[Chimera-users] morph volumes after alignment

Elaine Meng meng at cgl.ucsf.edu
Tue Jun 30 09:31:53 PDT 2015


Dear David,

 believe you need to resample the fitted map on the grid of the reference map to create a third map.  Then you will have two maps on exactly the same grid (the reference and the third map), and can morph between those two.

For example, if I fitted map #2 onto map #0, I could resample it to create new map #3 with command:

vop resample #2 onGrid #0 model #3

Then try morphing between #0 and #3.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#resample>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#morph>

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 Jun 30, 2015, at 7:15 AM, Haselbach, David <david.haselbach at mpibpc.mpg.de> wrote:
> 
> Dear all, 
>  
> I have a few volumetric cryo EM Maps of the same protein in different conformations. And I would like to morph between those conformations. However, the volumes are not perfectly aligned in first place. So I align all of them on one of the maps using the “fit in map” functionality.  This works great and when I look through the different structures with the volume viewer, they are perfectly aligned. However, if I morph through the maps using the following command:
>  
> vop morph #0-19 playstep 0.003 constantVolume true frames 1000   
>  
> the maps are morphed in their original position so the morph is quite jumpy.
>  
> Is there a way to morph through them in the aligned coordinate system directly?    
>  
> Kind regards
>  
> David
> 



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