The H-Bonds tool uses atom types and
to identify hydrogen bonds (H-bonds). It is also implemented as the
Molecule Display icons:
Protein-Ligand Binding Sites
H-Bonds can be opened from the Structure Analysis section of the
Tools menu and manipulated like other panels
It is not necessary to add hydrogens first, as their
possible positions will be inferred if they are missing.
The number of H-bonds found is reported in the
This number includes all H-bonds consistent with the chosen options,
even if the H-bonds could not coexist simultaneously.
For example, both donor-acceptor and acceptor-donor H-bonds
could be found between the the same pair of atoms, and a hydroxyl group
could be found to donate a hydrogen bond to two different acceptors even
if only one or the other could be the acceptor at a given time.
If the hydroxyl group has an explicit hydrogen atom,
however, only H-bonds compatible with the position
of the hydrogen will be found.
Clicking Apply (or OK, which also dismisses the dialog)
runs the calculation. Several of the dialog settings are remembered as
preferences when the calculation is run.
- Display as pseudobonds (initial default on)
– whether to show H-bonds as
The pseudobonds will be drawn between the donor and acceptor atoms,
or if hydrogens are present, between the hydrogens and acceptor atoms.
H-bond pseudobonds can be removed with the command
hbonds delete or
A pseudobond model can also be closed
with the Model Panel
or the close command.
- Color (initial default deep sky blue
– color of H-bond pseudobonds; can be
changed later with color,
color hbonds goldenrod
- Radius (initial default 0.075 Å)
– radius for H-bond pseudobonds;
can be changed later with size
- Dashes (initial default 6) –
number of dashes in H-bond pseudobonds;
can be changed later with style.
Currently, odd numbers are rounded down to give an even number of dashes.
- Distance label (initial default off)
– whether to show Å distances as bond labels;
the number of decimal places and whether to show the Å symbol can be
changed with distance style
or set beforehand in the
and label height in Å can be changed with
or set beforehand in the
The distances (pseudobond lengths) can also be plotted as a histogram with
- Retain pre-existing H-bonds (initial default off)
- Relax distance and angle criteria (initial default on)
– whether to add tolerance values to the
precise criteria for identifying
H-bonds (several different distance and angle cutoffs depending on the
atom types involved). As the precise
cutoffs were based on high-resolution small-molecule crystal structures,
relaxing them is generally recommended for macromolecules and
structures at a broader range of resolutions.
- Distance tolerance (initial default 0.4 Å)
- Angle tolerance (initial default 20°)
- Color H-bonds not meeting precise criteria differently
(initial default off)
– whether to use a different color for
representing H-bonds within the tolerance values but not meeting the
(initial default dark orange
- Limit results:
Any combination of the settings can be used, except that the first two
are mutually exclusive (cannot both be on).
To find H-bonds between sibling
of the same parent model,
use the hbonds command with
- Limit by selection (initial default off)
– whether to limit the results by the current
selection according to one of the following
choices in the pulldown menu:
- with at least one end selected
- with exactly one end selected
- with both ends selected
- between selection and atom spec...
The two sets of atoms may overlap, but will not overrule other restrictions.
- Salt bridges only (initial default off)
– whether to limit the results to salt bridges, that is,
H-bonds between formally charged functional groups.
Such groups are identified by their atom types,
where possible. In the absence of explicit hydrogens,
a histidine sidechain is assumed to be formally charged unless one of
its nitrogens is coordinating a metal ion or identified unambiguously
as an H-bond acceptor.
- Include intermodel (initial default on)
- Include intramodel (initial default on)
- Include intramolecule (initial default on)
– whether to include intramolecular H-bonds,
where a molecule is defined as a covalently bonded set of atoms
- Include intraresidue (initial default on)
- Treatment of results:
- Select atoms (initial default off)
– whether to select the H-bonding atoms
- Reveal atoms of H-bonding residues
(initial default on) –
since a pseudobond
is only shown when both of its endpoint atoms are shown,
whether to ensure all showing all H-bonds by displaying all of the endpoint
atoms. To avoid showing disconnected atoms, the entire residues will be shown,
except that amino acid and nucleic acid residues are split into
moieties separately displayed by this option.
Displayed backbone atoms may still be invisible where cartoon is shown,
unless their simultaneous display has been enabled with
cartoon suppress false.
- Write information to: Where to write H-bond information,
including donor and acceptor atom specifications
(see the Labels preferences
for specifier style), donor-acceptor distances, and when hydrogens are present,
hydrogen atom specifications and hydrogen-acceptor distances.
- Log (initial default off)
– show the information in the Log
- File (initial default off)
– save the information to a text file
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