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 > > > ------------------------------------------------------------------------------ > 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 > Jmol-users@lists.sourceforge.net > 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 Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users