eMol* Visualization User Guide
Necessary Disclaimers and Legal
Users are responsible for reviewing and complying with the license requirements of the software and data referenced in this documentation.
Users are responsible for compute and storage costs incurred within their DNAnexus project spaces.
Instance type availability and pricing are subject to the agreement between the user (or their organization) and DNAnexus.
Citations and Acknowledgments
When using Mol*, please cite: Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures.
Detail user guide from Mol*: https://molstar.org/viewer-docs/ and PDB: https://www.rcsb.org/news/627c18149c3931864b072866.
Overview of Mol* applet
Mol* (v5.6.1) is deployed on DNAnexus as an integrated web-based applet for interactive 3D molecular visualization. Users can visualize structure files (PDB or mmCIF) generated by the nf-core/proteinfold pipeline. Mol* also supports visualization of any protein structure files stored within a user’s project space or shared projects to which they have access. The viewer also enables direct retrieval and rendering of structures from external resources such as the Protein Data Bank (PDB), AlphaFold Protein Structure Database (AlphaFold DB), PubChem, and the SWISS-MODEL repository.
Mol* Interface overview
3D Canvas is the space where a PDB structure is displayed for manipulation in three dimensions (3D).
Toggle Menu provides users quick access to some commonly used operations for the 3D canvas. Go to Mol* official user guide to learn more about each function in the Toggle menu.
Control Panel is located on the right side of the screen and contains the following panels for structure manipulation: Structure, Measurements, Components, Density, Assembly Symmetry, Import, Session, and Superposition. Go to Mol* official user guide to explore each feature.
Log Panel is located at the bottom of the screen and displays logs of actions taken while viewing the structure.
Main Menu includes options such as Download Structure, Download Density, Open Files, Load Trajectory, and Download Tunnels.
State Tree is accessible via the second icon in the left sidebar. It displays the hierarchical structure of all loaded data, organized from the source file down to individual components and their representations. Each node can be hidden or deleted using the eye and trash icons respectively.
For detailed instructions on available features and controls, please refer to the official Mol* documentation.
Using Molstar Applet on DNAnexus
Copying the applet and example dataset into a project
To explore the demo analyses, copy the applet and example dataset from the public project into your own project space:
Create a project for your analysis, billed to your own organization. Tutorials on how to set up a project can be found on this page.
Navigate to the Resources tab, locate the project titled "Public Datasets AWS US (East)," and select the "Molstar" folder.
Select the applet: molstar_v5.6.1, examples folder and read me file.
Click "Copy" in the top-right menu and select the project created in Step 1.
Return to your project space to begin exploring the applet.
Example dataset for testing
We provided four example files in the examples folder for testing this applet:
Quick Start
Click the applet to run the analysis.
Click Start to launch the analysis, then go to MONITOR tab and go to the Mol* job and click Open Worker URL to access the interface.
In the Main Menu, you can click to Source and scroll down to select AlphaFold DB and use the default ID.
Click Apply to load the structure.
For additional ways to load structures into the viewer, refer to the Example use cases section.
Example use cases
Download structure
Load a structure from Protein Data Bank (PDB)
In the Main Menu, go to Download Structure and click on the Source dropdown and select PDB
A PDB Id(s) field will appear with the default ID 1tqn. Enter your desired PDB ID.
Click Apply to load the structure into the 3D Canvas
Note: The same steps apply for other sources such as PDB-IHM, SWISS-MODEL, AlphaFold DB, and PubChem by selecting the desired source and entering the accession ID.
Loading a structure from DNAnexus platform
Note: To load a structure by using a file ID, you must have access to the project where the file is stored. If you are using the example files from the Public Datasets project and are unable to copy the file ID, copy the files into your own project first, then copy the file ID from there.
The Download Structure menu supports two DNAnexus-specific sources:
DNAnexus-proteinfold source is designed specifically for loading prediction outputs from the nf-core/proteinfold pipeline. The structure is colored by pLDDT confidence score upon loading.
DNAnexus source is designed to load any accessible PDB or CIF file stored on the DNAnexus platform.
Both sources require a DNAnexus file ID as input. To obtain the file ID, navigate to your file on DNAnexus, click on it to open the detail panel on the right, then click Copy ID under the ID field.
For testing, navigate to the examples folder and select a file (e.g. ma-bak-cepc-0003.cif). The file ID will appear as file-xxx.
For nf-core/proteinfold outputs, navigate to ProteinFold/results/test_full_alphafold/alphafold2/standard/ and select the .alphafold.pdb file (e.g. T1024.1.alphafold.pdb, file ID: file-xxx).
For output from nf-core/proteinfold, you can use an output from the example results available on Public Dataset project at /ProteinFold/results/test_full_alphafold/alphafold2/standard/
To load the structure:
In the Main Menu, expand Download Structure and select DNAnexus or DNAnexus-proteinfold from the Source dropdown.
Paste the copied file ID into the input field.
Click Apply to load the structure into the 3D Canvas.
Loading structure from URL.
Files stored on DNAnexus can also be loaded into Mol* using a download URL.
To obtain the download URL:
Navigate to the examples folder on DNAnexus.
Click on the file (e.g. 9YNC.cif), then click Download in the top menu.
In the Download Data dialog, click the Copy URL button to copy the download link.
To load the structure:
In the Main Menu, expand Download Structure and select URL from the Source dropdown.
Paste the copied URL into the Url field.
Set the Format to the appropriate file format (e.g. mmcif for .cif files).
Click Apply to load the structure into the 3D Canvas.
Changing Representation and Style
Mol* provides quick options to change how a structure is displayed using the Quick Styles section in the Controls Panel.
In this example, we use the structure 4HHB (Human Hemoglobin) loaded from PDB.
Apply Representation:
Load 4HHB from PDB following the steps in Load a structure from PDB.
In the Controls Panel, locate the Quick Styles section.
Under Apply Representation, click one of the following options: Default, Cartoon, Spacefill , Surface.
Under Apply Style, click one of the following options: Default or Illustrative.
Coloring a Structure
In this example, we color the Polymer component of 4HHB by secondary structure using the Components Panel.
In the Controls Panel, open the Components panel.
Click the three dots (...) button next to Polymer.
Under Chain Property, select Chain Id to color each chain a different color.
The structure will be recolored on the 3D Canvas accordingly.
Note: Other coloring methods such as custom color selection and validation report-based coloring are also available. Refer to the Mol* official user guide for more details.
Making Measurements
Mol* supports several types of measurements: label, distance, angle, and dihedral. Measurements require atoms to be selected in Selection Mode before they can be applied.
In this example, we use 4HHB to measure the distance between two atoms.
Load 4HHB from PDB following the steps in Load a structure from PDB.
In the Toggle Menu, activate Selection Mode by clicking the cursor icon.
Choose the residue such as HIS 72
In the Controls Panel, open the Measurements panel, click Add and select Label.
Repeat steps 3–4 for ASP 75 to add a second label.
Select the desired measurement type from the dropdown. Only options matching the number of selected atoms will be available.
The measurement will be displayed on the 3D Canvas and listed in the Measurements panel.
For further guidance about measurement, please check Mol* official document.
Load trajectory
In this example, we load an MD simulation of MDM2 protein using a topology file (.pdb) and a trajectory file (.dcd) from https://www.bahargroup.org/prody/tutorials/trajectory_analysis/outputtraj.html
Download the example dataset zip file (MDM2 files (ZIP)).
Unzip the file to obtain the following files:
trajectory_analysis_files/
├── mdm2.pdb # topology/structure file
└── mdm2.dcd # trajectory file
In the Main Menu, expand Load Trajectory, and select files for Model and Coordinates.
Click Apply to load the trajectory into the 3D Canvas.
Click Select Animation to open the animation settings.
Click Start to play the trajectory animation.
Export image
Mol* allows users to capture and download the current view of the 3D Canvas as an image.
In the Toggle Menu, click the Screenshot / State Snapshot icon.
A preview of the current view will appear in the Screenshot / State panel with the following options:
Resolution: set to Viewport by default
Format: PNG by default
Transparent: toggle background transparency On/Off
Auto-crop: toggle to automatically crop the image
Axes: toggle to show/hide the orientation axes in the image
Click Download to save the image to your local computer, or Copy to copy it to clipboard.
Limitations
API Dependency for External Sources
Loading structures directly from external databases (e.g. PDB, AlphaFold DB, SWISS-MODEL) depends on the availability of their respective APIs. If a structure fails to load due to API restrictions or downtime, we recommend downloading the file locally and uploading it to DNAnexus, then loading it using the file ID via the DNAnexus source in Download Structure.
Session and Snapshot Management
Mol* does not automatically sync sessions or snapshots to DNAnexus. Users must manually save the session or state as a .molj or .molx file to their local machine and re-upload it to DNAnexus if needed for future use or sharing.
Note: Session and state saving is an experimental feature. Saved files might not be openable in a future version of Mol*.
Terminate Instance
After finishing your session, close the browser tab and terminate the job in the MONITOR panel on DNAnexus to avoid unnecessary compute costs.
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