PyMOL Molecular Graphics System

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PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is free to everyone!



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An interactive viewer for three-dimensional chemical structures.

PyMOL Plugins

PyMOL Plugins aims to provide many plugins for the PyMOL software. You can find further informations about PyMOL on this website:


SBEVSL is a collaborative project between Dowling and RIT on the development of a Structural Biology Extensible Visualization Scripting Language, so that users can move freely among various molecular graphics tools, such as rasmol, pymol, raster3d, etc.

Pymlp - pyMLP is a program computing the molecular lipophilicity potential map of proteins.

pyMLP: Molecular Lipophilicity Potential evaluator pyMLP takes a protein .pdb file as input and output a .dx map file easily visualized in many molecular visualization packages such as VMD, Pymol, Chimera, ... This program was developed in python as a platform independent equivalent of MLPP (see references in README). As a result pyMLP may run on any platform supported by Python and Numpy.

Pdbfs - Mount the Protein Data Bank as a filesystem with FUSE

IntroductionThe Protein Data Bank (PDB) is an excellent repository of protein structures determined by X-ray crystallography, which has yet to be used to its full potential. pdbfs hopes to facilitate the writing of tools to data-mine the PDB by making it possible to mount the PDB as a filesystem. This package concerns itself with getting a list of structures and on the fly downloading and decompressing the proper files, so that other packages don't have to! Prerequisitesbuild tools: gcc, make, e

Molecular-biology-tools - Multiplatform calculator and sequence manipulator for molecular biologists

Native application for multiple platforms aimed at on-the-fly DNA manipulation, especially focused on use of a smartphone. Emphasis on smooth GUI, ease-of-use, and completeness of each tool added. Completeness, here, is to be understood as giving the user the option to readily modify the calculations in as many ways as are known to exist, such that the user does not need to move his or her data to another program to finish calculations. Development is currently focused on very basic functionalit

Immersive-viz - PyMol script to view molecules with the HTDP

ImmersiveViz is a PyMol script to interface with the Head Tracking Driver Project in order to control the molecule by moving around in physical space. The script requires Python and wxPython to be installed, and currently only works on the Mac operating system. In time, it will be released for Linux and Windows as well. This project extends from the MolViz Project of Christian Muise and Ryan Lilien at the University of Toronto. InstallationMake sure you have Python, wxPython, and PyMol installed

Pdbbot - A bot to automate PDB image edits on Wikipedia and Wikimedia Commons

PDBbot is a small application which generates high-quality images of protein structures for Wikipedia. It is written primarily in Python, and interacts with PyMOL and GIMP. The application has three main functions: generating images, uploading them to Wikimedia Commons, and updating protein articles on Wikipedia to use the new images. More detailed documentation is in the code itself.

Exser - Extracts the amino acid sequences of the secondary structural regions

Detailed structural analysis of proteins necessitates investigation at primary, secondary and tertiary levels, respectively. Protein Data Bank (PDB) is an internationally referred protein structure database,it comprise of the atomic coordinates of the threedimensional (3D) structures of proteins that are solved experimentally, and as well theoretically. Molecular visualization tools such as RASMOL, PyMOL etc., help to visualize the coordinates of the PDB file in a 3D form, the information pertai

pymol - pymol scripts

pymol scripts