!pip install git+https://github.com/njzjz/dpdata@3dmol py3Dmol

import dpdata
import numpy as np
dpdata.System(data={
    "atom_names": ["N"],
    "atom_numbs": [2],
    "atom_types": np.zeros((2,), dtype=int),
    "coords": np.array([[[0,0,0],[1,1,1]]], dtype=np.float32),
    "cells": np.zeros((1, 3, 3), dtype=np.float32),
    "orig": np.zeros(3, dtype=np.float32),
    "nopbc": True,
}).to_3dmol()