PyMOL

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.

PyMOL alternatives ➤

What is PyMOL?

PyMOL is a popular open-source molecular visualization system created by Warren DeLano and currently maintained by Schrödinger. It is designed specifically for visualizing and animating 3D structures of small molecules and biological macromolecules such as proteins and nucleic acids.

Some key features and capabilities of PyMOL include:

High-quality rendering and ray tracing for publication-ready images and movies
Support for a wide range of molecular data file formats
Interactive visualization with rotations, selections, coloring, etc.
Measurement tools for distances, angles, surface areas, etc.
Sequence and structure alignment capabilities
Integrated Python scripting for automation and customization
Plugins and library for advanced features like electrostatics and visualization of large structures

PyMOL can be used on Windows, Mac, and Linux systems. The intuitive GUI combined with flexible scripting has made it one of the most widely used platforms in molecular modeling, structural biology education, and molecular visualization in research publications and presentations.

Some alternatives with similar functionality include UCSF Chimera, VMD, Swiss PDB Viewer, and others. But PyMOL remains popular as a free tool for high-quality molecular graphics and flexible customization via scripting.

Official Links

Official Website
pymol.org/2

The Best PyMOL Alternatives

Top Apps like PyMOL

Rasmol, Jmol, VMD - Visual Molecular Dynamics, UCSF Chimera, RasTop, BioBlender, QuteMol, Calistry.org, Space Ball are some alternatives to PyMOL.

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Rasmol

RasMol is a popular free and open-source molecular visualization software used to visualize and analyze 3D molecular structures such as proteins, DNA, RNA, and small molecules. Originally developed in the early 1990s for computational molecular graphics teaching and research, RasMol has evolved into one of the most widely used tools...

Jmol

Jmol is an open-source molecular viewer and visualization software for 3D chemical structures, with features for chemical education, research, and commercial use. It is written in Java so that it can run on desktops and servers, online or locally. Jmol allows users to visualize, animate, manipulate, measure, and analyze a...

VMD - Visual Molecular Dynamics

VMD (Visual Molecular Dynamics) is a molecular visualization program designed for the display, animation, and analysis of large biomolecular systems using 3-D graphics and built-in scripting. VMD can read standard protein databank files and display the contained structure's secondary structure cartoon, displaying molecules as lines, ribbons, cylinders, spheres, and other...

UCSF Chimera

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.Chimera includes complete documentation and several tutorials. Core attributes include:highly integrated...

RasTop

RasTop is an open source, free system monitoring tool for Linux operating systems. It provides a graphical interface to monitor various metrics and resources in real time, including:CPU usage and loadMemory and swap usageDisk I/O and file system usageNetwork bandwidth and packet statisticsSome key features of RasTop include...

BioBlender

BioBlender is an open-source 3D animation software application designed specifically for visualizations in molecular and cellular biology. It is built on top of the popular open-source 3D creation suite Blender, providing tools tailored for biological data visualization and animation.Key features of BioBlender include:Importing common molecular file formats like...

QuteMol

QuteMol is an open-source, cross-platform molecular visualization application designed for proteins, small molecules, and quantum chemistry. It enables users to visualize and analyze the structures and properties of molecular systems interactively.Some key features of QuteMol include:Intuitive user interface for manipulating molecular structures in 3DSupport for common file formats...

Calistry.org

Calistry.org is a comprehensive free online calculator and unit conversion tool. It features hundreds of built-in calculators and unit converters spanning various categories including math, finance, health, fitness, science, engineering, and more.Users can easily convert between units for length, volume, temperature, time, speed, area, pressure, energy, power, data...

Space Ball

Space Ball is a classic 2D arcade-style spaceship shooter set in outer space. Players control a small but powerful spaceship and must make their way through hordes of menacing enemy ships and asteroid fields.The goal is to get the highest score possible by destroying as many alien ships as...