[Proteopedia] Arbitrary scripts vs. state scripts

[Dan Bolser]

2009/2/4 Eric Martz <emartz at microbio.umass.edu>:
> 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
> http://proteopedia.org/wiki/index.php/Lac_repressor

Unfortunately that doesn't appear to work for me. I see a multi-model
PDB file (all models visible), and clicking 'Toggle Animation' has no
effect.

This is Mozilla/5.0 (X11; U; Linux i686; en-GB; rv:1.9.0.5)
Gecko/2008121911 CentOS/3.0.5-1.el5.centos Firefox/3.0.5

about:plugins says Java(TM) Plug-in 1.6.0_07-b06 File name:
libjavaplugin_oji.so Java(TM) Plug-in 1.6.0_07

Is everyone else seeing the animation correctly?

Cheers,
Dan.

> 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:
> http://proteopedia.org/wiki/index.php/Template:Button_Toggle_Animation
> 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:
> http://proteopedia.org/wiki/index.php/User:Eric_Martz/Sandbox_3
>
> 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".
>
> -Eric
>
>
> 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.
>>
>> Jaim
>> --
>>  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)
>>  ------------------------------------------------------------------------
>>
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>
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