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User:Eric Martz/JSmol Notes: Difference between revisions

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Atoms (Kilo)
Atoms (Kilo)
</td><td>
</td><td>
KD ([[Asymmetric Unit]])
kDa* ([[Asymmetric Unit]])
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</td>
</tr>
</tr>
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1.7
1.7
</td><td>
</td><td>
28
24 (28)
</td>
</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)
</td>
</td>
</tr>
</tr>
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23
23
</td><td>
</td><td>
233
220 (233)
</td>
</td>
</tr>
</tr>
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45
45
</td><td>
</td><td>
826
602 (826)
</td>
</td>
</tr>
</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.)
</td><td>
</td><td>
416 (20K x 20 NMR models)
416 = 19.8K x 21 NMR models (416)
</td>
</td>
</tr>
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<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.
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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, Edge, Chrome and Opera====
====Poor performance in Internet Explorer & Edge====


JSmol runs in the javascript of the browser. Different web browsers operate JSmol with very different performances (see [[JSmol/Rotation Speeds]]). '''Firefox runs JSmol best''' (Safari is equally good). '''Chrome''' and '''Opera''' are up to several fold slower, and '''Edge''' is about 4-fold slower. '''Internet Explorer is unacceptably slow''' (all versions, including version 11), but since early 2016, it is [http://www.netmarketshare.com no longer the most widely used browser]. Thus, Firefox is by far the best browser for JSmol. For details, see  [[JSmol/Rotation Speeds]].
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 not in Firefox.
<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.
<!--<table style="background:#ffffa0;" border="1" cellpadding="10"><tr><td>
Snapshot graphic table is temporarily unavailable in Proteopedia but '''[https://flic.kr/p/zHpKBU can be viewed here]'''.
</td></tr></table>-->
[[Image:Jsmol-vs-browsers.png|center|450px]]
The above snapshot is taken from [[FirstGlance in Jmol]]. For more details, see the [http://bioinformatics.org/firstglance/fgij/notes.htm#browsers Notes for FirstGlance].


==Converting Websites from Jmol to JSmol==
==Converting Websites from Jmol to JSmol==
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