3D Molecular Models Data Viewer

About the 3D Molecular Models Data Viewer

The 3D Molecular Models Data Viewer visualizes molecular and crystallographic data in an interactive 3D viewer.

The 3D Molecular Models Data Viewer provides authors and readers with many benefits. It:

  • Lets authors enrich the content of their articles with 3D visualizations of their data
  • Enables readers to browse through 3D models, zoom into each model, rotate and pan the model, change viewing modes and display settings
  • Enables users to open the viewer in a new window
  • Lets users download original data files

The viewer was developed in collaboration with Kitware SAS.

Example Articles

Author Instructions


The 3D viewer supports the following data formats: PDB, PSE, MOL/MOL2 and CIF.

  • PDB is the Protein Data Bank file format. It is a textual file format describing 3D structures of molecules held in the RCSB Protein Data Bank (PDB). The format specification can be found here.
  • PSE (PyMOL Session file format) is a dictionary representation of a PyMOL session. A session is one particular conformation of a molecule (color scheme, camera, lighting effects, etc.). This format is very specific and requires the use of the application PyMOL.
  • MOL (also called MDL) is a file format created by MDL for holding information about the atoms, bonds, connectivity and coordinates of a molecule. The format specification can be found here.
  • MOL2 is a Tripos Mol2 file. It is a complete, portable representation of a SYBYL molecule. The format specification can be found here.
  • CIF (Crystallographic Information File) is an archiving and information interchange standard for crystallographic and related structural science data promoted by the International Union for Crystallography. The format specification can be found here.

To prepare or export your 3D molecular model in one of these formats, you can use various tools, including: PyMOL, RasMol, MolView, YASARA, QuteMol, Coot, UCSF Chimera.


Software to view and validate CIF files can be found at: http://www.iucr.org/resources/cif/software.


In your manuscript, you can indicate where you want the material to appear in the article, for example, by writing ‘File1.mol here’.

  • Upload each 3D molecular model file to EES separately under the “3D molecular models” submission category
  • Only data in the following formats will be processed: PDB (.pdb), PSE (.pse), MOL (.mol) and MOL2 (.mol2)
  • You can zip together 3D crystallographic data (.cif) files and upload as a single archive

The 3D viewer will be provided in the online version of your article. The PDF or print version of your article will feature static figures only (if those figures are included in the article manuscript).

For Reviewers

Instructions are included in the reviewer invitation letter.

Reviewers will find PDB, PSE, MOL and MOL2 files associated with the 3D Molecular Models Data Viewer in the supplementary material submitted with the manuscript.

  • EES: the files can be downloaded via links on the final pages of the reviewer PDF
  • EVISE: the files can be downloaded directly from the system [details TBC]

For more information, read the general reviewer instructions for Content Innovation.


If you wish to provide feedback on the 3D Molecular Models Data Viewer or have a suggestion for another innovation that would further enhance the online article please get in touch.