[Proteopedia] movie?

Eric Martz emartz at microbio.umass.edu
Wed Sep 2 20:53:46 EDT 2009

Dear Ramiro,


It seems to me that you can make a slideshow fairly easily now. 
Consider an existing article in Proteopedia with, for example, five 
or ten green links (scenes). Normally, these green links will be 
buried in text that describes the scenes. All you would have to do is 
add (on the same page, or maybe better, a separate page) a numbered 
list of the scenes with short green-linked descriptions. Jmol could 
be larger next to this list (larger than it would be in the main 
article with text wrapping around Jmol). I'm not sure how to make a 
"next" button, but perhaps Eran and Jaime will think about a way to 
put the list of scenes somewhere for the "next" button to utilize? 
Even without a "next" button, as long as you remember where you are, 
you can run the slideshow from the list of green links. Actually, 
having the short green-linked descriptions of the slides could be 
useful to the audience as well as the presenter! They could be in large font.


The subject of your message is "movie?". Changing to that subject, 
Proteopedia is designed to show either a static scene (rotatable and 
zoomable), or an animation of a multiple-model PDB file (e.g. see 
http://proteopedia.org/wiki/index.php/Lac_repressor ). However, it is 
possible to put more complex movies into Proteopedia using a "button" 
instead of a green link. The button calls an uploaded script. 
Currently, files of type .spt cannot be uploaded (Eran and Jaime, 
this should be changed!), but you can upload a file of type .spt.gz 
(gzipped, which Jmol automatically unzips). I have just done two such 
complex movies:



I am not finished with the second page, but the animation is in final 
form (or close to it). I plan to add a new article highlighting the 
simulation of drug binding, which is now shown for the first time in 
Jmol -- it was developed in Chime (http://atlas.molviz.org/atlas.htm#enzymes).

Incidentally, the scripts are
- http://proteopedia.org/wiki/index.php/Image:MP_tamiflu.spt.gz

- http://proteopedia.org/wiki/index.php/Image:MP_hivdrug.spt.gz
Click on the link to e.g. MP_hivdrug.spt.gz at the top of this page, 
and the .spt file will be downloaded. On OS X, it is automatically 
unzipped. Not sure if this is OS X or the Proteopedia server doing 
the unzipping.


At 8/31/09, you wrote:
>I just gave a presentation using proteopedia and one thing that 
>would be useful, and perhaps not that hard, is to allow the creation 
>of proteopedia "slideshows".  Be able to create a "storyboard" with 
>all the sequence of scenes that one would like to show.  Then when 
>the screen appears it would be on "slideshow mode", and it would 
>have controls for next, prev, play, pause and one could go through 
>the whole sequence by pressing those buttons (or perhaps even with a 
>remote).  Since we are already spending so much time creating our 
>proteopedia scenes, then making a movie out of that perhaps wouldn't 
>be that bad.  The transitions between scenes might be tricky I am 
>sure, but I just wanted to "throw this out there" as an idea..
>Proteopedialist-for-users mailing list
>Proteopedialist-for-users at bioinformatics.org

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