Introduction to Electron Density Maps

The PDB archive contains two types of data for structures determined by X-ray crystallography. Coordinate files include atomic positions for the final model of the structure and the structure factor file which represents the intensity (or amplitude) for each reflection (X-ray spots) in the diffraction pattern.

These two types of data are combined to create electron density maps to represent how well the model fits the data.

There are two common types of electron density maps used by researchers, the 2Fo-Fc map and Fo-Fc map. The 2Fo-Fc map uses observed structure factors (Fo) and calculated structure factors (Fc) to show the fit of the model to the experimental data. 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, surface loops of the model, or at the N-terminal or C-terminal regions.

wwPDB Validation Reports provide users with detailed information that includes an analysis of the quality of the coordinate model compared with the experimental data. The resulting analysis is available in PDF, XML and CIF formats. For X-ray crystallography structures, 2Fo-Fc and Fo-Fc map coefficient files (weighted amplitudes and phases) containing the data that are used in wwPDB Validation Reports are provided in PDBx/mmCIF format.

These coefficient files may be downloaded from the Structure Summary Page of an entry and can be visualized in the “Structure” tab.

The downloaded coefficient files can be converted to electron density maps that may be visualized in Coot(DSN6 format) or produce CCP4 formatted map files (MTZ format) that can also be used in other visualization programs.

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

In this diagram, files provided by the PDB are outlined in red, dashed lines.

The following table shows the main items generally included in the _refln category of the mmCIF format structure factor file and coefficient files. Notice that the structure factor file includes the experimental structure factors, while the coefficients files contain weighted structure factor amplitudes (_refln.pdbx_DELFWT; _refln.pdbx_FWT) and weighted phases for the (_refln.pdbx_DELPHWT; _refln.pdbx_PHWT ) as well as a figure of merit (_refln.fom ).

Downloading Structure Factor Files or Validation Map Coefficients

One can download the validation-produced electron density map coefficient files manually from Structure Summary Pages, or with a Unix system, a simple shell script may be used:

#!/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 Coefficient files to MTZ File Format

There are several options to convert coefficient files to MTZ formatted files 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

Coot can utilize this combined file to visualize the electron density maps.

Using MTZ Map Coefficient Files to Produce CCP4 Maps

There are several ways to convert MTZ 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 way to convert the file is with the CCP4 program FFT. This is what is used by the RCSB.org website.

For a 2fo-fc map:

fft HKLIN 2fo.mtz MAPOUT 2fo.map << EOF
LABIN F1=FWT PHI=PHWT
END
EOF

For a fo-fc map:

F1=DELFWT SIGI=SIGFP PHI=PHDELWT

Downloading Maps for Electron Microscopy Entries

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/

References

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].

Chimera: UCSF Chimera--a visualization system for exploratory research and analysis. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. J Comput Chem. 2004 Oct;25(13):1605-12.

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

GEMMI: Wojdyr, M., (2022). GEMMI: A library for structural biology. Journal of Open Source Software, 7(73), 4200, https://doi.org/10.21105/joss.04200

PyMOL: Schrödinger, L., & DeLano, W. (2020). PyMOL. Retrieved from http://www.pymol.org/pymol

Resources

• May 09, 2024 Announcement: EDMAPS.rcsb.org Shutdown
• June 06, 2024 Download and Display Electron Density Maps
• September 24, 2024 Announcement and FAQ: EDMAPS.rcsb.org Shutdown October 16