Help:Contents
From Proteopedia
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**To keep this page visible, right-click on ''Random'' (Ctrl-click on Macs) and then click on ''Open Link in New Tab''. | **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]]. | *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]]. | ||
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| - | ===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 [[Java#How_to_be_as_safe_as_possible_with_Java|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]]. | ||
===Teaching and Education=== | ===Teaching and Education=== | ||
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*[[Proteopedia:News#Adoptions in College and University Classes|Adoptions in College and University Classes]] | *[[Proteopedia:News#Adoptions in College and University Classes|Adoptions in College and University Classes]] | ||
*[[Molecular Workbench]] | *[[Molecular Workbench]] | ||
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| + | ===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 [[Java#How_to_be_as_safe_as_possible_with_Java|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]]. | ||
Revision as of 15:54, 3 August 2014
Contents |
Using Proteopedia
You can use Proteopedia as a reference resource, without authoring any content yourself.
- 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.
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.
The sections below concern authoring new content, or improving existing content, in Proteopedia.
Getting Started Authoring
- 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.
- 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.
- 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 Page Contributors and Editors (what is this?)
Eric Martz, Jaime Prilusky, Karsten Theis, Joel L. Sussman, Angel Herraez, Eran Hodis, Wayne Decatur
