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Download and Display Electron Density Maps
06/06
Electron density maps combine the structural model (coordinates) and the experimentally-collected data from an X-ray structure determination and serve to represent the fit of the model to the data. There are two types of electron density maps commonly used by researchers: 2fo-fc and fo-fc. The fo-fc map (also called a difference or omit map) map shows what has been overrepresented or not accounted for by the model, while the 2fo-fc map includes the fo-fc map and electron density around the model.
These two maps are then used to correct the model when possible. Areas of poor electron density can be viewed in even in the best quality structures. This may represent sections of the model that exist in multiple conformations, as seen in long side chains or surface loops of the model.
Electron density maps calculated using the program DCC can be downloaded in DSN6 format from Structure Summary pages at rcsb.org. DSN6 format files (for use with programs including O, pymol, JSmol/Jmol, and Chimera) and MTZ format coefficient files (for CCP4) are available from edmaps.rcsb.org/persist and can be used to open electron density maps in Coot. Additional documentation is available.
Learn more about “Structure Factors and Electron Density” at PDB-101.
These electron density maps can be viewed in 3D at rcsb.org using NGL. Both 2fo-fc and fo-fc maps are available, and can be displayed at different sigma levels and styles. Shown: Electron density 2fo-fc map for PDB structure 1CBS centered around Retinoic Acid (REA) at 1 sigma contour level.
Electron density maps calculated using the program DCC can be downloaded in DSN6 format files (for use with programs including O, pymol, JSmol/Jmol, and Chimera) and map coefficients are contained in the MTZ file available at the "Download File" page of the Structure Summary Page of an entry and can be used to open electron density maps in Coot.
