Rigid body fitting of atomic strucures in cryo-electron microscopy density maps
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README.md

PowerFit

DOI

About PowerFit

PowerFit is a Python package and simple command-line program to automatically fit high-resolution atomic structures in cryo-EM densities. To this end it performs a full-exhaustive 6-dimensional cross-correlation search between the atomic structure and the density. It takes as input an atomic structure in PDB-format and a cryo-EM density with its resolution; and outputs positions and rotations of the atomic structure corresponding to high correlation values. PowerFit uses the local cross-correlation function as its base score. The score can optionally be enhanced by a Laplace pre-filter and/or a core-weighted version to minimize overlapping densities from neighboring subunits. It can further be hardware-accelerated by leveraging multi-core CPU machines out of the box or by GPU via the OpenCL framework. PowerFit is Free Software and has been succesfully installed and used on Linux and MacOSX machines.

Requirements

Minimal requirements for the CPU version:

  • Python2.7
  • NumPy 1.8+
  • SciPy
  • GCC (or another C-compiler)

Optional requirement for faster CPU version:

  • FFTW3
  • pyFFTW 0.10+

To offload computations to the GPU the following is also required

  • OpenCL1.1+
  • pyopencl
  • clFFT
  • gpyfft

Recommended for installation

  • git
  • pip

Installation

If you already have fulfilled the requirements, the installation should be as easy as opening up a shell and typing

git clone https://github.com/haddocking/powerfit.git
cd powerfit
sudo python setup.py install

If you are starting from a clean system, follow the instructions for your particular operating system as described below, they should get you up and running in no time.

Linux

Linux systems usually already include a Python2.7 distribution. First make sure the Python header files, NumPy, SciPy, and git are available by opening up a terminal and typing for Debian and Ubuntu systems

sudo apt-get install python-dev python-numpy python-scipy git

If you are working on Fedora, this should be replaced by

sudo yum install python-devel numpy scipy git

Sit back and wait till the compilation and installation is finished. Your system is now prepared, follow the general instructions above to install PowerFit.

MacOSX

First install git by following the instructions on their website, or using a package manager such as brew

brew install git

Next install pip, the Python package manager, by following the installation instructions on the website or open a terminal and type

sudo easy_install pip

Next, install NumPy and SciPy by typing

sudo pip install numpy scipy

Wait for the installation to finish. Follow the general instructions above to install PowerFit.

Installing pyFFTW for faster CPU version can be done as follows using brew

brew install fftw
sudo pip install pyfftw

Windows

First install git for Windows, as it comes with a handy bash shell. Go to git-scm, download git and install it. Next, install a Python distribution with NumPy and Scipy included such as Anaconda. After installation, open up the bash shell shipped with git and follow the general instructions written above.

Usage

After installing PowerFit the command line tool powerfit should be at your disposal. The general pattern to invoke powerfit is

powerfit <map> <resolution> <pdb>

where <map> is a density map in CCP4 or MRC-format, <resolution> is the resolution of the map in ångstrom, and <pdb> is an atomic model in the PDB-format. This performs a 10° rotational search using the local cross-correlation score on a single CPU-core. During the search, powerfit will update you about the progress of the search if you are using it interactively in the shell.

Options

First, to see all options and their descriptions type

powerfit --help

The information should explain all options decently. In addtion, here are some examples for common operations.

To perform a search with an approximate 24° rotational sampling interval

powerfit <map> <resolution> <pdb> -a 24

To use multiple CPU cores with laplace pre-filter and 5° rotational interval

powerfit <map> <resolution> <pdb> -p 4 -l -a 5

To off-load computations to the GPU and use the core-weighted scoring function and write out the top 15 solutions

powerfit <map> <resolution> <pdb> -g -cw -n 15

Note that all options can be combined except for the -g and -p flag: calculations are either performed on the CPU or GPU.

Output

When the search is finished, several output files are created

  • fit_N.pdb: the top N best fits.
  • solutions.out: all the non-redundant solutions found, ordered by their correlation score. The first column shows the rank, column 2 the correlation score, column 3 and 4 the Fisher z-score and the number of standard deviations (see N. Volkmann 2009, and Van Zundert and Bonvin 2016); column 5 to 7 are the x, y and z coordinate of the center of the chain; column 8 to 17 are the rotation matrix values.
  • lcc.mrc: a cross-correlation map, showing at each grid position the highest correlation score found during the rotational search.
  • powerfit.log: a log file, including the input parameters with date and timing information.

Creating an image-pyramid

The use of multi-scale image pyramids can signicantly increase the speed of fitting. PowerFit comes with a script to quickly build a pyramid called image-pyramid. The calling signature of the script is

image-pyramid <map> <resolution> <target-resolutions ...>

where <map is the original cryo-EM data, <resolution is the original resolution, and <target-resolutions> is a sequence of resolutions for the resulting maps. The following example will create an image-pyramid with resolutions of 12, 13 and 20 angstrom

image-pyramid EMD-1884/1884.map 9.8 12 13 20

To see the other options type

image-pyramid --help

Licensing

If this software was useful to your research, please cite us

G.C.P. van Zundert and A.M.J.J. Bonvin. Fast and sensitive rigid-body fitting into cryo-EM density maps with PowerFit. AIMS Biophysics 2, 73-87 (2015).

For the use of image-pyramids and reliability measures for fitting, please cite

G.C.P van Zundert and A.M.J.J. Bonvin. Defining the limits and reliability of rigid-body fitting in cryo-EM maps using multi-scale image pyramids. J. Struct. Biol. 195, 252-258 (2016).

Apache License Version 2.0

The elements.py module is licensed under MIT License (see header). Copyright (c) 2005-2015, Christoph Gohlke

Tested platforms

Operating System CPU single CPU multi GPU
Linux Yes Yes Yes
MacOSX Yes Yes Yes
Windows Yes Fail No

The GPU version has been tested on:

  • NVIDIA GeForce GTX 680 and AMD Radeon HD 7730M for Linux
  • NVIDIA GeForce GTX 775M for MacOSX 10.10