Thank you, Miguel. Right, there are many ways to do this. This note is
intended specifically for those users who already have "hbonds on"
built into their pages that involve links or buttons. The key point is
to make sure you do not use just
connect hbonds auto;
in your scripts as a replacement for "hbonds on", as those are not
equivalent, and that you check your pages for instances of "hbonds on"
prior to installing Jmol version 10.1. In this context,
connect hbonds auto (*) (*)
or
connect hbonds auto (nitrogen) (all)
are precise replacements for "hbonds on" in this context. The first is
fine. I introduced the second merely for emphasis -- that not ALL
nitrogens have to be selected, and as Angel pointed out, Rasmol
hydrogen bonds are specifically between nitrogens and either oxygens
(in proteins) or nitrogens and oxygens (in nucleic acids).
I do not recommend using
select *; connect hbonds auto
as a general replacement, because that has lingering implications on
the current selection, which the former "hbonds on" does not. That
would not be a safe replacement in all scripts. (It's fine to use
this, just not as a blanket replacement for "hbonds on", I think.)
Bob
--
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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