PyMOL is described as 'Powerful and comprehensive molecular visualization product for rendering and animating 3D molecular structures' and is an app in the education & reference category. There are more than 10 alternatives to PyMOL for a variety of platforms, including Mac, Windows, Linux, Web-based and Android apps. The best PyMOL alternative is Avogadro, which is both free and Open Source. Other great apps like PyMOL are UCSF Chimera, Calistry.org, Jmol and Rasmol.
Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
United States
UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data.
Calistry is an online Chemistry Calculator. Till date Calistry contains 70+ calculators in the field of Chemistry. Everything in the website is entirely free to use. Other than calculators, Calistry also provides online molecular viewers that visualizes coordinate file of...
Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems.
RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures, such as those found in the Protein Data Bank.
QuteMol is an open source (GPL), interactive, high quality molecular visualization system. QuteMol exploits the current GPU capabilites through OpenGL shaders to offers an array of innovative visual effects.
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX can be downloaded free of charge for academic, government, nonprofit, and...
Explore detailed 3D cell biology down to the molecular level, or tour life’s molecular machines. CellWalk is a beautiful new way for students to learn biology.
Canada
Jalview is a free cross-platform program for multiple sequence alignment editing, visualisation and analysis. Use it to align, view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures...
United Kingdom
RasTop is a molecular visualization software adapted from the program RasMol, which was initially developed by Roger Sayle. RasTop is particularly adapted for educational purposes and for the rapid analysis of macromolecules at the bench.
