XYZ File Extraction and Visualization

This README provides instructions on how to extract compressed .xyz files and visualize them using Python libraries MDAnalysis and nglview.

File Extraction

The .xyz files are compressed and split into multiple .tar.gz files. Use the following bash commands to extract them:

# For files split into multiple parts (e.g., R19P.xyz and T30P.xyz):
cat R19P.tar.gz.* | tar xzf -
cat T30P.tar.gz.* | tar xzf -

# For files in a single part (e.g., C30P.xyz and O30P.xyz):
tar xzf C30P.tar.gz.00
tar xzf O30P.tar.gz.00

After extraction, you should have the following .xyz files:

• C30P.xyz
• O30P.xyz
• R19P.xyz
• T30P.xyz

Visualization

To visualize the extracted .xyz files, you can use Python with MDAnalysis and nglview libraries. Here's a Python script to visualize any of the extracted .xyz files:

import MDAnalysis as mda
import nglview as nv

# Replace 'filename.xyz' with the name of the .xyz file you want to visualize
filename = 'filename.xyz'

# Create a universe object from the .xyz file
universe = mda.Universe(filename)

# Create a view of the universe
view = nv.show_mdanalysis(universe)

# Add a ball and stick representation
view.add_representation('ball+stick')

# Center the view
view.center()

# Display the view
view

To use this script:

1. Make sure you have MDAnalysis and nglview installed. You can install them using pip:

   pip install MDAnalysis nglview
   

2. Replace 'filename.xyz' with the name of the .xyz file you want to visualize (e.g., 'R19P.xyz').
3. Run the script in a Jupyter notebook or in an environment that supports nglview visualization.