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

[Elaine Meng]

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  
dragging)
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ 
volumepathtracer/volumepathtracer.html#dragplace

(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)
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ 
volumepathtracer/volumepathtracer.html#surfaces

(e) use the command "mask" to use the surface to divide the data
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html

Best,
Elaine
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html