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| ==Use the [[Sandbox]] for practice editing==
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| The [[Sandbox]] is a special page for practice editing. Changes you make there are not permanent. Feel free to try out the methods explained below in the ''Sandbox'' before saving permanent edits on other pages.
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| ==How To Create A New Page==
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| If you plan to edit the text or the molecular scenes in an existing page, you can skip this section. If you want to create a new page, you must first decide whether it should be a normal page that any user can edit, or a protected page, that only you can edit. If you want it to be protected, please see [[Help:Protected_Pages]]. If you want it to be publicly editable, continue with the steps below.
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| # Type the title of your new page in the search slot at the left near the top of the page.
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| # Click the '''Search''' button.
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| # Examine the search results carefully to make sure the page you want to create does not already exist, and that the content you have in mind cannot fit perfectly well into an existing page.
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| # If you still need to create a new page, click on the red link to the proposed page title at the top of the search results page.
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| # Enter some text into the new page, and save it.
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| ==For edits of text, not involving Proteopedia Scenes==
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| If the page you wish to edit does not display an ''edit'' tab at the top:
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| * Make sure you are logged in. If you do not have a login account, go to the [[Special:Userlogin | Login / User Account]] page, and click '''request one'''.
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| * If you are logged in (you see your name at the top of the page), and there is still no ''edit'' tab, please see [[Help:Protected_Pages]] for how to copy protected text into a new page that you can edit.
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| Please visit http://en.wikipedia.org/wiki/Wikipedia:Cheatsheet and http://en.wikipedia.org/wiki/Wikipedia:How_to_edit_a_page, as they have a much more complete help reference dealing with wikitext, and Proteopedia uses the same wiki software.
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| ==To create or edit Proteopedia Scenes==
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| "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.
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| '''SCENE TUTORIAL MOVIE:''' There is also a rough and brief, temporary video tutorial available at http://www.weizmann.ac.il/ISPC/Proteopedia.html.
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| 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.
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| ==Proteopedia Jmol Applets==
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| 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 typed into the page by hand following the format below. But 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.)
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| : <nowiki><applet load='X' size='X' frame='X' align='X' caption='X' scene='X'/></nowiki>
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| Each X represents a parameter that you enter (and many of them are Optional). For example, this generates the Jmol applet on this page:
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| : <nowiki><applet load='1ea5' size='300' color='white' frame='true' align='right' caption='testcaption' /></nowiki>
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| <applet load='1ea5' size='300' frame='true' align='right' caption='testcaption' />
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| The order of the parameters does not matter. Explanations of each parameter follow:
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| ====load='X'====
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| 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]].
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| ====size='X'====
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| Optional (default value is 400 pixels).
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| This is the size in pixels of the applet's height and width. It will be square.
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| ====frame='X'====
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| Optional (default value is 'true').
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| 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.
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| ====align='X'====
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| Optional and only relevant if the frame parameter is set to true.
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| Determines where on the page the Jmol applet should appear. align='right' would have it right-aligned. Options include 'left' and 'center'.
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| ====caption='X'====
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| Optional and only relevant if the frame parameter is set to true.
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| This is what will appear under the Jmol applet if frame is not set to 'false'.
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| ====scene='X'====
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| Optional.
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| The scene specified here uses the same format used to specify the "name" parameter when typing the wikitext to insert a scene: Pagename/Scriptname/Versionnumber (ex: scene='Hemoglobin/Cavity/14').
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| ====name='X'====
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| Optional.
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| 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.
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| ==Proteopedia Scenes==
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| To insert a scene, type <nowiki><scene name='PageName/SceneName/Version#'>Text Displayed On Page</scene></nowiki>
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| This wikitext for inserting a scene will be automatically generated for you to copy and paste into place when you save a scene using the authoring tools. It will also be automatically generated for you to copy and paste into place when you load a scene using the authoring tools.
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| Do not put blank spaces in front of the wikitext for a scene if you are putting the wikitext for a scene as the first text on a new line. If you do this, the error will generate boxes with dashed lines on the page.
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| ===More than one Jmol applet on a page===
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| 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.
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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.
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| ==Jmol extension==
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| The Jmol extension is part of Proteopedia, so all use of the Jmol extension is allowed. [http://wiki.jmol.org/index.php/MediaWiki Usage and syntax of the Jmol extension].
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| ==Including One Page in Another Page==
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| Suppose you want to include an entire existing "donor" page in another "recipient" page. For example, suppose there is a page with scenes of a molecule you would like to include in a page you are editing. There are two ways to do this.
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| # '''Copy and Paste:''' You can copy all or part of the donor page (from its editing box) and paste it into the editing box of the recipient page. This has two advantages. First, you can copy only a portion of the donor page. Second, the copy in the recipient page can be edited or adapted. Thus, it may diverge from the donor content.
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| # '''Inclusion:''' Suppose the donor page title is "Serine Protease". Then you can include it in a recipient page by inserting this in the editing box of the recipient page: <nowiki>{{:Serine_Protease}}</nowiki> (note the colon!). This method includes the ''entire'' donor page, and when the donor page is edited, the changes will appear automatically in the recipient page.
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