Thanks for that confirmation, Bob.... I downloaded 11.6RC7 and -- sure
enough -- that version does *NOT *show the behavior. So, it was either
11.6RC5 or a combination of that version and something that I'm doing....
Happily, RC7 seems to tolerate me!
Thanks very much,
Tom
On Sat, Aug 16, 2008 at 10:10 PM, Bob Hanson <[EMAIL PROTECTED]> wrote:
> Thomas, I'm not able to reproduce that problem. See, for example:
>
> http://chemapps.stolaf.edu/jmol/docs/examples-11/simple.htm?3bzi
>
> or
>
> http://chemapps.stolaf.edu/pe/protexpl?id=3bzi
>
> Either it was something about 11.6.RC5 or there's still something odd
> there that I don't see.
>
> Bob
>
>
>
> Thomas Stout wrote:
>
> >
> > 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
> >
> >
> >
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>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
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