## 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

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