Proteopedia - User contributions [en]

Help:Editing

2025-02-18T04:40:19Z

Pooja Rajak:

<Structure load=''''Insert PDB code or filename here'''''''''4RF1'''Bold text'''''''''' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /><center><table style='background:#ffd8d8;' cellpadding='6'><tr><td>
Before using this page, you may find it useful to consult [[Proteopedia:Getting_Started|Help:Getting Started in Proteopedia]], the [[Proteopedia:Video Guide|Video Guides]], and the main [[Help]] Page.
</td></tr></table></center>

==<big>Help with Wikitext Syntax</big>==
Please visit the <big>[http://en.wikipedia.org/wiki/Wikipedia:Cheatsheet Cheatsheet] and [http://en.wikipedia.org/wiki/Help:Wiki_markup A Reference On Wikitext Syntax]</big>, 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==
[[Help:Sandboxes|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 [[Help:Sandboxes|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 [[Proteopedia:How to Make a Page|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.
# Type the title of your new page in the search slot at the left near the top of the page.
# Click the '''Search''' button.
# 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.
# A good place to develop a new page is in a [[Help:Sandboxes|protected sandbox]]. After it is completed, you can move the contents to a publically editable, permanent page with an appropriate article title.
# 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.
# Enter some text into the new page, and save it.

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

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

== Problems while editing ==

=== 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 [[Special:Userlogin | 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]].

=== If you get '''We could not process your edit due to a loss of session data''' ===
The full message says
:'''Sorry! We could not process your edit due to a loss of session data. Please try again. If it still doesn't work, try logging out and logging back in.'''
just under the 'Preview' heading.

This is an infrequent error. See instructions at [[Help:Errors]].

==<big>To create or edit Proteopedia Scenes</big>==
"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|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 <nowiki><scene ...>...</scene></nowiki> 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. )

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

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:

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

<Structure load='1ea5' size='300' frame='true' align='right' caption='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: <nowiki>[[Image:someImageName.jpg|frame|someCaption]]</nowiki>. 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 <nowiki><scene name='PageName/SceneName/Version#'>Text Displayed On Page</scene></nowiki>

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

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

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

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

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:

'''<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==

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:
<blockquote><big>
{{Template:ColorKey Composition Protein}}
{{Template:ColorKey Composition DNA}}
{{Template:ColorKey Composition RNA}}
{{Template:ColorKey Composition Ligand}}
{{Template:ColorKey Composition Solvent}}
</big></blockquote>

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. [http://wiki.jmol.org/index.php/MediaWiki 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.

# '''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.
# '''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.

==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:

<nowiki>#REDIRECT [[Target Page]]</nowiki>

==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<ref>This is just some text to illustrate that you can put any text in a reference/footnote.</ref>. 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 <nowiki>==References==</nowiki>.

'''Examples:''' This paragraph contains several citations to literature indexed in PubMed, and one citation of a paper not indexed in PubMed.
<blockquote>
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). [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]].
</blockquote>
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.)
<blockquote>
David and Jane Richardson introduced Kinemages in 1992 <ref>PMID:1304880</ref>. The following year, Roger Sayle released <nowiki>[[RasMol]]</nowiki> <ref name="rasmol">PMID:7482707</ref>. For web-based molecular visualization, <nowiki>[[Chime]] was very popular after its release in 1996, but in recent years, [[Jmol]]</nowiki> has become the best solution <ref name="jmol">Angel Herráez. Biomolecules in the computer: Jmol to the rescue. <nowiki>[http://www3.interscience.wiley.com/journal/113449000/abstract Biochem. Mol. Biol. Ed. 34:255-261]</nowiki> (2006). <nowiki>[http://dx.doi.org/10.1002/bmb.2006.494034042644 DOI: 10.1002/bmb.2006.494034042644]</nowiki></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 <nowiki>[http://wiki.jmol.org/index.php/Literature recently implemented JSmol], a version that operates without [[Java]]</nowiki>.
</blockquote>

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

===Citing by PubMed ID Number===

When citing a publication indexed at [http://pubmed.gov PubMed.Gov], type "PMID:" followed by the PubMedID number of the publication, and then enclose it between <ref> and </ref>. For example, type '''<nowiki><ref>PMID: 18673581</ref></nowiki>''' 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 <nowiki>"<references/>"</nowiki>). The example reference: <ref>PMID: 18673581</ref>.

====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 "<nowiki><ref group="xtra">PMID:15068885</ref></nowiki>". If you type the PubMedID in this manner, the properly formatted reference will be created automatically wherever you place the necessary wikitext <nowiki>"<references group="xtra"/></nowiki>"". 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, 
<nowiki>Additional Literature and Resources</nowiki> 
<nowiki><ref group="xtra">PMID:15068885</ref><ref group="xtra">PMID:14749769</ref><ref group="xtra">PMID:1304880</ref></nowiki> 
<nowiki><references group="xtra"/></nowiki>

will appear on the article page, as below: 
  
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"/>

===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 '''<nowiki><ref>DOI: 10.1002/bmb.2005.494033022442</ref></nowiki>''' 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)

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

The resulting citation: <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>.

===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
<blockquote>
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.
</blockquote>

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 <ref>This is an example of digressive text placed in a footnote.</ref>.

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:

<nowiki>==References==</nowiki>

<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
*[[Proteopedia:Video_Guide]]
*[[User:Tom_Gluick/glutamine_synthetase]]
*[[Help:Contents]] has a list of all tutorials and help within Proteopedia.

==References==
<references/>

==See Also==
* [[Proteopedia:How to Make a Page|How to Make a Page]]
* [[Help:Language Translation]] and [[Help:Text Directionality]]

Help:Editing

2025-02-18T04:33:53Z

Pooja Rajak:

<Structure load=''''Insert PDB code or filename here''''''Crystal Structure of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Papain-like Protease Bound to Ubiquitin'''' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /><center><table style='background:#ffd8d8;' cellpadding='6'><tr><td>
Before using this page, you may find it useful to consult [[Proteopedia:Getting_Started|Help:Getting Started in Proteopedia]], the [[Proteopedia:Video Guide|Video Guides]], and the main [[Help]] Page.
</td></tr></table></center>

==<big>Help with Wikitext Syntax</big>==
Please visit the <big>[http://en.wikipedia.org/wiki/Wikipedia:Cheatsheet Cheatsheet] and [http://en.wikipedia.org/wiki/Help:Wiki_markup A Reference On Wikitext Syntax]</big>, 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==
[[Help:Sandboxes|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 [[Help:Sandboxes|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 [[Proteopedia:How to Make a Page|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.
# Type the title of your new page in the search slot at the left near the top of the page.
# Click the '''Search''' button.
# 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.
# A good place to develop a new page is in a [[Help:Sandboxes|protected sandbox]]. After it is completed, you can move the contents to a publically editable, permanent page with an appropriate article title.
# 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.
# Enter some text into the new page, and save it.

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

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

== Problems while editing ==

=== 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 [[Special:Userlogin | 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]].

=== If you get '''We could not process your edit due to a loss of session data''' ===
The full message says
:'''Sorry! We could not process your edit due to a loss of session data. Please try again. If it still doesn't work, try logging out and logging back in.'''
just under the 'Preview' heading.

This is an infrequent error. See instructions at [[Help:Errors]].

==<big>To create or edit Proteopedia Scenes</big>==
"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|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 <nowiki><scene ...>...</scene></nowiki> 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. )

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

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:

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

<Structure load='1ea5' size='300' frame='true' align='right' caption='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: <nowiki>[[Image:someImageName.jpg|frame|someCaption]]</nowiki>. 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 <nowiki><scene name='PageName/SceneName/Version#'>Text Displayed On Page</scene></nowiki>

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

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

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

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

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:

'''<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==

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:
<blockquote><big>
{{Template:ColorKey Composition Protein}}
{{Template:ColorKey Composition DNA}}
{{Template:ColorKey Composition RNA}}
{{Template:ColorKey Composition Ligand}}
{{Template:ColorKey Composition Solvent}}
</big></blockquote>

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. [http://wiki.jmol.org/index.php/MediaWiki 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.

# '''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.
# '''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.

==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:

<nowiki>#REDIRECT [[Target Page]]</nowiki>

==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<ref>This is just some text to illustrate that you can put any text in a reference/footnote.</ref>. 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 <nowiki>==References==</nowiki>.

'''Examples:''' This paragraph contains several citations to literature indexed in PubMed, and one citation of a paper not indexed in PubMed.
<blockquote>
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). [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]].
</blockquote>
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.)
<blockquote>
David and Jane Richardson introduced Kinemages in 1992 <ref>PMID:1304880</ref>. The following year, Roger Sayle released <nowiki>[[RasMol]]</nowiki> <ref name="rasmol">PMID:7482707</ref>. For web-based molecular visualization, <nowiki>[[Chime]] was very popular after its release in 1996, but in recent years, [[Jmol]]</nowiki> has become the best solution <ref name="jmol">Angel Herráez. Biomolecules in the computer: Jmol to the rescue. <nowiki>[http://www3.interscience.wiley.com/journal/113449000/abstract Biochem. Mol. Biol. Ed. 34:255-261]</nowiki> (2006). <nowiki>[http://dx.doi.org/10.1002/bmb.2006.494034042644 DOI: 10.1002/bmb.2006.494034042644]</nowiki></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 <nowiki>[http://wiki.jmol.org/index.php/Literature recently implemented JSmol], a version that operates without [[Java]]</nowiki>.
</blockquote>

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

===Citing by PubMed ID Number===

When citing a publication indexed at [http://pubmed.gov PubMed.Gov], type "PMID:" followed by the PubMedID number of the publication, and then enclose it between <ref> and </ref>. For example, type '''<nowiki><ref>PMID: 18673581</ref></nowiki>''' 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 <nowiki>"<references/>"</nowiki>). The example reference: <ref>PMID: 18673581</ref>.

====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 "<nowiki><ref group="xtra">PMID:15068885</ref></nowiki>". If you type the PubMedID in this manner, the properly formatted reference will be created automatically wherever you place the necessary wikitext <nowiki>"<references group="xtra"/></nowiki>"". 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, 
<nowiki>Additional Literature and Resources</nowiki> 
<nowiki><ref group="xtra">PMID:15068885</ref><ref group="xtra">PMID:14749769</ref><ref group="xtra">PMID:1304880</ref></nowiki> 
<nowiki><references group="xtra"/></nowiki>

will appear on the article page, as below: 
  
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"/>

===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 '''<nowiki><ref>DOI: 10.1002/bmb.2005.494033022442</ref></nowiki>''' 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)

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

The resulting citation: <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>.

===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
<blockquote>
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.
</blockquote>

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 <ref>This is an example of digressive text placed in a footnote.</ref>.

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:

<nowiki>==References==</nowiki>

<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
*[[Proteopedia:Video_Guide]]
*[[User:Tom_Gluick/glutamine_synthetase]]
*[[Help:Contents]] has a list of all tutorials and help within Proteopedia.

==References==
<references/>

==See Also==
* [[Proteopedia:How to Make a Page|How to Make a Page]]
* [[Help:Language Translation]] and [[Help:Text Directionality]]

Proteopedia:How to Make a Page

2025-02-18T03:43:31Z

Pooja Rajak:

These steps are meant to help you create an excellent, top-quality Proteopedia page. You may choose to deviate from these steps in creating your page, if you wish, but these are the standards we have adopted and recommend for top-quality page creation. If you believe we should change some of these standards, please give us feedback at {{Template:Contact}}. For an example of an excellent Proteopedia page, see [[HMG-CoA Reductase]] (while the HMG-CoA Reductase page could always be improved, it represents most of the points on quality page creation listed below).

==Before you begin==

Before you begin, if this is your first time editing a Proteopedia page you should begin by watching the [[Proteopedia:Video Guide|video guide]] and referring to the [[Help:Editing|editing help]] reference pages.
Crystal Structure of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Papain-like Protease Bound to Ubiquitin
==Creating the page==
Crystal Structure of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Papain-like Protease Bound to Ubiquitin
# choose your topic (generally: a protein, a molecule, or a concept)
# check that a page on your topic doesn't exist already by using:
## the search box
## looking in the [[Proteopedia:Table of Contents|table of contents]]
# choose a title that is appropriate following rules at [[Proteopedia:Page name]]. You can always rename the page later if necessary.
#if a page on your topic already exists, you may edit that page to improve it
# you don't have permission to edit [[1h88|PDB entry pages]]. Please contact {{Template:Contact}} if you need
## to add links to other Proteopedia pages
## to correct wrong information about the PDB entry
## to add information relevant to the PDB entry but not to the protein or molecule in general
#if you need to create a new page, search for the exact title of the new page, then in the "not found" results, click on the red link to the non-existent page. Now you can edit it, and after the first save, you have created the page.

==The new page template==

[[Image:Proteopedia New Page Annotated.JPG|right|thumb|New page template with highlighted code: 3D Jmol window, yellow; green links, green; references, tan.]]When you start a new page, it opens with a template to get you started. The elements highlighted in yellow place a 3D Jmol browser window on the right side of the page, with scrolling text on the left. The initial scene that shows in the 3D window is specified in the code as well, either by providing the PDB ID of a structure (here: 1STP) or by specifying a 3D scene (left blank in this example). The elements highlighted in green are the code that create green links on your page. The elements in tan show how to cite literature and show the references at the end of the page. You should modify these elements to fit your page. You could also delete the entire template and start from scratch if that is easier.

==The basic beginnings of your page==
Every new Proteopedia page should begin with an introduction, a 2D image, and a 3D structure.

===Adding an introduction===
#3-7 sentences about what the protein or topic is and why it is important
#first sentence should contain the name of the topic and it should be an interwiki link (so on the Hemoglobin page, you might start by writing "<nowiki>[[Hemoglobin]] is the protein...</nowiki>")
#touch on medical relevance if there is any
#absolutely no external links

===Add a 2D image===
#preferably that show a different view of the protein compared to the 3D structure in the introduction, (i.e. if the introductory 3D structure is in cartoon, make the 2D image in spacefill)
#PyMOL is good for producing high-quality raytraced images for this purpose and you can use the [http://polyview.cchmc.org/polyview3d.html POLYVIEW-3D] webserver as a facile interface to rendering images with PyMol. Save the file to your computer.
#[[Special:Upload|Upload]] the image file to Proteopedia using the '[[Special:Upload|Upload File]]' function under the toolbox section in the lower left hand side panel of each Proteopedia page. It will get a name such as 'Image:YourImageName.png'.
#Build a reference to the uploaded image into your page. Example syntax: <nowiki>[[Image:YourImageName|300px|left|thumb| Your Caption Text]]</nowiki>::Example syntax if your image is derived from a PDB entry: <nowiki>[[Image:1dqa opening.png|300px|left|thumb| Human HMG-CoA Reductase Catalytic Domain, [[1dqa]]]]</nowiki>
#around 200 or 300 px is a good size
#the custom is to align the 2D image to the left
#mention the PDB entry as an interwiki link in the caption of the image

===Add a 3D structure===
#standard practice is to use a "StructureSection", i.e. a window on the right with scrollable text on the left.
##new pages contain the code for this already
##example wikitext: <nowiki><StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> ... </StructureSection>
</nowiki>
#if your page lacks a StructureSection and you need one, click on the "green window" icon in the editing tools
#use an initial scene (by setting "load=''" and inserting the scene in the "scene=" parameter)
#make sure all your scenes have captions
#include an interwiki link to the PDB entry in the captions
#preferably show a different view of the protein compared to the 2D structure in the introduction, (i.e. if the introductory 2D image is in cartoon, make the 3D structure in spacefill)

==Planning the rest of the page==
# it is best to sketch out your plan for the page on paper
# start with a broad focus that gets increasingly narrow
# think about bringing the reader through a tour of the most interesting and important features of your structure
# plan for 1 or 2 sections that will feature a structural description with a 3D structure and green scene links
# in exceptional cases, you might have more than one 3D applet on the page but this makes loading slower
# plan for a section about how your topic is related to disease, if relevant

==Rules to keep in mind==
* max number of applets on the entire page is 3 (use StructureSections to help reduce the number of applets on the page, follow the examples here: [[Glutamate receptor (GluA2)|Glutamate receptor]])
* use wikitext rather than HTML
* mention all PDB ids whenever appropriate, and link to their page in Proteopedia

==Structural Description==
# the page should have 1 or 2 sections that feature a structural description with a 3D structure adjacent to descriptive text with green scene links
# if the section is short, use a regular applet for the 3D structure (ex: <nowiki><applet load='1ea5'...</nowiki>)
# if you have a long section with a lot of text, use a StructureSection (click on the button with 4 green squares above the text-editing area when you are editing your page to add the syntax for a StructureSection)

===Scenes===
#make a list of the most important structural features of your biomolecule (look at figures from publications about your biomolecule for inspiration)
#create a story to lead the reader through the most important structural features of your biomolecule
#minimize unnatural jumps
##by creating a natural flow between scenes
##by using the same PDB structure for consecutive scenes, where possible
#use different transitions where appropriate (for tips refer to [[Proteopedia:How to Make a Scene]])
#choose text for the green links that relates to the scene
#try to minimize the text used for a green scene link (i.e. have a link that is "You can see the <scene name=''>structure</scene> of HMGR'' instead of ''<scene name=''>You can see the structure of HMGR</scene>'')
#use as few structures as possible
#make it obvious which structures you are using either in the text of the page, or in the caption of the 3D applet, or in the caption of the scene
#use morphs to illustrate conformational changes
#refer to these instructions for making excellent scenes: [[Proteopedia:How to Make a Scene]]

==Images==
# images should ideally be big enough to look at without having to click to enlarge
# [[Special:Upload|Upload]] the image file to Proteopedia using the '[[Special:Upload|Upload File]]' function under the toolbox section in the lower left hand side panel of each Proteopedia page. It will get a name such as 'Image:YourImageName.png'.Upload your image using the toolbox on the left
# try to use this style of wikitext for images <nowiki>[[Image:YourImageName|300px|left|thumb| An informative caption here]]</nowiki>
## change the caption, size and alignment (left, right, center) as necessary
# provide a descriptive caption
# if the image is of a PDB entry, provide an interwiki link to that PDB entry in the caption, for example <nowiki>[[Image:1dqa opening.png|300px|left|thumb| Human HMG-CoA Reductase Catalytic Domain, [[1dqa]]]]</nowiki>
# images should have proper copyrights that allow for their use in Proteopedia (do not use images from copyrighted sources like journal articles or textbooks)

==Add External Links==
# add any external links in a section at the end of the page called "External Resources"
# consider adding a link to the relevant Wikipedia page
# any external links that you wish to place in the body of your page should be added as references

==References==
#add references to papers using their PubMed id
##example wikitext: <nowiki><ref>PMID:1234235</ref></nowiki>
#create a section titled "References" as the second to last section on the page (the last will be "External Resources")
#in the "References" section add this wikitext: <nowiki><references/></nowiki>
#for more information on how to use references, refer to [[Help:Editing#Citing_Literature_References]]
#make sure you cite, at the minimum, the most important references

==Add Internal Links==
# do a google search on your topic prepending it with "site:proteopedia.org" to discover which other pages are relevant to your topic.# if there are topics mentioned in your page that have their own Proteopedia article, make them into interwiki links
## example wikitext: <nowiki>[[Hemoglobin]]</nowiki>
# add a "See Also" section directly before the "References" section with a list of links to other Proteopedia pages (use the wikitext syntax for lists)
# consider editing the pages you linked to, adding a link to the new page. This way, Proteopedia becomes a web of linked pages, and it becomes easier to navigate. You can quickly find out about links from the "What links here" item in the toolbox on the left side panel.

==List of all related PDB ids==
#before the "See Also" section add a section titled "Additional 3D Structures of X" where you replace "X" with the name of your protein or biomolecule
#in this section create an organized list of all other PDB entries of the same protein or biomolecule
#try to follow the example here: [[Ferredoxin]]

==When finished==
# read through your page again, making sure the text and the scenes have a natural flow
# check that your page illustrates the most important features of the topic of the page
# add your page to the [[Proteopedia:Table of Contents]]
# create redirects for alternative spellings or capitalizations of your page name
# link to your page from other relevant Proteopedia pages
# add categories to the bottom of your page
# if page topic fits within one of the subcategories listed in the table of contents, i.e. "Diabetes" or "Lyase" add a section at bottom of page, before the references section called "Additional Resources" with the phrase <nowiki>"See [[Diabetes]] for more information"</nowiki>.

==See Also==
* [[Help:Editing]]