Measurements & Annotations
Measure molecular geometry accurately and attach review context to specific locations in the structure.
Use measurements for quantitative geometry and annotations for review context. Both are tied to the molecular scene, but they serve different purposes: a distance answers “how far?”, while an annotation records “why does this location matter?”.
Measurement types
| Measurement | Required atom picks | Result |
|---|---|---|
| Distance | 2 | Length in ångström (Å) |
| Angle | 3 | Angle in degrees |
| Dihedral | 4 | Torsion in degrees |
The order of picks matters for angles and dihedrals. Choose atoms in the same logical order you would use to describe the geometry.
Create a measurement
Measurement mode targets individual atoms even if your previous working granularity was broader. Zoom into the area and use a detailed representation before picking crowded atoms.
Make a measurement presentation-ready
For each active measurement, adjust the available appearance controls:
- Font size.
- Text and outline color.
- Line color for distance, angle, and dihedral geometry.
Choose colors that remain legible against both the background and the molecule. Avoid placing many overlapping measurements in one scene; create separate saved states for separate conclusions.
Remove or clear measurements
Remove an individual measurement from its entry when you no longer need it. Use Clear All Measurements only when you intend to remove every measurement from the active scene.
Save a named viewer session before clearing a review scene with important measurements. History is useful during the current session, but a saved viewer session is the durable recovery point.
Measurements in trajectories
Measurements stay anchored as you move through trajectory frames, allowing the displayed value to follow the changing coordinates. For a reliable comparison:
- Pause on the frame of interest.
- Confirm the atom identities and pick order.
- Create the measurement.
- Scrub to additional frames and observe the change.
- Record important frame numbers in an annotation or review note.
Add an annotation
Annotations are 3D pins attached to a molecular location. A pin can include a title, note, author, time, and type/color. Built-in categories include Note, Clash, Question, Idea, and Important, with support for custom types where available.
Write annotations for handoff
A useful annotation answers three questions:
- What did you observe?
- Where is it anchored?
- What should the next reviewer decide or do?
Prefer “Possible steric clash between ligand O3 and THR A:54; review pose refinement” over “Check this.”
Measurements versus annotations
| Use | Measurement | Annotation |
|---|---|---|
| Quantitative geometry | Yes | Mention the result only as context |
| Review question or decision | No | Yes |
| Visible geometric line in the scene | Yes | No |
| Authored note with category | No | Yes |
| Dynamic value across trajectory frames | Yes | Use the note to record relevant frames |
Annotations are an interface overlay and may not be included in exported images or story scenes. If text must appear in the exported result, validate the export preview and use supported labels, measurements, or story subtitles.