[Jmol-users] possible display bug in 11.6RC5

[Thomas S. <tho...@gm...>]

Hi Folks --

I'm working with the applet (version 11.6RC5 -- I can't keep up with the
versions!) and have just noticed the following: the display of proteins in
"backbone" or "cartoon" mode seems to be non-functional for me.  This is
true for all PDB files that I've loaded so far, but one example would be
"3BZI".

If I issue the following:

load 3BZI.pdb     # structure comes up in wireframe mode, all visible
select protein
backbone 0.33   # everything disappears except the waters and a formate

spacefill off;
wireframe off;
backbone 0.33;   # again, nothing visible
wireframe 0.1;     # now the protein is visible again
wireframe off;
cartoon on;         # now I see only the hetatms again


Using the pop-up menu gives the same results:

> Select > protein > All                          # 1,865 atoms selected
> Style > Scheme > Ball-and-Stick        # All visible
> Style > Scheme > Trace                     # Only waters and a formate
visible
> Style > Scheme > Cartoon                 # Only waters and a formate
visible
> Style > Scheme > Spacefill                # All visible
> Style > Scheme > Sticks                    # All visible
> Style > Scheme > Wireframe             # All visible

Finally, I tried in the console: "calculate structure" and re-displaying
cartoons, backbone trace, etc and still had the same above behavior.

Has anyone seen -- or specifically NOT seen -- this as well?   I don't know
if it just here or a general issue....
Thanks,
Tom