Looks like a bug to me. Will get back to you.
On Fri, Jan 13, 2017 at 12:29 PM, Kubasik, Matthew A. <
mkuba...@fairfield.edu> wrote:
> Angel,
>
> I am unfamiliar with the syntax you are using.
>
> However, placing the bonds into a variable has worked for me, as in:
>
> select {oxygen and connected(1) and connected(carbon)} or {carbon and
> (connected(oxygen))}
> x1={selected}.bonds
> select x1
> bondorder 2
> select none
>
> I use the above code to make carbonyl bonds “double”. Works for my small
> peptides, but will give odd bonding structures to things like carboxylates.
>
> Matt
>
> > On Jan 13, 2017, at 11:51 AM, Angel Herráez <angel.herr...@uah.es>
> wrote:
> >
> > Hi all
> >
> > I am not familiar with the use of "select bonds" command, so I am asking
> > here.
> >
> > We have somewhat old state scripts (saved in Proteopedia scenes) that
> > were generated by an older version of Jmol (# Jmol state version 11.8.24
> > 2010-04-26 08:00;).
> >
> > Right now, Jmol 14.6.0 fails to select the bonds and render their
> thickness
> > and color.
> > The commands in state are of this type:
> >
> > select BONDS ({5 16 27});
> >
> > Q: Has this syntax changed, or is it broken?
> >
> > I've just tried Jmol app 14.6.4 and don't know how to select bonds, my
> > simple test is failing
> >
> > load $caffeine
> > select bonds ({2 3})
> >
> > Should that work as such?
> >
> > ·
> > Dr. Angel Herráez
> > Biochemistry and Molecular Biology,
> > Dept. of Systems Biology, University of Alcalá
> > E-28871 Alcalá de Henares (Madrid), Spain
> >
> >
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--
Robert M. Hanson
Larson-Anderson 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.
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