Note: V005 addes a new tab which generates a 3D representation of the helix and Relion command for making initial model. This needs a newer version of Matplotlib (>3.6).
Written by Xuewu Zhang, Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, USA.
A video demo on how to use it: https://www.youtube.com/watch?v=KxAeo90CIt4
A more detailed description can be found at (Citation:Xuewu Zhang, Protein Sci. 2021. doi: 10.1002/pro.4186): https://onlinelibrary.wiley.com/doi/10.1002/pro.4186
This is a Python-based GUI program for indexing power spectra of helical assemblies. The program is a Python script that runs under Python version 3.7. The script depends on the following Python libraries: Mrcfile 1.1.2 (Burnley et al., 2017), numpy 1.18.3 (Harris et al., 2020), matplotlib 3.4.2 (Hunter, 2007), Pillow 7.2.0 (https://pillow.readthedocs.io/en/stable/), PyQt5 5.15.0 (https://pypi.org/project/PyQt5/), SciPy 1.4.1 (Virtanen et al., 2020) and mplsursors 0.4 (https://mplcursors.readthedocs.io/en/stable/). Newer versions of these packages should work as well. These libraries can be installed on modern operating systems with standard Python library management tools such as PIP (Python Package Installer; https://pip.pypa.io/en/stable/) and anaconda (https://docs.conda.io/en/latest/).
For example, you can download Miniconda from here: https://docs.conda.io/en/latest/miniconda.html
Follow the intruction to install the python 3 version of Miniconda. To activate Conda:
$ source /directory/to/miniconda/bin/activate
Now you can directly install the dependency packages by using commands such as:
$ conda install numpy
Or you can create a virtual environment for PyHI:
$ conda create --name PyHI
To activate this new virtual environment:
$ source /directory/to/miniconda/bin/activate PyHI
Now you can install the packages within this envirnoment. To run PyHI, change to the directory where PyHI_v003.py resides and then:
$ python3 PyHI_v004.py