Avogadro!

ACD/ChemSketch is a chemically intelligent drawing interface that allows you to draw almost any chemical structure including organics, organometallics, polymers, and Markush structures. Use it to produce professional looking structures and diagrams for reports and publications.

Marvin is a great alternative to the subscription based ChemDraw by CambridgeSoft. It is a collection of tools for drawing, displaying and characterizing chemical structures, substructures and reactions.It will also convert structures you create to various molecular visualiztion formats, such as .pdb and .mol, compatible with programs such as PyMOL and SwissPDB Viewer.

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. It was originally developed by Roger Sayle in the early 90s.Historically, it was an important tool for molecular biologists since the extremely optimized program allowed the software to run on (then) modestly powerful personal computers. Before RasMol, visualization software ran on graphics workstations that, due to their expense, were less accessible to scholars. RasMol has become an important educational tool as well as continuing to be an important tool for research in structural biology.RasMol has a complex version history. Starting with the series of 2.7 versions, RasMol is licensed under a dual license (GPL or custom license RASLIC).RasMol includes a language (for selecting certain protein chains, or changing colors etc.). Jmol and Sirius has incorporated the RasMol scripting language into its commands.Protein Databank (PDB) files can be downloaded for visualization from members of the Worldwide Protein Data Bank (wwPDB). These have been uploaded by researchers who have characterized the structure of molecules usually by X-ray crystallography, NMR spectroscopy or electron microscopy. »

The Gnome Chemistry Utils include six chemistry related programs: - GChemPaint, a 2D chemical formula editor. - a chemical calculator (computes raw formule, molar weight, mass composition and isotopic pattern). - a molecule 3d viewer using OpenGL to display molecular models. - a crystal structure editor and viewer. - a periodic table of the elements. - a spectrum viewer.

BKChem is a free (as in free software :o) chemical drawing program. It was conceived and written by Beda Kosata and is currently maintained by Reinis Danne.

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.

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 leading molecular dynamic pakages.

Cool Chemistry Tool - educational app for Students.Chemist will help you in chemical tasks! Use the Periodic Table just like a computer keyboard. With the Chemist you will learn everything you need to know about the elements, compounds and chemical reactions.

What's your favorite molecule? With ChemJuice, chemical structure drawing is now at your fingertips.

Ghemical is computational chemistry package, which is licensed under GNU GPL . The ghemical authors are listed here .

XDrawChem is a free software program for drawing chemical structural formulas, available for Unix and Mac OS. It is distributed under the GNU GPL. In Microsoft Windows this program is called WinDrawChem.Major features Fixed length and fixed angle drawing Automatic alignment of figures Detection of structures, text, and arrows, and their automatic placement Can automatically draw rings and other structures - has all standard amino acids and nucleic acids in a built-in library Retrieval of structures from a network database based on CAS number, formula, or name Retrieval of information on a molecule based on a drawing Symbols such as partial charge and radicals Reading MDL Molfiles, CML (Chemical Markup Language), ChemDraw binary format, ChemDraw XML text format Writing MDL Molfiles, CML, ChemDraw XML text format Integration with OpenBabel, allowing XDrawChem to read and write over 20 different chemical file formats. Image export in Portable Network Graphics (PNG), Windows bitmap, Encapsulated PostScript (EPS), and Scalable Vector Graphics (SVG) 3D structure generation with the help of the external program BUILD3D Simple spectra predictions, including 13C-NMR, 1H-NMR (based on additive rules and functional group lookup methods), and IR Simple property estimation, including pKa, octanol-water partition coefficient, and gas-phase enthalpy change. »