Help:Contents

For users: browsing and displayingFor users: browsing and displaying

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

• Overview of Proteopedia's Users, Modes and Areas

Generic help in using ProteopediaGeneric 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 ~150,000 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.
  • 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 SpeedProteopedia 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 EducationTeaching 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
• New educational pages may be announced to subscribers to the Proteopedia:Email list.

Software for use with ProteopediaSoftware 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)

For authors: contributing contentFor authors: contributing content

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

Getting Started Authoring (including Beginners Primer)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 with 4 slides per page, or same file walkthrough of a Proteopedia workshop with 1 slide per page.
• 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 ScenesCreating 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.
• If rotating model looks different than the still rendering read Rotating vs still models
• For simple recipes for including Flash, Imagemap, Floating quote Box, Movies (.mov, .mpeg) etc., try Proteopedia:Cookbook.
• If you do not see the Scene Authoring Tool (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).

Static ImagesStatic 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 PublicationsInteractive 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 PagesProtecting Pages

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

LanguagesLanguages

• 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 SpeedProteopedia 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.

CommentsComments

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

ContactContact

Feel free to contact us with any questions or suggestions.