CrystalMaker Help > Guide > Building

Icon

Model Type

CrystalMaker provides a number of pre-set model types for every structure. You can instantly switch between these structural representations using the Model menu:

Space Filling

Space Filling models plot atoms at their correct relative sizes. If bonds have been defined, then atom overlap corrections are applied, so that spheres appear to blend into each other.

Ball-and-Stick

Ball-and-Stick models are a popular way of visualizing atomic positions and connectivity. By default, atoms are plotted as spheres, at 40% of their space-filling radii, with a minimum size of 0.15 Å.

You can customize the relative sizes of ball-and-stick spheres, using the Model Options window (Model > Model Options). Choose the Atoms pane, then edit the Relative Radius and Minimum Radius fields.

Different styles of atom spheres (e.g., rendered, translucent, "beach ball", etc.) can be chosen from the scrolling list in the Atoms pane.

Stick

Stick models hide the individual atom spheres and emphasize the connectivity of a structure. Bond cylinders or lines are drawn between atom centres.

You can customize bond colours and styles (e.g., rendered cylinders, striped segments, etc.) using the Bonds pane of the Model Options window.

Wireframe

Wireframe models are similar to stick models, but faster to manipulate because there is less rendering required. These models are ideal for complex structures, where you need to visualize large-scale topologies.

Polyhedral

Polyhedral plots provide great flexibility, with the possibility of displaying both coordination polyhedra and ball-and-stick styles within the same model.

Use the Atoms pane of the Model Options window to specify different styles for each site or chemical element.

Thermal Ellipsoid

Thermal Ellipsoid plots are available when your crystal structure has temperature factor data (sometimes called "atomic displacement parameters").

The directions and extents of atomic motions, or positional disorder, are indicated by probability surfaces - in the shape of ellipsoids (for the general case), or spheres (isotropic temperature factors).

You can control many aspects of your thermal ellipsoid model using the Atoms pane of the Model Options window.

  • Choose an ellipsoid style from the Ellipsoid column of the scrolling list.
  • Disable ellipsoid rendering for certain sites, by turning off the Ellipsoid checkbox for those sites (small spheres will be drawn instead, with radii given by the Sphere Radius text field)
  • Choose the probability level using the Probability text field