Nomosis Docs
Getting started

Your First Structure

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

This guided exercise uses 1CBS, a compact protein–ligand structure that loads quickly and exposes the main Viewer controls. The goal is not only to open the model, but to finish with a scene that is clear, reproducible, and ready for a scientific conversation.

Watch the walkthrough

Load 1CBS, frame the complete model, rotate it, color the protein by secondary structure, and show the ligand as Spacefill (CPK). The tutorial has no audio and lasts 27 seconds.

Before you load

Confirm the project name in the viewer's top bar. For the Nomosis test environment, use test-1. Then make sure no unsaved work in the current viewer needs to be preserved.

Loading another structure does not have to replace the current one. The Viewer can keep multiple structures open, each with its own display state.

Load 1CBS

Click the PDB ID field in the top bar.
Enter 1CBS and choose Load.
Wait until 1CBS appears under Structures on the left and the molecule appears in the viewport.
Choose Fit → All (reset) to center the complete model.

Checkpoint: successful load

The active structure should show a protein component and a ligand component. If the model is listed on the left but you cannot see it, choose Fit → All (reset). If loading fails, confirm that the identifier contains exactly four characters and retry.

Establish a useful camera view

Left-drag across the viewport to rotate the model.
Scroll until the structure fills most of the viewport without touching its edges.
Middle-drag if you need to reposition the model without changing its orientation.
Use Fit → All (reset) at any time to return to a known starting point.

A strong review view keeps the full protein fold readable while leaving enough space around the ligand for labels, interactions, or measurements.

Separate protein and ligand visually

Open Display in the right sidebar.
Set Protein to Cartoon / Ribbon. This emphasizes the overall fold and secondary structure.
Set the protein color scheme to Secondary Structure.
Set Ligand to Spacefill (CPK) for volume and packing, or Ball & Stick for atom and bond detail.
Keep the ligand colored by Element so heteroatoms remain easy to identify.
Hide Water if it obscures the initial overview. You can restore it when water-mediated contacts matter.

Choose the representation for the question

QuestionProteinLigand
What is the overall fold?Cartoon / RibbonBall & Stick
How tightly is the ligand packed?Cartoon / RibbonSpacefill (CPK)
Which atoms make a contact?Ribbon with atom overlayBall & Stick
What is the pocket envelope?Surface or Cartoon / RibbonBall & Stick

Inspect a residue

Set picking granularity to Residue in the top bar.
Click a residue near the ligand.
Double-click if you want the camera to focus on the picked location.
Use the Structure Hierarchy to confirm the chain, residue name, and residue number.
Clear the selection before starting a different selection-based task.

For atom-level measurements, switch granularity to Atom before choosing endpoints. For an entire protein chain, switch to Chain.

Save a reproducible state

Open File → Save as….
Use a descriptive name such as 1CBS — initial ligand review.
Add a short description or tags if the save dialog offers them.
Confirm the project shown in the dialog, then save.
Open File → Open session… and verify that the named session is available.

A viewer session preserves the scene so that you can return to the same camera, components, representations, colors, measurements, annotations, and other supported viewer state.

Optional next steps

  • Use Fit → Ligand to move from the overview to the binding site.
  • Open Applications → Ligand Interaction → 2D Diagram for a schematic view of the ligand environment.
  • Open Interactions to focus on specific contact types.
  • Add a distance measurement between two atoms.
  • Use Studio when you are ready to export a high-resolution image.

Troubleshooting

Continue learning

Components & Hierarchy

Isolate chains, residues, ligands, solvent, and custom elements.

Non-Covalent Interactions

Inspect contacts around the ligand in 3D and in a table.

Measurements & Annotations

Capture precise geometric and review context.

Saving Work: Viewer Sessions

Understand exactly what a saved viewer session preserves.

A Tour of the Interface

Learn the purpose of each major area in the Nomosis Viewer and where to begin common tasks.

The Nomosis Viewer

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

On this page

Watch the walkthroughBefore you loadLoad 1CBSCheckpoint: successful loadEstablish a useful camera viewSeparate protein and ligand visuallyChoose the representation for the questionInspect a residueSave a reproducible stateOptional next stepsTroubleshootingContinue learning