Jmol vs PyMOL

Struggling to choose between Jmol and PyMOL? Both products offer unique advantages, making it a tough decision.

Jmol is a Science & Education solution with tags like chemistry, 3d, molecular-structure, education, research.

It boasts features such as 3D visualization of molecules and chemical structures, Support for common chemical file formats like PDB, Mol, SDF, Interactive manipulation and measurement of molecular models, Analysis tools like molecular orbitals, electrostatics, etc, Scripting and programming interface for automation and customization, Platform independent (Java-based), Integration with web pages and applications and pros including Free and open source, Cross-platform compatibility, Powerful visualization and analysis capabilities, Support for major chemical file formats, Customizable and extensible via scripts, Actively developed and maintained.

On the other hand, PyMOL is a Science & Education product tagged with molecular-visualization, protein-structure, molecular-graphics, 3d-structure.

Its standout features include Molecular visualization and modeling, High quality rendering, Support for animations and movies, Plugin architecture for extensibility, Python scripting interface, Command line interface, Support for multiple structure alignment, Measurement tools, Session saving, and it shines with pros like Powerful visualization capabilities, High quality graphics, Extensive scripting options, Cross-platform availability, Free and open source.

Feature	Jmol	PyMOL
Overall Score	N/A	N/A
Primary Category	Science & Education	Science & Education

Product Overview

Jmol

Description: Jmol is an open-source Java viewer for 3D chemical structures that allows users to visualize, manipulate, and analyze molecular models. It supports a variety of chemical file formats and can be used for education, research, and commercial purposes.

PyMOL

Description: PyMOL is an open-source molecular visualization system. It can produce high-quality 3D images of small molecules and biological macromolecules such as proteins. PyMOL is designed for interactive visualization and generating publication-quality images and animations.

Key Features Comparison

Jmol Features

• 3D visualization of molecules and chemical structures
• Support for common chemical file formats like PDB, Mol, SDF
• Interactive manipulation and measurement of molecular models
• Analysis tools like molecular orbitals, electrostatics, etc
• Scripting and programming interface for automation and customization
• Platform independent (Java-based)
• Integration with web pages and applications

PyMOL Features

• Molecular visualization and modeling
• High quality rendering
• Support for animations and movies
• Plugin architecture for extensibility
• Python scripting interface
• Command line interface
• Support for multiple structure alignment
• Measurement tools
• Session saving

Pros & Cons Analysis

Jmol

Pros

• Free and open source
• Cross-platform compatibility
• Powerful visualization and analysis capabilities
• Support for major chemical file formats
• Customizable and extensible via scripts
• Actively developed and maintained

Cons

• Steep learning curve
• Limited documentation and support
• Some features require programming skills
• User interface could be more intuitive
• Lacks some features of commercial alternatives

PyMOL

Pros

• Powerful visualization capabilities
• High quality graphics
• Extensive scripting options
• Cross-platform availability
• Free and open source

Cons

• Steep learning curve
• Limited support and documentation
• Some features only in paid versions
• Can be resource intensive for large structures

Pricing Comparison

Jmol

• Open Source
• Free

PyMOL

• Free
• Open Source