Excluding Hydrogen Atoms from Contact Surfaces
Applicability: The option "Exclude hydrogens" is not applicable
to X-ray crystallographic models which lack hydrogen atoms, or to MEP
calculations which require hydrogens and model in the missing ones
automatically. (Checking the option will harmlessly have no effect in
these cases.) To find out if the displayed model contains hydrogens,
just issue the command "select hydrogens" and see whether the
resulting count of atoms selected is zero or nonzero.
Many X-ray crystallographic models and all NMR
models contain hydrogen atoms, usually only a portion of those
actually present in the molecule.
Excluding hydrogens when coloring by distance.
As presently implemented here, the
Distance Color Scheme option for contact surfaces is most informative
when hydrogen atoms are excluded from
Checking "Exclude hydrogens for Distance Color Scheme" effects all of
the above by automatically adding "and not hydrogen" to the
appropriate "select" commands. However the terms
are defined to include hydrogens. This makes it easy to display hydrogens
if you wish, for example if you have checked Show bonded receptor
atoms, O/N and Exclude hydrogens ..., the display will omit
hydrogens from the "bonded receptor oxygen/nitrogen" ("bron") atoms shown.
You can add the hydrogen atoms to this display by issuing
these commands manually:
- Generation of the contact surface shape on the receptor.
- The ligand atom group from which distances to receptor are calculated
for applying isocontour coloring.
- The ligand atoms shown as balls and/or sticks (when these options
- The receptor atoms shown when "Show 'bonded' receptor atoms, O/N or C/S"