OpenScience / Software / Chemistry / Molecule Viewers and Editors

molPX is an Ipython module that provides, within a Jupyter notebook, interactive molecular visualization of virtually any type of coordinate that a molecular dynamics (MD) trajectory has been projected to. From the more intuitive coordinates, such as distances, contacts, angles … Continue reading →

IQmol is a easy to use molecular editor and visualization package with the ability to connect to remote servers to run ab initio calculations. Find IQmol at: http://iqmol.org

Molekel is an open-source multi-platform molecular visualization program. Find Molekel at: http://molekel.cscs.ch/wiki/pmwiki.php

Zeobuilder is a user-friendly GUI toolkit for the construction of advanced molecular models. The program contains several advanced tools to build, align, manipulate and analyze molecular structures. Most of its novel functionality is based on a hierarchical data-structure of reference … Continue reading →

EasyChem is a program designed to draw chemical molecules, written under Linux and using Gtk+ 2. Focus is on press-quality final drawings, drawing very easily ornaments (non-bonding electron pairs, …) and exporting to EPS/PDF formats with LaTeX fonts (Computer Modern). … Continue reading →

A molecular builder and conformational editor. AGM Build can be used for interactive model preparation for molecular dynamics simulations, including association of atom types and partial charges. Features: * Geometry editing * Lattice building * Building of chain molecules (for … Continue reading →

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers a flexible rendering engine and a powerful plugin architecture. Find Avogadro at: http://avogadro.cc/wiki/Main_Page

This is an Applescript Studio application that provides a front-end for a variety of Cheminformatics tools. To date these include file conversion (between a vast range of chemical file formats), SMARTS-based substructure searching, similarity searching, list manipulation, overlaying using OpenBabel, … Continue reading →

The CCP1GUI project aims to develop a free, extensible Graphical User Interface to various computational chemistry codes developed by the worldwide academic community, with an emphasis on ab initio Quantum Chemistry codes. Find The CCP1GUI at: http://www.cse.scitech.ac.uk/ccg/software/ccp1gui/

Useful for viewing PDB files, etc. Relatively powerful configuration for graphical representation of molecule. Find VMD at: http://www.ks.uiuc.edu/Research/vmd/