[PyMOL] Hydrogen Bond Parameters

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Hello,

Any help with the following would be greatly appreciated:

The online PyMOL documentation
(http://delsci.info/dsc/dokuwiki/doku.php?id=setting:h_bond&s=hydrogen%20bond)

describes the h_bond parameters as follows:

1. h_bond_cone (float, default: 180.0) is a hydrogen-bond
geometry parameter.
2. h_bond_cutoff_center (float, default: 3.6) is the maximum
distance for ideal hydrogen bonds.
3. h_bond_cutoff_edge (float, default: 3.6) is the maximum
distance for a marginal hydrogen bond.
4. h_bond_exclusion (integer, default: 3) controls suppression
of hydrogen bonds around adjacent atoms.
5. h_bond_max_angle (float, default: 63.0) is the maximum
angle for a marginal hydrogen bond.
6. h_bond_power_a (float, default: 1.6) is a hydrogen-bond
geometry parameter.
7. h_bond_power_b (float, default: 5.0) is a hydrogen-bond
geometry parameter.

I was hoping someone (Warren?) might be able to elaborate on
parameters 1-3 and 5-7 (or alternatively provide a reference
and/or thread). Specifically, if a hydrogen bond consists of a
donor (D), hydrogen (H), acceptor (A), and acceptor antecedent
(B) illustrated as:

D--H--A--B

or alternatively:
      
  H--A
 /    \
D      B

Then how are parameters 1-3, and 5-7 defined in terms of
distances (HA, DA) and angles (DHA, DAB, HAB)? I would guess
that "h_bond_cutoff_center" and "h_bond_cutoff_edge" both
refer to the donor-acceptor (DA) distance, and I can make
additional guesses about the other parameters, but I would
prefer to proceed with a set of exact definitions if possible.

Three additional questions: 

1. Once the hydrogen bond parameters have been set, one uses
the 'dist' command with mode=2 to find all hydrogen bonds,
correct? For instance, if mc_H is the set generated by the
command 'select mc_H, name h' and mc_O is the set generated by
the command 'select mc_O, name o'  then will the following
command find all main-chain/main-chain hydrogen bonds for a
given structure (using the previously-defined h_bond
parameters as selection criteria):

	dist mcmc, mc_H, mc_O, mode=2
?
	 

2. Are hydrogen bonds considered a subset of "polar contacts"
in PyMOL or are the two sets equivalent ({hydrogen bonds} =
{polar contacts})?

3. At the risk of belaboring the point, what set of commands
combined with the distance command would yield the same
results as those generated by following menu selection:

	find > polar contacts > within selection

assuming that the selection under consideration is an entire
structure?

Thanks in advance,

Christopher