Name

find_3d_threshold - Compute the density threshold of a 3D density map.

Usage

• thrd=image.find_3d_threshold(mass, pixel_size)

Input

mass

Molecular mass of the protein complex in (kilo Daltons)

pixel_size

The pixel size of the structure (Angstrom)

Output

thrd

The density threshold for display.

Description

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

Keywords

category 1

FUNDAMENTALS

Files

emdata_sparx.cpp

Maturity

stable

works for most people, has been tested; test cases/examples available.

Bugs

None. It is perfect.