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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

Volume (last edited 2008-11-26 04:42:30 by localhost)