Help:Contents

From Proteopedia

Revision as of 08:07, 14 May 2015

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 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 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.

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

• 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.