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.