10 Free SDF File Viewer Software for Windows

Here is a list of 10 free SDF file viewer software for Windows. SDF is Structural Data File and not to be mistaken for Spatial Data File (AutoDesk). A molecular SDF file contains data about its structural arrangement, atoms, residue, bond connectivity, and more. If you are looking for SDF viewers then you can check out this list. You can find the main feature of each software along with a brief description. With that, you can easily pick the software that is best suited for your needs.

Most of these software are open-source with cross-platform availability. Any of all ten software can easily open an SDF file and visualize the molecular structure data. Some software offer two-dimensional visualization and some also offer three-dimensional visualization. You can open multiple molecules to analyze the structure and find structural errors. You can also visualize the orbital and density surfaces of the molecules.

Some software are packed with many more features apart from SDF viewer. You can open various file types and data files from other computational chemistry programs. Last but not least, you can export the visualization to various formats including PDF, PNG, JPG, POV-ray, WRL, OBJ, etc.

My Favorite SDF Viewer

Jmol is my favorite SDF file viewer. It is open-source and available for Windows, macOS, and Linux. This software has a simple-to-navigate interface where you can visualize the 2D and 3D structures of molecules. It can visualize 60+ file formats including support for various quantum chemistry software data files. Last but not least, it allows you to export the visualization to many different formats including JPG, GIF, PDF, POV-ray, etc.

You can also check out lists of best free PES File Viewer, GDS File Viewer, and DST File Viewer software for Windows.

Jmol

Jmol is an open-source molecule viewer program. It can visualize 3D chemical structures. This program can run in four different modes: standalone Java program, HTML-5 web application, Java applet, and a “headless” server-side component. This program can read various types of file and can also open output from QuantumEspresso, Gaussian, MOPAC, GAMESS, CASTEP, CRYSTAL, VMD, and many other popular programs.

Main Features:

• Run in 4 different modes
• Multi-language support
• View molecule and material structures
• Supports 60+ file formats including PDB, PyMOL, SDF, MOL, CIF, SDF, MOL, PSE, etc.
• Supports file types from various quantum chemistry software
• Open and compare multiple files
• Full crystallographic symmetry capability
• Export to PDF, GIF, PNG,  JPG, WRL, POV-Ray, and OBJ formats
• Customizable User Interface and more

IQmol

IQmol is a free open-source molecule editor and visualizer program. This program can easily open SDF and many other file types. It comes with a molecular editor that can also generate orbital and density surfaces with animation. IQmol is integrated with the Q-Chem quantum chemistry package. This offers users an intuitive environment to set up, run, and analyze Q-Chem calculations.

Main Features:

• Open-source and Cross-platform
• Multi-language support
• Draw and view molecule and material structures
• Free-form builder with integrated molecular mechanics
• Supports various computational chemistry file formats
• Hierarchical Model View
• Visualization of molecular orbitals and densities
• 4 model views including tubes, wireframes, VDW, and CPK
• OpenBabel library support
• Generate movie files of molecule animation
• Export to Export of spectra and POV-ray

Avogadro

Avogadro is another free cross-platform molecule editor and visualizer program. It is available for Windows, macOS, and Linux. This program is used for computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Avogadro can easily open SDF files with high-quality renders.

Main Features:

• Open-source and Cross-platform
• Multi-language support
• Draw molecule and material structures
• Supports various computational chemistry file formats
• Open Babel import of chemical files
• Input generation for multiple computational chemistry packages
• Extensions for additional functionality

Molekel

Molekel is a free molecule visualization program that can view SDF files. This is an open-source program available for Windows, macOS, and Linux. It uses different methods to quickly render the molecule structures and visualizes the orbital surfaces, SAS surfaces, SES surfaces, Van der Waals surfaces, Iso-surface from density matrix, and Iso-surface from Gaussian cube grid data.

Main Features:

• Open-source and Cross-platform
• Multi-language support
• Visualize molecule and material structures
• Supports various computational chemistry file formats
• Animation of molecular surfaces
• Animation of vibrational modes
• Programmable shaders
• Export to high-resolution image, PDF, PostScript, and animation

Swiss-PdbViewer

Swiss-PdbViewer is a free cross-platform program that can visualize SDF files. It is also known as DeepView. This program can view and analyze multiple proteins at the same time. It can superimpose molecules to compare and deducted their structure alignments. It can compare models to find model errors, compute surfaces, electrostatic potentials, examine electron-density maps, and much more.

Main Features:

• Cross-platform
• Multi-language support
• Visualize molecule and material structures
• Supports various computational chemistry file formats
• Color surfaces via atoms or cavities
• Export to POV-ray
• Extensive Integration with Web Servers

Molegro Molecular Viewer

Molegro Molecular Viewer is a free software to visualize molecules and Molegro Virtual Docker results. This software is available for Windows only. It can automatically prepare molecules and visualize the molecule surfaces and backbone. It can crop the molecules and clip the planes. This software supports Molegro Virtual Docker MVDML files and aligns the protein structure.

Main Features:

• View and share molecular and material structures
• Multi-language support
• Imports and exports common molecular file formats such as PDB, SDF, Mol2, etc.
• Supports Molegro Virtual Docker MVDML files
• Built-in raytracer for high-quality images
• Labels, sequence viewer
• Biomolecule generator
• Support for KNIME workflows

CueMol

CueMol is another cross-platform program to view SDF files. This program is available for macOS and Linux as well along with Windows. It is good for macromolecular structure visualization and can also create molecular structures. CueMol can easily open molecular coordinates (PDB format), MSMS surface data, APBS electrostatic potential map (OpenDX format), and electron density (CCP4, CNS, and MTZ formats).

Main Features:

• Cross-platform
• Tab-based molecular views
• Visualize molecule with edge rendering
• Support for multi-molecular scenes
• Supports various formats including PDB, MSMS, OpenDX, X-PLOR/CNS, MAP, etc.
• Store and restore scenes in XML format
• Animate Camera motion and Structure morphing
• Export to POV-ray and movie creation

iMol

iMol is another free open-source molecule visualization program. It is available for Windows and Linux. It can visualize common computational chemistry structural data file-formats including MDL MOL format. It can open multiple molecular structures at the same time with multiple rendering styles and can also animate the molecular dynamics trajectories and molecular dynamics trajectories, residues, and atoms.

Main Features:

• Open-source
• Multi-language support
• Hierarchical view of molecules
• Stereo rendering
• Animate molecular atoms, dynamics trajectories
• Surface and backbone coloring
• Export to POV-ray

BALLView

BALLView is a standalone program offered by BALL Project. This program is designed for easy molecular modeling and visualization. It can easily visualize atoms, bonds, and surfaces. Additionally, it also supports grid-based visualizations like electrostatic potentials. It can open multiple molecules simultaneously.

Main Features:

• Multi-language support
• Visualize molecule and material structures
• Supports common computational chemistry file formats
• Different stereo mode with space navigator
• VRPN-supported Input devices

SDFReader

SDFReader is a free program to view Structure Data Files. This is an open-source program available for Windows and Linux. It is a simple program with a minimal interface. Users can directly open the SDF file to visualize it. This program then shows the structure of the molecule along with additional data stored in the SDF file.

Main Features:

• Open-source
• Multi-language support
• View molecule and material structures
• Sve data in sqlite3 database format