User:Karsten Theis/Sandbox 2

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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.

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===<i class="fas fa-directions"></i> 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.

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===<i class="fas fa-glasses"></i> 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.

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===<i class="fas fa-user-clock"></i> 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.

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===<i class="fas fa-id-card"></i> 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.

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===<i class="fas fa-user-edit"></i> For authors: contributing content===

Proteopedia entries contain text and 3D scenes (interactive images). Help for editing text is in this section, and help for creating 3D scenes is in the section on the right. 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]]). If you are copying or paraphrasing content from other authors, 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]].

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===<i class="fas fa-cubes"></i> For authors: creating 3D scenes===

Proteopedia entries contain text and 3D scenes (interactive images). Help for creating 3D scenes is in this section, and help for editing text is in the section on the left.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]]/

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=== <i class="fas fa-film"></i> For authors: multimedia===

You can insert static images (and other media) and embed videos. Proteopedia hosts images as long as they come with the appropriate licence (see [[Proteopedia:Terms of Service]]). For uploading images, see [[Proteopedia:Video_Guide#Video_5:_Uploading_an_image_or_file_and_adding_an_image_to_a_page|Video Guide 5]]. For help on formatting the image within the page, see [http://en.wikipedia.org/wiki/Help:Wiki_markup#Images Wiki markup: Images] or for even more detail, [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Wikipedia:Extended image syntax]. Embedding videos is described in the [[Proteopedia:Cookbook]] in the section called [[Proteopedia:Cookbook#Embedded Youtube|Embedded Youtube]].

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===<i class="fas fa-atom"></i> For authors: advanced topics===

Some 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]]). For more help on using Jmol to achieve advanced representations in 3D scenes, see the pages listed under [[Special:Allpages/Jmol]]. To use other entries as examples for your own pages, go to those pages and choose the tab "edit this page" to see the source code. Sometimes, templates [https://proteopedia.org/wiki/index.php?title=Special%3AAllpages&from=Abstract&namespace=10] and [[Proteopedia:Macros|macros]] can help to achieve effects with less typing. If you encounter error messages, consult [[Help:Errors]], feel free to [[#Contact|contact us directly]], or subscribe to, and post questions on the [[Proteopedia:Email list]].

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==<div class="bg-yellow"> <i class="fas fa-chalkboard-teacher"></i> For teachers</div>==

*[[Proteopedia:Practical Guide to Advanced Proteopedia Authoring and Its Use in Teaching]]

* [[Proteopedia:Primer]]

* [[Media:Proteopedia tutorial step by step.pdf]]

*For Teaching with Proteopedia, see [[Teaching_Strategies_Using_Proteopedia|Teaching Strategies Using Proteopedia]] and [[Teaching_Scenes%2C_Tutorials%2C_and_Educators'_Pages|Teaching_Scenes, Tutorials, and Educators' Pages]].

*[[High school teachers' resources]]

*[[Proteopedia:News#Adoptions in College and University Classes|Adoptions in College and University Classes]]

*[[Molecular Workbench]]

*New educational pages may be announced to subscribers to the [[Proteopedia:Email list]].