PDBUnits is an accessory tool that can be used to identify the orientation and translations of a repeating subunit (given in a Subunit PDB file} in a complex supramolecular structure (given in a Large PDB file). The program also gets the tolerance, given by the maximum root-mean-squared-displacement (RMSD)
value, within which repeating subunits can be considered similar. 
The program reads the PDB file of the complete structure and finds all the instances
of the subunit. If subunits are splitted at different location in a PDB file, the parts
should be combined into complete subunits, before using the tool. 
For each instance the rotation and translation with respect to the original subunit are computed. The tool
exports the so called Assembly Symmetry of the subunit as a docking list (DOL) text file, which is a required input for D+, to compute the entire structure using
the reciprocal grid algorithm of D+.  

The *.dol text file contains a list of the center of mass coordinates, x, y, and z, and the Tait–Bryan rotation angles a,b, and g about the corresponding axes, of each subunit instance, within the large PDB file. 

The program asks for the following items:

The complete structure as a Large unit PDB file path
The Subunit PDB file path
The RMSD value, which sets the maximum RMSD allowed difference between the given Subunit PDB file and any instance of the subunit, within the Large unit PDB file.
The Output DOL file path, in which the list of translations and rotations of repeating subunit instances will be stored.   
 

The program can also be used from the Command Prompt. The default file path is: 

C:\Program Files\D+\bin>

Within the folding, typing 
PDBUnits --help

gives the command line format: 
    
PDBUnits <Large unit PDB file> <subunit PDB file> <RMSD> <Output DOL file path>

For more details see our user's manual.