A blog about free research software, alternative to commercial paid software.

One way to help people is to share your knowledge with those who could benefit from it. As a researcher , constant effort to solve scientific problems have exposed me to various scientific resources that can be accessed free of charge. Especially these knowledge is useful to labs and institution unable to access expensive software or novice users due to lack of expertise. In this blog, I have provided a comprehensive list of freely available softwares, alternative to commercial software. I shall share with you all that I have learned, as I make the changes or learn something new, I shall document them. Hope this blog will help those finding the way………….

Research software and books

Feb 11, 2011

List of free molecular viewers

Given here are list of freely available molecular viewer with outstanding features. Individually comparing the features of each of these programs are really too much of work for me. Most of these programs have general features including standard representation ( ribbon, ball and stick, space filling etc) and various coloring features.

Cn3D Integrated sequence alignment view; embeddable
Chime Widely used; structure editing; electrostatic maps; embeddable
Chimera Popular; integrated sequence alignment viewer (EDM, MD)
DS Visualizer Free version of Accelrys’s powerful viewer/editor program
ICM-Browser High quality images; integrates with sequence alignment viewer
IMOD Tomogram alignment, display, segmentation (EDM, optical)
Jmol Widely used; embeddable
KiNG Generic tool for creating ‘kinemages’
Mage Generic tool for creating ‘kinemages’; allows structure editing
Molscript Useful for preparing manuscript images
MolSurfer Shows macromolecular interfaces, for example, by electrostatic potential
MOLMOL Many features, particularly suited for NMR structures
OpenAstexViewer Embedded in many PDBe (see below) services
ProSAT2 Displays sequence features on three-dimensional structure
PMV Dynamically extensible; multiple structures, large assemblies  (MM)
PyMOL Widely used; embeddable; high-quality images (EDM, MM)
RasMol Widely used; fast; scripting
Raster3D High-quality, photorealistic rendering
SPICE Adds DAS features to three-dimensional structures
STRAP Editor for structural alignments of proteins (HM)
Swiss-PdbViewer Integrated sequence view (EDM, MM)
VMD Widely used; extensible, many add-ons (EDM, MD, MM, NMR)
Innovative ‘virtual reality’ graphical user-interface (EDM, MM, NMR)

Abbreviations: EDM, electron density maps; HM, homology modeling; MD, molecular dynamics; MM, molecular modeling and molecular orbital visualization; MRI, magnetic resonance imaging; NMR, nuclear magnetic resonance; optical, optical microscopy.