MicrographModeller
Simulation of electron microscopy tilt- and frame-series, focused on modelling whole samples.
Dependencies
Micrograph-modeller is a python(>=3.8) package that can be installed. The base of the code runs on CPU's due to the large memory requirements for the tomography models. For sampling atoms to electrostatic potential a part of the code can be accelerated with GPU's. You will need to install cupy and CUDA toolkit to access it (see below).
To add hydrogens and remove water molecules from pdb/cif files I call chimerax from the command line. So for the full functionality you need to have chimerax installed.
Installation
I assume you have miniconda3 installed.
First create an environment with cupy in case you want to use the GPU acceleration. Conda will also automatically install a CUDA toolkit version compatible with cupy in this environment. You can specify more recent versions of cupy, but just keep in mind everything has been developed with 10.6.
conda create --name micrograph_modeller python=3.8 cupy=10.6.0
If you need a specific version of cudatoolkit you can specify it as well.
conda create --name micrograph_modeller python=3.8 cupy=10.6.0 cudatoolkit=11.6
You can also install a wheel of cupy via pip that is build against an installed versions of CUDA toolkit on your system. This can be preferred because CUDA toolkit takes up a lot of disk space.
conda create --name micrograph_modeller python=3.8
conda activate micrograph_modeller
pip install cupy-cuda116=10.6.0
If you did not do so already, activate the environment.
conda activate micrograph_modeller
And then install micrograph-modeller.
pip install micrograph-modeller
Tests
You can run the unittests as follows.
Running
UNDER CONSTRUCTION