[Chimera-users] Suggestion for adding a volume map to morph conformation

Trevor Harris tmh08 at my.fsu.edu
Tue Apr 24 08:27:43 PDT 2018

Great! Thank you, I will take a look. 


> On Apr 24, 2018, at 11:26 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hello Trevor,
> There is a separate tool to morph volume data: Morph Maps (or command “vop morph”).  It was developed mostly for EM density maps and I don’t know if anybody has ever tried it with orbital isosurfaces, so I don’t know how the results would look… but it’s worth a try.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morphmap/morphmap.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#morph>
> Since this is a separate tool, it is not automatically synchronized with morphing atoms (Morph Conformations).  I would try just morphing the orbital data and seeing how that looks; if it looks good enough to you, then you can “worry” about synchronizing with the atoms.  How to synchronize the two is explained in this previous post and links therein:
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-April/008752.html>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Apr 23, 2018, at 10:27 PM, Trevor Harris <tmh08 at my.fsu.edu> wrote:
>> Hello,
>> I would like to use the Morph Conformation show the changes of the molecular orbitals from starting material to transition state to product. I can show the changes structurally of the atoms which is great, but this would be amazing with the molecular orbitals overlaid the structures. If this option is available to add volumes into morph conformation, then I couldn’t find it. Would it be possible to add this feature? It would be similar to IBOView. 
>> Thank you!
>> Trevor Harris
>> Postdoctoral Fellow
>> UPenn Chemistry, Chenoweth Group

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