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

Trevor Harris trevorha at sas.upenn.edu
Wed Apr 25 09:36:51 PDT 2018

This worked! Thank you.


> On Apr 24, 2018, at 8:29 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Trevor,
> As mentioned in the Morph Map page:
> "The data sets should have the same grids: dimensions, spacing, and numbers of points. Note the command vop resample can be used to make a copy of one map that has the same grid as another.”
> For running Morph Map, I don’t think it matters what kind of data are on those grids, as they are treated simply as values at grid points.  I only meant in my previous reply that I wasn’t sure how good the linear interpolation of orbital data would look, i.e. if the shapes of the isosurfaces would change in the way you expect.
> For resampling, you would want to use the grid that encloses all your isosurfaces of interest.  If both map’s grids do that, it doesn’t really matter which way you do it (resample A on B or resample B on A). You can show the grid outline boxes of your maps, for example with command: 
> volume all showoutline true
> (this setting is also in the Volume Viewer dialog, menu: Features… Data display options)
> The “vop resample” command mentioned above is described here:
> <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample>
> Just setting min & max the same may not be helpful if the grids are offset from one another, with origins in different places.
> I hope this helps,
> Elaine
>> On Apr 24, 2018, at 4:08 PM, Trevor Harris <trevorha at sas.upenn.edu> wrote:
>> So I tried the morph map feature first to see if I could get it to interpolate between two sets of orbital isosurfaces and nothing happens when i move the fraction slider. It does say at the bottom of the morph map window “Map sizes differ”. I tried to adjust the region min max to be the same values but I don’t know if that would really fix anything or if it just doesn’t work using MOs. 
>> Trevor
>>> 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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