Commands for data deposition:

[1] excs ?FileName? ?Residue_number?
Extract chemical shifts from .str file generated by NMRView5. All the chemical shifts will be converted to NMR-STAR format (V3) and saved in "cs.txt" file with calibrated residue number in current folder.
For example, extract CS from test.str and decrease residue number by 8: 'excs test.str -8'

[2] adppm ?FileName? ?H_ppm? ?N_ppm? ?C_ppm?
Calibrate H/15N/13C chemical shifts in STAR format (V3). A new file with calibrated CS will be saved in current folder.
For example, increase 13C CS by 2.7ppm only: 'adppm cs.txt 0 0 2.7 '

[3] dihednum ?FileName? ?Residue_number?
Change residue number in dihedral angle constraint file. A new file with calibrated residue number will be saved in current folder.
For example, increase residue number by 8: 'dihednum dihed.tab 8 '

[4] noefile
In the popup window, change residue number in upper and/or low limit files. A new file with calibrated residue number will be saved in current folder.
By default, residue numbers of NOE pairs will be changed together.

Commands for PDB file processing after refinement in AMBER:

Step 1

exeng ?Step_Number?
Extract energy of each structure based on step number of refinement to a new file, energy.txt. Another new file, min.nam, containing names of all structures arranged from lower to higher energy, will also be generated.
For example, 'exeng 200'

Step 2

amber1 ?Residue_Number?
Convert residue/atom names and combine all the pdb files into all.pdb. Default chain ID (A) will be added. Residue number can also be changed at this step.
For example, 'amber1 0'

For a dimer:

amber2 ?Residue_Number1? ?Residue_Number2?

[Note] For larger oglimers: you will have to modify their pdb files manually.

Step 3