scipion-em-hax 1.0.0

Plugin to execute Hax package inside Scipion

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).