Install and Run Molywood in Ubuntu

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/#linux
2. Be sure that the Linux tab is selected and and copy the Download Python 3.x version link.
   
   
3. Open terminal and download the link copied in the step above:
   
   

   wget https://repo.anaconda.com/archive/Anaconda3-2019.10-Linux-x86_64.sh .

4. Now we have the file downloaded but we need to give it execution permissions:
   
   

   chmod +x Anaconda3-2019.10-Linux-x86_64.sh

   
   
5. Once we have execution permissions, let's execute the file and follow the installation instructions:
   
   

   sh ./Anaconda3-2019.10-Linux-x86_64.sh

6. 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
  - vmd
  - ffmpeg
  - imagemagick
  - conda

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

Download environment.yml

Create conda environment

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

3. 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