Visualize HOMO LUMO with psi4 #RDKit #psi4 #psikit

Now thin wrapper of psi4 named psikit can generate cube file which has frontier orbital information. After calling getMOview, I would like to check the orbital shape.

Psi4 provides script which generates cool view on VMD. To run the script on python3, it is needed to change line 332 from ‘for k,v in options.iteritems():’ to ‘for k,v in options.items():’.

After changed the code. Ready to visualize molecular orbital! Let’s check it.
I run the following code on jupyter notebook.

import os
import sys
import pandas as pd
import numpy as np
from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
from psikit import Psikit
pk = Psikit()
>Optimizer: Optimization complete!

Then call getMOview() to generate MO cube files.

Next, run the The script has many options. To check the option, -h gives help.

I run the code interactive mode. After run the code, I could see MO on VMD.

To run the code, reader need install VMD in your PC. Of course the script generates image of each MO.

I think it is interesting that visualize MO of protein-ligand complex because it will show interaction of protein and ligand. It is very useful for understanding of the interaction. Any comments or suggestions are greatly appreciated. ;)


Published by iwatobipen

I'm medicinal chemist in mid size of pharmaceutical company. I love chemoinfo, cording, organic synthesis, my family.

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

This site uses Akismet to reduce spam. Learn how your comment data is processed.

%d bloggers like this: