[Proteopedia] Arbitrary scripts vs. state scripts

Eric Martz emartz at microbio.umass.edu
Wed Feb 4 13:17:55 EST 2009

Re the thread: Script compiler error

I'd like to remind everyone that there is already a mechanism with 
which you can send any arbitrary script to Jmol in Proteopedia. The 
minor disadvantage (?) is that it uses a button instead of a green 
link. I have used this mechanism in the "Toggle Animation" buttons at

Because toggling animation was something I needed at multiple places 
in this article, and expect to use in other articles, I did it in a Template:
but for a one-off script, it could equally well be literally embedded 
in the page wiki text.

This mechanism could be used to load a saved surface data file, which 
would provide a solution to Karl's problem that does not require 
intervention from Eran or Jaim, the sys admins.

It is also possible to have a button that changes its text label, 
e.g. shows [ ] vs. [x] when clicked. An example is here:

So you could have a button "Show Surface" that changes to "Hide 
Surface" when it is clicked, or even goes through an intermediate 3rd 
mode "Transparent Surface".


At 1/30/09, lsprilus at weizmann.ac.il wrote:
>According to "Karl Oberholser" <oberhols at messiah.edu>:
> > The upgrade may have solved one problem, but there is still a problem.  The
> > surface is still not displayed when the green link is clicked and the
> > following error is displayed in the Jmol console: io error reading
> > http://proteopedia.org/wiki/scripts/second.spt:
>Dear Karl,
>Fixed. Somehow the green link was altered and had "name='second'" instead
>of "target='second'" as it is generated by SAT. At the end, your page had
>name= twice on the same link, confusing Proteopedia on what to request from
>the server.
>The surface shows up now. Very nice, although it takes so long that your
>warning at the top might not be enough for keeping people on the same page.
>  Dr Jaime Prilusky                      | Jaime.Prilusky at weizmann.ac.il
>  Head of Bioinformatics ISPC            |
>  R&D Bioinformatics and Data Management |
>  Weizmann Institute of Science          | fax: 972-8-9344113
>  76100 Rehovot - Israel                 | tel: 972-8-9344959
>  OCA, http://oca.weizmann.ac.il (the protein structure/function database)
>  Proteopedia, http://www.proteopedia.org (because life has more than 2D)
>  ------------------------------------------------------------------------
>Proteopedialist-for-users mailing list
>Proteopedialist-for-users at bioinformatics.org

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