Site Highlighting¶
Open the Site Highlighting dialog with View → Highlight Sites (Ctrl+Shift+S).
Site highlighting lets you colour-code specific lattice sites while showing the rest of the crystal in a uniform background colour. This is useful for identifying particular crystallographic positions, comparing sites from different analysis groups, or marking sites of interest.
Background Colour¶
The Background Colour controls how non-highlighted sites appear:
| Option | Behaviour |
|---|---|
| Colour picker | All non-highlighted points use this colour |
| None (Use Existing) | Non-highlighted points keep their current colouring |
Highlight Groups¶
Each group assigns a colour to a set of site numbers. You can define any number of groups simultaneously.
Adding a Group¶
- Enter site numbers in the input field using any combination of the formats below
- Pick a colour for the group
- Click Add
Site Number Syntax¶
| Format | Example | Meaning |
|---|---|---|
| Single | 5 |
Site number 5 |
| List | 1,2,3 |
Sites 1, 2, and 3 |
| Range | 10-20 |
Sites 10 through 20 inclusive |
| Mixed | 1,5-10,15 |
Sites 1, 5 through 10, and 15 |
Managing Groups¶
- Edit — modify the site numbers or colour for a selected group
- Remove — delete the selected group
- Clear All — remove all highlight groups
Applying Changes¶
- Apply All — update the viewport with all current group definitions
- OK — apply and close the dialog
- Cancel — discard changes and close
Use Cases¶
- Compare faces: Highlight (100) face sites vs (010) face sites in different colours
- Mark crystallization order: Highlight sites that crystallized first vs last
- Quality control: Check that site numbers from analysis match the expected crystal positions
Notes¶
- Site numbers correspond to the
site_numbercolumn in the XYZ data (column 7 if present) - If a site number does not exist in the loaded crystal, it is silently ignored
- Highlighted groups are cleared when a new XYZ file is loaded