Yes, that's the unit cell. Maybe a lesson there. But mostly an unfortunate
distraction for you and your students. Very sorry.
This is an issue with
set defaultlattice
that I thought I had worked out. I have worked on that recently. Jmol was
writing
set DefaultLattice "{0 0 0}"
in states, and while that SHOULD have turned off the unit cell, as it
happens, the parser was not successfully interpreting that string, and I
had the poor choice of default of {1 1 1} when that happened. Is it
possible they were reading a state for some other model prior to reading
the 2lyz file? That could have set that parameter incorrectly, but you
would only see it on the next loaded model.
My guess is that some of these students were using older versions of Jmol,
some newer. It's always a problem to clear these from the cache, as it's
the Java cache, not the browser cache when you are using Java.
The fact that when they reopened the session it went away suggests that
it's gone for good. Generally the instructions should be "Close your
browser completely -- all windows of any kind -- and restart it." At least,
I hope that's gone.
If you can spot it again, please go to the bottom menu item "about" and
tell me the version of Jmol being used. Then, if you can, please under File
(now at the top of the menu) ...Export...PNG+JMOL and send that image to
me.
Bob
On Thu, Feb 20, 2014 at 4:48 PM, Jeffrey Cohlberg <
jeffrey.cohlb...@csulb.edu> wrote:
> I just gave my students an assignment in which they worked with the files
> 1PGB (immunoglobulin-binding domain) and 2LYZ (lysozyme). About a third
> of the class, upon loading either 1pgb.pdb.gz or pdb1pgb.ent, saw six
> copies of the molecule on their screen instead of one. About half of
> those students, upon loading the files for 2LYZ, saw eight molecules of
> lysozyme instead of one. I have posted one sample image of each file at
> http://www.csulb.edu/~cohlberg/multipleimages.pdf.
>
> Students who had this problem included both PC and Mac users. They were
> all using versions of Jmol downloaded within the last 10 days.
>
> Strangely, whenever a student who had this problem reopened the same file
> in Jmol in a new Jmol session, only one molecule was seen in the image.
>
> Any idea what is going on?
>
> Jeff Cohlberg
> --
> Dr. Jeffrey Cohlberg
> Department of Chemistry and Biochemistry
> California State University, Long Beach
> 1250 Bellflower Blvd
> Long Beach, CA 90840
> 562-985-4944 FAX 775-248-1263
> cohlb...@csulb.edu
>
>
>
>
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--
Robert M. Hanson
Larson-Anderson 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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