[Chimera-users] using chimera on 3D EM map

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 10 09:50:43 PDT 2008

On Mar 6, 2008, at 11:21 AM, Weimin Wu wrote:
> Thanks for your reply. I will try the eraser ball again. To add the
> density, I really need something like 3D brush. I have tried a  
> series of
> Markers and split by colors, however it is hard to choose marker
> position and choose color zone radius, because we need separate the
> signals within 4A distance, especially when two subunits cross over  
> and
> one beta sheet is very close to the beta sheet on the other  
> subunit. For
> statistical comparison of two maps, I need not only correlation, but
> also rotation degrees, translation, especially for the hinge region,
> something like rmsd in pdb comparison.

Hi Weimin,
Another possibility is to make a surface, and then use the surface to  
divide the density map. This can be done with recent versions of  
Chimera.  I don't know if this is a good way to work with your data,  
but if you want to try, here are more details:

(a) in Volume Viewer, show a single density plane (Features... Planes  
in Volume Viewer menu)

(b) use Volume Tracer to draw a line in that plane, actually a string  
of markers (Place markers on data planes and Place markers while  

(c) repeat (a) and (b) for a stack of planes

(d) use Volume Tracer to join the stack of lines into a surface  
(Features... Surfaces in Volume Tracer menu)

(e) use the command "mask" to use the surface to divide the data

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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