Make structure part of the conversation
Keep the molecule beside the conversation.
The Mol* workspace makes structure state part of the project. Load a PDB, mmCIF, AlphaFold result, or generated structure, then inspect it with the Agent while keeping that context intact.
Load and cite a structure
Start from an active project conversation. Bring a PDB, mmCIF, AlphaFold result, or generated structure into the current Mol* workspace. Its source, chains, and selections stay with the project. Describe what you need and let the Agent find and load it, or open Hello Mol* to import a local file from the project folder. When the structure is ready, type # in the composer and choose the current entry, or select Add to Chat in Mol*. Loading, viewing, and citing all happen in one workspace.
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Method 1Ask the Agent to find and load it
Describe the target in the project conversation, such as “Find 1CRN in PDB and load it into Mol*” or “Open this protein's AlphaFold structure.” Levin finds an available source, downloads the file, and brings it into the current workspace. If the name is ambiguous, confirm the species, chain, or version first.
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Method 2Open Hello Mol* directly
If the structure is already on your computer or in the project folder, open Hello Mol* from the project tools and choose a PDB, mmCIF, or another supported protein structure file. The imported entry appears in the current workspace. You can do this without starting a new conversation.
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ShortcutCite the current structure
Type
#in the project composer and choose the current entry. You can also select Add to Chat in Mol*. For a narrower reference, select a chain, residue range, or measurement before attaching the structured context.
Load first, then cite. Ask the Agent to find the structure or import it with Hello Mol*. When you need it in the conversation, use # or Add to Chat. The source, selection, and measurements stay together, so Levin never has to guess from a screenshot.
Work across both Mol* views
Every Mol* action changes what you see. Choose the interaction that fits the question, then continue with the next step.
1. Click to focus. Confirm the target.
Start in the 3D view to inspect and lock onto a candidate, then use the Sequence panel to confirm its residue number or extend it into a continuous range. The 3D view, sequence highlight, and target bar stay synchronized.
Select a target
Click a residue or region to select it and keep the target synchronized with the current view.
Open the shortcut menu
Right-click a residue to open its shortcut menu and continue with the relevant selection action.
Select a continuous range
Drag from the first residue to the last to define an exact interval, such as residues 42–58 in chain A.
Use the molecular control panel
Open the control panel to manage layers, selections, representations, tags, measurements, and actions for the current structure.
2. Say what you need. Stay in control.
Once the target is exact, tell Levin what you want to inspect, compare, tag, measure, present, or export. Lévin™ Harness includes built-in Mol* tools in the Agent, so you do not need to prescribe each click; the Agent acts on the structured selection in the current project context.
| Category | Capability | What it does |
|---|---|---|
| Structure controls | Focus and selection | Focuses a residue, continuous range, spatial neighborhood, or entire chain, then confirms that the selection is exact. |
| Project annotations | Tags and layers | Names a target selection, switches layers, and checks or removes existing tags. |
| Structure analysis | Read structure state | Reads residue properties, sequences, and secondary structure, bringing exact structure data into the analysis. |
| Visual presentation | Styles and motion | Changes representations and color, and controls trajectory playback to make structural changes easier to see. |
| Delivery | Exports and evidence | Saves the current view, a trajectory video, or a structure file as a project deliverable. |
A reliable flow: make a selection with the mouse or Sequence panel, confirm it in the target bar, then ask the Agent to inspect it. To continue in Chat, select Add to Chat or type # to attach the same structure context.
Style, animate, and export
Mol* is also a workspace for scientific figures and output. Preserve the structural evidence first, then shape the presentation and export the result. Selections and measurements support reproducibility; rendered views support communication.
Style the structure
Use the Molecular Graphics control panel to adjust 3D representations, colors, and rendering until the structure reads clearly.
Trajectory and video export
Play, pause, step through frames, and adjust speed with the trajectory controls. Pause on the frame you want to cite, then export the selected trajectory as a video.
Export high-resolution scientific images
Preview the frame in the capture menu, choose the output size up to 8K, pixel density, and background, then export a high-resolution PNG or JPEG for a report or project deliverable.
Switch molecular representations
Open the Style menu to switch between Research, Cinematic, Cartoon, and X-Ray presets, then refine the active rendering for the current structure.
Image export clears temporary selections and hover highlights while preserving focus, giving you a cleaner scientific figure. Keep the exact selection, tag, measurement, or structure file as the evidence record.
Measurements and visualization
A measurement is structured Mol* data, not decoration on a screenshot. Open the measurement tools, choose a type, then select atoms or residues in order. After creating it, verify the selected objects, value, unit, and order in the measurement list. A distance uses two positions, an angle uses three, and a dihedral uses four. Labels add text annotations. Orientation shows the principal directions of a selection. A plane creates a best-fit plane from selected points. To share the result with the Agent, use # to attach the current entry and measurement, so Levin can inspect the same structural positions.
| Measurement | How to create it | What to verify in Mol* | What it can show |
|---|---|---|---|
| Distance | Select two atoms or residue positions in order. | The numeric distance, Å unit, and both selected endpoints. | Bond length, interatomic distance, or spacing within a pocket. |
| Angle | Select three positions in order. The middle position is the vertex. | The angle in degrees and the order of all three positions. | Bond angles, local geometry, or ligand pose. |
| Dihedral | Select four positions in order to form three connected segments. | The torsion angle in degrees and the order of all four positions. | Backbone torsion, side-chain conformation, or conformational change. |
| Label | Select an atom or residue and add a text label at that position. | The label is attached to the right position and its layer is visible. | An active site, mutation site, or residue that needs review. |
| Orientation | Select a structural region, add an orientation, then choose a box, axes, or ellipsoid. | The principal directions, axes, or ellipsoid cover the intended selection. | A domain's overall orientation, long axis, or shape distribution. |
| Plane | Select several points across a target surface and add a best-fit plane. | The plane fits the selected points and its layer is visible. | A membrane surface, interface, or coplanar trend across positions. |
| Rendered view | Preserve the measurements, selections, and camera state, then capture or export. | The camera, layers, labels, and lighting show the full context. | A report figure or visual appendix. It does not replace structured measurement evidence. |
Review in this order: confirm the structure entry, confirm the selected positions and units, then cite the measurement with #. Treat the image as supporting evidence only. Before export, choose a clear project path and retain the structure identifier in the accompanying note.
Keep the context precise
Ask the Agent to inspect the current structure, selected residues, or a measurement. Levin can combine that state with project files, plugin output, and workflow steps, without asking you to describe the same location again.
Structure is a working medium. Treat Mol* state as part of the project context, alongside files, code, and conversation.
When the view is not what you expect
The structure will not open
Confirm that an active project conversation exists, then check that the file contains readable PDB or mmCIF data rather than a screenshot or compressed archive.
The selection is missing from the conversation
Make the selection in Mol* first. Then type # in the composer and choose the current structure or selection. Plain text does not create a structured reference.
The camera changed, but the model did not
Check the current entry and layer visibility. Focus the selected residue, then confirm that the target layer is visible in the dashboard.