Dear Bob,
Here are some suggestions for the Jmol command manual:
-------------------------
Under set (visibility), set solvent,
PRESENTLY SAYS
Turns on and off display of solvent "probe" that can be
displayed using dots. The radius of this probe is set with set
radius (above). After set solent ON, you must (re)issue
dots ON for it to take effect.
REPLACE WITH
When set solvent is ON, a subsequent dots ON shows the
surface of the aggregate of selected atoms, using dots. This surface is
defined by the contact of a spherical probe (representing a solvent
molecule) rolled over the surface of the selected atoms. The radius of
the probe sphere is customarily 1.4 Angstroms, which approximates a water
molecule. Note that the default radius for Jmol is 1.2 Angstroms. The
radius of the probe is set with set radius (above). (More
information on molecular surfaces:
http://www.netsci.org/Science/Compchem/feature14.html ) After set
solvent ON, you must (re)issue dots ON for it to take
effect.
----------------------------
Under 'dots':
PRESENTLY SAYS
Turns dotted surface on or off for Van der Waals radii or solvent probe
(if in addition set dots ON).
CORRECTION:
Change next to last word from 'dots' to 'solvent', so it ends 'set
solvent ON'.
(There is no 'set dots ...' command.)
-Eric
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- [Jmol-users] Suggestions for dots, set solvent DOCUMENTATION Eric Martz
