User:Mary Ball/Scenes: Difference between revisions
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==Overview== | {{STRUCTURE_1acj| PDB=1acj | SCENE= }} | ||
On the right is a JMol applet showing the crystal structure of ''[http://en.wikipedia.org/wiki/Torpedo_californica Torpedo californica]'' [[acetylcholinesterase]] (''Tc''AChE) complexed with [http://en.wikipedia.org/wiki/Tacrine tacrine]. | |||
To zoom in on acetylcholinesterase's active site, click on the following green phrase: <scene name='1acj/Active_site_of_1acj/2'>AChE's active site</scene>. | |||
Clicking on the green phrase triggers a transition to what is called a Scene. For more information on creating and using scenes in Proteopedia pages, see the rest of this Tutorial. | |||
=='''Overview'''== | |||
===What are scenes?=== | |||
Scenes are "frozen" moments in Jmol that can be later accessed by the page-viewer by clicking on "green text". A scene stores viewpoint, representations, colors, labels, and generally everything that is necessary to recreate the way things looked when the scene was saved. | Scenes are "frozen" moments in Jmol that can be later accessed by the page-viewer by clicking on "green text". 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 '''Scene authoring tools''' are used for the creation and editing of | The '''Scene authoring tools''' are used for the creation and editing of scenes. Scenes created using the ''Scene authoring tools'' can then be inserted into [[Proteopedia]] pages. | ||
The basic steps of using the ''Scene authoring tools'' are as follows: | The basic steps of using the ''Scene authoring tools'' are as follows: | ||
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===Additional Resources=== | ===Additional Resources=== | ||
A good place to start is the [[Proteopedia:Video_Guide#Video_7:_Adding_scenes_.28green_links.29| | A good place to start is the [[Proteopedia:Video_Guide#Video_7:_Adding_scenes_.28green_links.29|Video on Adding Scenes]]. | ||
Next you may want to look at the [[Proteopedia:DIY:Scenes|Instructions for creating a molecular scene with Proteopedia's Scene Authoring Tools]]. This gives you step-by-step directions to recreate the sample scene. | |||
=='''Where are the ''Scene-authoring tools''?'''== | |||
===Accessing the Scene-authoring Tools=== | |||
The ''Scene authoring tools'' are accessible when you are editing a page. Click the tab '''edit this page''' at the top of the page where you wish to create a molecular scene. On the edit page, near the top, you'll see a big box 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 [show]'''. Click on '''show''' to expand and open the ''Scene authoring tools''. | The ''Scene authoring tools'' are accessible when you are editing a page. Click the tab '''edit this page''' at the top of the page where you wish to create a molecular scene. On the edit page, near the top, you'll see a big box 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 [show]'''. Click on '''show''' to expand and open the ''Scene authoring tools''. | ||
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--> | --> | ||
==Using the 'load scene' tab to edit an existing scene== | ===How can I preview the results of using the Scene-authoring Tools?=== | ||
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. | |||
=='''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). | ||
==Using the 'load molecule' tab to "start fresh" to create a scene== | =='''Using the 'load molecule' tab to "start fresh" to create a scene'''== | ||
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). | ||
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 | 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 through [http://bip.weizmann.ac.il/oca-bin/ocamain OCA]. | ||
To load a file that is not part of the PDB, first upload the file to Proteopedia at [[Special:Upload]] (you can get there also by using the link called 'upload file' on the left hand column-toolbar of Proteopedia). Do NOT upload any image from a scientific publication or website unless you have permission to display that image on Proteopedia. Uploading an image that you have created or a PDB file that you have modified is always okay. | |||
Once a file has been uploaded, you can specify its name in the input area next to the words "From Proteopedia uploaded file" and click load. | |||
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". | ||
==Using the '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. | ||
==Using the options under the '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. | ||
==Using the tools under the '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. | ||
==Using the tools under the '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, | The first area is the 'all or nothing and halo toggle' area. This provides a button to select all atoms, deselect all atoms (select none), and a checkbox to turn selection halos on or off. | ||
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 '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. | ||
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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. | ||
==Using the '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. | ||
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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). | 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). | ||
After saving, wikitext for inserting your scene into the Proteopedia page will appear in the 'Wikitext' area. | After saving, wikitext for inserting your scene into the Proteopedia page will appear in the 'Wikitext' area. Copy this and paste it into the text-editing window. (To preview its effect on the page and/or save the edited page, you must hide the Scene-authoring tools to make the '''Save page''' and '''Show preview''' buttons active.) | ||
=== | ===Choosing a non-standard scene transition=== | ||
If you select the checkbox entitled ' | If you select the checkbox entitled 'show scene transition options', you get two choices for non-standard transitions. This means you can choose different transitions for how your scene will be recalled when the user clicks on the green scene link. Here's the breakdown of transition options: | ||
# If you don't select any checkbox (i.e. do not select the checkbox next to "show advanced options") then the most basic and standard transition will be used : when the scene is recalled, the molecule will zoom out to 100% zoom, rotate to the new scene's orientation, and then zoom to the new scene's correct zoom. | # If you don't select any checkbox (i.e. do not select the checkbox next to "show advanced options") then the most basic and standard transition will be used : when the scene is recalled, the molecule will zoom out to 100% zoom, rotate to the new scene's orientation, and then zoom to the new scene's correct zoom. | ||
