Scene authoring tools

The Scene authoring tools are used for the creation and editing of scenes. Scenes created using the Scene authoring tool can then be inserted into Proteopedia pages.

Where are the Scene authoring toolsWhere are the Scene authoring tools

The Scene authoring tools are accessible when you are editing a page. On the edit page, near the top, you'll see a big text area where all the wikitext of the page lives--here you can change the text of the page. If you scroll down some, near the bottom, you'll find in bold letters Scene authoring tools [+/-]. Click on the plus/minus sign to expand and open the Scene authoring tools.

OverviewOverview

The Scene authoring tools are meant to make scene management easier and to make scene creation easier. Scenes are "frozen" moments in Jmol that can be later restored. A scene stores viewpoint, representations, colors, labels, and generally everything that is necessary to recreate the way things looked when the scene was saved.

The steps of using the Scene authoring tools are as follows:

1. Either load an existing scene using the 'load scene' tab, or start fresh with the 'load molecule' tab.
2. Manipulate the scene view using the mouse. Change the scene appearance by choosing selections from your scene using the 'selections' tab and setting the appearance of selections using the 'representations', 'colors' and 'labels' tabs.
3. Save the scene using the 'save scene' tab, and wikitext for inserting the scene into a Protepedia page will be automatically generated.

So the idea is to begin by either loading an existing scene, or by loading a molecule. Once something is loaded onto the Jmol applet, you can begin to change the viewpoint, the representations, the colors, the labels, and other settings, in order to create a scene that conveys your desired message. When you're done creating the scene, you save it and then put it into the page.

'load scene' tab'load scene' tab

The first input box asks for the page name (on which the scene you wish to load resides). The default page name is the name of the page currently being entered. Next, you proceed to choose the scene name using the drop-down selector (all scenes associated with the entered page name will be listed). Once a scene is selected, all of its versions are available for selection using the drop-down version number menu. When a version number is selected, that version of the scene is loaded onto the Jmol applet that is part of the Scene authoring tools and the description that was given to the scene is also recalled. At the same time, the wikitext that is needed for insertion of the scene into the page is displayed.

Each distinct scene has 3 parameters to distinguish it from all other scenes: pagename, scenename, and versionnumber. A scene's "pagename" is automatically determined by the name of the Proteopedia page on which the scene was initially created. The scenename is given by the user. The versionnumber is incremental: If no scene by the given name exists for the given page, then the first version will be version 1. If there exist previous versions of the same scenename on the same pagename, then the newest saved version will not overwrite older versions of the scene, but will instead be automatically saved as the newest version (by incrementing the versionnumber by one). A scene's full name is in this format: Pagename/Scenename/Versionnumber (ex: Hemoglobin/Cavity/14).

Manipulating Jmol with your mouseManipulating Jmol with your mouse

• Rotate: left click
• Zoom: scroll button or left click + shift
• Drag: right click + ctrl
• Measure distance: dbl click on 1st atom, dbl click on 2nd atom
• Measure angle: dbl click on 1st atom, click on 2nd atom, dbl click on 3rd atom
• Measure dihedral angle:' dbl click on 1st atom, click on 2nd and 3rd atoms, dbl click on 4th atom