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 <[email protected]> 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
>
>
> ------------------------------------------------------------------------------
> Developer Access Program for Intel Xeon Phi Processors
> Access to Intel Xeon Phi processor-based developer platforms.
> With one year of Intel Parallel Studio XE.
> Training and support from Colfax.
> Order your platform today. http://sdm.link/xeonphi
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
