User:Mary Ball/Scenes: Difference between revisions
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==Where are the ''Scene authoring tools''== | ==Where are the ''Scene-authoring tools''?== | ||
A good place to start is the [[Proteopedia:Video_Guide#Video_7:_Adding_scenes_.28green_links.29|Video on Adding Scenes]]. | A good place to start is the [[Proteopedia:Video_Guide#Video_7:_Adding_scenes_.28green_links.29|Video on Adding Scenes]]. | ||
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=='load scene' tab== | ==Using the 'load scene' tab to edit an existing scene== | ||
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. | 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). | 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). | ||
=='load molecule' tab== | ==Using the 'load molecule' tab to "start fresh" to create a scene== | ||
[[Image:Load_molecule.png|thumb|The load molecule tab in action]] | [[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). | 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). | ||
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The "currently loaded" text area displays the name of the currently loaded file in the Jmol applet of the "Scene authoring tools". | The "currently loaded" text area displays the name of the currently loaded file in the Jmol applet of the "Scene authoring tools". | ||
=='selections' tab== | ==Using the 'selections' tab== | ||
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. | 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. | ||
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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. | 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. | ||
=='representations' tab== | ==Using the options under the 'representations' tab== | ||
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 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. | ||
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Clicking on 'hide selection' turns off all representations for the selection. | Clicking on 'hide selection' turns off all representations for the selection. | ||
=='colors' tab== | ==Using the tools under the 'colors' tab== | ||
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 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. | ||
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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 '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. | ||
=='labels' tab== | ==Using the tools under the 'labels' tab== | ||
The first area is the 'all or nothing and halo toggle' area. This provides a button to select all atoms, disselect all atoms (select none), and a checkbox to turn selection halos on or off. | The first area is the 'all or nothing and halo toggle' area. This provides a button to select all atoms, disselect all atoms (select none), and a checkbox to turn selection halos on or off. | ||
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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. | 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. | ||
=='save scene' tab== | ==Using the 'save scene' tab== | ||
Once you have created your scene, you can save it here. | Once you have created your scene, you can save it here. | ||
