CIF File Viewer

Our CIF File Viewer is an easy-to-use online tool for viewing 3D models of macromolecular and crystalline structures. Researchers, students, and academics can quickly analyze structural files, especially in mmCIF and CIF formats. Our CIF file reader includes many valuable features, connects with major structural databases, and can handle even very large structures at high speed.

The Viewer Features

1. High-Performance 3D Visualization: Fast and smooth rendering of complex and large structures.
2. Support for Various Formats: Ability to load standard formats like mmCIF, CIF, PDB, MMTF, as well as density data such as CCP4 and MRC.
3. Load from Multiple Sources:
   • Direct file upload from your computer (Upload Your Files).
   • Import structures from major databases (like RCSB PDB, PDB-Dev, EBI) using only their ID.
   • Load directly from a URL.
4. Analytical and Measurement Tools:
   • Measure distances, angles, and dihedral angles.
   • Display and analyze non-covalent interactions.
5. Diverse Representation Styles (Quick Styles): Quickly change the structure’s display style between Cartoon (for proteins), Spacefill (volumetric view of atoms), Surface (molecular surface), and Default (ball-and-stick).
6. Full Display Control: Ability to select atoms, chains, or residues and change their color, transparency, or representation independently.

How to Use

This is the most important section for users and should be step-by-step.

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:

1. 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).

Applications

For structural biology and drug discovery, our viewer excels with mmCIF files, the modern standard for large biomolecular data. Researchers can load protein, DNA, or enzyme structures to investigate biological function at an atomic level. This includes studying active sites, analyzing protein-ligand (drug) interactions, and understanding the molecular mechanisms of disease. For example, you can load an mmCIF file of a viral protein to precisely analyze how an inhibitory drug binds to it.

Separately, the viewer fully supports traditional CIF files, which are essential in materials science, chemistry, and crystallography. Materials scientists can use the tool to load and visualize cif file contents, such as complex crystal structures like zeolites, Metal-Organic Frameworks (MOFs), and alloys. The tool facilitates the detailed inspection of the unit cell, crystal symmetries, and pore analysis, making it a powerful resource for research and an excellent educational tool for students learning 3D structural concepts.

Our tool is ideal for understanding structural data across different fields, specializing in both mmCIF and CIF formats. While related, these formats serve distinct purposes (for a detailed comparison, see this guide on CIF vs. mmCIF).

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
2. Brown, I. D., & McMahon, B. (2002). CIF: the computer language of crystallography. Acta Crystallographica Section B Structural Science, 58(3), 317–324. https://doi.org/10.1107/s0108768102003464
3. Brown, I. D. (1996). CIF (Crystallographic Information File). A standard for crystallographic data interchange. Journal of Research of the National Institute of Standards and Technology, 101(3), 341. https://doi.org/10.6028/jres.101.035