Molecular Playground/Authoring - Revision history

Eric Martz: /* Notes and References */

Eric Martz — Sun, 20 Jan 2013 22:44:02 GMT

Notes and References

←Older revision		Revision as of 22:44, 20 January 2013
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	==Notes and References==		==Notes and References==
	<references />		<references />
		+
		+	==See Also==
		+	* [[Molecular Playground]]
		+	* [[CBI Molecules]]

	[[Category: Molecular Playground]]		[[Category: Molecular Playground]]

Eric Martz: /* Facilitate rotation by onlookers */

Eric Martz — Mon, 03 Oct 2011 16:27:42 GMT

Facilitate rotation by onlookers

←Older revision		Revision as of 16:27, 3 October 2011
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	===Facilitate rotation by onlookers===		===Facilitate rotation by onlookers===

-	MP invites onlookers to interact by rotating the structure at any time. Therefore, scripts should be designed to permit rotation as much of the time as possible. Furthermore, it may be desirable for the ~~user~~-set orientation to remain while the script proceeds, perhaps all the way to the end of the script. ~~For example,~~ a ''moveto'' command precludes rotation until the specified orientation is completed. In the version of Jmol currently used in Proteopedia (11.8.9 in December, 2009), ''zoomto'' commands also enforce the current orientation, "fighting" with the onlooker who attempts rotation during the timed zoomto. Therefore, the support script provided for MP includes a function ''zoomRotatableTo()'' that performs the zoom while permitting rotation.	+	MP invites onlookers to interact by rotating the structure at any time. Therefore, scripts should be designed to permit rotation as much of the time as possible. Furthermore, it may be desirable for the onlooker-set orientation to remain while the script proceeds, perhaps all the way to the end of the script. One command that goes counter to this goal is a ''moveto'' command, which precludes rotation until the specified orientation is completed. In the version of Jmol currently used in Proteopedia (11.8.9 in December, 2009), ''zoomto'' commands also enforce the current orientation, "fighting" with the onlooker who attempts rotation during the timed zoomto. Therefore, the support script provided for MP includes a function ''zoomRotatableTo()'' that performs the zoom while permitting rotation.

	===Avoid displays that seriously slow Jmol===		===Avoid displays that seriously slow Jmol===

Eric Martz: /* Technical (All Three Levels) */

Eric Martz — Wed, 13 Apr 2011 16:01:05 GMT

Technical (All Three Levels)

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	* PlaygroundContentPath # the path on the MP server to your .spt and .pdb files. The filename must be appended to this.		* PlaygroundContentPath # the path on the MP server to your .spt and .pdb files. The filename must be appended to this.
	* PlaygroundSupportScriptPath # the path on the MP server to MPSupportVersion01.spt and MPSceneVersion01.spt. The filename must be appended.		* PlaygroundSupportScriptPath # the path on the MP server to MPSupportVersion01.spt and MPSceneVersion01.spt. The filename must be appended.
		+
		+	<!-- Adam plans in April 2011 that these will become:
		+	PlaygroundModelPath
		+	PlaygroundScriptPath
		+	PlaygroundSupportPath
		+	-->

	==Web Pages==		==Web Pages==

Eric Martz: /* Level I: A single script file */

Eric Martz — Tue, 16 Mar 2010 12:50:44 GMT

Level I: A single script file

←Older revision		Revision as of 12:50, 16 March 2010
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	There are two ways to prepare the script file.		There are two ways to prepare the script file.
-	* In Proteopedia, using its [[SAT\|Molecular Scene Authoring Tool]]. You don't need to be familiar with Jmol command scripting language. You save the "state script" from Jmol in Proteopedia.	+	* '''Recommended:''' In Proteopedia, using its [[SAT\|Molecular Scene Authoring Tool]]. You don't need to be familiar with Jmol command scripting language. You save the "state script" from Jmol in Proteopedia.
		+	** An '''example''' of a web page created by this method is [[Molecular Playground/Relenza]].
	** '''Instructions for creating your custom scene and saving the state script are in [[Molecular_Playground/Procedures]].'''		** '''Instructions for creating your custom scene and saving the state script are in [[Molecular_Playground/Procedures]].'''
	**''' Instructions for creating your web page are below, under [[#Web Page Procedure in Proteopedia]].'''		**''' Instructions for creating your web page are below, under [[#Web Page Procedure in Proteopedia]].'''
-	* By hand. This requires familiarity with the [http://chemapps.stolaf.edu/jmol/docs/ Jmol Command Scripting Language]. No instructions are provided here for this method, either for constructing the script file, or for making a supporting web page. See [[#Technical (All Three Levels)]] below for how your script will operate on MP.	+
		+	* '''For Advanced Jmol Users:''' By hand. This requires familiarity with the [http://chemapps.stolaf.edu/jmol/docs/ Jmol Command Scripting Language]. No instructions are provided here for this method, either for constructing the script file, or for making a supporting web page. See [[#Technical (All Three Levels)]] below for how your script will operate on MP.

	===Level II: A Single Molecular Scene With A Color Key===		===Level II: A Single Molecular Scene With A Color Key===

Eric Martz: /* Technical (All Three Levels) */

Eric Martz — Tue, 16 Mar 2010 12:44:33 GMT

Technical (All Three Levels)

←Older revision		Revision as of 12:44, 16 March 2010
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	===Technical (All Three Levels)===		===Technical (All Three Levels)===
		+
		+	MP takes responsibility for loading the PDB file before your script is run, and it adds a delay after your script is run so that your scene will spin for a while before a repeat cycle of your script, or a different script, is run. For all three levels, MP defines the following variables before any master script is run:
		+	* PlaygroundProjection = true; # this if false if undefined
		+	* PlaygroundContentPath # the path on the MP server to your .spt and .pdb files. The filename must be appended to this.
		+	* PlaygroundSupportScriptPath # the path on the MP server to MPSupportVersion01.spt and MPSceneVersion01.spt. The filename must be appended.

	==Web Pages==		==Web Pages==

Eric Martz: /* Level I: A single script file */

Eric Martz — Tue, 16 Mar 2010 12:44:11 GMT

Level I: A single script file

←Older revision		Revision as of 12:44, 16 March 2010
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	** '''Instructions for creating your custom scene and saving the state script are in [[Molecular_Playground/Procedures]].'''		** '''Instructions for creating your custom scene and saving the state script are in [[Molecular_Playground/Procedures]].'''
	**''' Instructions for creating your web page are below, under [[#Web Page Procedure in Proteopedia]].'''		**''' Instructions for creating your web page are below, under [[#Web Page Procedure in Proteopedia]].'''
-	* By hand. This requires familiarity with the [http://chemapps.stolaf.edu/jmol/docs/ Jmol Command Scripting Language]. No instructions are provided here for this method, either for constructing the script file, or for making a supporting web page.	+	* By hand. This requires familiarity with the [http://chemapps.stolaf.edu/jmol/docs/ Jmol Command Scripting Language]. No instructions are provided here for this method, either for constructing the script file, or for making a supporting web page. See [[#Technical (All Three Levels)]] below for how your script will operate on MP.
-		+
-	~~'''~~Technical~~''': MP takes responsibility~~ for ~~loading the PDB file before~~ your script ~~is run, and it adds a delay after your script is run so that your scene~~ will ~~spin for a while before a repeat cycle of your script, or a different script, is run. For all three levels, MP defines the following variables before any master script is run:~~	+
-	* PlaygroundProjection = true; # this if false if undefined	+
-	* PlaygroundContentPath # the path on the MP server to your .spt and .pdb files. The filename must be appended to this.	+
-	* PlaygroundSupportScriptPath # the path on ~~the~~ MP ~~server to MPSupportVersion01.spt and MPSceneVersion01.spt. The filename must be appended~~.	+

	===Level II: A Single Molecular Scene With A Color Key===		===Level II: A Single Molecular Scene With A Color Key===

Eric Martz: /* Level III: A Complex Animation */

Eric Martz — Tue, 16 Mar 2010 12:42:37 GMT

Level III: A Complex Animation

←Older revision		Revision as of 12:42, 16 March 2010
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	* growSpacefill() and growWireframe() make the selected atoms "grow" slowly into spacefilled or wireframe representations, permitting rotation by the onlooker during these transitions.		* growSpacefill() and growWireframe() make the selected atoms "grow" slowly into spacefilled or wireframe representations, permitting rotation by the onlooker during these transitions.
	If you need a transition or function that is not included, don't hesitate to ask for help in adding it. Please contact {{Template:Martz_email}}.		If you need a transition or function that is not included, don't hesitate to ask for help in adding it. Please contact {{Template:Martz_email}}.
		+
		+	===Technical (All Three Levels)===

	==Web Pages==		==Web Pages==

Eric Martz: /* Level I: A single script file */

Eric Martz — Tue, 16 Mar 2010 12:41:02 GMT

Level I: A single script file

←Older revision		Revision as of 12:41, 16 March 2010
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	**''' Instructions for creating your web page are below, under [[#Web Page Procedure in Proteopedia]].'''		**''' Instructions for creating your web page are below, under [[#Web Page Procedure in Proteopedia]].'''
	* By hand. This requires familiarity with the [http://chemapps.stolaf.edu/jmol/docs/ Jmol Command Scripting Language]. No instructions are provided here for this method, either for constructing the script file, or for making a supporting web page.		* By hand. This requires familiarity with the [http://chemapps.stolaf.edu/jmol/docs/ Jmol Command Scripting Language]. No instructions are provided here for this method, either for constructing the script file, or for making a supporting web page.
		+
		+	'''Technical''': MP takes responsibility for loading the PDB file before your script is run, and it adds a delay after your script is run so that your scene will spin for a while before a repeat cycle of your script, or a different script, is run. For all three levels, MP defines the following variables before any master script is run:
		+	* PlaygroundProjection = true; # this if false if undefined
		+	* PlaygroundContentPath # the path on the MP server to your .spt and .pdb files. The filename must be appended to this.
		+	* PlaygroundSupportScriptPath # the path on the MP server to MPSupportVersion01.spt and MPSceneVersion01.spt. The filename must be appended.

	===Level II: A Single Molecular Scene With A Color Key===		===Level II: A Single Molecular Scene With A Color Key===

Eric Martz: /* Web Page Procedure in Proteopedia */

Eric Martz — Tue, 16 Mar 2010 02:07:30 GMT

Web Page Procedure in Proteopedia

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	'''Identify the page''' in Proteopedia where you will develop your article to provide more information as a supplement to your module in MP. Most likely you already set up this page and developed your scene there (see [[Molecular_Playground/Procedures#Create_a_Customized_Molecular_Scene_in_Proteopedia]]).		'''Identify the page''' in Proteopedia where you will develop your article to provide more information as a supplement to your module in MP. Most likely you already set up this page and developed your scene there (see [[Molecular_Playground/Procedures#Create_a_Customized_Molecular_Scene_in_Proteopedia]]).
	We recommend that you develop your web page in a temporary, protected page that you create named '''User:Your Name/Sandbox 1''' (or 2 or higher if you already have a Sandbox 1). For instructions on how to create this page, see [[Help:Sandboxes#Protected_Sandbox_Pages]]. After you have completed the development of the content in your page, you can move the content to a new permanent page named '''Molecular Playground/Your Molecule''' (see the last item below).		We recommend that you develop your web page in a temporary, protected page that you create named '''User:Your Name/Sandbox 1''' (or 2 or higher if you already have a Sandbox 1). For instructions on how to create this page, see [[Help:Sandboxes#Protected_Sandbox_Pages]]. After you have completed the development of the content in your page, you can move the content to a new permanent page named '''Molecular Playground/Your Molecule''' (see the last item below).
-	</li><li>
-	Write the text for your page, dividing it into logical sections. See the example pages linked [[#Web Pages\|above]]. On the [[#Web Pages\|example pages]], use the ''edit this page'' tab to see how the wikitext is done, then Cancel editing (so that you don't change the example pages).
	</li><li>		</li><li>
	When you were developing your molecular scene, you installed a rectangular Jmol into your page. Now, you can specify that your custom scene will be automatically displayed when the page loads, rather than having to press a green link. To do this, insert the <font color="red">red</font> line below into your <applet ... /> tag.		When you were developing your molecular scene, you installed a rectangular Jmol into your page. Now, you can specify that your custom scene will be automatically displayed when the page loads, rather than having to press a green link. To do this, insert the <font color="red">red</font> line below into your <applet ... /> tag.
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	Replace 'YYY' with a descriptive caption for your scene. This is a good place to mention the [[PDB code]] for the model you are showing. Put the lower case PDB code between double square brackets, like this <nowiki>[[3ckz]]</nowiki>, which will make a link like this: [[3ckz]].		Replace 'YYY' with a descriptive caption for your scene. This is a good place to mention the [[PDB code]] for the model you are showing. Put the lower case PDB code between double square brackets, like this <nowiki>[[3ckz]]</nowiki>, which will make a link like this: [[3ckz]].
	</li><li>This step applies '''only to Level II''' modules, and even for those, it is '''optional''': Insert a button that will show the scene as projected in MP. See [[Molecular Playground/Procedures#Displaying a Level II Scene in a Proteopedia Web Page]].		</li><li>This step applies '''only to Level II''' modules, and even for those, it is '''optional''': Insert a button that will show the scene as projected in MP. See [[Molecular Playground/Procedures#Displaying a Level II Scene in a Proteopedia Web Page]].
		+	</li><li>
		+	Write the text for your page, dividing it into logical sections. See the example pages linked [[#Web Pages\|above]]. On the [[#Web Pages\|example pages]], use the ''edit this page'' tab to see how the wikitext is done, then Cancel editing (so that you don't change the example pages).
	</li><li>		</li><li>
	Insert <nowiki>{{Template:MP_masthead}}</nowiki> at the top of your page to show the MP masthead photographs. Depending on what follows, you may need to put several blank lines after it to force the ''Contents'' table down, as done in [[Molecular_Playground/HIV_Protease_Inhibitor]]. Or you may need to insert <nowiki>{{Clear}}</nowiki> as done in [[Molecular Playground/Tamiflu]].		Insert <nowiki>{{Template:MP_masthead}}</nowiki> at the top of your page to show the MP masthead photographs. Depending on what follows, you may need to put several blank lines after it to force the ''Contents'' table down, as done in [[Molecular_Playground/HIV_Protease_Inhibitor]]. Or you may need to insert <nowiki>{{Clear}}</nowiki> as done in [[Molecular Playground/Tamiflu]].

Eric Martz: /* Level I: A single script file */

Eric Martz — Tue, 16 Mar 2010 01:38:07 GMT

Level I: A single script file

←Older revision		Revision as of 01:38, 16 March 2010
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	There are two ways to prepare the script file.		There are two ways to prepare the script file.
	* In Proteopedia, using its [[SAT\|Molecular Scene Authoring Tool]]. You don't need to be familiar with Jmol command scripting language. You save the "state script" from Jmol in Proteopedia.		* In Proteopedia, using its [[SAT\|Molecular Scene Authoring Tool]]. You don't need to be familiar with Jmol command scripting language. You save the "state script" from Jmol in Proteopedia.
-	** Instructions for creating your custom scene and saving the state script are in [[Molecular_Playground/Procedures]].	+	** '''Instructions for creating your custom scene and saving the state script are in [[Molecular_Playground/Procedures]].'''
-	** Instructions for creating your web page are below, under [[#Web Page Procedure in Proteopedia]].	+	**''' Instructions for creating your web page are below, under [[#Web Page Procedure in Proteopedia]].'''
	* By hand. This requires familiarity with the [http://chemapps.stolaf.edu/jmol/docs/ Jmol Command Scripting Language]. No instructions are provided here for this method, either for constructing the script file, or for making a supporting web page.		* By hand. This requires familiarity with the [http://chemapps.stolaf.edu/jmol/docs/ Jmol Command Scripting Language]. No instructions are provided here for this method, either for constructing the script file, or for making a supporting web page.