> 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/rcsb-saguaro.md).

# RCSB Saguaro

## Specs

| Label                     | Value                                  |
| ------------------------- | -------------------------------------- |
| **Version**               | Not documented (updated on 2026-06-14) |
| **Developer**             | Labii Inc.                             |
| **Type**                  | Section                                |
| **Support Configuration** | Yes                                    |

## Overview

The RCSB Saguaro widget embeds a protein feature viewer inside a Labii record so researchers can inspect sequence-based annotations from Protein Data Bank entries without leaving their experimental documentation. Built around the RCSB Saguaro 1D feature viewer concept, it helps teams review positional features such as domains, annotated regions, and other sequence-linked information associated with a selected structure or protein entry. This makes the widget useful for structural biology, protein characterization, target review, and record-centered collaboration where sequence context needs to stay connected to protocols, assay data, and conclusions.

## Use Cases

* **Sequence Annotation Review**: Display protein sequences together with position-based annotations while reviewing a record.
* **Target Characterization**: Inspect annotated domains and feature regions when documenting proteins, antibodies, or engineered constructs.
* **Assay Interpretation**: Relate sequence features to assay outcomes, binding regions, or mutation studies stored in the same record.
* **Record-Centered Collaboration**: Keep protein feature summaries attached to the record for shared review and handoff.
* **Training and Knowledge Transfer**: Use the widget to help team members understand how annotated features map onto a protein sequence in a project record.

## Interface

### Read-only View

In read-only mode, the widget displays the protein feature viewer associated with the saved Protein Data Bank identifier from the configured column. Users can inspect sequence-position annotations directly inside the record without opening an external RCSB page.

* **Data Display**: Shows protein sequence features and annotations linked to the configured PDB entry.
* **Navigation**: Supports interactive inspection of sequence regions and feature tracks within the embedded viewer.
* **Record Context**: Keeps the annotation view visible alongside related experimental notes, structure viewers, and result sections.
* **Review Use**: Useful for reviewing feature summaries during experiment interpretation, design review, or project handoff.

<figure><img src="/files/kLTCu28a0MQpnLKrbpRt" alt="Read-only view of the RCSB Saguaro widget"><figcaption><p>The read-only view displays sequence-position features and protein annotations associated with the configured Protein Data Bank entry.</p></figcaption></figure>

### Edit View

In edit mode, users configure which record column contains the Protein Data Bank identifier that drives the RCSB Saguaro viewer. This setup allows the same widget to work across records as long as the table stores PDB IDs consistently.

* **Input Methods**: Select the record column that stores the PDB ID.
* **Configuration Focus**: The edit flow binds the widget to the correct identifier source rather than editing annotations directly.
* **Validation**: The selected field must contain a valid PDB ID for the viewer to return the expected sequence features.
* **Workflow Fit**: After configuration, the widget can be reused across structure- or protein-focused records in the same table.

{% hint style="info" %}
RCSB Saguaro focuses on protein sequence features and annotations. It complements 3D viewers by showing where biologically relevant features fall along the sequence.
{% endhint %}

## Configuration

### Initial Setup

{% stepper %}
{% step %}
Open the record and add the **RCSB Saguaro** 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 sequence features load.
{% endstep %}
{% endstepper %}

### Required Settings

* **PDB Column**: Select the column that contains the Protein Data Bank identifier used to retrieve the protein feature summary.

### Optional Settings

* **None**: The current documentation does not indicate any additional widget-level settings.

{% hint style="info" %}
If the widget does not show features, first confirm that the selected field contains a valid PDB ID for the current record.
{% endhint %}

### Advanced Configuration

For teams documenting many proteins, standardize PDB ID storage so the widget configuration can be reused across table templates and recurring record layouts.

{% stepper %}
{% step %}
Create or reuse a dedicated field for Protein Data Bank identifiers in the relevant table.
{% endstep %}

{% step %}
Populate each record with normalized PDB IDs before adding the widget to standard record templates.
{% endstep %}
{% endstepper %}

{% hint style="warning" %}
If the selected field is empty, malformed, or points to an unsupported entry, the widget cannot display the expected sequence annotations.
{% endhint %}

## Additional Functions

### Interactive Feature Inspection

The embedded viewer helps users examine protein annotations in their positional sequence context.

* **Feature Review**: Inspect annotated regions such as domains, motifs, or other sequence-linked summaries associated with the entry.
* **Contextual Interpretation**: Compare sequence features with notes, mutations, assay findings, or structure-oriented sections in the same record.
* **Presentation Support**: Use the embedded feature view during team review when discussing protein regions of interest.

### Record-Driven Annotation Loading

Because the widget is driven by a record field, it supports repeatable loading of protein feature data across datasets without manual re-entry.

{% stepper %}
{% step %}
Store the relevant PDB ID in the configured record column.
{% endstep %}

{% step %}
Open any record that contains the RCSB Saguaro section.
{% endstep %}

{% step %}
Review the loaded sequence features directly inside the record.
{% endstep %}
{% endstepper %}

### Integration Features

* **Record Metadata Integration**: Uses a Labii field as the source of truth for the protein entry being displayed.
* **Documentation Integration**: Fits naturally alongside sequence notes, assay interpretations, and other protein-related sections.
* **Structural Review Integration**: Pairs well with 3D structure viewers when teams need both positional features and structural context.

### Version Control and Audit Trail

* **Tracked Record Changes**: Updates to the source PDB ID remain part of the record history.
* **Configuration Traceability**: The selected source column remains part of the widget configuration for repeatable use.
* **Documentation Integrity**: Sequence feature references stay attached to the same electronic record as the associated scientific work.

## Best Practices

### Data Organization

* Store Protein Data Bank identifiers in a dedicated field rather than in narrative text.
* Keep identifier formatting consistent across records so the viewer loads predictable results.
* Place RCSB Saguaro near related sections such as MolStar, protein notes, or assay interpretation to keep the biological context together.

### Review and Interpretation

* Use the widget to confirm where annotated features fall before discussing mutations, epitopes, or functional regions in adjacent notes.
* Review sequence-position annotations together with structure views when both linear and 3D context matter.
* Document why a specific PDB entry was chosen if multiple entries could represent the same target.

### Scientific Documentation

* Treat the widget as a reference and interpretation aid rather than the sole source of protein documentation.
* Capture conclusions about domains, regions, or annotations in nearby text sections so the record preserves the scientific reasoning.
* Cite the underlying RCSB resource appropriately when feature summaries contribute to reports, figures, or formal analyses.

{% hint style="success" %}
RCSB Saguaro is most useful when the record already contains a curated PDB identifier and the surrounding sections explain why the displayed protein features matter to the experiment.
{% endhint %}

### Common Pitfalls to Avoid

* **Avoid using the wrong source field**, because the widget depends on a valid PDB ID to retrieve the correct feature summary.
* **Avoid assuming the viewer replaces narrative interpretation**, since important conclusions about annotated regions should still be written into the record.
* **Avoid separating feature review from structure review** when both are relevant, because sequence and 3D context often need to be interpreted together.

## Related Widgets

* [MolStar](/widgets/section-widgets/biology/protein/molstar.md): Use MolStar when you need a 3D molecular structure view to complement the linear sequence-feature perspective provided by RCSB Saguaro.
* [Plasmid Editor](/widgets/section-widgets/biology/molecular-biology-suite/plasmid-editor.md): Pair with Plasmid Editor when construct design and downstream protein feature review need to stay in one record workflow.

## References

### External Resources

* [RCSB Saguaro 1D Tools and Services](https://doi.org/10.1093/bioinformatics/btaa1012): Publication describing the RCSB Protein Data Bank 1D tools and services that underpin feature-display workflows.

### Citation

* Joan Segura, Yana Rose, John Westbrook, Stephen K. Burley, and Jose M. Duarte. [RCSB Protein Data Bank 1D tools and services](https://doi.org/10.1093/bioinformatics/btaa1012). Bioinformatics, 2020.


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