Re: [Jmol-users] use of select bonds

Yes, that seems to be our issue. So we need to redo the state scripts. Thanks On 13 Jan 2017 at 18:07, Robert Hanson wrote: Ah, yes! bonds are indexed COMPLETELY differently -- and are not even the same set of bonds -- in PDB, mmCIF, and MMTF. --- El software de antivirus Avast ha

Re: [Jmol-users] use of select bonds

Ah, yes! bonds are indexed COMPLETELY differently -- and are not even the same set of bonds -- in PDB, mmCIF, and MMTF. On Fri, Jan 13, 2017 at 2:29 PM, Robert Hanson wrote: > This works fine: > > load $caffeine > select bonds ({0 3 4}) > color bonds yellow > > so that

Re: [Jmol-users] use of select bonds

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

Re: [Jmol-users] use of select bonds

Thank you, Matt Further testing indicates that he command itself is working as it used to be. Suspicion is now on a possible change in the way bonds are indexed, between old PDB files and recent mmCIF files (this is in Proteopedia which changed the source of files last year) --- El software

Re: [Jmol-users] use of select bonds

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

Re: [Jmol-users] use of select bonds

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