Help:Editing

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Contents 1 Help with Wikitext Syntax 2 Use the Sandbox for practice editing 3 How To Create A New Page 4 If the page you wish to edit does not display an edit tab at the top 5 To create or edit Proteopedia Scenes 6 Proteopedia Jmol Applets 6.1 load='X' 6.2 size='X' 6.3 frame='X' 6.4 align='X' 6.5 caption='X' 6.6 scene='X' 6.7 name='X' 7 Proteopedia Scenes 7.1 More than one Jmol applet on a page 8 Jmol extension 9 Including One Page in Another Page 10 Redirecting One Page to Another Page 11 Citing Literature References 12 References

Help with Wikitext Syntax

Please visit the Cheatsheet and How to edit a page, both in Wikipedia, as they have a much more complete help reference dealing with wikitext, and Proteopedia uses the same wiki software.

Use the Sandbox for practice editing

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.

How To Create A New Page

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.

1. Type the title of your new page in the search slot at the left near the top of the page.
2. Click the Search button.
3. 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.
4. 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.
5. Enter some text into the new page, and save it.

If the page you wish to edit does not display an edit tab at the top

• Make sure you are logged in. If you do not have a login account, go to the Login / User Account page, and click request one.
• 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.

To create or edit Proteopedia Scenes

"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. After you create a scene, you must insert it using the appropriate wikitext that the Scene Authoring Tools will generate for you.

SCENE TUTORIAL MOVIE: There is also a rough and brief, temporary video tutorial available at http://www.weizmann.ac.il/ISPC/Proteopedia.html.

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

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

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

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

spinqualitylabelsall models testcaption Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

The order of the parameters does not matter. Explanations of each parameter follow:

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.

size='X'

Optional (default value is 400 pixels).

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

frame='X'

Optional (default value is 'true').

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: [[Image:someImageName.jpg|frame|someCaption]]. If frame is set to false than no caption can be displayed.

align='X'

Optional and only relevant if the frame parameter is set to true.

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

caption='X'

Optional and only relevant if the frame parameter is set to true.

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

scene='X'

Optional.

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').

name='X'

Optional.

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.

Proteopedia Scenes

To insert a scene, type <scene name='PageName/SceneName/Version#'>Text Displayed On Page</scene>

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.

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.

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 <scene ...>...</scene> 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: <scene name='PageName/SceneName/Version#' target='AppletName'>Text Displayed On Page</scene> 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.

Jmol extension

The Jmol extension is part of Proteopedia, so all use of the Jmol extension is allowed. Usage and syntax of the Jmol extension.

Including One Page in Another Page

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.

1. 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.
2. 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: {{:Serine_Protease}} (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.

Redirecting One Page to Another Page

Sometimes it is desirable to have one page automatically take you to another page. This is called redirection. This is useful when there are synonomous titles for two or more pages, for example, Non-Standard Residue was created, and later Non-Standard Residues (plural) was created and redirected to the former page. Sometimes a page is renamed. For example, a page called Proteopedia: Interesting Pages was later renamed to Proteopedia: Topic Pages. The former now redirects to the latter.

Whenever the page you requested redirects you to another page, you will see a small notice to that effect beneath the title. For example, see Proteopedia: Interesting Pages.

To redirect one page to another page (which we'll call the Target Page), the redirecting page should contain only a single line in this format:

#REDIRECT [[Target Page]]

Citing Literature References

To provide examples, this paragraph contains several citations to literature references. David and Jane Richardson introduced Kinemages in 1992 ^[1]. The following year, Roger Sayle released RasMol ^[2]. 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 ^[3] If you want to know whether your protein will fold, or prefer not to fold, try consulting FoldIndex ^[4]

Other pages that cite references correctly include Photosystem II.

When citing a publication in the text of a page, type the citation into the text as you wish it to appear in the reference list below, and then enclose it between <ref> and </ref>. Only a number in brackets will be displayed in the text. 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 <ref name="rasmol">...</ref>. Then, you can re-cite the same reference with this: <ref name="rasmol"/>. (Note the trailing slash.) Here is how this will actually appear: Although Sayle released RasMol in 1993, his publication did not appear until 1995^[2].

The only thing you need to type into the wikitext at the bottom of your page, in order to display the references there, are these two lines:

==References==

<references/>

The title of the References section can be any appropriate title, such as Literature Cited.

References

1. ↑ Richardson DC, Richardson JS. The kinemage: a tool for scientific communication. Protein Sci. 1992 1:3-9. PMID:1304880
2. ↑ ^{2.0 2.1} Sayle RA, Milner-White EJ. RASMOL: biomolecular graphics for all. Trends Biochem Sci. 1995 20:374. PMID:7482707
3. ↑ Angel Herráez. Biomolecules in the computer: Jmol to the rescue. Biochem. Mol. Biol. Ed. 34:255-261 (2006).
4. ↑ FoldIndex©: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Jaime Prilusky, Clifford E. Felder, Tzviya Zeev-Ben-Mordehai, Edwin Rydberg, Orna Man, Jacques S. Beckmann, Israel Silman, and Joel L. Sussman, 2005, Bioinformatics PMID:15955783