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Star Republic: Guide for Biologists

Visulization of 3D structures

Several programs are available for visualizing 3D structures of proteins or chemicals.

RasMol
Description: View molecular structure in 3D. Show any molecule with an atomic coordinate (PDB) file (e.g., structures in Brookhaven Protein DataBank (PDB) ).
System requirements: Works for both Windows and Machitosh.
Download http://www.umass.edu/microbio/

Chime
Description: Derived from RasMol. Web plug-in.
System requirements: Works for Windows, Machitosh, SGI, linux, etc. Best if using Netscape. Works sometimes with Explorer.
Download http://www.umass.edu/microbio/chime/

Protein Explorer
Description: Derived from RasMol and Chime.
System requirements: Works for both Windows and Machitosh. Best if using Netscape. Works with Netscape on Mac.
Download http://molvis.sdsc.edu/protexpld/index.htm

Cn3D
Description: View 3D structures for molecules in the NCBI's Molecular Modeling Database (MMDB), a subset of Brookhaven Protein DataBank (PDB).
System requirements: Works for Windows, Machitosh and Unix. Works with both Explorer and Netscape.
Download http://www.ncbi.nlm.nih.gov/structure/cn3d/cn3d.shtml

VMD --- Visual Molecular Dynamics
Description: Displaying, animating, and analyzing large biomolecular systems.
System requirements: Works for Windows, Machitosh and Unix.
Download http://www.ks.uiuc.edu/Research/vmd/