• Volume

volume

• This program calculates the volume/mass of a 3D map

Usage

• volume <input file> <A/pix> [thr=<thresh>] [calc=<mass>] [set=<mass>] [plot]

Parameters

• <input file>	3D map to work with
  <A/pix>	Angstroms/voxel in the map
  [thr=<thresh>]	Calculate the volume/mass at a given threshold
  [calc=<mass>]	Determine the threshold for a given mass
  [set=<mass>]	Rescale the map densities so a threshold of 1 gives the specified mass
  [plot]	Output a x/y file containing a plot of threshold vs mass

  Typical usage: volume threed.1a.mrc 4.667 set=2500

Description

This routine calculates volumes enclosed by isosurfaces. The algorithm used is approximate. It doesn't calculate subvoxel volumes. It is fairly accurate as long as a substantial fraction of the voxels are 'inside' the volume.

For convenience, mass is specified rather than volume. Volume/mass conversions assume a density of 1.35 g/ml (0.81 Da/A³).

Please note that an earlier version of the docs cited 1.35 Da/A³. This was an error in the documentation only. The program was using the correct value.

EMAN Manual page, generated Mon Jan 8 17:35:59 2007