For twenty years, PyMOL was the default choice for visualizing a protein. But the landscape has changed. An overview of 17 alternatives and a practical decision grid.
Detailed comparison
17 molecular visualization tools
Stacked cards to compare at a glance. Filter by use case, click on a name to go to the official website.
Publication-quality renderings, Python scripting. The historical standard for scientific paper figures.
The official viewer of the RCSB PDB and AlphaFold DB, now the de facto standard on the web.
The modern successor to Chimera. Native handling of large cryo-EM assemblies and AlphaFold, VR support.
Versatile, homology modeling. The historical version, now transitioning to ChimeraX.
The molecular dynamics standard, handling very large systems and NAMD/GROMACS trajectories.
Molecule editing, computational chemistry. Ideal for organic chemistry and small molecules.
Web integration and teaching. The historical standard for interactive pages and university tutorials.
Lightweight, embeddable in a product page or a scientific dashboard.
Goodsell-style renderings, server-side PyMOL ray tracing. Ideal for educational illustrations without installing anything.
Interactive homology modeling, to test virtual mutations or align sequences.
The absolute reference for X-ray crystallography and structure refinement.
A historical, very lightweight tool. Still used for basic teaching and introductions to 3D visualization.
High-quality renderings via GPU/OpenGL shaders. Very aesthetic, but a dated project (unmaintained).
Photorealistic graphics, VR, built-in MD simulations. All-in-one modeling and visualization.
A complete drug design suite. Aimed at pharma: docking, ADMET, virtual screening, library management.
Drug design and cheminformatics. The industrial pharma reference, with a very rich SVL script ecosystem.
Immersive VR visualization (Meta Quest and others). Multi-user collaboration in virtual reality.
