Help:Editing

For edits of text, not involving Proteopedia ScenesFor edits of text, not involving Proteopedia Scenes

Please visit http://en.wikipedia.org/wiki/Wikipedia:Cheatsheet and http://en.wikipedia.org/wiki/Wikipedia:How_to_edit_a_page, as they have a much more complete help reference dealing with wikitext, and Proteopedia uses the same wiki software.

To create or edit Proteopedia ScenesTo create or edit Proteopedia Scenes

"Proteopedia Scenes" are customized molecular views displayed in the Jmol applet. To create them, use the Scene Authoring Tools. After you create a scene, you must insert it using the appropriate wikitext that the Scene Authoring Tools will generate for you. Also if you need to insert an applet or check on the wikitext for a scene, continue reading this page.

There is also a rough and brief, temporary video tutorial available at http://www.weizmann.ac.il/ISPC/Proteopedia.html.

Proteopedia Jmol AppletsProteopedia Jmol Applets

Displaying a Proteopedia Scene requires an instance of the Jmol applet on the page, in order to display the molecular scene. The wikitext for inserting a Jmol applet is automatically generated by the Scene Authoring Tools. However, if you wish to modify an already inserted Jmol applet, or insert a Jmol applet without using the Scene Authoring Tools, type

<applet load='X' size='X' color='X' frame='X' align='X' caption='X' script='X'/>

Each X represents a parameter that you enter. For example, this generates the Jmol applet on this page:

<applet load='1ea5' size='300' color='white' frame='true' align='right' caption='testcaption' />

spinqualitylabelsall models testcaption Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

The order of the parameters does not matter. Explanations of each parameter follow:

load='X'load='X'

Specify a PDB code (ex: load='2ace') to have the applet load the protein with the matching PDB code from the PDB database. Specify a file name (ex: load='2ace.pdb') to have the applet load the file from Proteopedia's uploaded files. If your desired file is not in the PDB database and not yet uploaded to Proteopedia, you may upload it here Special:Upload.

size='X'size='X'

This is the size in pixels of the applet's height and width. It will be square.

color='X'color='X'

Background color.

frame='X'frame='X'

If this value is not 'false' then the Jmol applet will appear on the page surrounded by a frame similar to inserting in image in wikitext and using its "frame" parameter like so: [[Image:someImageName.jpg|frame|someCaption]]. If frame is set to false than no caption can be displayed.

align='X'align='X'

Determines where on the page the Jmol applet should appear. align='right' would have it right-aligned. Options include 'left' and 'center'.

caption='X'caption='X'

This is what will appear under the Jmol applet if frame is not set to 'false'.

script='X'script='X'

The script specified here uses the same format used to specify the "name" parameter when typing the wikitext to insert a scene: Pagename/Scriptname/Versionnumber (ex: script='Hemoglobin/Cavity/14').

Proteopedia ScenesProteopedia Scenes

To insert a scene, type <scene name='PageName/SceneName/Version#'>Text Displayed On Page</scene>

This wikitext for inserting a scene will be automatically generated for you to copy and paste into place when you save a scene using the authoring tools. It will also be automatically generated for you to copy and paste into place when you load a scene using the authoring tools.

Do not put blank spaces in front of the wikitext for a scene if you are putting the wikitext for a scene as the first text on a new line. If you do this, the error will generate boxes with dashed lines on the page.

Jmol extensionJmol extension

The Jmol extension is part of Proteopedia, so all use of the Jmol extension is allowed. Usage and syntax of the Jmol extension.