pschmidtke / mobcal-shm

Mobcal-shm analysis Pipeline

This package includes the mobcal fork, called mobcal-shm and several supplementary utilities allowing to a more straightforward analysis of protein structures especially with mobcal.

Using the package

Here you can find the how to use the package with the docker image.

Transforming a pdb to a mobcal input file

The scripts directory contains a python script allowing you to convert a PDB file to a mfj file, which is the accepted input format of mobcal. The script prepares the PDB file as well, completing missing atoms, it optionally protonates the structure to a provided pH. Charges are subsequently calculated for the system and written out in the resulting mfj file.

cd scripts;
python pdb2mfj.py examples/1mty.pdb examples/1mty.mfj 

Installation

NB: This is only required if you want to continue development of this package, else, please refer to the docker image of the package to avoid the huzzle of installing & compiling all dependencies.

Conda Development environment

Import the conda environment for mobcal using the provided environment file. This is especially required when you want to use the pdb2mfj utility provided in the repo:

conda env create -f mobcal.yml

Next activate the environment using

conda activate mobcal

Compiling mobcal-shm

Now we also need to compile mobcal-shm itself for you environment, unless the provided executable works for you. Simply run the following commands:

cd src;
make

Docker Image

Building the docker image

docker build -t mobcalshm .

Running the docker image