[Chimera-users] Morphing surface

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 5 23:47:24 PST 2011

Oops, my reply only pertains to conformational changes, not creation/destruction of atoms.  The morphing trajectory created by Morph Conformations only includes the set of atoms that are present in both endpoint structures, because the coordinates are simply interpolated from one endpoint to the other.  Thus if you are changing an amino acid from one type to another, the morph trajectory will only include the backbone atoms of that residue.

One idea, but I really don't know how well it would work, would be to simulate a density map from each structure with the "molmap" command, display isosurfaces for the two maps using Volume Viewer, then use Morph Map (under Tools... Volume Data) to morph between the two density maps.


It might be hard to set the density map isosurface levels so that the isosurfaces well approximate the molecular surfaces.  You could display the molecular surfaces for comparison while adjusting the density isosurface levels in Volume Viewer.

If you try this, I'd be interested in hearing how well it worked.  Best,

On Jan 5, 2011, at 4:25 PM, Elaine Meng wrote:

> Hi Sumitro,
> If you use Morph Conformations on atomic structures, that creates a trajectory with a bunch of intermediate structures.  Then just show a surface on the trajectory model before playing it back.  There may be a message saying playback will be slow because it has to recalculate the surface at each step, but you can continue anyway.  Basically, it will just calculate a surface for each intermediate structure in the trajectory -- it is not exactly morphing the surface, but the result is similar and should be what you want.  One drawback is that if an intermediate structure is weird, the surface calculation might fail at that step. The test case I tried worked fine, however.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Jan 4, 2011, at 5:00 PM, Sumitro Harjanto wrote:
>> Hi elaine, 
>> Thanks for the prompt responses on earlier queries. I have one more question:
>> Is it possible to morph between 2 surfaces? 
>> Basically, I would like to show the effect in the surface contour due to a residue change.
>> Thanks,
>> Sumitro
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