This is the main dialog for creating and modifying Representations. It can be opened by either The dialog can be used in two modes, depending on what items the user selected:
  • If a Representation in the GeometricControl is selected, the dialog will modify this Representation.
  • If a molecular entity in the MolecularControl is selected, the dialog will create a new Representation.
To distinguish between these two modes, the caption of the dialog and the apply button differ, depending on which mode is currently active.

Model Settings

The left side of the dialog contains all control elements for the model settings.


In the upper left side the user can select the model. Currently BALLView provides the following models:

Model Note
Line very fast, first choice for very slow computers
Ball and Stick can also show aromatic and multiple bonds dashed (see Advanced Options)
Van der Waals  
Solvent Excluded Surface  
Solvent Accessible Surface Currently still very slow and buggy
Cartoon Use best with coloring mode SecondaryStructure
H-Bonds See here
Forces Invisible if no forces are acting on atoms.


Every model can be created in at least four different resolutions to comply with vastly different graphic performances of today's computers. Try setting the detail level to "low" if the graphics are bucking while rotating the view. The detail level of all surfaces can be set in smaller steps by using the according slider below. The image below shows a Ball and Stick model in three different detail levels.

Drawing Mode

BALLView provides three drawing modes: solid, wireframe and dots.
Hint: For images like above try the wireframe mode for surfaces with a resolution below 3.5 and with a transparency around 80%.

Coloring Settings

Coloring Method

BALLView currently supports these coloring methods:
  • by element
  • by residue index
  • by residue name (a different color for every amino acid)
  • by residue type (polar, hydrophobic, ...)
  • by secondary structure
  • by atom charge
  • by atom distance (use with Selection)
  • by temperature factor (read from PDB files)
  • by occupancy (read from PDB files)
  • by forces
  • by chain
  • custom (one single color)
Informations on how to color Representations from three-dimensional data grids can be found here.