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

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

[Jmol-users] use of select bonds

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

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] coloring surface residues

OK, Dan, I found and fixed that one. The problem was that the command *color isosurface range 1 122* because it did not specify color scheme user: *color isosurface "user" range 1 122* reverted to the default color scheme, which is RGB. I consider that a bug -- the scheme already specified

Re: [Jmol-users] coloring surface residues

That works. Thank you! On Fri, Jan 13, 2017 at 8:20 AM, Robert Hanson wrote: > OK, Dan, I found and fixed that one. The problem was that the command > > *color isosurface range 1 122* > > because it did not specify color scheme user: > > *color isosurface "user" range 1 122*