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| ''This program is used to produce a skeleton representation of a 3D map. 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.'' | ''This program is used to produce a skeleton representation of a 3D map.'' |
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| ||< threshold>||Iso-surface value of the map|| | || <threshold>||Iso-surface value of the map|| |
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| == 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. |
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:
- Typical usage: skeleton 6 1grl.mrc atoms_1grl.pdb 1.5 0.38 3 3 out_1grl.pdb
<[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.
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