= 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