Proteopedia:How to Make a Page

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 . 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 beginBefore you begin

Before you begin, if this is your first time editing a Proteopedia page you should begin by watching the video guide and referring to the editing help reference pages.

Creating the pageCreating the page

1. choose your topic (generally: a protein, a molecule, or a concept)
2. check that a page on your topic doesn't exist already by using:
   1. the search box
   2. looking in the table of contents
3. choose a title that is appropriate. it should be:
   1. the name of the topic
   2. 5 words or fewer
   3. (you can always rename the page later if necessary)
4. don't edit a PDB entry page except:
   1. to add links to other Proteopedia pages
   2. to correct wrong information about the PDB entry
   3. to add information relevant to the PDB entry but not to the protein or molecule in general
5. if a page on your topic already exists, you may edit that page to improve it

The basic beginnings of your pageThe basic beginnings of your page

Every new Proteopedia page should begin with an introduction, a 2D image, and a 3D structure.

Adding an introductionAdding an introduction

1. 3-7 sentences about what the protein or topic is and why it is important
2. 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 "[[Hemoglobin]] is the protein...")
3. touch on medical relevance if there is any
4. absolutely no external links

Add a 2D imageAdd a 2D image

1. 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)
2. PyMOL is good for producing high-quality raytraced images for this purpose
3. example syntax: [[Image:1dqa opening.png|300px|left|thumb| Human HMG-CoA Reductase Catalytic Domain, [[1dqa]]]]
4. around 200 or 300 px is a good size
5. the custom is to align the 2D image to the left
6. mention the PDB entry as an interwiki link in the caption of the image

Add a 3D structureAdd a 3D structure

1. standard practice is to use a STRUCTURE Box
   1. example wikitext: {{STRUCTURE_1dq8| right| PDB=1dq8 | SCENE=HMG-CoA_Reductase/1dq8_starting_scene/1 |CAPTION= Crystal Structure of Human HMG-CoA Reductase Catalytic Domain, [[1dq8]] }}
2. if STRUCTURE Box is not ideal, use a regular applet
3. custom is to align 3D structure to the right
4. use an initial scene (by changing the "scene=" parameter) that shows a good overview of the protein
5. have a descriptive caption
6. include an interwiki link to the PDB entry in the caption
7. preferably that show a different view of the protein compared to the 3D 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 pagePlanning the rest of the page

• good to write down on paper
• plan for 1 or 2 sections with structural description
• plan for no more than 3 applets on the page in total
• plan for a section about how your topic is related to disease, if relevant

Structural descriptionStructural description

• structuresection is ideal for this

Rules to live byRules to live by

• max number of applets (absolute max is 3 including the upper right one) - if you need more use structuresection
• use wikitext rather than HTML

ScenesScenes

• 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 jumps
• use different transitions where appropriate (where appropriate?)
• 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 structure of HMGR instead of You can see the structure of HMGR)
• make them tell a story about the structure
• use as few structures as possible
• make it obvious which structures you are using
• use morphs to illustrate conformational changes
• use a structuresection if you have a section with many green scene links

ReferencesReferences

1. add references to papers using their PubMed id
   1. example wikitext: <ref>PMID:1234235</ref>
2. create a section titled "References" as the 2nd to last section on the page (the last will be "External Resources")
3. in the "References" section add this wikitext: <references/><nowiki> #for more information on how to use references, refer to [[Help:Editing#Citing_Literature_References]] ==Add Internal Links== # if there are topics mentioned in your page that have their own Proteopedia article, make them into interwiki links ## example wikitext: <nowiki>[[Hemoglobin]]
4. 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)

Add External LinksAdd External Links

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

When finishedWhen finished

1. read through your page again, making sure the text and the scenes have a natural flow
2. check that your page illustrates the most important features of the topic of the page
3. add your page to the Proteopedia:Table of Contents
4. create redirects for alternative spellings or capitalizations of your page name
5. link to your page from other relevant Proteopedia pages
6. add categories to the bottom of your page

ImagesImages

• images should ideally be big enough to look at without having to click to enlarge
• try to use this wikitext for images [[Image...thumb etc]]
• provide a descriptive caption
• images should have proper copyrights that you can use them

Extra stuff need to be organizedExtra stuff need to be organized

• applet on the upper right should be a representative structure
• mention all PDB ids (where?)
• use references correctly
• make sure your scenes meet these guidelines -> Proteopedia:How to Make a Scene
• start broad and go narrow (use headlines, start with two equal signs, never use a single equal sign heading)
• use captions for your images
• if your protein has any medical relevance whatsoever, make sure to talk about it
• cite the most important references
• 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 "See Diabetes for more information".
• add a list of all PDB entries, organized (say, similar to XXX page)