Vpython accessing object loaded from pdb protein file

Question

using this.cif file:

https://files.rcsb.org/download/1MSC.cif and parsing in with https://pypi.org/project/pdbx-mmcif/

with this code (main.py) that uses Vpython 7.6.1 in python3:

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Nov  11 17:40:03 2020

@author: Pietro

"""
import sys
from pdbx.reader.PdbxReader import PdbxReader

import time

from vpython import *


scene = canvas(title='Examples of Tetrahedrons',
     width=800, height=800,
     center=vector(0,0,0), background=color.black)

openz = open('./1msc.cif')

pRd = PdbxReader(openz)

data = []

pRd.read(data)

block = data[0]

atomsite = block.getObj("atom_site")

i=0
while True:
        atom =  atomsite.getValue("group_PDB",i)
        atomid = atomsite.getValue('label_atom_id',i)
        if atom =='ATOM':
            if atomid == 'CA':
                    aa = sphere(pos=vector(float(atomsite.getValue('Cartn_x',i)),float(atomsite.getValue('Cartn_y',i)),
                                           float(atomsite.getValue('Cartn_z',i))),radius=0.5)  
    
            i +=1
    
        else:
        
            break
      
print('fine')          

I can show CA atoms in space as spheres. What I am missing is how to access the singles spheres ( objects as I understood) created by vpython, to be able to apply something like

sphere-object-number-1.color = color.red

sphere-object-number-1.color = color.blue

obviusly not in the same loop I created to display all the spheres? Please be kind I am not a Python expert.

Answer 1

A standard method is to make a list atoms = [] and when you create a sphere add it to the list, as atoms.append(sphere(.....)). Then you access the nth sphere with atoms[n], where n runs from 0 to atoms.length-1.