Using Java for Rendering Structures - Revision history

Angel Herraez: remind users of browsers not supporting Java any more

2016-10-15T11:29:37Z

remind users of browsers not supporting Java any more

← Older revision		Revision as of 11:29, 15 October 2016
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	Starting January 26, 2014, Proteopedia uses a newer version of [[Jmol]] that operates either with ~~HMTL5~~/Javascript, or alternatively with the traditional [[Java]]. Proteopedia defaults to the ~~HMTL5~~/Javascript mode, called JSmol. When using Java, Proteopedia no longer offers the unsigned Jmol applet, but only the signed applet (Jmol_S). This is because Oracle, the makers of Java, plan to prohibit unsigned applets to improve security.		Starting January 26, 2014, Proteopedia uses a newer version of [[Jmol]] that operates either with HTML5/Javascript, or alternatively with the traditional [[Java]]. Proteopedia defaults to the HTML5/Javascript mode, called JSmol. When using Java, Proteopedia no longer offers the unsigned Jmol applet, but only the signed applet (Jmol_S). This is because Oracle, the makers of Java, plan to prohibit unsigned applets to improve security.

	However, as [[Testing PDB File Sizes\|Java remains the best for performance]], '''when present we encourage you to use [[Java]] to render the 3D visualizations on Proteopedia'''.		However, as [[Testing PDB File Sizes\|Java remains the best for performance]], '''when present we encourage you to use [[Java]] to render the 3D visualizations on Proteopedia'''.

	Users with Java installed on their computer can select Proteopedia to run Jmol in Java mode on a page-by-page basis or registered users can set Java mode as your default option. (Registration is free.) How to do each of these two options is explained below.		Users with Java installed on their computer and using a compatible browser can select Proteopedia to run Jmol in Java mode on a page-by-page basis or registered users can set Java mode as your default option. (Registration is free.) How to do each of these two options is explained below.

	If you may need to update Java on your computer, or have difficulty enabling Java to work in your favorite web browser, please see [[Installing and enabling Java]].		If you may need to update Java on your computer, or have difficulty enabling Java to work in your favorite web browser, please see [[Installing and enabling Java]].

	'''NOTE: TABLETS AND PORTABLE DEVICES THAT DO NOT HAVE THE OPTION TO INSTALL JAVA ONLY HAVE THE CHOICE OF RUNNING ~~JMOL~~ WITH ~~HMTL5~~/Javascript.''' See [[Java#Detecting your Java version]] to look into whether you have Java installed.		'''NOTE: TABLETS AND PORTABLE DEVICES THAT DO NOT HAVE THE OPTION TO INSTALL JAVA ONLY HAVE THE CHOICE OF RUNNING JSmol WITH HTML5/Javascript.''' See [[Java#Detecting your Java version]] to look into whether you have Java installed.

			'''NOTE: COMMON BROWSERS ARE DROPPING SUPPORT FOR RUNNING JAVA APPLETS WITHIN WEB PAGES, SO THE ONLY CHOICE IS RUNNING JSmol WITH HTML5/Javascript.''' For details, please see [[Installing and enabling Java]].

	__FORCETOC__		__FORCETOC__
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	<pre>http://proteopedia.org/wiki/index.php/G_protein-coupled_receptor</pre> using Java-based Jmol, the URL of the Proteopedia page would be <pre>http://proteopedia.org/wiki/index.php/G_protein-coupled_receptor?use=java</pre>		<pre>http://proteopedia.org/wiki/index.php/G_protein-coupled_receptor</pre> using Java-based Jmol, the URL of the Proteopedia page would be <pre>http://proteopedia.org/wiki/index.php/G_protein-coupled_receptor?use=java</pre>

	* You may now be prompted to accept the certificate for the signed Java applet. Note, you will not see this if you have already selected the checkbox option to remember you trusted it already. (It is suggested you toggle that option on so you are not bothered in the future.) <br/>		* You may now be prompted to accept the certificate for the signed Java applet. Note, you will not see this if you have already selected the checkbox option to remember you trusted it already. (It is suggested you toggle that option on so you are not bothered in the future, but even when doing so, it may reappear repeatedly.) <br/>
	[[Image:Jmol app permission needed toggled.png]]		[[Image:Jmol app permission needed toggled.png]]

Jaime Prilusky at 04:50, 29 August 2014

2014-08-29T04:50:05Z

← Older revision		Revision as of 04:50, 29 August 2014
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	==Java-mode on a page-by-page basis for rendering structures in Proteopedia==		==Java-mode on a page-by-page basis for rendering structures in Proteopedia==
	Append the code below to the URL of a Proteopedia page to render structures with Jmol using Java.		Append the code below to the URL of a Proteopedia page to render structures with Jmol using Java.
	<pre>?~~_use~~=java</pre>		<pre>?use=java</pre>

	For, example to view the page		For, example to view the page
	<pre>http://proteopedia.org/wiki/index.php/G_protein-coupled_receptor</pre> using Java-based Jmol, the URL of the Proteopedia page would be <pre>http://proteopedia.org/wiki/index.php/G_protein-coupled_receptor?~~_use~~=java</pre>		<pre>http://proteopedia.org/wiki/index.php/G_protein-coupled_receptor</pre> using Java-based Jmol, the URL of the Proteopedia page would be <pre>http://proteopedia.org/wiki/index.php/G_protein-coupled_receptor?use=java</pre>

	* You may now be prompted to accept the certificate for the signed Java applet. Note, you will not see this if you have already selected the checkbox option to remember you trusted it already. (It is suggested you toggle that option on so you are not bothered in the future.) <br/>		* You may now be prompted to accept the certificate for the signed Java applet. Note, you will not see this if you have already selected the checkbox option to remember you trusted it already. (It is suggested you toggle that option on so you are not bothered in the future.) <br/>

Jaime Prilusky at 04:46, 29 August 2014

2014-08-29T04:46:57Z

← Older revision		Revision as of 04:46, 29 August 2014
Line 13:		Line 13:
	==Java-mode on a page-by-page basis for rendering structures in Proteopedia==		==Java-mode on a page-by-page basis for rendering structures in Proteopedia==
	Append the code below to the URL of a Proteopedia page to render structures with Jmol using Java.		Append the code below to the URL of a Proteopedia page to render structures with Jmol using Java.
	<pre>?~~_USE~~=~~SIGNED~~</pre>		<pre>?_use=java</pre>

	For, example to view the page		For, example to view the page
	<pre>http://proteopedia.org/wiki/index.php/G_protein-coupled_receptor</pre> using Java-based Jmol, the URL of the Proteopedia page would be <pre>http://proteopedia.org/wiki/index.php/G_protein-coupled_receptor?~~_USE~~=~~SIGNED~~</pre>		<pre>http://proteopedia.org/wiki/index.php/G_protein-coupled_receptor</pre> using Java-based Jmol, the URL of the Proteopedia page would be <pre>http://proteopedia.org/wiki/index.php/G_protein-coupled_receptor?_use=java</pre>

	* You may now be prompted to accept the certificate for the signed Java applet. Note, you will not see this if you have already selected the checkbox option to remember you trusted it already. (It is suggested you toggle that option on so you are not bothered in the future.) <br/>		* You may now be prompted to accept the certificate for the signed Java applet. Note, you will not see this if you have already selected the checkbox option to remember you trusted it already. (It is suggested you toggle that option on so you are not bothered in the future.) <br/>

Eric Martz at 04:40, 27 April 2014

2014-04-27T04:40:06Z

← Older revision		Revision as of 04:40, 27 April 2014
Line 4:		Line 4:

	Users with Java installed on their computer can select Proteopedia to run Jmol in Java mode on a page-by-page basis or registered users can set Java mode as your default option. (Registration is free.) How to do each of these two options is explained below.		Users with Java installed on their computer can select Proteopedia to run Jmol in Java mode on a page-by-page basis or registered users can set Java mode as your default option. (Registration is free.) How to do each of these two options is explained below.

			If you may need to update Java on your computer, or have difficulty enabling Java to work in your favorite web browser, please see [[Installing and enabling Java]].

	'''NOTE: TABLETS AND PORTABLE DEVICES THAT DO NOT HAVE THE OPTION TO INSTALL JAVA ONLY HAVE THE CHOICE OF RUNNING JMOL WITH HMTL5/Javascript.''' See [[Java#Detecting your Java version]] to look into whether you have Java installed.		'''NOTE: TABLETS AND PORTABLE DEVICES THAT DO NOT HAVE THE OPTION TO INSTALL JAVA ONLY HAVE THE CHOICE OF RUNNING JMOL WITH HMTL5/Javascript.''' See [[Java#Detecting your Java version]] to look into whether you have Java installed.
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	==See also==		==See also==
	*[[Java]]		*[[Java]]
			*[[Installing and enabling Java]]
	*[[Jmol]]		*[[Jmol]]
	*[[Distinguishing the modes of Jmol on Proteopedia]]		*[[Distinguishing the modes of Jmol on Proteopedia]]

Eric Martz: /* Java-mode: setting a preference to use Jmol_S (Java) automatically for rendering structures in Proteopedia */

2014-01-29T23:17:29Z

Java-mode: setting a preference to use Jmol_S (Java) automatically for rendering structures in Proteopedia

← Older revision		Revision as of 23:17, 29 January 2014
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	==Java-mode: setting a preference to use Jmol_S (Java) automatically for rendering structures in Proteopedia==		==Java-mode: setting a preference to use Jmol_S (Java) automatically for rendering structures in Proteopedia==
	Registered users of Protopepedia can set Java mode as your default preference for rendering structures on Proteopedia. Registration is free~~: click on ''Login / request account'' at the upper right corner of any page in Proteopedia~~.		Registered users of Protopepedia can set Java mode as your default preference for rendering structures on Proteopedia. Registration is free.

	How to do this follows:		How to do this follows:

Eric Martz: /* Java-mode: setting a preference to use Jmol_S (Java) automatically for rendering structures in Proteopedia */

2014-01-29T23:14:23Z

Java-mode: setting a preference to use Jmol_S (Java) automatically for rendering structures in Proteopedia

← Older revision		Revision as of 23:14, 29 January 2014
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	*When the structure scene appears, you'll see <font color="maroon">Jmol_S</font> in the bottom right corner of the Proteopedia structure scenes on that page, indicating you are viewing it with the signed Java-based Jmol applet.		*When the structure scene appears, you'll see <font color="maroon">Jmol_S</font> in the bottom right corner of the Proteopedia structure scenes on that page, indicating you are viewing it with the signed Java-based Jmol applet.
			<br>
			'''β-2 Adrenergic Receptor'''
			<br>
	[[Image:Making image of GPCR page with Jmol S shown.png]]		[[Image:Making image of GPCR page with Jmol S shown.png]]


	See [[Distinguishing the modes of Jmol on Proteopedia~~\|here~~]] ~~for more information about distinguishing the modes~~.		See also [[Distinguishing the modes of Jmol on Proteopedia]].


	==See also==		==See also==

Eric Martz: /* Rendering Structures with Jmol in Java-mode on a page-by-page basis */

2014-01-29T22:56:23Z

Rendering Structures with Jmol in Java-mode on a page-by-page basis

← Older revision		Revision as of 22:56, 29 January 2014
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	__FORCETOC__		__FORCETOC__

	==~~Rendering Structures with Jmol in~~ Java-mode on a page-by-page basis==		==Java-mode on a page-by-page basis for rendering structures in Proteopedia==
	Append the code below to the URL of a Proteopedia page to render structures with Jmol using Java.		Append the code below to the URL of a Proteopedia page to render structures with Jmol using Java.
	<pre>?_USE=SIGNED</pre>		<pre>?_USE=SIGNED</pre>
Line 20:		Line 20:

	Open a Proteopedia page with a structure on it. When the structure scene appears, you'll see <font color="maroon">Jmol_S</font> in the bottom right corner of the Proteopedia structure scenes on that page, indicating you are viewing it with the signed Java-based Jmol applet. See [[Distinguishing the modes of Jmol on Proteopedia\|here]] for more information about distinguishing the modes.		Open a Proteopedia page with a structure on it. When the structure scene appears, you'll see <font color="maroon">Jmol_S</font> in the bottom right corner of the Proteopedia structure scenes on that page, indicating you are viewing it with the signed Java-based Jmol applet. See [[Distinguishing the modes of Jmol on Proteopedia\|here]] for more information about distinguishing the modes.


	==Java-mode: setting a preference to use Jmol_S (Java) automatically for rendering structures in Proteopedia==		==Java-mode: setting a preference to use Jmol_S (Java) automatically for rendering structures in Proteopedia==

Eric Martz at 22:53, 29 January 2014

2014-01-29T22:53:13Z

← Older revision		Revision as of 22:53, 29 January 2014
Line 1:		Line 1:
	Starting January 26, 2014, Proteopedia uses a newer version of [[Jmol]] that operates either with HMTL5/Javascript, or alternatively the traditional [[Java]]. Proteopedia defaults to the HMTL5/Javascript mode, called JSmol. When using Java, Proteopedia no longer offers the unsigned Jmol applet, but only the signed applet (Jmol_S). This is because Oracle, the makers of Java, plan to prohibit unsigned applets to improve security.		Starting January 26, 2014, Proteopedia uses a newer version of [[Jmol]] that operates either with HMTL5/Javascript, or alternatively with the traditional [[Java]]. Proteopedia defaults to the HMTL5/Javascript mode, called JSmol. When using Java, Proteopedia no longer offers the unsigned Jmol applet, but only the signed applet (Jmol_S). This is because Oracle, the makers of Java, plan to prohibit unsigned applets to improve security.

	However, as [[Testing PDB File Sizes\|Java remains the best for performance]], '''when present we encourage you to use [[Java]] to render the 3D visualizations on Proteopedia'''.		However, as [[Testing PDB File Sizes\|Java remains the best for performance]], '''when present we encourage you to use [[Java]] to render the 3D visualizations on Proteopedia'''.

Eric Martz at 22:52, 29 January 2014

2014-01-29T22:52:50Z

← Older revision		Revision as of 22:52, 29 January 2014
Line 1:		Line 1:
	Starting January 26, 2014, Proteopedia uses a newer version of [[Jmol]] that operates either with HMTL5/Javascript, or alternatively the traditional [[Java]]. Proteopedia defaults to the HMTL5/Javascript mode, called JSmol.		Starting January 26, 2014, Proteopedia uses a newer version of [[Jmol]] that operates either with HMTL5/Javascript, or alternatively the traditional [[Java]]. Proteopedia defaults to the HMTL5/Javascript mode, called JSmol. When using Java, Proteopedia no longer offers the unsigned Jmol applet, but only the signed applet (Jmol_S). This is because Oracle, the makers of Java, plan to prohibit unsigned applets to improve security.

	However, as [[Testing PDB File Sizes\|Java remains the best for performance]], '''when present we encourage you to use [[Java]] to render the 3D visualizations on Proteopedia'''.		However, as [[Testing PDB File Sizes\|Java remains the best for performance]], '''when present we encourage you to use [[Java]] to render the 3D visualizations on Proteopedia'''.

	Users with Java installed on their computer can select Proteopedia to run Jmol in Java mode on a page-by-page basis or registered users can set Java mode as your default option. How to do each of these two options is explained below.		Users with Java installed on their computer can select Proteopedia to run Jmol in Java mode on a page-by-page basis or registered users can set Java mode as your default option. (Registration is free.) How to do each of these two options is explained below.

	'''NOTE: TABLETS AND PORTABLE DEVICES THAT DO NOT HAVE THE OPTION TO INSTALL JAVA ONLY HAVE THE CHOICE OF RUNNING JMOL WITH HMTL5/Javascript.''' See [[Java#Detecting your Java version]] to look into whether you have Java installed.		'''NOTE: TABLETS AND PORTABLE DEVICES THAT DO NOT HAVE THE OPTION TO INSTALL JAVA ONLY HAVE THE CHOICE OF RUNNING JMOL WITH HMTL5/Javascript.''' See [[Java#Detecting your Java version]] to look into whether you have Java installed.
Line 22:		Line 22:


	==~~Defaulting~~ to rendering ~~Proteopedia's~~ structures ~~with Jmol~~ in ~~Java-mode~~==		==Java-mode: setting a preference to use Jmol_S (Java) automatically for rendering structures in Proteopedia==
	Registered users of Protopepedia can set Java mode as your default ~~option~~ for rendering structures on Proteopedia.		Registered users of Protopepedia can set Java mode as your default preference for rendering structures on Proteopedia. Registration is free: click on ''Login / request account'' at the upper right corner of any page in Proteopedia.

	How to do this follows:		How to do this follows:

Eric Martz at 22:44, 29 January 2014

2014-01-29T22:44:17Z

← Older revision		Revision as of 22:44, 29 January 2014
Line 1:		Line 1:
	Proteopedia ~~now~~ uses ~~the~~ version of [[Jmol]] that ~~supports running~~ with HMTL5/Javascript or the traditional [[Java]]. Proteopedia defaults to the HMTL5/Javascript ~~of Jmol~~.		Starting January 26, 2014, Proteopedia uses a newer version of [[Jmol]] that operates either with HMTL5/Javascript, or alternatively the traditional [[Java]]. Proteopedia defaults to the HMTL5/Javascript mode, called JSmol.

	However, as [[Testing PDB File Sizes\|Java remains the best for performance]], '''when present we encourage you to use [[Java]] to render the 3D visualizations on Proteopedia'''.		However, as [[Testing PDB File Sizes\|Java remains the best for performance]], '''when present we encourage you to use [[Java]] to render the 3D visualizations on Proteopedia'''.