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

Thomas Goddard goddard at cgl.ucsf.edu
Mon Mar 10 17:27:44 PDT 2008

Hi Weimin,

   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.
> Thanks,
> weimin

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