Methods for analyzing electron density maps in wwPDB
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 https://github.com/MoseleyBioinformaticsLab/pdb_eda.git
pdb_eda requires the following Python libraries:
To install dependencies manually:
pip3 install biopython pip3 install pandas pip3 install numpy pip3 install scipy pip3 install docopt pip3 install jsonpickle
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.