PDB File Viewer

The ScienceCodons PDB Viewer is a high-performance tool for visualizing, analyzing, and exploring macromolecular structures directly in your web browser. It offers seamless support for PDB, mmCIF, and density map formats, allowing you to inspect atomic details and perform molecular dynamics simulations without complex software installation.

How to Use (a step-by-step guide)

A) Loading a Structure

You have several ways to load data:

• Upload Your Files:
  1. Click the Select files… button and choose the desired file(s) from your system.
  2. You can manually select the file format (Format) or leave it on Auto for automatic detection.
  3. After selecting, click the Apply button.
• Import from Databases:
  1. Expand this section.
  2. Enter the structure ID (e.g., 1CRN for PDB) in the respective field and press Apply.
• Load from URL:
  • Enter the direct URL of the structural file in this section and press Apply.

B) Interacting with the Viewport

• Rotate: Click and drag the left mouse button (or one finger on mobile).
• Zoom: Use the mouse scroll wheel (or pinch with two fingers on mobile).
• Pan: Click and drag the right mouse button (or drag with two fingers on mobile).
• Select: Click on an atom, residue, or chain. You can select multiple items by holding the Shift key.
• Focus: After selecting a part, you can use the magnifying glass icon in the Tools Panel (right side) to focus on it.

C) Using the Tools Panel

In the right panel (Tools Panel), you can customize the structure’s appearance:

• Structure: Manage the different loaded components. You can hide or show parts of the structure.
• Measurements:
  1. To add a new measurement (e.g., distance), click + Add.
  2. Select the measurement type (e.g., Distance).
  3. Then, click on the desired atoms in the 3D viewport to register the measurement.
• Quick Styles:
  • The easiest way to change the entire structure’s appearance.
  • Choose one of the options: Default, Cartoon, Spacefill, or Surface to apply it instantly.
• Components:
  • For advanced tasks. Here, you can define a new representation for specific selections (e.g., a specific ligand) and change its color or style independently from the rest of the structure.

D) Saving & Exporting

After finishing your work, you can save your results:

• Save Screenshot: To capture a high-quality image of the current view, look for the camera icon (📸) or the Screenshot option in the main toolbar. You can often adjust the output resolution, making the captured image suitable for printing or publications.
• Save Session: To continue your work later, click the Session icon (which looks like a save disk 💾) in the main toolbar. From there, select Save Session or Export Session. This will create a file (often with a .molx extension). In the future, you can load this file to return to this exact state (with all settings, colors, and measurements intact).

Key Features

1) Fast & Versatile Rendering

Experience high-performance 3D visualization that handles everything from small proteins to massive biological assemblies. The viewer is optimized for speed, ensuring smooth rotation, zooming, and interaction even with large datasets.

2) Comprehensive Format Support

Upload and visualize a wide array of molecular data formats automatically. While fully optimized for Protein Data Bank (PDB) files, the tool also supports .cif, .mmcif, electron density maps, and molecular dynamics trajectories.

3) Flexible Visualization Styles

Customize your view to gain better insights. Switch instantly between representations to highlight different structural aspects:

• Cartoon: Ideal for visualizing secondary structures like alpha helices and beta sheets.
• Spacefill: View atoms at their van der Waals radii to understand packing and volume.
• Surface: Analyze accessible surface areas and pockets.
• Illustrative: Create publication-ready figures with artistic shading and outlines.

4) Integrated Analysis Tools

Go beyond simple viewing with built-in utilities:

• Measure: Calculate precise distances and angles between atoms.
• Analyze Sequences: View the amino acid sequence alongside the 3D structure.
• Inspect Density: Load electron density maps to validate structural models.
• Trajectory Support: Visualize molecular dynamics simulations and structural changes over time.

FAQ

Reference

1. Sehnal, D., Bittrich, S., Deshpande, M., Svobodová, R., Berka, K., Bazgier, V., Velankar, S., Burley, S. K., Koča, J., & Rose, A. S. (2021). Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Research, 49(W1), W431–W437. https://doi.org/10.1093/nar/gkab314