Before I begin I know that what I am asking will deform the M.O but for what I am doing this for that is okay if it is only around the atoms and bonds.

My question is in JMOL is there anyway to display the isosurface of the molecular orbital and have it leave a gap around the molecule. I am going to a conference soon and need to print a model of a cyclic molecule. I would like to be able to "mount" the MO to the molecule using tiny magnets at certain points so I may dislodge the two phases and show the structure of the molecule. Yes using two different models (one with MOs and one without) is possible but not preferred.

I have explored isosurface command and different syntax and have not been able to find anything that may be of help.

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    $\begingroup$ Perhaps someone will actually know how to do this in JMOL, but if klunky hacks are acceptable, you could export the isosurface and then try to edit it in a program like MeshMixer (free, but unfortunately not on Linux) $\endgroup$ – chipbuster Oct 4 '17 at 22:48
  • $\begingroup$ Kind of the direction I might have to go. I would use TinkerCAD or Meshlab. Increase size of atoms and bonds, then delete it, leaving a cavity, then replace the molecule. $\endgroup$ – Ryan Godbey Oct 4 '17 at 22:58
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    $\begingroup$ I've used VMD in the past to make 3D-printed molecular models: youtube.com/watch?v=8hdmBRxCrnw . Never done it with orbitals, though. I know VMD can visualize orbitals but whether converting JMOL format to VMD is easy, is another question. $\endgroup$ – khaverim Oct 4 '17 at 23:18

What I ended up doing was using jmol to produce the different phases of the MO and then I used TinkerCAD and made the molecule itself a "hole" structure. This created the space to actually put the molecule inside the orbital.


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