The BayesFold format palette contains options for decorating the structure drawing. This palette is broken into three tabs: Formatting, Advanced, and Print & Save. The first two are discussed here, while the third tab is covered in its own section, Chapter 8, Printing and Saving.
When changes are made an element on any tab, the palette's "Apply" and "Cancel" buttons are enabled. Click "Apply" to make the formatting changes that you have specified, or click "Cancel" to discard your changes. Clicking the "Reset" button will discard all existing formatting and return the structure drawing to its default appearance.
The Formatting tab (shown below) is displayed by default when the Format Palette is opened.
It includes three groups of formatting controls.
Visibility: These option buttons control the display of elements of the structure drawing. You can independently show or hide the drawing's backbone (lines connecting adjacent bases), pair connectors, or nucleotides.
Colorings: These list boxes allows you to color the nucleotide text and/or the pair connectors so that they display one of several sorts of data (including mismatches, mutual information, pair probability, etc.) For a full description of the various coloring options and how to apply them, see Section 4, “Displaying Data on the Structure Drawing”
Nucleotide Text: These settings control the weight and style of the nucleotide text. They can be adjusted to make the text bold, italic, etc.
The Advanced tab (shown below) also contains three groups of formatting controls.
Numbers and Labels: Base numbers and "5'" and "3'" labels can optionally be applied to the structure. By default, both numbers and labels are turned off.
Global Settings: BayesFold allows you to adjust several settings controlling the structure appearance. For instance, you can change the distance between adjacent nucleotides or the height of the stems. You can also alter the thickness of the backbone and/or pair connectors; this functionality is especially useful if you have applied a coloring to the pair connectors and want to make them more visible.