Help:Editing

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Before using this page, you may find it useful to consult Help:Getting Started in Proteopedia, the Video Guides, and the main Help Page.

Contents

Help with Wikitext Syntax

Please visit the Cheatsheet and A Reference On Wikitext Syntax, both in Wikipedia, as they have a much more complete help reference dealing with wikitext, and Proteopedia uses the same wiki software.


Use Sandboxes for practice editing

Sandboxes are a special pages for practice editing. Changes you make there are not permanent. Feel free to try out the methods explained below in a Sandbox before saving permanent edits on other pages. In fact, a protected Sandbox is a good place to develop a new page: instructions are at Help:Sandboxes.

How To Create A New Page

For fuller coverage, see How to Make a Page.
The basics:
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. A good place to develop a new page is in a protected sandbox. After it is completed, you can move the contents to a publically editable, permanent page with an appropriate article title.
  5. 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.
  6. Enter some text into the new page, and save it.

Once your new page is reasonably complete, please add it to the list What's New in Proteopedia?.

Please see Proteopedia:How to Make a Page for guidance as to how to make an excellent Proteopedia page.

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

  • 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.

If you get XML Error: Mismatched tags at line 1

Don't worry! You can fix this and recover your work. The instructions are at Help:Errors.

To create or edit Proteopedia Scenes

"Proteopedia Scenes" are customized molecular views displayed in the Jmol structure applet. Before you can create or edit a scene, there must be a Jmol structure applet already on the current page. Instructions for inserting a new structure applet are in the next section below. When there is a Jmol structure 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 a video tutorial available at Proteopedia:Video Guide

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

Proteopedia Jmol Structure Applets

Displaying a Proteopedia Scene requires an instance of the Jmol structure applet on the page, in order to display the molecular scene. The wikitext for inserting a Jmol structure applet must be entered on the page following the format below. The simplest way to get the wikitext for a structure applet is by clicking the "3D" button just above the wikitext area when editing a page. (Or you could copy and paste the structure applet wikitext from a different page, and then edit the parameters. You may sometimes see 'applet' in place of 'Structure' at the start of the code on older pages as this is the form, which still works. )

<Structure load='Insert PDB code or filename here' size='X' frame='X' align='X' caption='Insert caption here' scene='Insert optional scene name here' />

Parameters that you can enter are represented by descriptions of what you need to enter or an 'X' (and many of them are Optional). For example, this generates the Jmol structure applet on this page:

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

testcaption

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

load='Insert PDB code or filename here'

Specify a PDB code (ex: load='2ace') to have the structure applet load the protein with the matching PDB code from the PDB database. Specify a file name (ex: load='2ace.pdb') to have the structure 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 structure 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 structure 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 structure applet should appear. align='right' would have it right-aligned. Options include 'left' and 'center'.

caption='Insert caption here'

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

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

scene='Insert optional scene name here'

Optional.

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

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 structure applet. This is useful if you wish to have a green scene link act on a specific applet that is not the structure applet directly above the green scene link. See section entitled "More than one Jmol structure 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 structure applet on a page

When there is more than one Jmol structure 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 structure 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='StructureAppletName'>Text Displayed On Page</scene> where " target='StructureAppletName' " tells this scene link to act on the structure applet with the name 'StructureAppletName' on the page (set by using the structure applet's "name" parameter in the applet's wikitext). If the structure 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 structure 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 structure 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 structure applet with all of the functional annotation and other information in one big box looks like this:

{{STRUCTURE_3cs9| PDB=3cs9 | SCENE= }}

You may know that to add a 3D structure 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 structure applet on the page

<Structure load='Insert PDB code or filename here' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

The "Structure Box" is different than the plain structure applet in that it includes the 3D structure 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:

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

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 <scene in the front and the </scene> 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:

{{STRUCTURE_3cs9| PDB=3cs9 | SCENE=3cs9/Overall_structure/1 }}

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

Color Keys

Color keys will help your readers understand your molecular scenes. For example, if you use the Composition color scheme available in the Colors tab of the Scene Authoring Tool, you could include this in your wikitext:

Protein DNA RNA Ligand Solvent

For an explanation of how to include color keys in your Proteopedia pages, please see Help:Color Keys.

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

Each citation that is to appear as a numbered footnote at the bottom of an article should be enclosed between <ref> and </ref>. Only a number in brackets will be displayed in the text where you placed the reference, like this[1]. 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.

While you can place any text between the <ref> and </ref> tags, there is a time-saving shortcut for publications indexed in PubMed (details below).

To produce the list of numbered references at the bottom of the page, insert <references /> (note the slash!). Typically this is placed after a title such as ==References==.

Examples: This paragraph contains several citations to literature indexed in PubMed, and one citation of a paper not indexed in PubMed.

David and Jane Richardson introduced Kinemages in 1992 [2]. The following year, Roger Sayle released RasMol [3]. 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 [4]. Angel Herráez has been a major leader in educational molecular visualization[4]. Bob Hanson has been the primary developer of Jmol since 2006, and has recently implemented JSmol, a version that operates without Java.

Here is the wikitext for the previous paragraph with the <ref> tags in boldface. Notice how a reference can be named (see red below), and then cited again by name to avoid duplicating it in the reference list. (You could also see the wikitext by clicking the edit this page tab at the top of this article, but then be sure to click Cancel if you do not intend to change it.)

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, [[Jmol]] 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). [http://dx.doi.org/10.1002/bmb.2006.494034042644 DOI: 10.1002/bmb.2006.494034042644]</ref>. Angel Herráez has been a major leader in educational molecular visualization<ref name="jmol" />. Bob Hanson has been the primary developer of Jmol since 2006, and has [http://wiki.jmol.org/index.php/Literature recently implemented JSmol], a version that operates without [[Java]].

Other pages that cite references correctly include Photosystem II.

Citing by PubMed ID Number

When citing a publication indexed at PubMed.Gov, type "PMID:" followed by the PubMedID number of the publication, and then enclose it between <ref> and </ref>. For example, type <ref>PMID: 18673581</ref> in the wikitext box and save the page. 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 "<references/>"). The example reference: [5].

PubMed citations without footnote numbers

It is 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. An example is "<ref group="xtra">PMID:15068885</ref>". If you type the PubMedID in this manner, the properly formatted reference will be created automatically wherever you place the necessary wikitext "<references group="xtra"/>"". If you have a number of them to cite like this, putting all the additional references on one line eliminates excessive gaps in the page created when the items are hidden on the article page.
For example, the source,
Additional Literature and Resources
<ref group="xtra">PMID:15068885</ref><ref group="xtra">PMID:14749769</ref><ref group="xtra">PMID:1304880</ref>
<references group="xtra"/>

will appear on the article page, as below:
 
Additional Literature and Resources

Use DOI for citations not in PubMed

Nearly all recent publications have a DOI (Digital Object Identifier). Some journals, monographs, and other publications are not indexed in PubMed. For most of these references, it's enough to enter "DOI:" followed by the DOI identifier, and then enclose it between <ref> and </ref>. For example, type <ref>DOI: 10.1002/bmb.2005.494033022442</ref> in the wikitext box and save the page.

When citing a reference for which the DOI is not enough for automatically retrieving the full reference, you will need to type (or copy and paste) the entire reference text along with the DOI. You can hyperlink the DOI to go to the cited document. Suppose that the reference is

Martz, E. Book review of Introduction to protein science—architecture, function, and genomics: Lesk, Arthur M.. Biochem. Mol. Biol. Educ. 33:144-5 (2006). DOI: 10.1002/bmb.2005.494033022442

Then enter it in the wikitext like this (markup is bold; note two single quotes used for italics)

<ref>Martz, E. Book review of ''Introduction to protein science—architecture, function, and genomics: Lesk, Arthur M. Biochem. Mol. Biol. Educ.'' 33:144-5 (2006). [http://dx.doi.org/10.1002/bmb.2005.494033022442 DOI: 10.1002/bmb.2005.494033022442]</ref>

The resulting citation: [6].

Not in PubMed, no DOI

For references not indexed at Pubmed, and lacking a DOI, you will need to put the information as you want it to appear in the reference list between the <ref> and </ref> tags. You may include hyperlinks (see hyperlinked DOI example above). You can also use <ref> and </ref> tags for footnotes that are not citations of publications (see References section below).

Repeat citations

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 using two references already used in the first example of the Citing Literature References section

Although Sayle released RasMol in 1993, his publication did not appear until 1995[3]. Although Herráez wrote the cited paper on Jmol[4], he appropriately credits Miguel Howard and Robert Hanson for most of Jmol's development for macromolecular displays.

See the References section below and note how the each individual reference is listed only once with the separate instances linked.

Footnotes

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 <ref> and </ref> tags, for example [7].

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

==References==

<references />

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

Policies in Proteopedia

Please see the separate page Proteopedia:Policies for the policies on issues such as linking to Wikipedia, protected pages, theoretical models.

Tutorials

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

References

  1. This is just some text to illustrate that you can put any text in a reference/footnote.
  2. Richardson DC, Richardson JS. The kinemage: a tool for scientific communication. Protein Sci. 1992 Jan;1(1):3-9. PMID:1304880
  3. 3.0 3.1 Sayle RA, Milner-White EJ. RASMOL: biomolecular graphics for all. Trends Biochem Sci. 1995 Sep;20(9):374. PMID:7482707
  4. 4.0 4.1 4.2 Angel Herráez. Biomolecules in the computer: Jmol to the rescue. Biochem. Mol. Biol. Ed. 34:255-261 (2006). DOI: 10.1002/bmb.2006.494034042644
  5. Hodis E, Prilusky J, Martz E, Silman I, Moult J, Sussman JL. Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules. Genome Biol. 2008;9(8):R121. Epub 2008 Aug 3. PMID:18673581 doi:http://dx.doi.org/10.1186/gb-2008-9-8-r121
  6. Martz, E. Book review of Introduction to protein science—architecture, function, and genomics: Lesk, Arthur M.. Biochem. Mol. Biol. Educ. 33:144-5 (2006). DOI: 10.1002/bmb.2005.494033022442
  7. This is an example of digressive text placed in a footnote.

See Also

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Wayne Decatur, Eran Hodis, Jaime Prilusky, Daniel Mott, Tuhin Bhowmick

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