[Molvis-list] Running old Jmol tutorials (unsigned applets)

Eric Martz emartz at microbio.umass.edu
Thu Jul 3 15:50:56 EDT 2014

Hi, Malcolm,

Well it won't hurt for the entire list to be aware of this.

In the initial control panel ("molecule information", tab labeled 
with the PDB code), below the section on Asymmetric Unit, there is a 
link Biological Unit. Yes, viewing it is only a few clicks away.

There is also a link for getting the Biological Unit under the Resources tab.

It is always best to check the Biological Unit for every structure in 
order to be aware of how it may differ from the Asymmetric Unit 
published by crystallographers. Those terms are defined/explained in 
the help within FirstGlance in Jmol, and further via links within 
FirstGlance in Jmol.

In the case of 3b8e, the biological unit is half of the asymmetric 
unit, namely it is a 3-chain trimer (instead of two copies, six chains).

Regards, Eric

At 7/1/14, you wrote:
>When I use FirstGlance, is there a way to click a button to get the 
>biological unit to show up?
>This is the sodium pump which many students study, but the 
>biological unit is not what shows up.
>On Jun 22, 2014, at 1:57 PM, Eric Martz <emartz at microbio.umass.edu> wrote:
> > At http://proteopedia.org/w/Installing_and_enabling_Java
> >
> > I have added instructions (at the end) for enabling Java to 
> display unsigned Java applets. Its great that we can still do this 
> for all those legacy Jmol tutorials that are still out there!
> >
> > You can find links to many of these tutorials at http://molviz.org
> >
> > If you find these instructions to be incomplete or confusing, 
> please let me know!
> >
> > Eric
> > _______________________________________________
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> > http://www.bioinformatics.org/mailman/listinfo/molvis-list
>A. Malcolm Campbell, Ph.D.
>Professor of Biology
>Director, James G. Martin Genomics Program
>Davidson College
>Founding Director of GCAT (www.bio.davidson.edu/GCAT )
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