Electron Density Maps and Coefficient Files

06/03

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

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.

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.

A new help page provides an Introduction to Electron Density Maps, Downloading Structure Factor Files or Validation Map Coefficients, Converting Coefficient files to MTZ File Format, Using MTZ Map Coefficient Files to Produce CCP4 Maps, and Downloading Maps for Electron Microscopy Entries.

News Index

• 06/03 Electron Density Maps and Coefficient Files

• 05/28 Explore Integrative Structures at RCSB.org

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• 01/16 wwPDB News: PDB-Dev now PDB-IHM

• 01/16 Top Molecules of the Month in 2024

• 01/14 Winter Newsletter Published

• 01/12 Paper Published: Updated resources for exploring PDB structures and Computed Structure Models

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• 01/05 wwPDB News: Time-stamped Copies of PDB and EMDB Archives