[Proteopedia] Jmol scripts inside a pdb file

[Eran Hodis]

Hi Angel,

So the way it is currently set up does not "ignore" the inline script in those PDB files, but rather other scripts act after those inline scripts which can negate their effects.

The sequence of events is as follows:

1) You upload a PDB file with inline scripts to Ppdia
2) You have two choices, either load this PDB file "plain" with no scene, or else create a scene using that PDB.
3) If you chose to load the PDB file plain then you would add an applet to a page that would look something like "<applet load='Angel.pdb' size='300' />" (without any initial scene loaded. Angel.pdb will be loaded and then an 'initialview.spt' script will be executed, which is the same initial script that all seeded PDB entry pages employ since they load a raw pdb file with no human-made scene.
4) If instead you chose to first create a scene with that PDB file, then as soon as you open the Scene Authoring Tools and you load that PDB file, again a similar initialview script will be executed so that the pdb file does not load as a basic wireframe representation. 

Eran

-----Original Message-----
>From Angel Herráez <angel.herraez at uah.es>
Sent Sat 11/6/2010 1:12 AM
To Forum for the Proteopedia User Community <proteopedialist-for-users at bioinformatics.org>
Subject Re: [Proteopedia] Jmol scripts inside a pdb file

Thanks, Eran

These are the files:
http://proteopedia.org/wiki/index.php/Image:3L79_514-525.pdb
http://proteopedia.org/wiki/index.php/Image:2QD3_A_346-357.pdb
http://proteopedia.org/wiki/index.php/Image:1HHO_B_5-16.pdb

They are all used in
http://proteopedia.org/wiki/index.php/Helices_in_Proteins

Right now, there are scenes loaded initially, and I had to put all I wanted into the scenes, so 
you won't notice. But when I started, I was expecting the inline script to be loaded, and they 
seemed not to.


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