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==<big>To create or edit Proteopedia Scenes</big>== | ==<big>To create or edit Proteopedia Scenes</big>== | ||
"Proteopedia Scenes" are customized molecular views displayed in the Jmol applet. Before you can create or edit a scene, there must be a Jmol applet already on the current page. Instructions for inserting a new applet are in the next section below. When there is a Jmol applet present in the page, you create new scenes (green links) by using the [[Scene authoring tools|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. | "Proteopedia Scenes" are customized molecular views displayed in the Jmol structure applet. Before you can create or edit a scene, there must be a Jmol structure applet already on the current page. Instructions for inserting a new structure applet are in the next section below. When there is a Jmol structure applet present in the page, you create new scenes (green links) by using the [[Scene authoring tools|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. | ||
'''SCENE TUTORIAL MOVIE:''' There is a video tutorial available at [[Proteopedia:Video Guide]] | '''SCENE TUTORIAL MOVIE:''' There is a video tutorial available at [[Proteopedia:Video Guide]] | ||
When there is more than one Jmol applet on a page, scenes automatically go to the applet above the <nowiki><scene ...>...</scene></nowiki> tag in the wikitext. | When there is more than one Jmol structure applet on a page, scenes automatically go to the applet above the <nowiki><scene ...>...</scene></nowiki> tag in the wikitext. | ||
==Proteopedia Jmol Applets== | ==Proteopedia Jmol Structure 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 structure applet must be entered on the page following the format below. The simplest way to get the wikitext for a structure applet is by clicking the "3D" button just above the wikitext area when editing a page. (Or you could copy and paste the applet wikitext from a different page, and then edit the parameters. You may sometimes see 'applet' in place of 'Structure' at the start of the code on older pages as this is the form, which still works. ) | Displaying a Proteopedia Scene requires an instance of the Jmol structure applet on the page, in order to display the molecular scene. The wikitext for inserting a Jmol structure applet must be entered on the page following the format below. The simplest way to get the wikitext for a structure applet is by clicking the "3D" button just above the wikitext area when editing a page. (Or you could copy and paste the structure applet wikitext from a different page, and then edit the parameters. You may sometimes see 'applet' in place of 'Structure' at the start of the code on older pages as this is the form, which still works. ) | ||
: <nowiki><Structure load='Insert PDB code or filename here' size='X' frame='X' align='X' caption='Insert caption here' scene='Insert optional scene name here' /></nowiki> | : <nowiki><Structure load='Insert PDB code or filename here' size='X' frame='X' align='X' caption='Insert caption here' scene='Insert optional scene name here' /></nowiki> | ||
Parameters that you can enter are represented by descriptions of what you need to enter or an 'X' (and many of them are Optional). For example, this generates the Jmol applet on this page: | Parameters that you can enter are represented by descriptions of what you need to enter or an 'X' (and many of them are Optional). For example, this generates the Jmol structure applet on this page: | ||
: <nowiki><Structure load='1ea5' size='300' color='white' frame='true' align='right' caption='testcaption' /></nowiki> | : <nowiki><Structure load='1ea5' size='300' color='white' frame='true' align='right' caption='testcaption' /></nowiki> | ||
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====load='Insert PDB code or filename here' ==== | ====load='Insert PDB code or filename here' ==== | ||
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]]. | Specify a [[PDB code]] (ex: load='2ace') to have the structure applet load the protein with the matching PDB code from the [[PDB]] database. Specify a file name (ex: load='2ace.pdb') to have the structure 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'==== | ||
Optional (default value is 400 pixels). | Optional (default value is 400 pixels). | ||
This is the size in pixels of the applet's height and width. It will be square. | This is the size in pixels of the structure applet's height and width. It will be square. | ||
====frame='X'==== | ====frame='X'==== | ||
Optional (default value is 'true'). | Optional (default value is 'true'). | ||
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: <nowiki>[[Image:someImageName.jpg|frame|someCaption]]</nowiki>. If frame is set to false than no caption can be displayed. | If this value is not 'false' then the Jmol structure applet will appear on the page surrounded by a frame similar to inserting in image in wikitext and using its "frame" parameter like so: <nowiki>[[Image:someImageName.jpg|frame|someCaption]]</nowiki>. If frame is set to false than no caption can be displayed. | ||
====align='X'==== | ====align='X'==== | ||
Optional and only relevant if the frame parameter is set to true. | Optional and only relevant if the frame parameter is set to true. | ||
Determines where on the page the Jmol applet should appear. align='right' would have it right-aligned. Options include 'left' and 'center'. | Determines where on the page the Jmol structure applet should appear. align='right' would have it right-aligned. Options include 'left' and 'center'. | ||
====caption='Insert caption here'==== | ====caption='Insert caption here'==== | ||
Optional and only relevant if the frame parameter is set to true. | Optional and only relevant if the frame parameter is set to true. | ||
This is what will appear under the Jmol applet if frame is not set to 'false'. | This is what will appear under the Jmol structure applet if frame is not set to 'false'. | ||
====scene='Insert optional scene name here'==== | ====scene='Insert optional scene name here'==== | ||
Optional. | Optional. | ||
If you specify a scene using the "scene" parameter, when your page is loaded, the applet will immediately load this scene. | If you specify a scene using the "scene" parameter, when your page is loaded, the structure applet will immediately load this scene. | ||
The scene specified here uses the same format used to specify the "name" parameter when typing the wikitext to insert a scene: Pagename/Scriptname/Versionnumber (ex: scene='Hemoglobin/Cavity/14'). | The scene specified here uses the same format used to specify the "name" parameter when typing the wikitext to insert a scene: Pagename/Scriptname/Versionnumber (ex: scene='Hemoglobin/Cavity/14'). | ||
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Optional. | Optional. | ||
This sets the name of the applet. This is useful if you wish to have a green scene link act on a specific applet that is not the applet directly above the green scene link. See section entitled "More than one Jmol applet on a page" below for more information. | This sets the name of the structure applet. This is useful if you wish to have a green scene link act on a specific applet that is not the structure applet directly above the green scene link. See section entitled "More than one Jmol structure applet on a page" below for more information. | ||
==Proteopedia Scenes== | ==Proteopedia Scenes== | ||
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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. | 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. | ||
===More than one Jmol applet on a page=== | ===More than one Jmol structure applet on a page=== | ||
When there is more than one Jmol applet on a page, scenes automatically go to the applet above the <nowiki><scene ...>...</scene></nowiki> tag in the wikitext. | When there is more than one Jmol structure applet on a page, scenes automatically go to the applet above the <nowiki><scene ...>...</scene></nowiki> tag in the wikitext. | ||
If you wish to have a green scene link act on a specific applet that is not the applet directly above the green scene link, then you must set the "target" parameter inside the wikitext for a scene link like so: <nowiki><scene name='PageName/SceneName/Version#' target=' | If you wish to have a green scene link act on a specific structure applet that is not the applet directly above the green scene link, then you must set the "target" parameter inside the wikitext for a scene link like so: <nowiki><scene name='PageName/SceneName/Version#' target='StructureAppletName'>Text Displayed On Page</scene></nowiki> where " target='StructureAppletName' " tells this scene link to act on the structure applet with the name 'StructureAppletName' on the page (set by using the structure applet's "name" parameter in the applet's wikitext). If the structure applet you wish to target has not been given a name using the name parameter, you may instead set target to the applet's number. For instance setting target='2' would have the green scene link act on the 3rd structure applet on the page, because by default, if applets are not given names, they take the sequential names 0, 1, 2, ... in the order in which the structure applets appear on a page. | ||
==Setting the initial scene in the Structure Box of a PDB entry page== | ==Setting the initial scene in the Structure Box of a PDB entry page== | ||
The wikitext that draws the big "Structure Box", as we like to call it, on each PDB entry page with the 3D applet with all of the functional annotation and other information in one big box looks like this: | The wikitext that draws the big "Structure Box", as we like to call it, on each PDB entry page with the 3D structure applet with all of the functional annotation and other information in one big box looks like this: | ||
'''<nowiki>{{STRUCTURE_3cs9| PDB=3cs9 | SCENE= }}</nowiki>''' | '''<nowiki>{{STRUCTURE_3cs9| PDB=3cs9 | SCENE= }}</nowiki>''' | ||
You may know that to add a 3D applet to the page, you can click the "3D" button above the wikitext area, and you get wikitext that looks like this, and gives you a 3D applet on the page | You may know that to add a 3D structure applet to the page, you can click the "3D" button above the wikitext area, and you get wikitext that looks like this, and gives you a 3D structure applet on the page | ||
'''<nowiki><Structure load='Insert PDB code or filename here' size=' | '''<nowiki><Structure load='Insert PDB code or filename here' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /></nowiki>''' | ||
The "Structure Box" is different than the plain applet in that it includes the 3D applet as well as all the other information that you get inside the 'Structure Box' you find on each PDB entry page (like functional information and links to that PDB entry in other resources). You get a bit less flexibility with the Structure Box, as the only parameters you can change are the PDB id and the starting Scene. The wikitext for scenes that you want to create inside the text of a page are generated automatically for you when you create a scene, and that looks something like this: | The "Structure Box" is different than the plain structure applet in that it includes the 3D structure applet as well as all the other information that you get inside the 'Structure Box' you find on each PDB entry page (like functional information and links to that PDB entry in other resources). You get a bit less flexibility with the Structure Box, as the only parameters you can change are the PDB id and the starting Scene. The wikitext for scenes that you want to create inside the text of a page are generated automatically for you when you create a scene, and that looks something like this: | ||
'''<nowiki><scene name='3cs9/Overall_structure/1'>TextToBeDisplayed</scene></nowiki>''' | '''<nowiki><scene name='3cs9/Overall_structure/1'>TextToBeDisplayed</scene></nowiki>''' | ||
