User:Mary Ball/Scenes: Difference between revisions

After you load an existing scene or "start fresh" to create a new scene, a Jmol applet window will open on the right side of the '''Scene-authoring tools''' window.  As you make changes, they will show up in this window, leading up to the point where you use the 'save scene' tab to save the scene.  But to put the scene into your page and preview how it will look there, you must copy the wikitext that is created when you save the scene and then hide the Scene-authoring tools to enable the '''Save Page''' and '''Show Preview''' buttons.

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).

[[Image:Load_molecule.png|thumb|The load molecule tab in action]]

The load molecule tab is used to load molecules into Jmol. Currently only one file can be loaded into Jmol at a time through this interface (but Jmol can handle several files at a time).

To load a file that has PDB code, input a PDB code into the first input area and click the load button.  The file will be fetched from the PDB database throgh [http://bip.weizmann.ac.il/oca-bin/ocamain OCA].

The "currently loaded" text area displays the name of the currently loaded file in the Jmol applet of the "Scene authoring tools".

The selections tab is meant to be used to select particular groups of atoms so that you can later change that group's color, representations, or labels.  When you choose a representation, a color, or a label using the ''Scene authoring tools'' other tabs, the change is almost always applied ONLY to the currently selected atoms.  That is why it is important to be aware of what atoms are selected at any given time.

Choosing 'default' sets it so that mouse clicks on the Jmol applet are set to their default setting in Jmol.  In the default setting, clicking does not select or deselect any atoms, but clicking to create measurements is enabled.  Choosing 'center' makes it so that any click on an atom, centers both the view and the axis of rotation on the atom.  Choosing 'atom' is perhaps the most useful setting for creating selections as each click on an atom either adds it to the selection, or if it is already part of the selection, removes it from the selection.  Choosing 'element' makes it so that clicking on an atom will select all other atoms of the same element.  Choosing 'molecule' makes it so that clicking on an atom selects all other atoms of the same molecule.

The first area is the 'all and halo toggle' area.  This provides a button to select all atoms, and a checkbox to turn selection halos on or off.

Clicking on 'hide selection' turns off all representations for the selection.

The first area is the 'all and halo toggle' area.  This provides a button to select all atoms, and a checkbox to turn selection halos on or off.

The 'transparency' area allows you to render your selection transparent.  Zero percent transparent will be opaque,  100 percent transparent will be invisible, and anywhere in between will be transparent to a degree.

The 'mouse click selects' area is similar to the 'mouse click selects' area in the 'selections' tab and allows changing between the 'default' mouse picking style and the 'atom' mouse picking style.  See the 'selections' tab section above for an explanation about the different mouse picking styles.

The 'bonds' area allows control over disulfide and hydrogen bonds.  You can turn disulfide and/or hydrogen bonds on or off for a particular selection and can choose the colors for the bonds.  

Once you have created your scene, you can save it here.

You must choose a name for your scene, and enter a description.  If you started by loading a scene, then by default, its name will appear as a suggested name for the scene you are about to save because Proteopedia assumes you might be editing a scene to save an updated version.  If you specify the name of a scene that already exists, then your scene will be saved as the newest version (i.e. if versions 1 through 5 for that scene already exist, then your scene will be saved as version 6).

===Choosing a non-standard scene transition===