find_3d_threshold - Compute the density threshold of a 3D density map.
- thrd=image.find_3d_threshold(mass, pixel_size)
- Molecular mass of the protein complex in (kilo Daltons)
- The pixel size of the structure (Angstrom)
- The density threshold for display.
In find_3d_threshold a good guidance is provied by the total molecular mass of the protein complex M Da and the pixel size p Angstorm, assuming the average protein density `d = 1.36 x 10^(-24) g/(Angstrom)^3`. The number of voxels `N_v` occupied by the complex is
`N_v = M/(p^3dN_A)`
where `N_A = 6.02x10^(23) "atoms"/("mole")` is the Avogadro's number. Based on that, one can find, using a minimization procedure, the threshold that for a given structure encompasses the dertermined number of voxels `N_v`. Note: Works only in 3D.
Author / Maintainer
Bharath K Narayanan
- category 1
- works for most people, has been tested; test cases/examples available.
None. It is perfect.