This repository contains an example for the PowerFit package. The output of this example was generated using PowerFit release version 5.0.2.
First download the input files and install PowerFit:
# Downloads the input files
mkdir powerfit-example-data/
cd powerfit-example-data
curl -L -o 3zpz_C.cif.gz https://github.com/haddocking/powerfit-examples/raw/refs/heads/main/3zpz_C.cif.gz
curl -L -o EMD-2325.map.gz https://github.com/haddocking/powerfit-examples/raw/refs/heads/main/EMD-2325.map.gz
# Create an environment, on Windows use WSL
python3 -m venv .venv
.venv/bin/activate # or activate equivalent for your OS/shell
# Install PowerFit release version 5.0.2
pip install powerfit-em==5.0.2In this example chain C of the GroEL/ES chaperonin system (PDB entry 3zpz) was fitted into the corresponding cryo-EM density map of the full complex (EMDB entry 2325 - 8.9 Å resolution) with a rotational sampling interval of 5 degrees.
In this repository you find the following files:
The following command can be used to generate the output present in output.zip:
# Run the example
powerfit EMD-2325.map.gz 8.9 3zpz_C.cif.gz --angle 5 --directory output --report --delimiter , Dependent on your system and the amount of CPUs used to run the example, this run might take ~30 minutes
Please refer to the manual for an explanation
of all the files present in output.zip
You can visualize the fits by downloading the output files and opening the result page with
python3 -m http.server -d . and clicking report.html
While Powerfit clearly favors one location based on cross correlation score and sigma difference, there is still a major break in sigma difference between the 7 symetric orientations and the next best fit (Fit 8).
PowerFit is currently functional on Linux and Mac devices. If you want to run it on a Windows device, we recommend installing WSL. You could also run this example on our webservice