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