed with the command vdw and its dot density adjusted with vdwdensity. The VDW dot size and dot density can also be adjusted in the the molecule model attributes panel. Note that the sphere representation of atoms also reveals the VDW surface.

Other types of surfaces that can be shown in Chimera are: