> For the complete documentation index, see [llms.txt](https://docs.labii.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.labii.com/widgets/section-widgets/biology/protein/molstar.md).
# MolStar
## Specs
| Label | Value |
| ------------------------- | ------------------------------ |
| **Version** | v0.1.0 (updated on 2024-02-20) |
| **Developer** | Labii Inc. |
| **Type** | Section |
| **Support Configuration** | Yes |
## Overview
The MolStar widget embeds an interactive molecular structure viewer inside a Labii record so researchers can inspect protein and antibody structures without leaving their experimental documentation. It uses a Protein Data Bank identifier stored in a record column to load the corresponding structure, making it useful for structural biology, protein engineering, antibody discovery, and assay interpretation workflows. By keeping the molecular view next to sequence data, experimental notes, and analysis results, the widget improves traceability and reduces the need to switch between Labii and external visualization tools.
## Use Cases
* **Structure Review**: Display the 3D structure of a protein, antibody, or complex while reviewing experiment records.
* **Protein Engineering**: Compare saved constructs or targets against their reference Protein Data Bank entries during design discussions.
* **Assay Interpretation**: Inspect structural context when documenting binding studies, mutagenesis results, or epitope mapping experiments.
* **Record-Centered Collaboration**: Keep the molecular view attached to the same record that stores protocols, data, and conclusions for team review.
* **Training and Knowledge Transfer**: Help new team members understand structure-driven projects by embedding the relevant model in the record.
## Interface
### Read-only View
In read-only mode, the widget displays the molecular structure associated with the saved Protein Data Bank identifier from the configured column. Users can review the rendered model directly in the record while keeping the structure linked to the surrounding experiment context.
* **Data Display**: Shows the 3D molecular structure loaded from the configured PDB ID.
* **Navigation**: Supports normal interactive viewer behavior such as rotating, zooming, and re-centering the model for inspection.
* **Record Context**: Keeps the structure visible alongside other Labii fields and sections in the same record.
* **Review Use**: Useful for record handoff, collaborative review, and documentation of structure-based decisions.
The read-only view displays the molecular structure linked to the record's configured Protein Data Bank identifier.
### Edit View
In edit mode, users configure which record column contains the Protein Data Bank identifier used by the viewer. This keeps the widget flexible across tables that store structure identifiers in different fields.
* **Input Methods**: Select the column that stores the PDB ID for the current record.
* **Configuration Focus**: The edit workflow is primarily for binding the widget to the correct source column rather than editing the structure itself.
* **Validation**: A valid PDB ID is required in the selected column for the structure to load correctly.
* **Workflow Fit**: Once the column is selected, the widget can be reused across records in the same table structure.
{% hint style="info" %}
MolStar does not create or edit macromolecular coordinates inside Labii. It visualizes structures referenced by the Protein Data Bank identifier stored in the selected record field.
{% endhint %}
## Configuration
### Initial Setup
{% stepper %}
{% step %}
Open the record and add the **MolStar** widget to a section.
{% endstep %}
{% step %}
Switch the section to **Edit** mode.
{% endstep %}
{% step %}
Select the record column that stores the Protein Data Bank identifier.
{% endstep %}
{% step %}
Save the record and return to read-only mode to verify that the structure loads.
{% endstep %}
{% endstepper %}
### Required Settings
* **PDB Column**: Select the column that contains the Protein Data Bank identifier for the structure you want MolStar to display.
### Optional Settings
* **None**: The widget does not expose additional widget-level settings in the current documentation set.
{% hint style="info" %}
If the widget does not display a structure, first confirm that the selected column contains a valid PDB ID for the current record.
{% endhint %}
### Advanced Configuration
For teams using structure-based workflows across many records, standardize where PDB IDs are stored so the same widget setup can be reused consistently.
{% stepper %}
{% step %}
Create or reuse a dedicated text field for Protein Data Bank identifiers in your table design.
{% endstep %}
{% step %}
Populate records with normalized PDB IDs before adding the MolStar widget to templates or recurring record layouts.
{% endstep %}
{% endstepper %}
{% hint style="warning" %}
If the selected field is empty, misspelled, or contains an identifier that is not available in the Protein Data Bank, the widget will not be able to render the expected structure.
{% endhint %}
## Additional Functions
### Interactive Structure Inspection
The MolStar viewer is designed for direct visual inspection of macromolecular structures within the record.
* **3D Navigation**: Rotate, zoom, and reposition the model to inspect domains, interfaces, or overall fold.
* **Contextual Review**: Keep the structural view visible while reading protocols, sequence notes, assay data, or conclusions in the same record.
* **Presentation Support**: Use the embedded viewer during meetings or reviews when discussing structural findings directly from Labii.
### Record-Driven Structure Loading
Because the widget is driven by a field in the record, it supports repeatable structure display across datasets without manually re-entering identifiers.
{% stepper %}
{% step %}
Store the relevant PDB ID in the configured record column.
{% endstep %}
{% step %}
Open any record that uses the MolStar section.
{% endstep %}
{% step %}
Review the loaded structure directly from the record context.
{% endstep %}
{% endstepper %}
### Integration Features
* **Record Metadata Integration**: Uses a Labii field as the source of truth for structure selection.
* **Documentation Integration**: Pairs well with notes, assay outputs, and sequence-oriented widgets in the same record.
* **Review Integration**: Supports structure-centric review workflows without exporting data to a separate viewer page.
### Version Control and Audit Trail
* **Tracked Record Changes**: Updates to the selected PDB ID remain part of the record's versioned history.
* **Configuration Traceability**: The chosen source column stays attached to the widget configuration for consistent reuse.
* **Documentation Integrity**: Structure references remain embedded in the same electronic record as the related scientific work.
## Best Practices
### Data Organization
* Store Protein Data Bank identifiers in a dedicated field rather than mixing them into free-text notes.
* Use consistent identifier formatting across records so structures load predictably.
* Pair MolStar with nearby contextual sections such as protocol notes, assay interpretation, or sequence annotations.
### Performance and Usability
* Use MolStar for focused record-level review rather than as a replacement for large batch structure management workflows.
* Verify the PDB ID before troubleshooting the widget, since most loading issues originate from missing or incorrect identifiers.
* Keep record templates consistent so collaborators do not need to reconfigure the widget for each experiment.
### Scientific Documentation
* Record why a given structure was selected, especially when multiple Protein Data Bank entries could represent the same target.
* Use the viewer during review of binding sites, domains, or mutations, then capture the interpretation in adjacent text sections.
* Cite MolStar appropriately in publications or formal reports when the viewer contributes to figure generation or structure analysis.
{% hint style="success" %}
MolStar works best when the record already contains a curated PDB identifier and the surrounding sections explain how that structure supports the experiment or decision being documented.
{% endhint %}
### Common Pitfalls to Avoid
* **Avoid using an empty or non-standard field** for the PDB source, because the widget depends on a valid identifier to load a structure.
* **Avoid treating the widget as an annotation editor**, since its role in Labii is structure visualization rather than coordinate or sequence authoring.
* **Avoid separating the structure from the experiment narrative**, because the value of the widget is strongest when the model sits next to the relevant record context.
## Related Widgets
* [RCSB Saguaro](/widgets/section-widgets/biology/protein/rcsb-saguaro.md): Use this widget when you need sequence-position annotations and protein feature summaries to complement MolStar's 3D structural view.
## References
### External Resources
* [MolStar Viewer Documentation](https://molstar.org/viewer-docs/): Official viewer documentation and feature reference.
### Citation
* David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodova, Karel Berka, Vaclav Bazgier, Sameer Velankar, Stephen K. Burley, Jaroslav Koca, and Alexander S. Rose. [Mol\* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures](https://doi.org/10.1093/nar/gkab314). Nucleic Acids Research, 2021.
---
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