nurvus lab repository

Chemistry software & other resources

The following links provide free for use , often open source, chemistry modeling programs. These are great for STEM students of all ages. I use many of these myself in the lab. As a scientist it can be tough finding your way around the internet, especially finding what you want. Someone literally wrote a book on it. That said, I hope this helps.

Free Molecular Visualization Software: 

1. Avogadro -An all inclusive modeling program, Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture. Many consider this best for all platforms. It is available for Windows, Linux, and Mac OS X users. All source code is available under the GNU GPL.
2. Discovery Studio Visualizer – Commercial-grade graphics visualization is available for free to all academic, government and commercial researchers through Discovery Studio (DS) Visualizer. With DS Visualizer, you can visualize and share molecular information in a clear and consistent way, and in a wide variety of industry-standard formats. You can also create high quality graphics. DS Visualizer runs on Windows 8, Red Hat Enterprise Linux versions 3, 4 & 5 and SUSE Enterprise Linux 10. This is the successor of WebLab Lite from Accelrys. WebLab Lite (see after text) is still available from some sites online (That link is a live .exe from American Chemistry Society). There are several advanced features on Discovery Studio Visualizer including the ability to show ligand binding sites in proteins and create a surface around the ligand. New updates feature the ability to build small molecules, proteins and nucleic acids. See the Free vs. Commercial Software Datasheet.
   • WebLab – from Molecular Simulations, Inc. was free and ran on Windows and Macintoshes, and was in part derived from RasMol. It could represent alpha helices as cylinders, add missing hydrogen atoms, and rotate residues around a bond (torsion). It was excellent for selecting  a subset of atoms and saving them to a separate file.
3. Jmol – This program is a free, open source molecule viewer written in Java. It runs as a standalone application and as a web browser applet. Jmol was collaboratively developed as a visualization and measurement tool for both scientists and educators. New features are added often in updated versions. Users are encouraged to modify it to fit their needs and to contribute their changes to the project. JMol is a Chime/Rasmol replacement. Jmol runs on tablets and often works better on the Mac.
4. MolMol – (Win95, unix) makes publication quality images including surfaces, and has a graphical user interface with menus, dialog boxes and on-line help, including a hypertext manual and tutorial. Especially good support for multi-model NMR files. Supports limited modeling (addition or removal of atoms/bonds, and rotation around dihedral angles).
5. Cn3D  – This program is a new free viewer from the National Center for Biotechnology Information. It uses PDB files converted to ASN.1 format available thru The NCBI Entrez Database. Cn3D  will itself query the Entrez database for the user as well. Considerable effort has been applied to the ASN.1 data files to resolve ambiguities present in the PDB format and remove errors present in some PDB files. See the on-line article by Hogue et al. from University of Massachusetts for an explanation. Cn3D is more intelligent than RasMol, i.e. it provides a more informative first image of a structure.
6.  Molecule to Image Converter Engine – by Jozsef Ferincz is a web form which allows you to submit a PDB file URL, and get back a RasMol image.
7. MolView and MolView Lite  – These are freeware programs written for the Mac. The user cannot only display proteins in all of the various ways but can also analyze them (e.g. distances, Ramachandran plots, Edmunson wheels, hydrophathy plots, 3D structure alignments). Ribbon drawings can be drawn in many different ways – all controlled by graphical buttons. Subsets of structures can be written out to ‘MOL files’ to be read in at a later time. UI is graphical based and not script driven. In contrast to most other programs, the output images are mostly kept as object-oriented PICT files for very high quality prints. Finally, the user can also output 3 different kinds of QuickTime movies, line DXF files, and Apple’s new 3DMF files for interactively rendered ball&stick, ribbon, space filling, line, and ‘tube’ models.
8. LinusLite – is a free test version of a forthcoming enhanced version of the commercial viewer MacMolecule. These programs run only on the Mac, and require a special atomic coordinate data file format, generated from PDB files with a free translator provided.
9. ChemDraw & Chem3D, free demo software from CambridgeSoft Corp., which also provides a web-searchable database of molecules. (Windows, Mac, unix)
10. JME Molecular Editor – JME Molecular Editor is a Java applet which allows the user to draw and edit molecules and reactions. The applet can also depict molecules directly within an HTML page. The editor can generate SMILES or MDL mol files for export.

11. Oscail X -A Windows based Crystallography and Molecular Modelling program.It is free to ACADEMIC users, students are included. Commercial users must obtain permission for its use. The program provides an integrated high quality system for building and modelling molecules (Mopac and Iconc are included) and the system drives PC GAMESS and Tinker. The crystallographic software can solve, refine and examine small molecule crystal structures. The pictures produced range from high quality HPGL to photo realistic rendered 3D. Rendered movies are effective and easy to make using RASMOV. Software for Powder pattern simulation and the detection and display of voids is also available.

12. Tinker – This program is for molecular modeling. The software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. Tinker has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98 and ff99), CHARMM (19 and 27), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA and OPLS-AA/L). It can coordinate with the above program Oscail X.

MDL Chime and molviz.org: MDL Chime is being phased out, and as far as molvis.org, it may become an obsolete resource soon.

• The following are resourcesare related to molvis.org
  • Top Five 3D MolVis Technologies http://Top5.MolviZ.Org
  • FirstGlance, used by Nature – http://firstglance.jmol.or
  • 3D Wiki with Scene-Authoring Tools http://Proteopedia.Org
  • Biochem 3D Education Resources http://MolviZ.org
  • ConSurf – Find Conserved Patches in Proteins: http://consurf.tau.ac.il
  • Atlas of Macromolecules: http://atlas.molviz.org
  • Interactive Molecules in Public Spaces http://MolecularPlayground.Org
  • Workshops: http://workshops.molviz.org
  • Molecular Visualization EMail List (molvis-list): http://list.molviz.org Protein
  • Explorer – 3D Visualization: http://proteinexplorer.org

60 Carbon “buckyball”

Not free, but potentially useful:

• Midas+ – This program isn’t free but an academic license costs only $350. It is very powerful and runs on Silicon Graphics, DEC Alpha AXP, and NeXT workstations.

Major 3D Databases & other resources:

• The Protein Data Bank
• US National Center for Biotechnology Information
• NIH Center for Molecular Modeling
• The Protein Society
• Swiss-3D-Image of the ExPASy Molecular Biology Server at the Swiss Institute of Bioinformatics, Geneva.
• SCOP, Structural Classification of Proteins from the Medical Research Council (MRC) Laboratory of Molecular Biology and Centre for Protein Engineering, Cambridge, England UK.
• Chemistry Dept, Imperial College of Science, Technology and Medicine, London UK.
• Journal of Protein Science
• Mathematics & Molecules at NYU.
• The Teaching & Education in Crystallography section of the Crystallography section of the World Wide Virtual Library.
• VirusWorld developed by the Bock Laboratories, Institute for Molecular Virology, at the University of Wisconsin. (great graphics here)
• Molvis.org – MDL Chime resource

The above is by no means everything, but hopefully if you are studying in the STEM fields it can provide you with some helpful sources. As always, leave me a comment if any of the links are dead!