ChemEM is currently distributed via anaconda. To begin using ChemEM ensure you have an anaconda or miniconda installed.
First, create a new environment called chemem.
Note: ChemEM v0.0.3 is currently only available on python 3.11
conda create --name chemem_env python=3.11
Now, Activate the new environment with:
conda activate chemem_env
Install mamba to the environment:
Next, install the Mamba package manager which resolves conda dependencies faster:
conda install mamba
Should this fail try:
conda install -c conda-forge mamba
Now its time to install ChemEM
mamba install -c chemem -c conda-forge chemem
Once the installation is complete and you should be able to use ChemEM from the command line by specifying a configuration file with the necessary data like so:
chemem <configuration_file>
The minimum require data to run ChemEM is shown below:
#ChemEM config file
protein = ~/test_data/7jjo_protein.pdb
ligand = CC(C)NC[C@@H](c1ccc(c(c1)O)O)O
centroid = (134.087, 133.507, 174.180)
output = ~/some_directory
densmap = ~/test_data/7jjo.mrc
resolution = 2.6
Additionally, the enabled stages block must be included
#enabled stages
pre_process = 1
pre_process_split_density = 0
auto_split_point = 0
auto_split_zone = 0
fitting = 1
dock_only = 0
post_process = 1
rescore = 0
The enabled stages section allows the user to specify what functions ChemEM should run with the given data. To enable a stage set the value to 1 to disable a stage set the value to 1.
For more information see the documentation.