Thanks for the correction, very helpful. Would be great to include in
the documentation.
On Sep 5, 2007, at 6:16 PM, Bob Hanson wrote:
Except I don't quite think that does what you say. You mean
set dotSurface on/off
set dotSurface ON # (the default)
creates for the selected atoms only that part of the overall molecular
"dot surface" that is associated with that atom.
set dotSurface OFF
creates full, possibly overlapping, spheres of dots around each
selected
atom.
What
set dotsSelectedOnly ON
does is to tell Jmol to ignore all atoms not selected when any future
"dots on" command is given. This allows, for example, dots to fully
encase a ligand even though it is in contact with a protein.
Otherwise,
with (the default)
set dotsSelectedOnly OFF
Jmol creates for each selected atom only the dots that would be
attributed to that atom on the overall molecular "dot surface."
The setting of dotsSelectedOnly ON or OFF only has an effect when
dotSurface is set ON.
Frieda Reichsman wrote:
Information on 'set dotsSelectedOnly' is missing form the
documentation, except for a brief statement under the command
'calculate'.
Under 'dots', it could say something like,
set dotsSelectedOnly on
creates dots on subsets of bonded atoms, so that each atom is a
finished sphere of dots.
set dotsSelectedOnly off
(which is the default state)
creates dots only where the surface of the atoms is sovlent-
accessible.
Apologies if this is not an accurate description; at least its a
starting point...
Frieda
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Frieda Reichsman
Molecules in Motion
Interactive Molecular Structures
http://www.moleculesinmotion.com
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Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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