Summary:
Some macOS users report a display bug in EndNote 2025, where either:
- The entire application window appears purple, or
- A purple square appears when inserting PDFs
This issue is primarily observed on macOS versions like Sonoma (formerly referred to as “Tahoe”), but is not limited to it. The cause can vary, including layout constraints or Xcode interference.
Recommended solutions
1. Terminal command – reset layout constraints
Applies when: the entire EndNote program window appears purple due to macOS layout issues.
Tips! This YouTube link shows how to open the terminal server: How to open the terminal
Steps:
- Open the Terminal application (Applications > Utilities).
- Enter the following command:
defaults delete com.ThomsonResearchSoft.EndNote NSConstraintBasedLayoutVisualizeMutuallyExclusiveConstraints
- Press Enter, then restart EndNote.
2. Disable or remove Xcode
Applies when: the purple window or purple square appears and Xcode is installed on the machine.
Why: Xcode has been identified as a trigger for layout rendering bugs in EndNote.
Steps:
- Open Spotlight Search (⌘ + Space), type “Storage Management”, and press Enter.
- Select Applications in the left panel.
- Find Xcode, right-click and select Delete.
Note: this removes Xcode from your Mac and also prevents future automatic updates unless reinstalled.
3. Reset EndNote preferences
Applies when: the above solutions do not resolve the issue.
Steps:
Follow Clarivate’s official guide: EndNote - delete & recreate preferences