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) |
Yasara | Innovative ‘virtual reality’ graphical user-interface (EDM, MM, NMR)
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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.
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