Electron cryo-microscopy (cryo-EM) has emerged as a powerful method to obtain three-dimensional (3D) structures of macromolecular complexes at atomic or near-atomic resolution. However, de novo building of atomic models from near-atomic resolution (3-5 Å) cryo-EM density maps is a challenging task, in particular since poorly resolved side-chain densities hamper sequence assignment by automatic procedures at a lower resolution. Furthermore, segmentation of EM density maps into individual subunits remains a difficult problem when the structure of the subunits is not known, or when significant conformational rearrangement occurs between the isolated and associated form of the subunits. To tackle these issues, we have developed a graph-based method to thread most of the C-alpha trace of the protein backbone into the EM density map. The EM density is described as a weighted graph such that the resulting minimum spanning tree encompasses the high-density regions of the map. A pruning algorithm cleans the tree and finds the most probable positions of the C-alpha atoms, using side-chain density when available, as a collection of C-alpha trace fragments. By complementing experimental EM maps with contact predictions from sequence co-evolutionary information, we demonstrate that this approach can correctly segment EM maps into individual subunits and assign amino acids sequence to backbone traces to generate atomic models.
The following python packages are required and can be installed using pip:
- numpy
- mrcfile
- netCDF4
- scipy
- networkx
- matplotlib
- biopython
- mpi4py
EMEC makes use of map_align C++ implementation. This program can be installed using detailed instruction from the map_align repository:
https://github.com/sokrypton/map_align
For the final model building, Modeller software is used. This program can be installed using the standard installation procedure as described in:
https://salilab.org/modeller/download_installation.html
To install EMEC, just clone the current repository and add the files in a directory that is listed in your PYTHONPATH variable, or add the path to EMEC directory in the PYTHONPATH variable. See https://docs.python.org/3/using/cmdline.html#envvar-PYTHONPATH for more details.
The file emec.py can be linked as emec in a directory listed in your $PATH variable. If $HOME/bin is listed in $PATH:
cd $HOME/bin && ln -s path/to/emec.py emec
The main EMEC file is emec.py. This file read a configuration file called emec.conf. An example emec.conf file is in run/emec.conf.
To reproduce the results of the paper, just run the following command in the run/ directory:
emec emec.conf
The EM map is read from a NetCDF file format that can be created from an MRC file using the UCSF Chimera software (https://www.cgl.ucsf.edu/chimera/)