<[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 | <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. |
skeleton 6 1grl.mrc atoms_1grl.pdb 1.5 0.38 3 3 out_1grl.pdb