The ListHBo command lists all atoms in the first selection that are hydrogen bonded to atoms in the second selection. Atoms separated by up to three covalent bonds are always excluded from the analysis.

The definition of a hydrogen bond is that the distance between the hydrogen and the hydrogen bond acceptor is smaller than 2.5 A. This implies that hydrogens have been added .

For best results, the hydrogen bonding network should be optimized , using either the OptHyd command in the Twinset or an energy minimization in YASARA Dynamics.

Since residue numbers and molecule names may not be unique , the commands 'ListHBoRes' and 'ListHBoMol' return unique strings instead, as explained here.

Hydrogen bonds between different objects can only be listed when the objects share the same local coordinate system.

ListHBoMol A,B

List all hydrogen bonds between molecules A and B.

ListHBoRes Arg,Glu

List all hydrogen bonds between arginines and glutamates.

mylist() = ListHBoAtom Element N,Element O

Assign the numbers of all nitrogen atoms that are hydrogen bonded to oxygens to 'mylist'.

mylist() = ListHBoRes Mol A,Mol B

Assign the unique IDs of all residues in molecule A that are hydrogen bonded to molecule B to 'mylist'.