For this example we use a PDB file of a homology model of nucleosome, which corresponds to the one analyzed experimentally, (scCSE4_601TA_nucl.pdb). The model was build based on an experimental X-ray template (PDBid 3LZ0).
Theoretical DNA cleavage frequency profiles are built by calcualting the solvent accessible surface area of deoxyribose hydrogen atoms in the PDB structure (H-SASA profiles). Since X-ray structures do not contain information about the positions of hydrogen atoms they need to be added via specialized software.
NOTE: H-SASA profiles are sensitive to small variations of C-H bond length. Different programs that add hydrogen atoms may use different values for the C-H and other X-H bonds the affect the magnitude of H-SASA profiles. Particularly, they might be affected by the choice of electron cloud distances (~1.0A) versus nuclear distances (~1.1A). For further discussion of this topic see H-SASA_params.md.
reduce -NUClear scCSE4_601TA_nucl.pdb > scCSE4_601TA_nucl_H_Ndist.pdb
The -NUClear option instructs to use nuclear X-H distances (~1.09 A for sugars) rather than default electron cloud distances (~0.97A).NOTE: Small conformational fluctuation in the positions of hydrogen atoms affect H-SASA. Hence an averaging of H-SASA profiles from a large set of snapshots from molecular dynamics simulations is prefered. See exampleMD.