Visualize Molecular Orbital with pymol and psikit #RDKit #psi4 #psikit #pymol

I posted how to visualize MO with VMD, the data was generated from psikit.

I used VMD because psi4 provides visualize function for cubefile and I could not find the same method on pymol. Pymol is familier for me than VMD. So I would like to do same thing on pymol. And today I could do it.

It is very easy! Let’s try it. At first, geometry optimize and generate cubefile of acetic acid and tetrazole.

import sys
sys.path.append('/Users/iwatobipen/develop/chemoenv/psikit/psikit')
from psikit import Psikit
from rdkit import Chem
pk = Psikit()
# acetic acid
pk.read_from_smiles("CC(=O)[O-]")
pk.optimize()
Chem.MolToMolFile(pk.mol, 'acetic_acid.mol')
pk.getMOview()

# tetrazole
pk.read_from_smiles("CC1=NN=N[N-]1")
pk.optimize()
pk.getMOview()

The getMOview() to generate MO cube files. The function generates 4 files named Psi_a/b_n_n_A.cube. n is number of alpha electrons and number of alpha electrons + 1. It means HOMO and LUMO.

After file generation, launch pymol and load mol file and cubefiles. For acetic acid, acetic_acid.mol, Psi_a_16_16-A.cube and Psi_b_16_16-A.cube files are loaded for HOMO drawing.

Then, draw isomesh and set color from pymol command line.

isomesh HOMO_A,  Psi_a_16_16-A, -0.02
isomesh HOMO_B,  Psi_b_16_16-A, 0.02
color blue, HOMO_A
color red, HOMO_B

Now I could get following image on pymol.

And I could get HOMO of tetrazole with same manner.

Pymol can draw ligand-protein complex easily. I think it is interesting for rendering ligand MO on protein-ligand complex and think about new drug design.

Leave a Reply

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

WordPress.com Logo

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

Google photo

You are commenting using your Google 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.