The Proteins Preferences dialog lets you adjust how protein information is displayed.
On Windows, this dialog is accessed via the command Edit > Preferences. On Macintosh, it is accessed using Protean 3D > Preferences (macOS 12 and lower) or Protean 3D > Settings (macOS 13 and higher). If the Proteins section is not already active, click on the word "Proteins" on the left.
- In the Assignments drop-down menu, select whether you want the default rendering for protein structures to be Calculated (KSDSSP) (Kinase Sequence Database secondary structure prediction) or Annotated.
- In the Nomenclature drop-down menu, specify whether mutations should use 1-letter, 3-letter, or Genome (HGVS) (Human Genome Variation Society) amino acid codes.
- In the Cutoff distance (Å) section, specify the likelihood that an item will be considered a “neighbor” of the current selection. The default value of 4.0 Å is optimal for most circumstances.
Click Apply to save your changes while keeping the preferences dialog open, or Apply and Close to save the changes and exit from the dialog. If you instead wish to return to default settings for all four drop-down menus, click Restore Defaults. To leave the dialog without applying changes, choose Cancel.
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