3D Molecular Models and Crystallographic Data

About the 3D viewer for molecular and crystallographic models

Authors of Elsevier journals can enrich their online articles by providing supplementary 3D molecular and crystallographic models, which will be visualized using the interactive 3D viewer embedded next to the article. 

Using the 3D viewer, the reader can browse through 3D models, zoom into each model, rotate and pan the model, change viewing modes and display settings, and download original data files. It is also possible to open the 3D viewer in a new window.

The viewer has been developed in collaboration with Kitware SAS

3D viewer 

Article examples
 
3D molecular models:
http://www.sciencedirect.com/science/article/pii/S1568786414000299
http://www.sciencedirect.com/science/article/pii/S0022283612009138
http://www.sciencedirect.com/science/article/pii/S0969212612003814

3D crystallographic models:
http://www.sciencedirect.com/science/article/pii/S1387700314002160
http://www.sciencedirect.com/science/article/pii/S138770031400269X
http://www.sciencedirect.com/science/article/pii/S0162013414001445

Supported data formats

The Elsevier's 3D viewer for molecular and crystallographic models 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 three dimensional 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 application: PyMOL to be used.

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.

The following tools can be used to prepare/export 3D molecular models in/to the aforementioned data formats: PyMOL, RasMol, MolView, YASARA, QuteMolCoot, UCSF Chimera, etc.

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

Submission & publication

Each 3D molecular model file should be uploaded to EES separately via the "3D molecular models" submission category. The 3D molecular data should support the following formats: PDB (.pdb), PSE (.pse), MOL (.mol) and MOL2 (.mol2). Molecular data submitted in other formats will not be processed.

3D crystallographic data (.cif) files can be zipped together and uploaded as a single archive. 

The 3D viewer will be provided in the online version of the article. The PDF/printed version of the article will feature static figures only (if those figures are included in the article manuscript). In the online version, it will also be possible to download the original data files.

If you wish to provide feedback on the 3D viewer for molecular and crystallographic models or have a suggestion for another innovation that would further enhance the online article please get in touch.