<jupyter_start><jupyter_text>Trying directly using [ipymd](https://ipymd.readthedocs.io/en/latest/tutorial.htmlbasic-atom-creation-and-visualisation) requires: conda activate ipymd*installed via:**conda create -n ipymd -c cjs14 ipymd pyqt=4 pyopengl=3.1**conda activate ipymd*<jupyter_code>import ipymd
data = ipymd.data_input.cif.CIF()
data.setup_data('Cu.cif')
atoms = data.get_atom_data()
print(atoms)
meta = data.get_meta_data()
print(meta)
vis = ipymd.visualise_sim.Visualise_Sim()
vis.basic_vis(data.get_atom_data(), data.get_meta_data(), xrot=45,yrot=45)<jupyter_output><empty_output><jupyter_text>Tests directly from the ipymd website<jupyter_code>cif_path = ipymd.get_data_path('example_crystal.cif')
data = ipymd.data_input.cif.CIF()
data.setup_data(cif_path)
meta = data.get_meta_data()
vis = ipymd.visualise_sim.Visualise_Sim()
vis.basic_vis(data.get_atom_data(), data.get_meta_data(), xrot=45,yrot=45)
import ipymd
import pandas as pd
df = pd.DataFrame(\
    [[2,3,4,1,[0, 0, 255],1],\
    [1,3,3,1,'orange',1],\
    [4,3,1,1,'blue',1]],\
    columns=['x','y','z','radius','color','transparency'])
vis = ipymd.visualise_sim.Visualise_Sim()
vis.add_atoms(df)
img1 = vis.get_image(size=400,quality=5)
img1<jupyter_output><empty_output>
{'fraction_non_alphanumeric': 0.16613162118780098, 'fraction_numerical': 0.03130016051364366, 'mean_word_length': 7.6, 'pattern_counts': {'":': 0, '<': 9, '<?xml version=': 0, '>': 9, 'https://': 1, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'chain_length': '2', 'dir': 'jupyter-structured-clean-dedup', 'id': '572985', 'license': 'MIT', 'n_tokens_mistral': 550, 'n_tokens_neox': 516, 'n_words': 70, 'path': 'test/cifTest/ipymd_python2.ipynb', 'repo_name': 'ageller/EmeryInteractive', 'size': '1246'}