User:Karsten Theis/Sandbox 2

==Navigating Proteopedia==

==Joining Proteopedia==

*To edit pages or create new ones, you need an account

==For authors: contributing content==

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

==Getting Started Authoring (including Beginners Primer)==

Authoring can be anything from adding a reference to creating a new pag.

* First time here? Learn the basics by either watching the narrated videos in the [[Proteopedia:Video_Guide|Proteopedia Video Guide]] or follow [[Proteopedia:Getting Started|Getting Started in Proteopedia]].

* The [[Proteopedia:Primer|Primer]] guides you step-by-step through creating your first molecular scene. There is also a detailed, step-by-step [[Media:Proteopedia tutorial step by step 4.pdf| walkthrough of a Proteopedia workshop with 4 slides per page]], or same file [[Media:Proteopedia tutorial step by step.pdf| 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 [[Proteopedia:Getting Started|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 [[Proteopedia:How to Make a Page|How to Make a Page]].

*[[Proteopedia:Guidelines for Ethical Writing]] lists guidelines for avoiding plagiarism, for content attribution, and for re-use of images.

* Questions? Stuck? Need help? Feel free to [[#Contact|contact us directly]], or subscribe to, and post questions on the [[Proteopedia:Email list]].

===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 [[Help:Getting Started in Proteopedia|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 [[Proteopedia:Rotating vs still models|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 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 [[Proteopedia:Video_Guide#Video_5:_Uploading_an_image_or_file_and_adding_an_image_to_a_page|Video 5: Uploading an image or file and adding an image to a page]].

*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].

==Teaching==

*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]].

===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]].

[[Image:1ijw-150px-48c.gif|right]]

*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 ([[Help:Copying FirstGlance Scenes into 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 [[Help:Text Directionality|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 [[Create_fast_pages|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. <!--After you save your comments, a banner will appear automatically at the top of the page to alert people to the existence of comments.-->

* [[Proteopedia:Comments_on_Published_Structures|Published Structures with Comments]]

* [[Proteopedia:Comments_on_Articles|Articles with Comments]]

===Errors===

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

==Contact==

Feel free to [[Special:Contact|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 <code>my preferences</code> link at top-right.)

** To use Java occasionally on a one-page basis, add <code>?use=java</code> to the page URL, like this: [http://proteopedia.org/w/G_protein-coupled_receptor?use=java http://proteopedia.org/w/G_protein-coupled_receptor?use=java].

** For a complete description see [[Using_Java_for_Rendering_Structures|Using Java for Rendering Structures]].

==Your Heading Here (maybe something like 'Structure')==

<StructureSection load='4ins' size='340' side='right' caption='Caption for this structure' scene=''>

<scene name='60/609965/B_surface/1'>Chain a as cartoon, chain b as surface</scene>

source http://proteopedia.org/wiki/scripts/Green_Fluorescent_Protein/1ema_gfp_barrel/2.spt

</StructureSection>