[Chimera-users] using chimera on 3D EM map
goddard at cgl.ucsf.edu
Mon Mar 10 17:27:44 PDT 2008
I wonder if a 3d brush will be useful. The problem is you cannot see
the depth in a 3d view of the data clearly. Amira provides a 2d brush
which is much less trouble. The painting tool I suggested would have
you push a button to paint within a sphere (maybe some other shape) and
it would be a simple matter to allow you to drag it like a brush without
the button press to test if that is useful.
I'm not sure I understand the rotation and translation parameters you
want. Is it that you have one map fit within another in 2 orientations
and you want the rotation and translation relating those 2 orientations?
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.
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