Jan's observation that
connect 1.2 2.0 HBOND (carbon) (hydrogen)
may not have any observable effect, because HBONDS are by default
OFF, suggests that there is a more general problem with connect.
Specifically, what determines the displayed
radius of the bond being created?
Answer: HBONDS 0, others: wireframe
To address this issue, I'va added an optional parameter that allows
the radius to be specified:
connect
<min-dist> <max-dist> <type> <radius> (source set) (target set)
All parameters are optional except (target set). If ONLY one distance
is given, and a radius is also given, that radius must follow an
explicit <type>. (Otherwise, the two numbers would be taken to be
minimum and maximum distances.)
This is now at
<http://www.stolaf.edu/people/hansonr/jmol/test/json/express.htm>
examples:
connect 1.2 (carbon)(hydrogen)
#make single C-H bonds if < 1.2 angstroms apart
connect 1.2 single 0.1 (carbon)(hydrogen)
#make 0.1-radius single C-H bonds if < 1.2 angstroms apart
connect 1.2 2.0 HBOND 2 (carbon) (hydrogen)
#a 2-pixel-radius HBOND
connect 1.2 2.0 2 HBOND (carbon) (hydrogen)
#a 2-pixel-radius HBOND
connect 1.2 2.0 HBOND 0.01 (carbon) (hydrogen)
#a 0.01-angstrom radius HBOND
connect 1.2 2.0 HBOND (carbon) (hydrogen)
#a default HBOND (off)
connect 1.2 2.0 SINGLE (carbon) (hydrogen)
#a default SINGLE bond (based on wireframe)
connect 1.2 2.0 DOUBLE 0 (carbon) (hydrogen)
#a DOUBLE bond, but not shown, because it has no radius
Notice that there is a difference between "SINGLE 0" and "DELETE".
The first creates or modifies the bond but does not display it (yet);
the second actually removes the bond.
Sound OK?
Bob Hanson
--
Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:[EMAIL PROTECTED]
http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein
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