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@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