Name

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

Usage

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

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.

find_3d_threshold (last edited 2014-05-05 22:33:50 by penczek)