Scipion HAX Plugin

Plugin to execute Hax package from Scipion.

Installation

We recommend installing Hax in production mode using the Scipion Plugin manager or by running the command:

[!WARNING] The following command assumes that you have defined an alias to the Scipion executable named scipion3

  scipion3 installp -p scipion-em-hax

If you are a developer, you might want to install the plugin in development mode. In this case, please clone this repository to your machine and install the plugin with the following command:

[!WARNING] The following command assumes that you have defined an alias to the Scipion executable named scipion3

  scipion3 installp -p path/to/your/cloned/scipion-em-hax --devel

In both cases, the Plugin will automatically create a Conda environment to isolate Hax from other installations. So, you'll need to have Conda installed on your machine.

[!WARNING] Hax currently supports NVIDIA drivers version: >= 525 (Cuda 12/13 will be installed along the package, so there is no need to have CUDA already installed in your system).

References

• Herreros, D., Lederman, R.R., Krieger, J.M. et al. Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials. Nat Commun 14, 154 (2023).
• Herreros, D., Kiska, J., Ramirez-Aportela, E. et al. ZART: A Novel Multiresolution Reconstruction Algorithm with Motion-blur Correction for Single Particle Analysis. Journal of Molecular Biology 435, 168088 (2023).
• Herreros, D., Krieger, J.M., Fonseca, Y., et al. Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM. Acta Cryst. D 79, 569-584 (2023).
• Herreros, D., Mata, C.P., Noddings, C. et al. Real-space heterogeneous reconstruction, refinement, and disentanglement of CryoEM conformational states with HetSIREN. Nat Commun 16, 3751 (2025).
• Herreros, D., Perez Mata, C., Sanchez Sorzano, C.O. et al. Merging conformational landscapes in a single consensus space with FlexConsensus algorithm". Nat Methods (2023).