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. weimin 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