Plot IGM analysis with PyMol

Plot IGM analysis from Multiwfn using PyMol. IGM is an useful analysis of spatial distribution of steric hindrance. Plotting IGM result is much easier and looks better in PyMol.

Related Multiwfn Documents
http://sobereva.com/407

Related PyMol Documents
https://pymolwiki.org/index.php/Ramp_New

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Run IGM analysis

• Save optimized geometry as .mol2 file

So that can be opened by both Multiwfn and Gview

• load into Multiwfn & run IGM

  20
  10
  2               // 2 fragments
  [atom index]    // fragment #1 (atom group tool from Gview helps)
  [atom index]    // fragment #2
  2               // grid quality
  3               // save files to current dir

  Now we have dg_inter.cub, dg_intra.cub, dg.cub and sl2r.cub.

Plot with PyMol

• load the .mol2, dg_inter.cub and sl2r.cub into PyMol.
• Use “Other Visualization Settings for structures” from https://www.shaoqz.cn/2020/06/29/PyMol-Orbital/
• Build Isosurface

  isosurface IGM1, dg_inter.cub, 0.01
  set transparency, 0.2

  Grammer: isosurface {new object name}, {.cub name}, {isovalue}
• Color the surface with sl2r

  ramp_new ramp1, sl2r, [-0.05, 0, 0.05], [blue, white, red]
  color ramp1, IGM1