Help:Editing: Difference between revisions

== If you clicked on 'edit this page' but you cannot edit the page ==

"Proteopedia Scenes" are customized molecular views displayed in the Jmol applet. Before you can create or edit a scene, there must be a Jmol applet already on the current page. Instructions for inserting a new applet are in the next section below. When there is a Jmol applet present in the page, you create new scenes (green links) by using the [[Scene authoring tools|Scene Authoring Tools]].  After you create a scene, you must insert it using the appropriate wikitext that the ''Scene Authoring Tools'' will generate for you.  

When there is more than one Jmol applet on a page, scenes automatically go to the applet above the <nowiki><scene ...>...</scene></nowiki> tag in the wikitext.

==Proteopedia Jmol Applets==

Displaying a Proteopedia Scene requires an instance of the Jmol applet on the page, in order to display the molecular scene. The wikitext for inserting a Jmol applet must be entered on the page following the format below.  The simplest way to get the wikitext for an applet is by clicking the "3D" button just above the wikitext area when editing a page. (Or you could copy and paste the applet wikitext from a different page, and then edit the parameters.)  

: <nowiki><applet load='X' size='X' frame='X' align='X' caption='X' scene='X'/></nowiki>

Each X represents a parameter that you enter (and many of them are Optional). For example, this generates the Jmol applet on this page:

: <nowiki><applet load='1ea5' size='300' color='white' frame='true' align='right' caption='testcaption' /></nowiki>

<applet load='1ea5' size='300' frame='true' align='right' caption='testcaption' />

====load='X'====

Specify a [[PDB code]] (ex: load='2ace') to have the applet load the protein with the matching PDB code from the [[PDB]] database.  Specify a file name (ex: load='2ace.pdb') to have the applet load the file from Proteopedia's uploaded files.  If your desired file is not in the PDB database and not yet uploaded to Proteopedia, you may upload it here [[Special:Upload]].

This is the size in pixels of the applet's height and width.  It will be square.

If this value is not 'false' then the Jmol applet will appear on the page surrounded by a frame similar to inserting in image in wikitext and using its "frame" parameter like so: <nowiki>[[Image:someImageName.jpg|frame|someCaption]]</nowiki>.  If frame is set to false than no caption can be displayed.

Determines where on the page the Jmol applet should appear.  align='right' would have it right-aligned.  Options include 'left' and 'center'.

====caption='X'====

This is what will appear under the Jmol applet if frame is not set to 'false'.

====scene='X'====

If you specify a scene using the "scene" parameter, when your page is loaded, the applet will immediately load this scene.

This sets the name of the applet.  This is useful 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.  See section entitled "More than one Jmol applet on a page" below for more information.

===More than one Jmol applet on a page===

When there is more than one Jmol applet on a page, scenes automatically go to the applet above the <nowiki><scene ...>...</scene></nowiki> tag in the wikitext.   

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.

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:

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:

'''Examples:''' To provide examples, this paragraph contains several citations to literature references. David and Jane Richardson introduced Kinemages in 1992 <ref>PMID:1304880</ref>. The following year, Roger Sayle released [[RasMol]] <ref name="rasmol">PMID:7482707</ref>. For web-based molecular visualization, [[Chime]] was very popular after its release in 1996, but in recent years, the [[Jmol]] java applet has become the best solution <ref name="jmol">Angel Herráez. Biomolecules in the computer: Jmol to the rescue.

[http://www3.interscience.wiley.com/journal/113449000/abstract Biochem. Mol. Biol. Ed. 34:255-261] (2006).</ref>. If you are interested to know whether your protein is likely to fold, or not, try consulting FoldIndex

<ref>PMID:15955783</ref>.

Other pages that cite references correctly include [[Photosystem II]].

'''How To Cite:''' When citing a publication indexed at PubMed in the text of a page, either type "PMID:" followed by the PubMedID number of the publication, or else type the citation into the text as you wish it to appear in the reference list below, and then '''enclose it between &lt;ref&gt; and &lt;/ref&gt;'''. An example is "<nowiki><ref>PMID:15955783</ref></nowiki>". If you type the PubMedID in this manner, the properly formatted reference will created automatically at the bottom of the page (or wherever you place the necessary wikitext <nowiki>"<references/>"</nowiki>, read on..). For references not indexed at Pubmed, you will need to put the information as you want it to appear in the reference list between the &lt;ref&gt; and &lt;/ref&gt; tags. Only a number in brackets will be displayed in the text where you placed the reference. Clicking this bracketed number will jump to that reference at the bottom of the page, and block highlight it. Similarly, clicking the small upwards-pointing arrow that displays with the reference at the bottom of the page will jump to the place where it is cited, and block highlight the bracketed number.

If you want to cite the '''same publication again later''' in your text, you need to give a name to the first instance, for example &lt;ref name="rasmol"&gt;...&lt;/ref&gt;. Then, you can re-cite the same reference with this: &lt;ref name="rasmol" /&gt;. (Note the trailing slash.) Here is how this will actually appear: Although Sayle released RasMol in 1993, his publication did not appear until 1995<ref name="rasmol" />. Although Herráez wrote the cited paper on Jmol<ref name="jmol"/>, he appropriately credits Miguel Howard and Robert Hanson for most of Jmol's development for macromolecular displays.

'''Footnotes:''' Literature references cited with the above method will appear as footnotes, for example at the bottom of this page. Footnotes are also a good place to put any technical or digressive notes to avoid having them intrude in the main text. You can put any footnote text between &lt;ref&gt; and &lt;/ref&gt; tags.

 

 

The title of the References section can be any appropriate title, such as ''Literature Cited'', ''Footnotes'', ''Notes and References'', etc.

'''Note:''' It's also possible to list reference information from Pubmed without having them get assigned a bracketed number at the point of citation. This is done by adding them to the group '''xtra'''. For example this may be helpful when listing additional references indexed at Pubmed that don't contain items specifically cited in the text of the page.  

Here is a list of tutorials that may help you famliarize yourself with editing pages in Proteopedia