[Chimera-users] Working with Electron density map

Elaine Meng meng at cgl.ucsf.edu
Wed May 3 09:46:49 PDT 2017

Dear Rahman,
I have no idea how you tried to do the slicing.  If you fit the maps successfully, then they are already superimposed, right?  Then you could just make a thin slice of everything together by dragging the global clipping planes in the Side View, and only show one map at a time or both together by using the “S” (Shown) checkboxes in the Model Panel.  Both the Side View and Model Panel can be opened from the Favorites menu.

Global clipping:

Model panel:

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On May 3, 2017, at 12:53 AM, MOHD HOMAIDUR RAHMAN <rahmanhpu at gmail.com> wrote:
> Dear Chimera user's
> I am trying to super impose molecular dynamics calculated density on cryo EM density and then slice densities to visualize each in different colors.
> I fitted density successfully now during slicing their X Y Z co-ordinate is not matching. 
> The similar analysis were publish in Marzinek et al., 2016, Structure 24, 1–11 August 2, 2016 http://dx.doi.org/10.1016/j.str.2016.05.014 
> Please see figure 3 for more details and image attached here.
> Thank
> Regards
> Rahman 

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