Generating Cartesian Coordinates from Protein Internal Coordinates Using Python

Generating Cartesian coordinates of each atom in protein chain from the internal coordinates using python or some software

To generate Cartesian coordinates of each atom in a protein chain from internal coordinates, you can use a programming language like Python or utilize specialized software such as PyMOL or Biopython.

Here is an example implementation using Python and the Bio. PDB module from Biopython:

1. Install Biopython by running the command: `pip install biopython`

2. Create a Python script and import the required modules:
“`python
from Bio. PDB import PDBParser, PDBIO, PDBModel
import numpy as np
“`

3. Load the protein structure from a PDB file using the PDBParser:
“`python
parser = PDBParser()
structure = parser. get_structure(‘protein’, ‘protein. pdb’) # Replace ‘protein. pdb’ with your input PDB file name
“`

4. Extract the first model and chain from the structure (assuming it’s a single chain protein):
“`python
model = structure[0]
chain = model[‘A’] # Replace ‘A’ with your desired chain identifier
“`

5. Create a dictionary to store the atom coordinates:
“`python
cartesian_coordinates = {}
“`

6. Iterate through each residue in the chain:
“`python
for residue in chain:
res_id = residue. get_id()[1]
for atom in residue:
atom_id = atom. get_name()
internal_coordinates = atom. get_vector(). get_array()
# Convert internal coordinates to Cartesian coordinates
cartesian_coordinates[(res_id, atom_id)] = internal_to_cartesian(internal_coordinates)
“`

7. Define a helper function to convert internal coordinates (lengths, angles, and dihedral) to Cartesian coordinates:
“`python
def internal_to_cartesian(internal_coordinates):
# Implement conversion logic using NumPy and trigonometric functions
#. cartesian_coordinates =. # Calculated Cartesian coordinates
return cartesian_coordinates
“`

8. Finally, print or save the Cartesian coordinates of each atom:
“`python
for (res_id, atom_id), coordinates in cartesian_coordinates. items():
print(f’Residue {res_id}, Atom {atom_id}: {coordinates}’)
“`

Remember to complete step 7 by implementing the conversion logic from internal coordinates to Cartesian coordinates. This involves calculating the x, y, and z coordinates based on lengths, angles, dihedral angles, and the relationships between neighboring atoms

Note: If you prefer using PyMOL, it provides a more interactive and flexible environment for visualizing and manipulating protein structures, and it can generate Cartesian coordinates as well. Simply load the structure in PyMOL and use built-in commands or scripting functions to obtain the desired Cartesian coordinates

More Answers: