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
from psikit import Psikit
from rdkit import Chem
pk = Psikit()
# acetic acid
Chem.MolToMolFile(pk.mol, 'acetic_acid.mol')

# tetrazole

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.


Published by iwatobipen

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

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