Help:Contents

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Contents 1 For users: browsing and displaying 1.1 Generic help in using Proteopedia 1.2 Proteopedia Speed 1.3 Teaching and Education 1.4 Software for use with Proteopedia 2 For authors: contributing content 2.1 Getting Started Authoring (including Beginners Primer) 2.2 Creating Molecular Scenes 2.3 Static Images 2.4 Interactive 3D "Supplementary Materials" for Journal Publications 2.5 Protecting Pages 2.6 Languages 2.7 Proteopedia Speed

For users: browsing and displaying

You can use Proteopedia as a reference resource, without authoring any content yourself.

Generic help in using Proteopedia

• For assistance with searching for something in Proteopedia, try Help:Searching.
• Browse Proteopedia's Table of Contents.
• Check out the Structure Index.
• Each of the >100,000 macromolecular models in the Protein Data Bank has a page in Proteopedia. To see some examples, click on Random in the navigation box on the left side of this page (in Safari, it is at the left bottom).
  • To keep this page visible, right-click on Random (Ctrl-click on Macs) and then click on Open Link in New Tab.
• For definitions of terms, and explanations of concepts in structural biology, see About Macromolecular Structure. Many articles are listed there, for example Amino Acids and Resolution.

Proteopedia Speed

• Render faster: If you have Java available on your computer, molecular models in Proteopedia pages will be rendered faster:
  • If you are a registered user you can set the use of Java as a default, in one of the preferences in your personal profile. (Visit the my preferences link at top-right.)
  • To use Java occasionally on a one-page basis, add ?use=java to the page URL, like this: http://proteopedia.org/w/G_protein-coupled_receptor?use=java.
  • For a complete description see Using Java for Rendering Structures.

Teaching and Education

• For Teaching with Proteopedia, see Teaching Strategies Using Proteopedia and Teaching_Scenes, Tutorials, and Educators' Pages.
• High school teachers' resources
• Adoptions in College and University Classes
• Molecular Workbench

Software for use with Proteopedia

• Java can be used to improve performance of molecular scenes in Proteopedia. Please see Installing and enabling Java.
• Java may be a security risk. Please see How to be as safe as possible with Java.
• Any molecule that you see in Proteopedia can be explored further using FirstGlance in Jmol. Every page titled with a PDB identification code has a link to explore that model in FirstGlance.

For authors: contributing content

The sections below concern authoring new content, or improving existing content, in Proteopedia.

Getting Started Authoring (including Beginners Primer)

• First time here? Learn the basics by either watching the narrated videos in the Proteopedia Video Guide or follow Getting Started in Proteopedia.
• The Primer guides you step-by-step through creating your first molecular scene. There is also a detailed, step-by-step walkthrough of a Proteopedia workshop, or same file walkthrough of a Proteopedia workshop with one slide per page.

Image:Proteopedia tutorial step by step 4.pdf

• We recommend that the first page you try editing in Proteopedia should be a Sandbox page, as explained in Getting Started in Proteopedia. Please see Help:Sandboxes for an explanation, and instructions on how to create a Sandbox page for your own use.
• For editing help, try Help:Editing, which explains, among other things, how to easily insert references to scientific literature citations using PubMed ID numbers, without typing the reference itself! See also How to Make a Page.
• Proteopedia:Guidelines for Ethical Writing lists guidelines for avoiding plagiarism, for content attribution, and for re-use of images.

Creating Molecular Scenes

• For step-by-step instructions on creating example molecular scenes, try Proteopedia:DIY:Scenes.
• If your molecular scenes require a model that is not published in the Protein Data Bank, see Help:Uploading molecules. See also Biological Unit: Showing and instructions for hiding portions of a model at Getting Started.
• If you save a page and get XML Error: Mismatched tag at line 1, don't worry, you can recover your page: see Help:Errors.
• For simple recipes for including Flash, Imagemap, Floating quote Box, Movies (.mov, .mpeg) etc., try Proteopedia:Cookbook.

Static Images

• To show a static image (jpeg, png, gif) file in a Proteopedia page, first you need to be sure you have the right to share the image and allow unrestricted re-use by others (see Proteopedia:Terms of Service). If yes, then you need to upload the image into Proteopedia: see Video 5: Uploading an image or file and adding an image to a page.
• For help on formatting the image within the page, see Wiki markup: Images or for even more detail, Wikipedia:Extended image syntax.

Interactive 3D "Supplementary Materials" for Journal Publications

• For preparing interactive 3D complements to journal publications (similar to supplementary materials), please see Interactive 3D Complements in Proteopedia.
• For hiding these until the date of publication, please see Proteopedia:Workbench.

Protecting Pages

• If you would like to protect a personal page from editing by others, please see Proteopedia:Policy and Help:Protected_Pages.

Languages

• For examples of Proteopedia articles in non-English languages, and for the rules and policies for such articles, please see Proteopedia:Languages. *For instructions for translating articles to other languages, see Help:Language Translation.
• See also Text Directionality regarding right-to-left languages such as Arabic or Hebrew.

Proteopedia Speed

• Proteopdia will render faster in your computer if you enable the use of Java (see above).
• Create fast pages: Following these simple tips your Proteopedia pages might load and render faster.