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If you wish to have a green scene link act on a specific applet that is not the applet directly above the green scene link, then you must set the "target" parameter inside the wikitext for a scene link like so: <nowiki><scene name='PageName/SceneName/Version#' target='AppletName'>Text Displayed On Page</scene></nowiki> where " target='AppletName' " tells this scene link to act on the applet with the name 'AppletName' on the page (set by using the applet's "name" parameter in the applet's wikitext). If the applet you wish to target has not been given a name using the name parameter, you may instead set target to the applet's number. For instance setting target='2' would have the green scene link act on the 3rd applet on the page, because by default, if applets are not given names, they take the sequential names 0, 1, 2, ... in the order in which the applets appear on a page.

==Setting the initial scene in the Structure Box of a PDB entry page==

The wikitext that draws the big "Structure Box", as we like to call it, on each PDB entry page with the 3D applet with all of the functional annotation and other information in one big box looks like this:

'''<nowiki>{{STRUCTURE_3cs9| PDB=3cs9 | SCENE= }}</nowiki>'''

You may know that to add a 3D applet to the page, you can click the "3D" button above the wikitext area, and you get wikitext that looks like this, and gives you a 3D applet on the page

'''<nowiki><applet load='Insert PDB code or filename here' size='300' frame='true' align='right' caption='Insert caption here' /></nowiki>'''

The "Structure Box" is different than the plain applet in that it includes the 3D applet as well as all the other information that you get inside the 'Structure Box' you find on each PDB entry page (like functional information and links to that PDB entry in other resources). You get a bit less flexibility with the Structure Box, as the only parameters you can change are the PDB id and the starting Scene. The wikitext for scenes that you want to create inside the text of a page are generated automatically for you when you create a scene, and that looks something like this:

'''<nowiki><scene name='3cs9/Overall_structure/1'>TextToBeDisplayed</scene></nowiki>'''

Now, the name of the scene is 3cs9/Overall_structure/1 which comes from the following format PageName/SceneName/VersionNumber. That whole todo with the <nowiki><scene</nowiki> in the front and the <nowiki></scene></nowiki> at the end tells Proteopedia to make a green scene link in the text. If you, on the other hand, want to make that scene the initial scene in the Structure Box, you need to enter just the scene's name into the Scene parameter of the Structure Box like so:

'''<nowiki>{{STRUCTURE_3cs9| PDB=3cs9 | SCENE=3cs9/Overall_structure/1 }}</nowiki>'''

Now your scene (3cs9/Overall_structure/1) will load as the initial scene within the Structure Box.

==Color Keys==

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@@ Line 76: / Line 76: @@
 If you wish to have a green scene link act on a specific applet that is not the applet directly above the green scene link, then you must set the "target" parameter inside the wikitext for a scene link like so:  <nowiki><scene name='PageName/SceneName/Version#' target='AppletName'>Text Displayed On Page</scene></nowiki> where " target='AppletName' " tells this scene link to act on the applet with the name 'AppletName' on the page (set by using the applet's "name" parameter in the applet's wikitext).  If the applet you wish to target has not been given a name using the name parameter, you may instead set target to the applet's number.  For instance setting target='2' would have the green scene link act on the 3rd applet on the page, because by default, if applets are not given names, they take the sequential names 0, 1, 2, ... in the order in which the applets appear on a page.
+==Setting the initial scene in the Structure Box of a PDB entry page==
+The wikitext that draws the big "Structure Box", as we like to call it, on each PDB entry page with the 3D applet with all of the functional annotation and other information in one big box looks like this:
+'''<nowiki>{{STRUCTURE_3cs9|  PDB=3cs9  |  SCENE=  }}</nowiki>'''
+You may know that to add a 3D applet to the page, you can click the "3D" button above the wikitext area, and you get wikitext that looks like this, and gives you a 3D applet on the page
+'''<nowiki><applet load='Insert PDB code or filename here' size='300' frame='true' align='right' caption='Insert caption here' /></nowiki>'''
+The "Structure Box" is different than the plain applet in that it includes the 3D applet as well as all the other information that you get inside the 'Structure Box' you find on each PDB entry page (like functional information and links to that PDB entry in other resources). You get a bit less flexibility with the Structure Box, as the only parameters you can change are the PDB id and the starting Scene. The wikitext for scenes that you want to create inside the text of a page are generated automatically for you when you create a scene, and that looks something like this:
+'''<nowiki><scene name='3cs9/Overall_structure/1'>TextToBeDisplayed</scene></nowiki>'''
+Now, the name of the scene is 3cs9/Overall_structure/1 which comes from the following format PageName/SceneName/VersionNumber. That whole todo with the <nowiki><scene</nowiki> in the front and the <nowiki></scene></nowiki> at the end tells Proteopedia to make a green scene link in the text. If you, on the other hand, want to make that scene the initial scene in the Structure Box, you need to enter just the scene's name into the Scene parameter of the Structure Box like so:
+'''<nowiki>{{STRUCTURE_3cs9|  PDB=3cs9  |  SCENE=3cs9/Overall_structure/1  }}</nowiki>'''
+Now your scene (3cs9/Overall_structure/1) will load as the initial scene within the Structure Box.
 ==Color Keys==