Applications
Choose the correct context-aware workflow from the Viewer Applications menu.
The Applications menu launches complete scientific workflows that sit above the everyday Viewer controls. Entries become available only when the active data provides the required context.
Applications and prerequisites
| Application | Entry point | Required context | Result |
|---|---|---|---|
| Docking | Applications → Docking → Analysis | A compatible docking result | Docking-focused analysis workspace |
| MD | Applications → MD → Analysis | An active trajectory with multiple frames | Time-series and event analysis for the simulation |
| Ligand Interaction | 2D Diagram, Interactions Table, or 3D Diagram | A detected ligand in the active structure | Complementary views of ligand contacts |
| Annotations | Applications → Annotations → Show / Hide | Any active structure for anchored annotations | Annotation pins and review cards |
| Capsules | Applications → Capsules → My capsules | Capsule access in the current account context | Protected molecular data and provenance |
| Stories | Applications → Stories | An active scene for a new story, or access to a saved story | Full-screen narrative authoring and playback |
Context determines availability
Applications inspect the active structure, not merely everything loaded in the Viewer. If an entry is unavailable:
For example, loading a trajectory in one structure does not enable MD analysis while a different static structure is active.
Ligand Interaction views
The three ligand entries answer different questions:
| View | Best for |
|---|---|
| 2D Diagram | Reading the ligand, nearby residues, and interaction pattern as a compact schematic |
| Interactions Table | Filtering contacts and checking donors, acceptors, types, and distances |
| 3D Diagram | Understanding the spatial direction and geometry of contacts in the binding site |
Use the same ligand and interaction scope when comparing these views so that the story remains consistent.
Applications versus right-side tools
Use the right-side tools for direct scene control and focused operations such as styling, measurements, interaction visibility, collaboration, and export. Use Applications when the task has its own multi-step workspace, such as ligand analysis, MD analysis, docking, capsules, or Story Studio.
A disabled Run entry or other unavailable command is not a loading failure. It indicates that the action cannot be started in the current product or data context.
Before you open an application
- Verify the project in the top bar.
- Activate the correct structure on the left.
- Save the current viewer session if you may need to restore it.
- Confirm that the current scene shows the components relevant to the analysis.
- Use a clear active-structure name when several similar models are open.
Related
Docking Analysis
Review ranked poses, binding modes, interaction fingerprints, and pharmacophore consensus.
Ligand Analysis
Use the 2D, table, and 3D ligand views together.
Molecular-Dynamics Trajectories
Prepare and validate a trajectory before MD analysis.
Story Studio
Build a controlled narrative from viewer scenes.
Encrypted Capsules
Open protected data and verify its provenance.