Scene authoring tools - Revision history

Eric Martz: /* 'load molecule' tab */

2022-11-12T18:35:26Z

'load molecule' tab

← Older revision		Revision as of 18:35, 12 November 2022
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	There is a checkbox to add calculated positions of '''hydrogen''' atoms to the structure as it is loaded. This allows to show the multiplicity of bonds (i.e. whether a bond is a single, double or triple bond) in the 3D scenes.		There is a checkbox to add calculated positions of '''hydrogen''' atoms to the structure as it is loaded. This allows to show the multiplicity of bonds (i.e. whether a bond is a single, double or triple bond) in the 3D scenes.

	Another optional field allows to enter ~~a text~~ that will be used to '''filter''' which atoms of the original model will be either loaded or ignored.		Another optional field allows to enter instructions that will be used to '''filter''' which atoms of the original model will be either loaded or ignored.
	For example, to load just the alpha carbons, to exclude water, include or exclude other hetero groups (ligands), load ~~several~~ biomolecule ~~units~~, etc. See [[Biological Unit: Showing]] for instructions.		For example, to load just the alpha carbons, to exclude water, include or exclude other hetero groups (ligands), load a specified biomolecule (biological unit), etc. See [[Biological Unit: Showing]] for instructions.
	You can also check the [{{ScriptingDoc}} Jmol Scripting Documentation] for details about the syntax of such filter specifications (in that page, search for <code style="color:maroon">load "filename" FILTER</code>).		You can also check the [{{ScriptingDoc}} Jmol Scripting Documentation] for details about the syntax of such filter specifications (in that page, search for <code style="color:maroon">load "filename" FILTER</code>).

Eric Martz: /* 'load molecule' tab */

2022-11-12T18:33:50Z

'load molecule' tab

← Older revision		Revision as of 18:33, 12 November 2022
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	Another optional field allows to enter a text that will be used to '''filter''' which atoms of the original model will be either loaded or ignored.		Another optional field allows to enter a text that will be used to '''filter''' which atoms of the original model will be either loaded or ignored.
	For example, to load just the alpha carbons, to exclude water, include or exclude other hetero groups (ligands), load several biomolecule units...		For example, to load just the alpha carbons, to exclude water, include or exclude other hetero groups (ligands), load several biomolecule units, etc. See [[Biological Unit: Showing]] for instructions.
	You can check the [{{ScriptingDoc}} Jmol Scripting Documentation] for details about the syntax of such filter specifications (in that page, search for <code style="color:maroon">load "filename" FILTER</code>).		You can also check the [{{ScriptingDoc}} Jmol Scripting Documentation] for details about the syntax of such filter specifications (in that page, search for <code style="color:maroon">load "filename" FILTER</code>).

	=='load scene' tab==		=='load scene' tab==

Angel Herraez: /* 'load molecule' tab */

2022-07-30T17:00:30Z

'load molecule' tab

← Older revision		Revision as of 17:00, 30 July 2022
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	Uploaded file can have various formats recognized by Jmol's "load" command. For example, you can load a .PNGJ file to load coordinates and a 3D scene in one step.		Uploaded file can have various formats recognized by Jmol's "load" command. For example, you can load a .PNGJ file to load coordinates and a 3D scene in one step.

	There is a checkbox to add calculated positions of hydrogen atoms to the structure as it is loaded. This allows to show the multiplicity of bonds (i.e. whether a bond is a single, double or triple bond) in the 3D scenes.		There is a checkbox to add calculated positions of '''hydrogen''' atoms to the structure as it is loaded. This allows to show the multiplicity of bonds (i.e. whether a bond is a single, double or triple bond) in the 3D scenes.

	Another optional field allows to enter a text that will be used to filter which atoms of the original model will be either loaded or ignored. You can check the [{{ScriptingDoc}} Jmol Scripting Documentation] for details about the syntax of such filter specifications (in that page, search for <code style="color:maroon">load "filename" FILTER</code>).		Another optional field allows to enter a text that will be used to '''filter''' which atoms of the original model will be either loaded or ignored.
			For example, to load just the alpha carbons, to exclude water, include or exclude other hetero groups (ligands), load several biomolecule units...
			You can check the [{{ScriptingDoc}} Jmol Scripting Documentation] for details about the syntax of such filter specifications (in that page, search for <code style="color:maroon">load "filename" FILTER</code>).

	=='load scene' tab==		=='load scene' tab==

Angel Herraez: 'load molecule' tab - help with FILTER

2022-07-30T09:19:52Z

'load molecule' tab - help with FILTER

← Older revision		Revision as of 09:19, 30 July 2022
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	To load a file that has a PDB ID, input the ID 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 a PDB ID, input the ID into the first input area and click the load button. The file will be fetched from the PDB database.

	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). Once a file has been uploaded, you can specify its name in the input area next to the words "From Proteopedia ~~upladed~~ file" and click load.		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). 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.

	Uploaded file can have various formats recognized by Jmol's "load" command. For example, you can load a .PNGJ file to load coordinates and a 3D scene in one step.		Uploaded file can have various formats recognized by Jmol's "load" command. For example, you can load a .PNGJ file to load coordinates and a 3D scene in one step.

	There is a checkbox to add calculated positions of hydrogen atoms to the structure as it is loaded. This allows to show the multiplicity of bonds (i.e. whether a bond is a single, double or triple bond) in the 3D scenes.		There is a checkbox to add calculated positions of hydrogen atoms to the structure as it is loaded. This allows to show the multiplicity of bonds (i.e. whether a bond is a single, double or triple bond) in the 3D scenes.

			Another optional field allows to enter a text that will be used to filter which atoms of the original model will be either loaded or ignored. You can check the [{{ScriptingDoc}} Jmol Scripting Documentation] for details about the syntax of such filter specifications (in that page, search for <code style="color:maroon">load "filename" FILTER</code>).

	=='load scene' tab==		=='load scene' tab==

Karsten Theis: /* Where are the ''Scene authoring tools''? */

2022-07-02T09:41:34Z

Where are the ''Scene authoring tools''?

← Older revision		Revision as of 09:41, 2 July 2022
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	[[Image:SAT show.JPG\|350px]]		[[Image:SAT show.JPG\|350px]]

	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 '''SAT (Scene authoring tools) [show]'''. Click on '''show''' to expand and open the ''Scene authoring tools''. If, however, the page does not contain a Jmol window yet (~~not~~ <Structure> or <StructureSection> tags), ~~there~~ will be access to the SAT. In this case, first edit the page to include ~~one~~ (using the [[Image:Structure buttons.JPG\|50px]] buttons above the text-editing area), save and then edit again to see the link to the SAT. New pages have placeholder content that includes these tags, but this page for example does not.		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 '''SAT (Scene authoring tools) [show]'''. Click on '''show''' to expand and open the ''Scene authoring tools''. If, however, the page does not contain a Jmol window yet (no <Structure> or <StructureSection> tags), the page will lack access to the SAT. In this case, first edit the page to include a Jmol window (using the [[Image:Structure buttons.JPG\|50px]] buttons above the text-editing area), save and then edit again to see the link to the SAT. New pages have placeholder content that includes these tags, but this page for example does not.

Rachel Butz at 21:29, 11 November 2020

2020-11-11T21:29:04Z

← Older revision		Revision as of 21:29, 11 November 2020
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	<!--		<!--<Structure load='
			----
			Insert PDB code or filename here' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />
	A short and rough, temporary video tutorial can be viewed here: http://www.weizmann.ac.il/ISPC/Proteopedia.html.		A short and rough, temporary video tutorial can be viewed here: http://www.weizmann.ac.il/ISPC/Proteopedia.html.
	-->		-->

Jaime Prilusky at 19:37, 31 October 2020

2020-10-31T19:37:38Z

← Older revision		Revision as of 19:37, 31 October 2020
Line 43:		Line 43:

	=='load scene' tab==		=='load scene' tab==
	The first box shows the '''current page name'''. First, you proceed to choose the '''scene name''' using the drop-down selector. All scenes associated with the scenes inserted in the page you edit will be listed (see ~~reusing~~ scenes) . 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 and caption that were given to the scene are also recalled. At the same time, the wikitext that is needed for insertion of the scene into the page is displayed.		The first box shows the '''current page name'''. First, you proceed to choose the '''scene name''' using the drop-down selector. All scenes associated with the scenes inserted in the page you edit will be listed (see [[Remixing#Remixing_3D_scenes_from_Proteopedia\|remixing scenes]]) . 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 and caption that were given to the scene are 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 4 parameters to distinguish it from all other scenes: domain, pageId, scenename, and versionnumber (e.g. 77/778341/Ballstick/1). The '''domain''' are the first two digits of the pageId, and the '''pageId''' is the unique internal identifier 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). To find out which page is associated with a scene, create the URL of the script by prepending "proteopedia.org/wiki/scripts/" and appending ".spt". e.g. the scene called 77/778341/Ballstick/1 is stored at [https://proteopedia.org/wiki/scripts/77/778341/Ballstick/1.spt]. Inspection of the first couple of lines of the file shows, after the keyword "documentBase", that it originated from a user page.		Each distinct scene has 4 parameters to distinguish it from all other scenes: domain, pageId, scenename, and versionnumber (e.g. 77/778341/Ballstick/1). The '''domain''' are the first two digits of the pageId, and the '''pageId''' is the unique internal identifier 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). To find out which page is associated with a scene, create the URL of the script by prepending "proteopedia.org/wiki/scripts/" and appending ".spt". e.g. the scene called 77/778341/Ballstick/1 is stored at [https://proteopedia.org/wiki/scripts/77/778341/Ballstick/1.spt]. Inspection of the first couple of lines of the file shows, after the keyword "documentBase", that it originated from a user page.

Jaime Prilusky at 16:41, 31 October 2020

2020-10-31T16:41:49Z

← Older revision		Revision as of 16:41, 31 October 2020
Line 43:		Line 43:

	=='load scene' tab==		=='load scene' tab==
	The first ~~input~~ box shows the current page name ~~(if you want to start with a scene from a different page, enter the page name here)~~. ~~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 box shows the '''current page name'''. First, you proceed to choose the '''scene name''' using the drop-down selector. All scenes associated with the scenes inserted in the page you edit will be listed (see reusing scenes) . 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 and caption that were given to the scene are 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 (e.g. Hemoglobin/Cavity/14). Current scenes have numerical page names (e.g. 77/778341/Ballstick/1~~). To find out which page is associated with a scene, create the URL of the script by prepending "proteopedia.org/wiki/scripts/" and appending ".spt". e.g. the scene called 77/778341/Ballstick/1 is stored at [https://proteopedia.org/wiki/scripts/77/778341/Ballstick/1.spt]. Inspection of the first couple of lines of the file shows, after the keyword "documentBase", that it originated from a user page.		Each distinct scene has 4 parameters to distinguish it from all other scenes: domain, pageId, scenename, and versionnumber (e.g. 77/778341/Ballstick/1). The '''domain''' are the first two digits of the pageId, and the '''pageId''' is the unique internal identifier 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). To find out which page is associated with a scene, create the URL of the script by prepending "proteopedia.org/wiki/scripts/" and appending ".spt". e.g. the scene called 77/778341/Ballstick/1 is stored at [https://proteopedia.org/wiki/scripts/77/778341/Ballstick/1.spt]. Inspection of the first couple of lines of the file shows, after the keyword "documentBase", that it originated from a user page.

	==Controls below the Jmol window==		==Controls below the Jmol window==

Karsten Theis: /* 'load molecule' tab */

2020-10-28T11:48:55Z

'load molecule' tab

← Older revision		Revision as of 11:48, 28 October 2020
Line 41:		Line 41:

	There is a checkbox to add calculated positions of hydrogen atoms to the structure as it is loaded. This allows to show the multiplicity of bonds (i.e. whether a bond is a single, double or triple bond) in the 3D scenes.		There is a checkbox to add calculated positions of hydrogen atoms to the structure as it is loaded. This allows to show the multiplicity of bonds (i.e. whether a bond is a single, double or triple bond) in the 3D scenes.

	Several files can also be loaded into Jmol, one at a time, using the "append" button. Note that by default Jmol will not display both together; they will be in different frames which you need to manage.

	=='load scene' tab==		=='load scene' tab==

Karsten Theis at 10:45, 28 October 2020

2020-10-28T10:45:47Z

← Older revision		Revision as of 10:45, 28 October 2020
Line 1:		Line 1:
	The '''Scene authoring tool''' (SAT) is used to create and edit molecular scenes. Scenes created using the ''Scene authoring tool'' can then be inserted into [[Proteopedia]] pages. This is a reference page explaining ~~everything~~. For a tutorial introduction, see [[Proteopedia:DIY:Scenes\|Instructions for creating a molecular scene with Proteopedia's Scene Authoring Tools]], and watch the introductory videos, e.g. [https://youtu.be/P-LsB2U8rNM].		The '''Scene authoring tool''' (SAT) is used to create and edit molecular scenes. Scenes created using the ''Scene authoring tool'' can then be inserted into [[Proteopedia]] pages. This is a reference page explaining the details once you are familiar with the basics. For a tutorial introduction, see [[Proteopedia:DIY:Scenes\|Instructions for creating a molecular scene with Proteopedia's Scene Authoring Tools]], and watch the introductory videos, e.g. [https://youtu.be/P-LsB2U8rNM].

	==Where are the ''Scene authoring tools''?==		==Where are the ''Scene authoring tools''?==