This program takes as input a low-resolution electronic density map (e.g. from electron microscopy) for a protein and a structure of the same protein in some other conformation. It then deforms the conformation to fit into the electronic density while preserving the protein structure through the use of low-energy normal modes.

Type "density_fit" without arguments to get a short description of how to use this program.

The algorithm used in this program is described in

K Hinsen, N Reuter, J Navaza, D L Stokes, and J J Lacapere Normal mode based fitting of atomic structure into electron density maps:

application to SR Ca-ATPase

Biophys. J. 88:818-827 (2005)

Please cite this article in your publications that make use of this program.



  • Python 2.2 or higher
  • Numerical Python 20.0 or higher
  • netCDF 3.4 or higher
  • ScientificPython 2.4 or higher
  • MMTK 2.4 or higher

To install this package, type (in this directory)

python build python install

The second command may require root privileges on Unix systems. Alternatively, users can install the package in their private directory. For more information about installation options, type

python --help install

Users of RPM-based Linux distributions can build RPM files (source and binary) by typing

python bdist_rpm