X-ray Electron Density Maps
What are electron density maps – and what is 2fo-fc and fo-fc?
Electron density maps are the end results of an X-ray structure determination. The maps combine the structural model and the experimentally collected data to produce a representation that provides information as to the fit of the model to the data.
There are two common forms of electron density maps used by researchers, the 2fo-fc map and fo-fc map. The fo-fc map will show what has been overfit by the model or not accounted for by the model, while the 2fo-fc map will include the fo-fc map and electron density around the model.
These two maps are then used to correct the model when possible. Even in the best quality structures, there are areas of poor electron density, which may represent sections of the model that exist in multiple conformations. This can be seen in long side chains or surface loops of the model.
How are the maps calculated?
Electron density maps are calculated using the program [Yang2016]. DCC calculates the phases of the map and then produces the electron density maps.
For which archival entries are the maps available?
For most entries in which a structure factor file is available for a model, electron density maps are available. We are not using any cutoff of how well the model fits the data.
What about EM maps?
At this time, maps from electron microscopy experiments are not being delivered at this time. They are already in a map form and may used directly.
In what format are the maps available
Electron density maps from the edmaps.rcsb.org service are being provided in both DSN6 format and as a separate phases file (MTZ) which may be loaded directly in some molecular viewers like COOT. See below for download options.
Why in that format?
DSN6 files are smaller in size than CCP4 maps, and compress well for web delivery. These may be loaded by molecular viewers like COOT. The DSN6 maps have two different version available. In the first the grid spacing in the maps are fixed at 1/3 of the high resolution of the map. In the other, the spacing varies from 1/3 to 1/2 of the high resolution limit for higher resolution structures. This provides for a smaller size without much of a compromise on quality.
MTZ files contain the phase information for the map in question. COOT can use this information to produce an electron density map as well.
Will there be other formats in the future?
In the future, CCP4 maps might be considered if the demand is there. For now, downloading the phase file and using in COOT is more efficient.
Where to download the maps?
Maps can be downloaded in DSN6 format from the "Download Files" menu of the Structure Summary and 3D View pages. The maps are also available from edmaps.rcsb.org. The DSN6 map files are in the "dsn6" folder (with fixed grid spacing at "high resolution/3") and in the "ngl" folder (with variable grid spacing from "high resolution/3" to "high resolution/2"). The MTZ phase files are in the "persist" folder. Entries are grouped by the middle two characters of the 4-character PDB identifier. For example, the DSN6 files for PDB entry 3PQR can be found in edmaps.rcsb.org/dsn6/pq/3pqr/.
- [Yang2016] H Yang, E Peisach, JD Westbrook, J Young, HM Berman and SK Burley. DCC: a Swiss army knife for structure factor analysis and validation (2016) Journal of Applied Crystallography 93:569-575 doi:10.1107/S1600576716004428