JSmol pros and cons - Revision history

AngelHerraez: note about obsolete content

2025-08-12T10:23:57Z

note about obsolete content

AngelHerraez: styling the table

2015-11-21T00:05:58Z

styling the table

AngelHerraez: link to PlatformSpeed

2015-11-20T23:56:15Z

link to PlatformSpeed

AngelHerraez: Chrome has dropped Java support

2015-06-15T15:25:37Z

Chrome has dropped Java support

EricMartz: /* Disadvantages of Selecting use:HTML5 (no Java) */

2014-08-07T22:00:00Z

‎Disadvantages of Selecting use:HTML5 (no Java)

EricMartz: /* Disadvantages of Selecting use:HTML5 */

2014-08-07T21:58:19Z

‎Disadvantages of Selecting use:HTML5

EricMartz: /* Advantages of Selecting use:HTML5 */

2014-08-07T21:57:56Z

‎Advantages of Selecting use:HTML5

EricMartz at 21:57, 7 August 2014

2014-08-07T21:57:31Z

EricMartz at 15:20, 1 August 2014

2014-08-01T15:20:35Z

Hansonr at 13:25, 1 August 2014

2014-08-01T13:25:15Z

← Older revision		Revision as of 10:23, 12 August 2025
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−	<~~span~~ style="font-size:130%;">This page could also be titled '''Things To Be Aware Of When Deciding between JSmol/Java and JSmol/HTML5 (no Java)'''.~~</span>~~	+	<div style="font-size:130%; color:#B30000;">
		+	Information in this page is obsolete, since the possibility of running Java Applets inside web pages has long been deprecated by most web browsers based on security concerns.
		+
		+	Content is being kept here for historical interest.
		+	</div>
		+
		+	<hr>
		+	.
		+
		+	<hr>
		+
		+
		+	This page could also be titled '''Things To Be Aware Of When Deciding between JSmol/Java and JSmol/HTML5 (no Java)'''.

	For other pages about JSmol, please see [[JSmol]].		For other pages about JSmol, please see [[JSmol]].

@@ Line 16: / Line 16: @@
 ===JavaScript is slower than Java by a factor of 6-10===
-<table width="300" cellpadding="4" style="background:#e0e0e0" align="right" hspace="10">
+<table class="wikitable" style="width:300px; background:#e0e0e0; float:right; margin-left:1ex;">
-<tr><td colspan=3>
+<caption>Macromolecules of Various Sizes</caption>
 <tr>
 <td>
@@ Line 26: / Line 24: @@
 Atoms (Kilo)
 </td><td>
-KD ([http://proteopedia.org/w/Asymmetric_Unit Asymmetric Unit])
+kDa ([http://proteopedia.org/w/Asymmetric_Unit Asymmetric Unit])
 </td>
 </tr>

@@ Line 98: / Line 98: @@
 </table>
-HTML5 is significantly '''slower''' than Java. For large systems it is strongly advised to use the '''set platformSpeed''' setting (or allow the user to set that). Smaller molecules (<10,000 atoms) are handled quite well. '''Large molecules''' (>20,000 atoms; see table at right) may be slow to load and process. (FirstGlance, when using HTML5, sometimes freezes for up to a minute, even more. These delays tend to happen with large molecules but are not simply related to model size.) Multiple-model ensembles (such as from [http://proteopedia.org/w/NMR NMR] experiments) may cause the page to freeze while taking minutes to load the ensemble, or loading may never finish.
+HTML5 is significantly '''slower''' than Java. For large systems it is strongly advised to use the [[PlatformSpeed|'''set platformSpeed''']] setting (or allow the user to set that). Smaller molecules (<10,000 atoms) are handled quite well. '''Large molecules''' (>20,000 atoms; see table at right) may be slow to load and process. (FirstGlance, when using HTML5, sometimes freezes for up to a minute, even more. These delays tend to happen with large molecules but are not simply related to model size.) Multiple-model ensembles (such as from [http://proteopedia.org/w/NMR NMR] experiments) may cause the page to freeze while taking minutes to load the ensemble, or loading may never finish.
 Here is how two websites that now use no-Java-JSmol by default have handled these issues:
@@ Line 108: / Line 108: @@
 ===Poor performance in Internet Explorer and Opera===
-Different web browsers have JavaScript engines with different performances. '''Chrome runs HTML5 best''', Safari is good, and Firefox is usually OK (see note under table below). '''Internet Explorer is unacceptably slow''' (all versions, including version 11). In '''Opera, rotation of the molecule is slow and jerky''' when setPlatformSpeed is not utilized.
+Different web browsers have JavaScript engines with different performances. '''Chrome runs HTML5 best''', Safari is good, and Firefox is usually OK (see note under table below). '''Internet Explorer is unacceptably slow''' (all versions, including version 11). In '''Opera, rotation of the molecule is slow and jerky''' when [[PlatformSpeed|setPlatformSpeed]] is not utilized.
 *[http://firstglance.jmol.org FirstGlance in Jmol] detects the browser being used, and recommends a different browser when being displayed in Internet Explorer or Opera.
-The findings below are based primarily on tests with [http://firstglance.jmol.org FirstGlance in Jmol] in its default HTML5 modality, not using '''set platformSpeed'''.  Results may be different for other JSmol websites.
+The findings below are based primarily on tests with [http://firstglance.jmol.org FirstGlance in Jmol] in its default HTML5 modality, not using [[PlatformSpeed|'''set platformSpeed''']].  Results may be different for other JSmol websites.
 [[Image:Jsmol-vs-browsers.png|center]]

@@ Line 3: / Line 3: @@
 For other pages about JSmol, please see [[JSmol]].
-JSmol allows development of a page that can use Java or just HTML5 (no Java), can use WebGL or not when using HTML5, and can also load molecules using a very small (50K) footprint (mostly nonscriptable) non-Jmol viewer option. When developing a page using JSmol, you need to decide which of these options you want. You specify that using the '''Info.use''' parameter that is passed to the JavaScript library that sets up your page.
+JSmol allows development of a page that can use Java or just HTML5 (no Java), can use WebGL or not when using HTML5, and can also load molecules using [[Lightweight JSmol]], a very small (50K) footprint (mostly nonscriptable) non-Jmol viewer option. When developing a page using JSmol, you need to decide which of these options you want. You specify that through [[Jmol_JavaScript_Object/Info#Modality|the '''Info.use''' parameter]] that is passed to the JavaScript library that sets up your page.
 ==Advantages of Selecting use:HTML5 (no Java)==
@@ Line 9: / Line 9: @@
 Advantages to using HTML5 (no Java) include:
 *Users of a website that does not use Java do not need to install Java.
 *A website using HTML5 will work on iPads and smart phones. (Java is not available for these platforms, so Java is not an option for them.)
 ==Disadvantages of Selecting use:HTML5 (no Java)==

@@ Line 99: / Line 99: @@
 HTML5 is significantly '''slower''' than Java. For large systems it is strongly advised to use the '''set platformSpeed''' setting (or allow the user to set that). Smaller molecules (<10,000 atoms) are handled quite well. '''Large molecules''' (>20,000 atoms; see table at right) may be slow to load and process. (FirstGlance, when using HTML5, sometimes freezes for up to a minute, even more. These delays tend to happen with large molecules but are not simply related to model size.) Multiple-model ensembles (such as from [http://proteopedia.org/w/NMR NMR] experiments) may cause the page to freeze while taking minutes to load the ensemble, or loading may never finish.
-Here is how two websites that now use JSmol by default have handled these issues:
+Here is how two websites that now use no-Java-JSmol by default have handled these issues:
-*[http://firstglance.jmol.org FirstGlance in Jmol], when using HTML5 (its default), loads only the first model when there are more than one. It offers using the signed Java applet as an option and a preference setting. When using FirstGlance it is recommended that one select Java when the molecule has >20,000 atoms, and especially when there are >50,000 atoms.
+*[http://firstglance.jmol.org FirstGlance in Jmol], when using HTML5 (no Java, its default), loads only the first model when there are more than one. It offers using the signed Java applet as an option and a preference setting. When using FirstGlance it is recommended that one select Java when the molecule has >20,000 atoms, and especially when there are >50,000 atoms.
 *[http://proteopedia.org Proteopedia] loads only amino acid alpha carbon atoms (or nucleic acid phosphorus atoms) and ligand atoms, since its ribbon view (secondary structure schematic) works fine without the other atoms. A prominent message is displayed that a ''simplified model'' is being shown, and there is a button to load the complete model. For registered users who are logged in, Proteopedia has a preference setting that will use Java instead of HTML5.

← Older revision		Revision as of 21:57, 7 August 2014
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−	<span style="font-size:130%;">This page could also be titled '''Things To Be Aware Of When Deciding between JSmol/Java and JSmol/HTML5'''.</span>	+	<span style="font-size:130%;">This page could also be titled '''Things To Be Aware Of When Deciding between JSmol/Java and JSmol/HTML5 (no Java)'''.</span>

	For other pages about JSmol, please see [[JSmol]].		For other pages about JSmol, please see [[JSmol]].

@@ Line 1: / Line 1: @@
 <span style="font-size:130%;">This page could also be titled '''Things To Be Aware Of When Deciding between JSmol/Java and JSmol/HTML5'''.</span>
 For other pages about JSmol, please see [[JSmol]].
-JSmol allows development of a page that can use Java or just HTML5, can use WebGL or not when using HTML5, and can also load molecules with  very small footprint simple (mostly nonscriptable) viewer. When developing a page using JSmol, you decide which of these options you want using the '''Info.use''' parameter that is passed to the JavaScript library that sets up your page.
+JSmol allows development of a page that can use Java or just HTML5, can use WebGL or not when using HTML5, and can also load molecules using a very small (50K) footprint (mostly nonscriptable) non-Jmol viewer option. When developing a page using JSmol, you need to decide which of these options you want. You specify that using the '''Info.use''' parameter that is passed to the JavaScript library that sets up your page.
 ==Advantages of Selecting use:HTML5==