MCCE quick start¶

Page last updated on: 2020-12-04

Get the code¶

MCCE runs on Linux and Mac OSX natively, on Windows in its Linux subsystem. Follow How to install WSL to install Linux Subsystem if you don't have one.

Install with conda¶

The mcce program comes with many small programs and tool scripts, so it is recommended to run mcce in a separate conda environment. Suppose we will run mcce under environment "mcce":

One-time setup of the environment:

conda create -n mcce
conda activate mcce

Install mcce:

conda install -c newbooks mcce

To exit conda mcce environment:

conda deactivate

Install from source¶

Of for some reason, installation of mcce from conda didn't work, you can install from the source.

Prerequisites¶

Compilers: C, gfortran

The C and gfortran compilers usually come with your operating system. If not, use the package manager to install.

On Ubuntu Linux:

$ sudo apt-get update
$ sudo apt-get upgrade
$ sudo apt-get install build-essential
$ sudo apt-get install gfortran

On Mac OS X:

For Mac users, the gcc compiler comes with Xcode from the App store. Once Xcode is installed, install command line tools. This provides gcc.

Gfortran is avalaible from https://github.com/fxcoudert/gfortran-for-macOS/releases, find your Mac OS X version and install appropriate gfortran package.

Python and modules

We need Python3 and optionally these modules: numpy, scipy, matplotlib, pygraphviz, pandas, xlrd, and openpyxl

Install Miniconda Python3: https://docs.conda.io/en/latest/miniconda.html
After installing Miniconda, install these optional modules for data analysis:

conda install numpy scipy matplotlib pygraphviz pandas xlrd openpyxl

Download from github¶

Under a terminal window, run:

git clone https://github.com/GunnerLab/Stable-MCCE.git

Compile the code¶

The above command creates a directory named Stable-MCCE, enter the directory and compile:

$ cd Stable-MCCE
$ make clean
$ make

Configure environment:

Find the path of Stable-MCCE installation directory:

(base) jmao@pc:~/projects/Stable-MCCE$ pwd
/home/jmao/projects/Stable-MCCE

In my case the installation directory is /home/jmao/projects/Stable-MCCE/

Add the executable to your path:

export PATH=/home/jmao/projects/Stable-MCCE/bin:$PATH

Remember to replace the installation directory /home/jmao/projects/Stable-MCCE/ with your own installation path.

Also put this line at the end of .bashrc file under your home directory so that the environment is properly set every time you open a terminal window.

Run MCCE¶

Prepare a working directory:¶

$ mkdir test_lysozyme
$ cd test_lysozyme

Get a pdb file¶

$ getpdb 1dpx

You now have a pdb file 1DPX.pdb in the working directory.

The simplest way to run mcce is do these four steps:

Step 1 convert PDB file into MCCE PDB¶

This step proof reads the structure file and cuts terminal residues and complex cofactors into smaller ones if necessary.

$ step1.py 1DPX.pdb

If this step quits and complain about unrecognized residues, please refere to the section of making new paramter files.

Step 2 make side chain conformers¶

This step makes alternative side chain locations and ionization states.

$ step2.py

Step 3 make energy table¶

This step calculates conformer self energy and pairwise interaction table.

$ step3.py

Step 4 Simulate a titration with Monte Carlo sampling¶

This step simulates a titration and writes out the conformation and ionization states of each side chain at various conditions.

$ step4.py

Notes¶

Command help "-h"¶

For more detailed command usages, use "-h" switch in each command above.

Run in background¶

Some steps take hours to finish, so it is recommended to run at the background. For example:
```
step3.py > run.log &
```

Jupyter notebook¶

Here is a Jupiter note book template: mcce.ipynb

Last update: 2020-12-04