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Methods for analyzing electron density maps in wwPDB

Project description


The pdb_eda package provides a simple Python tool for parsing and analyzing electron density maps data available from the world wide Protein Data Bank (PDB).

The pdb_eda package currently provides facilities that can:
  • Parse .ccp4 format file into their object representation.
  • Parse .pdb format file to get information that complimentary to the Bio.PDB module in BioPython package.
  • Analyze the electron density maps on atom/residue/chain level and interpret the electron densities in terms of number of electrons.

Full API documentation, user guide, and tutorial can be found on readthedocs


pdb_eda runs under Python 3.4+ and is available through python3-pip. Install via pip or clone the git repo and install the following dependencies and you are ready to go!

Install on Linux, Mac OS X

python3 -m pip install pdb_eda

GitHub Package installation

Make sure you have git installed:

git clone


pdb_eda requires the following Python libraries:

  • Biopython for creating and analyzing the pdb_eda atom objects.
  • pandas for calculating aggregated results.
  • numpy and scipy for mathmatical calculations.
  • docopt for better command line interface.
  • jsonpickle for formatted and reusable output.

To install dependencies manually:

pip3 install biopython
pip3 install pandas
pip3 install numpy
pip3 install scipy
pip3 install docopt
pip3 install jsonpickle

Basic usage

The pdb_eda package can be used in several ways:

  • As a library for accessing and manipulating data in PDB or CCP4 format files.

    • Create the pdb_eda.densityAnalysis.fromPDBid generator function that will generate (yield) single pdb_eda.densityAnalysis instance at a time.

    • Process each pdb_eda.densityAnalysis instance:

      • Generate symmetry atoms.
      • Generate red (negative density) or green (positive density) blob lists.
      • Process PDB structures to aggregate cloud.
      • Calculate atom blob list and statistics.
  • As a command-line tool:

    • Calculate statistics of a single PDB structure.
    • Calculate aggregated statistics of multiple PDB structures.

Project details

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