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Of course there are huge advantages to using JSmol:
Of course there are huge advantages to using JSmol:
*Users of a JSmol website do not need to install [[Java]] (which is a [[Java#Java_is_a_security_threat|likely security risk]]).
*Users of a JSmol website do not need to install [[Java]] (which is a [[Java#Java_is_a_security_threat|likely security risk]]).
*The very popular Google Chrome browser no longer supports Java, nor does Edge (the new browser in Windows 10). Opera plans to remove support for Java.
*A JSmol website will likely work on iPads and smart phones. (Java is not available for these platforms, so Jmol is not an option for them.)
*A JSmol website will likely work on iPads and smart phones. (Java is not available for these platforms, so Jmol is not an option for them.)


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Atoms (Kilo)
Atoms (Kilo)
</td><td>
</td><td>
KD ([[Asymmetric Unit]])
kDa* ([[Asymmetric Unit]])
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</td>
</tr>
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1.7
1.7
</td><td>
</td><td>
28
24 (28)
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</td>
</tr>
</tr>
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6
6
</td><td>
</td><td>
87
77 (87)
</td>
</tr>
<tr>
<td>
[[2v61]]
</td><td>
9
</td><td>
107 (120)
</td>
</td>
</tr>
</tr>
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</td><td>
</td><td>
12
12
</td>
<td>
142 (160)
</td>
</tr>
<tr>
<td>
[[5ibx]]
</td><td>
</td><td>
160
17
</td><td>
202 (215)
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</td>
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23
23
</td><td>
</td><td>
233
220 (233)
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</td>
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45
45
</td><td>
</td><td>
826
602 (826)
</td>
</td>
</tr>
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</td><td>
</td><td>
900
900
</td>
</tr>
<tr>
<td>
[[3j9q]]
</td><td>
99.6
</td><td>
1,314 (1,424)
</td>
</td>
</tr>
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57 (2.7K x 21 NMR models. Includes hydrogen.)
57 (2.7K x 21 NMR models. Includes hydrogen.)
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</td><td>
416 (20K x 20 NMR models)
416 = 19.8K x 21 NMR models (416)
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</td>
</tr>
</tr>
<tr><td colspan="3">
<tr><td colspan="3">
Models with &gt;10,000 atoms are in the largest ~10% of the [[PDB]]; with &gt;20,000 atoms, the largest ~5%; with &gt;50,000 atoms, the largest ~1.5% (counting all models for NMR ensembles).
Models with &gt;10,000 atoms are in the largest ~10% of the [[PDB]]; with &gt;20,000 atoms, the largest ~5%; with &gt;50,000 atoms, the largest ~1.5% (counting all models for NMR ensembles).
<br>
<nowiki>*</nowiki> kDa excluding water as reported by Jmol (print {not hoh}.mass.sum). RCSB molecular weights are sometimes much larger for obscure reasons. RCSB report is in parentheses.
</td>
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JSmol is significantly '''slower''' than Jmol. Rotation will be jerkier. 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. (Sometimes I’ve seen delays of up to a minute, even more, during which JSmol freezes. These delays tend to happen with large molecules but are not simply related to size.) Multiple-model ensembles (such as from [[NMR]] experiments) may cause JSmol to freeze while taking minutes to load the ensemble, or loading may never finish.
JSmol is significantly '''slower''' than Jmol. Rotation will be jerkier (see [[JSmol/Rotation Speeds]]). 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. (Sometimes I’ve seen delays of up to a minute, even more, during which JSmol freezes. These delays tend to happen with large molecules but are not simply related to size.) Multiple-model ensembles (such as from [[NMR]] experiments) may cause JSmol 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 JSmol by default have handled these issues:
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*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 Jmol_S instead of JSmol.
*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 Jmol_S instead of JSmol.


====Poor performance in Internet Explorer and Opera====
====Poor performance in Internet Explorer & Edge====


JSmol runs in the javascript of the browser (HTML5). Different web browsers operate JSmol with very different performances. '''Chrome runs JSmol best''', Safari is good, and Firefox is usually OK (see note under table below). '''Internet Explorer is unacceptably slow''' (all versions, including version 11), and [http://www.netmarketshare.com it is the most widely used browser]. In '''Opera, rotation of the molecule is slow and jerky'''.  
JSmol runs in the javascript of the browser. Different web browsers operate JSmol with very different performances (see [[JSmol/Rotation Speeds]]), and the performances vary as browser versions are updated. '''Internet Explorer has always been unacceptably slow''' (all versions, including version 11), but since early 2016, it is [http://www.netmarketshare.com no longer the most widely used browser].


*FirstGlance in Jmol detects the browser being used, and recommends a different browser when being displayed in Internet Explorer or Opera.
<center><span style="font-size:130%;">For current recommmendations, see  [[JSmol/Rotation Speeds]].</span></center>


The findings below are based primarily on tests with [[FirstGlance in Jmol]], and possibly results may be different for other JSmol websites.
FirstGlance in Jmol detects the browser being used, and recommends the optimal browser when another browser is used.
 
[[Image:Jsmol-vs-browsers.png|center]]
The above snapshot is taken from [[FirstGlance in Jmol]]. For more details, see the section ''Browser Pecularities'' in the [http://bioinformatics.org/firstglance/fgij/notes.htm Notes for FirstGlance].


==Converting Websites from Jmol to JSmol==
==Converting Websites from Jmol to JSmol==
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  --></pre>
  --></pre>


Add these two lines. Jmol2.js replaces Jmol.js, defining the same functions you were already using in Jmol.js.
Add these two lines. Jmol2.js replaces Jmol.js, defining the same functions you were already using in Jmol.js. The order of these two lines is critical: '''JSmol.min.js must come before Jmol2.js'''.


<pre><script type="text/javascript" src="jsmol/JSmol.min.js"></script>
<pre><script type="text/javascript" src="jsmol/JSmol.min.js"></script>
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===jmolInitialize()===
===jmolInitialize()===


Find jmolInitialize() in your code. If necessary, change the relative directory path argument of this function to reflect the location of the jsmol directory you have added. For example, if your main html file is in folder1/folder2/main.html, and the location of jsmol is folder1/jsmol, then from main.html, jmolInitialize("../../jsmol").
Find jmolInitialize() in your code. If necessary, change the relative directory path argument of this function to reflect the location of the jsmol directory you have added. For example, if your main html file is in folder1/folder2/main.html, and the location of jsmol is folder1/jsmol, then from main.html, jmolInitialize("../jsmol").
 
===(to be continued)===


I know that the above is incomplete. When I learn more I will add it here.
I know that the above is incomplete. When I learn more I will add it here.
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==See Also==
==See Also==
*[[Jmol]], where the four forms of Jmol are explained, and links are provided to other relevant articles.
*[[Jmol]], where the four forms of Jmol are explained, and links are provided to other relevant articles.
*[[JSmol/Rotation Speeds]] for the 6 most popular browsers, without and with Java.
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