[Chimera-users] Small molecules and orbitals/ESP's

Kenward Vaughan kay_jay at earthlink.net
Sat Aug 30 09:28:20 PDT 2014

On 08/29/2014 10:07 AM, Elaine Meng wrote:
> Hi Kenward,
> I’ve seen several publications using Chimera to view orbitals and spin-density isosurfaces from QM calculations, but I’m not sure which format they are using to pass the information to Chimera.  QM programs I’ve seen mentioned in these papers include ORCA and Gaussian.
> Chimera reads several “volume” formats (density maps, electrostatic potential, etc.) and the resulting volume models can be viewed with isosurfaces.  The ones most often associated with QM calculations are “Gaussian cube grid” and “gOpenMol grid”:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume>
> Several of the volume formats are most often used for electrostatic potential:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp>
>   There is also a program AOMix specifically for molecular orbital analysis that writes out associated atom attributes for visualization in Chimera.  That is different from visualizing the actual orbitals, but AOMix users could be doing both.
> <http://www.sg-chem.net/aomix/>
> I hope this addresses your question; if not, please ask again!
> Best,
> Elaine

Thanks for this information, Elaine!  It gives me great hope in getting 
to use my favorite viewer with those kinds of results. I will spend some 
time delving into these.



> On Aug 28, 2014, at 7:32 PM, Kenward Vaughan <kay_jay at earthlink.net> wrote:
>> Hi all,
>> I am searching for a way to show small molecules with orbitals and potential surfaces from their associated QM calculations, in stereos display using our planned 3D vision setups.  Cross eye works well for some in a class, but mant students simply never get it.
>> It doesn't appear that any small molecule viewers are out there with such capability.  Is there some way to pull such information into Chimera to do this?

In a completely rational society, the best of us would aspire to be
*teachers* and the rest of us would have to settle for something less,
because passing civilization along from one generation to the next
ought to be the highest honor and the highest responsibility anyone
could have.     - Lee Iacocca

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