This works fine:
load $caffeine
select bonds ({0 3 4})
color bonds yellow
so that syntax is fine. What can happen with old files, particularly from
PDB, is that the underlying file may have changed in such a way that that
bonds are in different orders. (Or, Jmol is reading the file slightly
differently.) So that particular command can be a problem.
On Fri, Jan 13, 2017 at 1:21 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> 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.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
--
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.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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