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Proteopedia is the 3D encyclopedia of proteins and other biological molecules. This is the directory of help pages for visitors and for registered users.

Navigating Proteopedia

Proteopedia is organized like an encyclopedia, with entries (also called pages or articles) on different topics. If you already know the topic you are interested in, you can search for relevant entries using the search box on the left side of the page. For help, go to Help:Searching. You can also browse the entries, starting with the suggestions on the Main Page or the table of contents or the structure index available in the navigation box on the left. Entries have links to other entries (if you right-click them, the current entry will stay available and the linked entry will open in a new tab). This is a way to browse entries on related topics.

Reading and viewing entries

The special feature of Proteopedia entries are the interactive 3D representations of molecules viewable on most pages. They appear in a window integrated into the page (often called "Jmol window"). As you read through the text of an entry, you will find "green links". When you click on them, you stay on the same page but the interactive 3D scene. To learn how to get the most out of the interactive 3D scenes, reference the Viewing guide and the cheat sheet that comes with it. If you encounter technical terms you are unfamiliar with, try searching for them to learn more about them (the About Macromolecular Structure entry is a good start.

Who wrote the entry when?

The section headed "Proteopedia Page Contributors and Editors" (on the bottom of the entry) lists all authors of the entry. If you are interested to learn who wrote what and when the entry was last updated, go to the history tab. Occasionally, the discussion tab contains information about how the entry was created or suggestions for improvement.

Becoming a registered user on Proteopedia

To edit pages or create new ones, you need an account. At the top right of each page, there is a link to login in or request an account. With an account, you can edit pages and create new ones. You will also have a user page to introduce yourself, and access to sandboxes where you can try out creating content.

For authors: contributing content

To get started, read Help:Getting Started in Proteopedia, or watch the videos linked there. You can start editing in a sandbox (see Help:Sandboxes). Before reusing content from others, consult Proteopedia:Guidelines for Ethical Writing for ethical aspects, and Help:Editing#Citing_Literature_References for formatting references. The text on Proteopedia has an open license that encourages remixing with attribution, see Remixing. For some suggestions how to improve the quality of a page, see Proteopedia:How to Make a Page.

For authors: creating 3D scenes

To show a 3D scene, you need structural data (typically from the protein database PDB) and need to decide how to show it. This is described in Proteopedia:DIY:Scenes. The 3D scenes are created and previewed using the Scene authoring tools. If you want to show a structure not in the PDB, you have to upload the structure first (Help:Uploading molecules). Tips how to make 3D scenes that have a lot of information yet are easy to understand is available at Proteopedia:How to Make a Scene.

For authors: multimedia

You can insert static images or animations directly in the text, embed videos, and integrate different data in 3D scenes, see Help:Multimedia. Proteopedia hosts images as long as they come with the appropriate license (see Proteopedia:Terms of Service). For uploading images, see Video Guide 5. For help on formatting the image within the page, see Wiki markup: Images or for even more detail, Wikipedia:Extended image syntax.

For authors: advanced topics

Advanced topics are discussed in Proteopedia:Cookbook, e.g. integrated quizzes (for details, see Help:Quiz), how to construct a URL showing a specific scene, and inserting interactive buttons (for details, see Jmol/Interactivity). Consult Help:Jmol for advanced 3D scenes. To look under the hood of other pages, use the "edit this page" tab. Templates and macros can help to achieve effects with less typing.

For teachers

For Teaching with Proteopedia, a good starting point is Help: Teaching with Proteopedia. Also consult Teaching_Scenes, Tutorials, and Educators' Pages and if applicable, High school teachers' resources. Students might benefit from studying Proteopedia:Primer and Media:Proteopedia tutorial step by step.pdf. If you need a space for students to draft pages, reserve some sandboxes for your students here.

More help? Contact us

Feel free to contact us, or subscribe to and post questions on the Proteopedia:Email list. As a registered user, you can also contact other users (e.g. if you have a question about a page they contributed to) by going to their user page and clicking on "contact this user" on the left side panel. If you encounter error messages, consult Help:Errors.

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Jaime Prilusky, Karsten Theis, Joel L. Sussman, Angel Herraez, Eran Hodis, Wayne Decatur

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