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

Weimin Wu wu49 at purdue.edu
Tue Mar 11 06:35:39 PDT 2008

My problem is that I have few subunits in the asymmetry unit. I fit one 
into the other subunit, and I try to figure out how good is the fit. 
Visually I can see they fit well, but  there is some difference which I 
think it is due to conformation difference, however I need quantitative 
data to report the difference, or a tool as simple as rmsd in the PDB 
comparison. I once tried to convert the density map to pseudo PDB 
(vol2pdb in situs), but it is hard to open that PDB in chimera.


Thomas Goddard wrote:
> 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?
>     Tom

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