Molecular editors are specialist applications for constructing, editing and visualizing molecular structures. They provide researchers and students with graphical tools for examining chemical systems without having to work solely with textual coordinate files or input decks.
The software in this roundup covers a fairly broad range of molecular modelling work. Typical capabilities include building molecules from atoms and fragments, manipulating bonds and geometry, displaying structures using different rendering styles, measuring distances and angles, and exploring three-dimensional molecular arrangements.
Some molecular editors also act as front ends for computational chemistry packages. This lets users prepare calculations, configure jobs and inspect the resulting molecular structures from a graphical environment. Other programs concentrate more heavily on high-quality visualization, structural biology, crystallography or programmable analysis.
These applications are useful to computational chemists, structural biologists, crystallographers, materials scientists and researchers working with molecular simulations. They can also be valuable teaching tools, helping students understand molecular geometry, bonding and three-dimensional chemical structures more intuitively.
We have selected applications that cover these different approaches to molecular editing and visualisation.
Here’s our verdict captured in a legendary LinuxLinks-style ratings chart. Only free and open source software is eligible for inclusion here.
Click the links in the table below to learn more about each application.
| Chemistry: Molecular Editors and Visualisation | |
|---|---|
| PyMOL | Molecular graphics system for visualizing structures and producing images |
| Avogadro | Advanced molecular editor and visualization application |
| Gabedit | Graphical interface for computational chemistry packages and modelling |
| Jmol | 3D molecular viewer for chemicals, crystals, materials and biomolecules |
| Patinae | Programmable molecular visualization toolkit with desktop and Python support |
| Coot | Interactive macromolecular model building, refinement and validation toolkit |
| IQmol3 | Molecular builder and visualization package for computational chemistry |
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