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."

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:

• the Actions menu can be used to switch among wire, stick, ball-and-stick, and CPK representations of atoms and bonds, change wire linewidth, add a ribbon to models containing protein or nucleic acid, or change the type of ribbon shown
• the command linewidth controls the thickness of lines drawn to show bonds in the wire representation
• the command represent can be used to switch among wire, stick, ball-and-stick, and CPK representations of atoms and bonds
• the command ribbon can be used to add a ribbon to models containing protein or nucleic acid
• the command ribrepr can be used to change which type of ribbon is shown (flat, edged, or rounded)
• Ribbon Style Editor can be used to change the ribbon cross-section (the width and height used to indicate different types of secondary structure)
• the molecule model attributes panel can be used to:
  • switch among wire, stick, ball-and-stick, and CPK representations of atoms and bonds
  • change wire linewidth and line type (can even be dotted or dashed)
  • change stick diameter and ball size
  • add a ribbon to models containing protein or nucleic acid
  • change which type of ribbon is shown (flat, edged, or rounded)
• the pseudobond attributes panel can be used to:
  • switch between wire and stick representations of groups of pseudobonds
  • change linewidth and line type for pseudobonds in the wire representation
  • change stick diameter for pseudobonds in the stick representation
• after a selection of atoms, bonds, and/or pseudobonds is made, its representation can be altered with the Selection Inspector
• PipesAndPlanks can be used to add a VRML pipes-and-planks representation if the model contains a protein with PDB secondary structure records

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.

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

• the Actions menu
• the command msms repr (same as surfrepr)
• the surface attributes panel (also allows changes in mesh line width, dot size, and dot density)

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). 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.