User:Karsten Theis/Sandbox 2

From Proteopedia

Revision as of 20:50, 11 February 2021

Proteopedia is the 3D encyclopedia of proteins and other biological molecules.

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), which is a way to browse entries on related topics.

• Help:Searching
• Proteopedia:Table_of_Contents
• Structure Index
• Protein database All pages

Users, Modes and Areas

• Right-click browsing

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.

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.

• Viewing guide
• History and discussion tabs
• Looking up technical terms at About Macromolecular Structure

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

Proteopedia entries contain text and 3D scenes (interactive images). Help for general editing is in this section, and specifically for 3D scenes are in the next section.

• Help:Editing
• Help:Sandboxes How to Make a Page.
• Proteopedia:Cookbook
• Proteopedia:How to Make a Page
• Proteopedia:Guidelines for Ethical Writing
• Remixing

For authors: creating 3D scenes

• Scene authoring tools
• Proteopedia:DIY:Scenes
• Proteopedia:How to Make a Scene
• Help:Quiz

• Proteopedia:Video_Guide
• Proteopedia:Getting Started.
• Proteopedia:DIY:Scenes
• Help:Uploading molecules
• Biological Unit: Showing
• Help:Errors
• Proteopedia:Rotating vs still models
• Proteopedia:Cookbook
• SAT) when editing a page: please disable 'Show preview on first edit' in the 'Editing' tab within 'my preferences'. Additionally, the SAT will never be displayed while the editing changes are being previewed (you clicked on the 'Show Preview' button).

For authors: multimedia

You can insert static images (and other media) and embed videos.

• 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.

For teachers

• 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 and Teaching_Scenes, Tutorials, and Educators' Pages.
• High school teachers' resources
• Adoptions in College and University Classes
• Molecular Workbench
• New educational pages may be announced to subscribers to the Proteopedia:Email list.

• Questions? Stuck? Need help? Feel free to contact us directly, or subscribe to, and post questions on the Proteopedia:Email list.

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.
  • Molecular views obtained in FirstGlance can become green links in Proteopedia (Instructions).
• You can make presentation-ready animations that can be dropped into Powerpoint slides from any scene in Proteopedia or FirstGlance. See Help:Making animations for Powerpoint. (At right: 1ijw)

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

• Proteopedia 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.

Comments

Users of Proteopedia are invited to comment on published structures. Comments can raise questions about the interpretation, validity or quality of the model, cite other pertinent resources, congratulate the authors on a job well done, discuss implications of the model, etc.

How to comment on articles or published structures: Log in to Proteopedia and add your comment by editing the discussion tab associated with each page. You can comment on any page in Proteopedia.

• Published Structures with Comments
• Articles with Comments

Errors

See Help:Errors for guidelines on how to proceed when your page seems gone forever.

Contact

Feel free to contact us with any questions or suggestions.

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.

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