Wireframe, Stick, Ball and stick, Space-filling/CPK
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Four different ways of visualizing molecules by showing all atoms are provided: Wireframe, Stick, Ball and stick, and Space-filling/CPK.
The visualizations are mutually exclusive meaning that only one style can be applied at a time for each selected molecule or atom group.
Six color schemes are available and can be accessed via right-clicking on the visualization style icons:
- Color by Element Classic CPK coloring based on atom type (e.g. oxygen red, carbon gray, hydrogen white, nitrogen blue, sulfur yellow).
- Color by Temperature For PDB files, this is based on the b-factors. For structure models created with tools in a CLC workbench, this is based on an estimate of the local model quality. The color scale goes from blue (0) over white (50) to red (100). The b-factors as well as the local model quality estimate are measures of uncertainty or disorder in the atom position; the higher the number, the higher the uncertainty.
- Color Carbons by Entry Each entry (molecule or atom group) is assigned its own specific color. Only carbon atoms are colored by the specific color, other atoms are colored by element.
- Color by Entry Each entry (molecule or atom group) is assigned its own specific color.
- Custom Color The user selects a molecule color from a palette.
- Custom Carbon Color The user selects a molecule color from a palette. Only carbon atoms are colored by the specific color, other atoms are colored by element.