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Powerfit Example

This example contains a sample input and ouput generated with PowerFit release version 5.0.2. The data is hosted on the powerfit-examples github repository.

Running the example

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==5.0.2

In 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 the repository you find the following files: - 3zpz_C.cif.gz - EMD-2325.map.gz - output.zip

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

If you want to quickly check the results of the run, you can directly downloads output.zip 

# Download ouput.zip
curl -L -o output.zip https://github.com/haddocking/powerfit-examples/raw/refs/heads/main/output.zip

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).