How to install

The first step in using Surfaces is to install Python. Details for installing Python can be found on the Python downloads page.

Another essential step is to install Pymol by following the instructions for your operating system.

Tip

We recommend Pymol installation for any OS as follows:

conda install -c conda-forge pymol-open-source

For Windows you must run it on Anaconda Powershell Prompt as Administrator.

For this installation you should first install Miniconda in case you do not have Anaconda installed.

To access all Surfaces codes, you can clone the repository using git:

git clone https://github.com/nataliateruel/Surfaces

or download the Surfaces repository at https://github.com/nataliateruel/Surfaces.

There are a few dependencies for Surfaces’ Python scripts. You can install them by running the following commands using pip:

cd Surfaces
pip install -r dependencies.txt

or also:

cd Surfaces
conda install --file dependencies.txt

Note

It is important to install the dependencies for the same version of Python that you plan to use for running the scripts.

Another necessary step is to compile Vcontacts. You can use:

clang Vcontacts-v1-2.c -o vcon

or also:

gcc -c Vcontacts-v1-2.c
gcc Vcontacts-v1-2.o -o vcon -lm

To test if the compilation step was successful you might run:

./vcon

Tip

If you are using Windows, make sure to have a functional C compiler installed. For that you might run conda install -c conda-forge m2w64-gcc on Anaconda Powershell Prompt as Administrator.

Note

For the subsequent usage steps, we recommend running your structure analyses within the Surfaces directory.