skeleton

• This program is used to produce a skeleton representation of a 3D map.

Usage

• skeleton <[4|5|6]> <input mrc> <pseudo atoms> <apix> <threshold> <min helix size> <min sheet size> <output score>

Parameters:

• <[4|5|6]>	Command flag. 4 for producing skeletons only, 5 for computing sheet/helix score only, 6 for both. If the skeletons (in MRC format) are to be generated, they come in three files: _helix.mrc, _sheet.mrc and _skeleton.mrc.
  <input mrc>	Input 3D map at 5-8A resolution
  <pseudo atoms>	Seeds locations to compute sheet/helix scores, generated by the Pseudoatom.py program.
  <apix>	Angstroms/pixel in 3D map.
  <threshold>	Iso-surface value of the map
  <min helix size>	Minimum size of curves in the skeleton (3 is a good choice )
  <min sheet size>	Minimum size of surfaces in the skeleton (3 is a good choice
  <output score>	The PDB file to which the sheet/helix scores will write.

  Typical usage: skeleton 6 1grl.mrc atoms_1grl.pdb 1.5 0.38 3 3 out_1grl.pdb

Description

The skeleton preserves the topology (i.e., connectivity) of the input map, yet with a reduced structure consisting only of curves (corresponding to tubular shapes in the map, such as helices) and surfaces (corresponding to platelike shapes in the map, such as beta-sheets). The skeleton can also be used to generate helix/sheet scores for given points in the map.

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