Proteopedia

Proteopedia:How to Make a Page

Revision as of 20:33, 19 October 2011 by Eric Martz (talk | contribs) (→‎References: corrected typo that failed to close nowiki tags)

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. if a page on your topic already exists, you may edit that page to improve it
  5. don't edit a PDB entry page. Please contact   if you need
    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

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 and you can use the POLYVIEW-3D webserver as a facile interface to rendering images with PyMol. Save the file to your computer.
  3. Upload the image file to Proteopedia using the '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'.
  4. Build a reference to the uploaded image into your page. Example syntax: [[Image:YourImageName|300px|left|thumb| Your Caption Text]]
Example syntax if your image is derived from a PDB entry: [[Image:1dqa opening.png|300px|left|thumb| Human HMG-CoA Reductase Catalytic Domain, [[1dqa]]]]
  1. around 200 or 300 px is a good size
  2. the custom is to align the 2D image to the left
  3. 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. Press the '3D' button at the top of the page while editing to easily insert the basic code for one.
    2. 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. the custom is to align 3D structure to the right
  3. use an initial scene (by changing the "scene=" parameter) that shows a good overview of the protein
  4. have a descriptive caption
  5. include an interwiki link to the PDB entry in the caption
  6. 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

  1. it is best to sketch out your plan for the page on paper
  2. start with a broad focus that gets increasingly narrow
  3. think about bringing the reader through a tour of the most interesting and important features of your structure
  4. plan for 1 or 2 sections that will feature a structural description with a 3D structure and green scene links
  5. plan for no more than 3 applets on the page in total
  6. plan for a section about how your topic is related to disease, if relevant

Rules to keep in mindRules 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)
  • use wikitext rather than HTML
  • mention all PDB ids whenever appropriate, and link to their page in Proteopedia

Structural DescriptionStructural Description

  1. 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
  2. if the section is short, use a regular applet for the 3D structure (ex: <applet load='1ea5'...)
  3. 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)

ScenesScenes

  1. make a list of the most important structural features of your biomolecule (look at figures from publications about your biomolecule for inspiration)
  2. create a story to lead the reader through the most important structural features of your biomolecule
  3. minimize unnatural jumps
    1. by creating a natural flow between scenes
    2. by using the same PDB structure for consecutive scenes, where possible
  4. use different transitions where appropriate (for tips refer to Proteopedia:How to Make a Scene)
  5. choose text for the green links that relates to the scene
  6. try to minimize the text used for a green scene link (i.e. have a link that is "You can see the of HMGR instead of )
  7. use as few structures as possible
  8. 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
  9. use morphs to illustrate conformational changes
  10. refer to these instructions for making excellent scenes: Proteopedia:How to Make a Scene

ImagesImages

  1. images should ideally be big enough to look at without having to click to enlarge
  2. Upload the image file to Proteopedia using the '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
  3. try to use this style of wikitext for images [[Image:YourImageName|300px|left|thumb| An informative caption here]]
    1. change the caption, size and alignment (left, right, center) as necessary
  4. provide a descriptive caption
  5. if the image is of a PDB entry, provide an interwiki link to that PDB entry in the caption, for example [[Image:1dqa opening.png|300px|left|thumb| Human HMG-CoA Reductase Catalytic Domain, [[1dqa]]]]
  6. 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 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

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 second to last section on the page (the last will be "External Resources")
  3. in the "References" section add this wikitext: <references/>
  4. for more information on how to use references, refer to Help:Editing#Citing_Literature_References
  5. make sure you cite, at the minimum, the most important references

Add Internal LinksAdd Internal Links

  1. if there are topics mentioned in your page that have their own Proteopedia article, make them into interwiki links
    1. example wikitext: [[Hemoglobin]]
  2. 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)

List of all related PDB idsList of all related PDB ids

  1. 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
  2. in this section create an organized list of all other PDB entries of the same protein or biomolecule
  3. try to follow the example here: Ferredoxin

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
  7. 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".

See AlsoSee Also

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eran Hodis, David Canner, Jaime Prilusky, Wayne Decatur, Eric Martz, Karsten Theis, Pooja Rajak
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