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The Nomosis Viewer

The Nomosis Viewer

Choose the right workflow to visualize, analyze, review, and present molecular structures and trajectories.

The Nomosis Viewer is the scientific workspace for molecular structures and simulations. Start with a guided path or move directly to the capability that matches your current scientific goal.

Nomosis Viewer with the 1CBS protein-ligand structure open, Structure Hierarchy on the left, the molecular scene in the center, and Display controls on the right.

Your scientific workspace

From molecular data to a clear, reviewable scene

Load a structure, establish the visual hierarchy, inspect the scientific question, and preserve the result for the next review.

Start your first structureExplore Viewer workflows

Choose your path

These three guides establish the core Viewer skills. Each one finishes with a visible result you can verify before moving to more advanced analysis.

1CBS entered in the PDB ID field with the structure loaded in the Nomosis Viewer.Start here

Load molecular data

Choose the correct path for a structure, MD trajectory, or docking result and verify the loaded state.

Open guide
1CBS protein shown as a ribbon colored by secondary structure with the ligand shown as spacefill.Visual clarity

Build a readable molecular scene

Choose representations and colors that separate the protein, ligand, and supporting context.

Open guide
Structure Hierarchy and Display panels for the 1CBS structure in the Nomosis Viewer.Precise control

Navigate components and hierarchy

Find chains, residues, ligands, and solvent, then control exactly what is visible.

Open guide

Keep the Viewer predictable

Most confusion comes from changing the right setting in the wrong context. Read the Viewer as four connected states:

1

Project

Where project-scoped work belongs

2

Loaded data

Structures and trajectories in the workspace

3

Active structure

The item currently targeted by the tools

4

Scene state

Camera, visibility, styling, and analysis

Before saving or starting a review, confirm both the project in the top bar and the active structure on the left. A correct sign-in does not guarantee that either context is correct.

Analyze structures and simulations

Non-Covalent InteractionsInspect and filter molecular contacts in 3D and in a table.Ligand AnalysisConnect 2D ligand chemistry with the 3D binding site.Measurements & AnnotationsCapture geometry and review context directly on the structure.Molecular-Dynamics TrajectoriesLoad, validate, play, scrub, and inspect a simulation.Docking AnalysisReview ranked poses, binding modes, interaction fingerprints, and pharmacophore consensus.ApplicationsChoose the context-aware workflow supported by the active data.Visual Settings & CameraControl the complete scene, lighting, effects, camera, and quality.

Preserve, collaborate, and present

Viewer SessionsSave the complete Viewer state and restore it later.History: Undo & RedoRevisit actions safely during the current Viewer session.Story StudioBuild a controlled narrative from validated scenes.ExportCreate structure files, high-resolution images, and video.Encrypted CapsulesProtect molecular data in encrypted, signed containers.

A reliable review sequence

Confirm the active project and intended structure.
Choose Fit → All (reset) and establish the scientific subject.
Use Display and Structure Hierarchy to create a clear visual hierarchy.
Select the appropriate granularity before choosing atoms, residues, chains, or entities.
Run only the analysis supported by the active structure, ligand, or trajectory.
Save a named Viewer session before switching projects or ending the review.

When a tool is unavailable

The Viewer exposes tools only when the active data supports them:

  • Ligand diagrams require a detected ligand in the active structure.
  • Trajectory controls and MD analysis require an active trajectory with multiple frames.
  • Docking-specific controls require a loaded docking result.
  • Save and open actions may require an active project and the relevant project permissions.

When in doubt, reactivate the intended structure, choose Fit → All (reset), and reopen the tool.

Your First Structure

Load 1CBS, inspect its protein and ligand, create a clear view, and save the result.

Loading Data

Choose the correct workflow for a structure, molecular-dynamics trajectory, or docking result and verify that the data is ready for analysis.

On this page

Choose your pathKeep the Viewer predictableAnalyze structures and simulationsPreserve, collaborate, and presentA reliable review sequenceWhen a tool is unavailable