Install and Run Molywood in Mac OS

Install Anaconda

Although the installation can be done without using Anaconda, we strongly recommend it as it contains numpy and matplotlib as a pre-installed package.

1. Go to the official Anaconda website:
   
   https://www.anaconda.com/distribution/#macos
2. Be sure that the macOS tab is selected and Download Python 3.x version.
   
   
3. Double click on the *.pkg file and follow the instructions:
   
   
4. The process of installation can last several minutes:
   
   
5. When the execution is finished, try to execute conda in the terminal window. If it doesn't work, the path must be exported:
   
   

   export PATH=/home/USER/anaconda3/bin:$PATH

   
   

Download environment.yml file

For creating a new conda environment, we need to download a YAML file with all the dependencies that must be installed into our environment. The structure of this file is as follows:

name: molywood
channels:
  - conda-forge
dependencies:
  - python
  - ffmpeg
  - imagemagick
  - conda

Download the YAML file environment.yml to your computer clicking the button below:

Download environment.yml

Create conda environment

Environment creation

Open your terminal and go to the folder where your environment.yml file has been downloaded and follow the next steps:

1. Create the molywood conda environment:
   
   

   conda env create -f environment.yml

2. Once the molywood conda environment is created, activate it:
   
   

   conda activate molywood

Packages installation

Once the environment has been successfully created, please follow the next steps for installing all the dependencies needed for the execution of :

VMD (Visual Molecular Dynamics)

1. As VMD is not available for macOS in Anaconda, we must install it manually. Please go to the following URL and download the *.dmg file:
   
   https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
   
   
2. Note that although VMD software is free for academic use, it is mandatory to be registered for downloading it. You must agree to the terms of the license:
   
   
3. As VMD is an external software, macOS will ask you for permissions in order to install it. Then run the installer:
   
   

Molywood

Run the Python Package Installer to install manually the last dependency:

pip install molywood

Run molywood

Now you can run molywood just typing molywood in your terminal.

(molywood) $ molywood

 Warning: no input data was provided. 

 To run Molywood, provide the name of the input file, e.g. 'molywood script.txt'. 

 To run a sample visualization, type 'y'. 

 To generate a sample input, type 'i'. 

 Pressing 'Enter' (or entering any other command) will terminate the script.
 >>> y
 Do you want to render the movie ('r'), or display only ('d')?
 >>> d
 Sample movie with pdb 1w0t, render mode off
Now rendering scene: scene