What are electron density maps?

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 represent how well the model fits the data.

What is a 2Fo-Fc map and how is it different from an Fo-Fc map?

There are two common types of electron density maps used by researchers, the 2Fo-Fc map and Fo-Fc map. The Fo-Fc map, known also as a difference or omit map, is used to show what has been overfit 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.

About Maps:

How are the maps calculated?

The program DCC ^[Yang2016] uses REFMAC to calculate phases and produce electron density maps.

For which PDB entries are the maps available?

Electron density maps are available for most entries for which a structure factor file is available. There is no consideration made of how well the model fits the data.

In what format are the maps available?

Electron density map coefficient files (2Fo-Fc and Fo-Fc) from the wwPDB validation pipeline are available in the public PDB archive alongside the wwPDB validation reports. Instructions for using the validation report electron density structure factor files are available here.

Note that as of June 28, 2024 EDMAPS.rcsb.org was shut down, including access to MTZ files with map coefficients from this service.

Using validation report map coefficient files

wwPDB validation reports provide users with detailed reports that include an analysis of the quality of coordinate model and experimental data. The resulting analysis is available in PDF, XML and CIF formats. In addition, for X-ray crystallography structures, the coefficients used to produce electron density maps are provided for download. These coefficient files contain the data that can be used to produce electron density maps. All validation data are available from the public archive at https://files.rcsb.org/pub/pdb/validation_reports/.

These electron density map data can be visualized in the “Structure” tab of a structure summary page by pressing on the “density” option from the right hand menu and then pressing the enable button.

This document describes how one may download the electron density map coefficient data and convert to a combined MTZ file, that may be visualized in COOT or produce CCP4 formatted map files that can also be used in other visualization programs.

Downloading Structure Factor File or Validation Map Coefficients

Assuming a UNIX based operating system, one can download the validation produced electron density map coefficient files, it can be done manually, but a simple shell script will do this, downloading the map coefficients for 2Fo-Fc and Fo-Fc maps.

#!/bin/sh
pdbid=$1
hash=${pdbid:1:2}
echo $pdid $hash
base="https://files.rcsb.org/pub/pdb/validation_reports"
vdir=$base/$hash/$pdbid
wget $vdir/${pdbid}_validation_2fo-fc_map_coef.cif.gz
wget $vdir/${pdbid}_validation_fo-fc_map_coef.cif.gz
if [ -e ${pdbid}_validation_2fo-fc_map_coef.cif.gz ]; then
gunzip ${pdbid}_validation_2fo-fc_map_coef.cif.gz
fi
if [ -e ${pdbid}_validation_fo-fc_map_coef.cif.gz ]; then
gunzip ${pdbid}_validation_fo-fc_map_coef.cif.gz
fi

Converting experimental data to MTZ file format

There are several options to convert to a MTZ formatted file for use in Phenix or other CCP4 programs. Two of the easiest are `cif2mtz` and `gemmi`. Both are distributed with CCP4, but the gemmi program is available for standalone use and may be installed with a local Python installation.
For instance:
cif2mtz hklin xxxx_validation_2fo-fc_map_coef.cif hklout 2fo.mtz << EOF
EOF

Or:
gemmi cif2mtz xxxx_validation_2fo-fc_map_coef.cif 2fo.mtz

With gemmi, one can combine multiple coefficient files at the same time:
gemmi cif2mtz xxxx_validation_2fo-fc_map_coef.cif --add xxx_validation_fo-fc_map_coef.cif comb.mtz

As mentioned above, COOT can utilize such a combined file to visualize the electron density maps.

Using MTZ map coefficient files to produce CCP4 maps

There are several ways to convert the map coefficient files to a CCP4 map. Only two are described here. Such map files can be used in Chimera, Pymol and other visualization software

With Gemmi
gemmi sf2map 2fo.mtz 2fo.map

Or more directly:
gemmi sf2map xxxx_validation_2fo-fc_map_coef.cif 2fo.map

The other common means to convert the file is with the CCP4 program FFT. This is what is used by the RCSB.org website.
fft HKLIN 2fo.mtz MAPOUT 2fo.map << EOF
LABIN F1=FWT PHI=PHWT
END
EOF

For an fo-fc map, use F1=DELFWT SIGI=SIGFP PHI=PHDELWT

Can maps for electron microscopy entries be downloaded?

Maps from electron microscopy experiments can be downloaded from the Structure Summary Page “Download Files" option and from the files download service at https://files.rcsb.org/pub/emdb/structures/

Reference

[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 49, 1081-1084 doi:10.1107/S1600576716004428.

COOT: Emsley P, Cowtan K (2004). Coot: model-building tools for molecular graphics. Acta Crystallogr. D60, 2126-2132.

Pymol: Schr?dinger, L., & DeLano, W. (2020). PyMOL. Retrieved from http://www.pymol.org/pymol

CCP4 Suite (for FFT): J. Agirre et al. Acta. Cryst. D79, 449-461 (2023) “The CCP4 suite: integrative software for macromolecular crystallography” [doi:10.1107/S2059798323003595].