A python package for flexible fitting of AFM images [1].
AFMfit can be installed with pip package manager :
git clone https://gricad-gitlab.univ-grenoble-alpes.fr/GruLab/afmfit.git
pip3 install afmfit
(Computation time : 1 min on a 16-core personal desktop)
Recommendation :
AFMfit uses ChimeraX for molecular visualizations.
It is recommended to have chimerax installed and available in the PATH variable.
Examples are available in the form of Jupyter notebooks. Make sure you have Jupyter installed :
pip3 install jupyter
The tutorial implements the data analysis of synthetic AFM images of Elongation Factor 2 (EF2) described in [1] and can be launched by :
python3 -m notebook examples/afmfit_tuto.ipynb
(Computation time : 5 min on a 16-core personal desktop)
You can now use most of AFMFit features through the GUI. Make sure you have Tkinter installed. For example (Ubuntu) :
sudo apt install python3-tk
Then you can simply run the script:
/path/to/afmfit/afmfit_gui
Rémi Vuillemot
LJK - Université Grenoble Alpes
e-mail: remi.vuillemot@univ-grenoble-alpes.fr
[1] Vuillemot, R., Pellequer, J. L., & Grudinin, S. (2024). AFMfit: Deciphering conformational dynamics in AFM data using fast nonlinear NMA and FFT-based search. bioRxiv, 2024-06.