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| | == Jmol extension for MediaWiki == | | == Jmol extension for MediaWiki == |
| | + | {{Anchor|SampleAnchor}} |
| | | | |
| − | This uses <code>uploadedFileContents</code> tag with an XYZ file:
| + | etc. |
| − | <jmol>
| |
| − | <jmolApplet>
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| − | <name>chair</name>
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| − | <size>200</size>
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| − | <uploadedFileContents>Chair.xyz</uploadedFileContents>
| |
| − | </jmolApplet>
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| − | <jmolLink>
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| − | <script>color atoms red</script>
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| − | <text>color atoms red</text>
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| − | </jmolLink>
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| − | <jmolLink>
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| − | <script>color atoms blue</script>
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| − | <text>color atoms blue</text>
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| − | </jmolLink>
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| − | <jmolCheckbox>
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| − | <scriptWhenChecked>color atoms lime</scriptWhenChecked>
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| − | <scriptWhenUnchecked>color atoms cpk</scriptWhenUnchecked>
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| − | <text>color atoms lime</text>
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| − | <target>chair</target>
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| − | </jmolCheckbox>
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| | | | |
| − | <jmolButton>
| + | etc. |
| − | <script>color atoms blue</script>
| |
| − | <text>color atoms blue</text>
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| − | </jmolButton>
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| | | | |
| − | </jmol>
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| − | For some reason, checkboxes are not working with the extension.
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| | | | |
| − | Color atoms:
| + | == Anchors == |
| − | <jmol>
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| − | <jmolMenu>
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| − | <item>
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| − | <script>color atoms cpk</script>
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| − | <text>default</text>
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| − | </item>
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| − | <item>
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| − | <script>color atoms yellow</script>
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| − | <text>yellow</text>
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| − | </item>
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| − | <item>
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| − | <script>color atoms blue</script>
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| − | <text>blue</text>
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| − | </item>
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| − | </jmolMenu>
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| − | </jmol>
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| | | | |
| | + | This is a test link to an [[#SampleAnchor|anchor]] which should take you near the top of the article. |
| | | | |
| − | This one uses the <code>inlineContents</code> tag, with straight MOL data on the left applet and with added pipe characters (|) on the right applet:
| |
| − | <table width="100%"><tr>
| |
| − | <td>
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| − | <jmol>
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| − | <jmolApplet>
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| − | <size>150</size>
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| − | <color>green</color>
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| − | <inlineContents>chair.mol
| |
| − | Conformational analysis
| |
| − | 0
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| − | 18 18 0 0 0 1 V2000
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| − | 1.6881 2.1572 -3.0193 C 0 0 0 0 0
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| − | 2.1484 3.6217 -2.9797 C 0 0 0 0 0
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| − | 2.9361 3.9126 -1.6942 C 0 0 0 0 0
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| − | 2.0927 3.5769 -0.4557 C 0 0 0 0 0
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| − | 1.6329 2.1120 -0.4898 C 0 0 0 0 0
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| − | 0.8532 1.8102 -1.7778 C 0 0 0 0 0
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| − | 2.5807 1.4887 -3.0652 H 0 0 0 0 0
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| − | 1.0897 1.9711 -3.9430 H 0 0 0 0 0
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| − | 1.2578 4.2927 -3.0282 H 0 0 0 0 0
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| − | 2.7791 3.8474 -3.8727 H 0 0 0 0 0
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| − | 3.8725 3.3053 -1.6844 H 0 0 0 0 0
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| − | 3.2413 4.9861 -1.6685 H 0 0 0 0 0
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| − | 1.2005 4.2467 -0.4224 H 0 0 0 0 0
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| − | 2.6835 3.7700 0.4714 H 0 0 0 0 0
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| − | 0.9957 1.8928 0.4002 H 0 0 0 0 0
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| − | 2.5240 1.4426 -0.4294 H 0 0 0 0 0
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| − | 0.5642 0.7322 -1.8031 H 0 0 0 0 0
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| − | -0.0919 2.4039 -1.7878 H 0 0 0 0 0
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| − | 1 2 1 0 0 0
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| − | 1 6 1 1 0 0
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| − | 1 7 1 0 0 0
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| − | 1 8 1 6 0 0
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| − | 2 3 1 1 0 0
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| − | 2 9 1 0 0 0
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| − | 2 10 1 6 0 0
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| − | 3 4 1 1 0 0
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| − | 3 11 1 0 0 0
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| − | 3 12 1 0 0 0
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| − | 4 5 1 0 0 0
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| − | 4 13 1 0 0 0
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| − | 4 14 1 1 0 0
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| − | 5 6 1 6 0 0
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| − | 5 15 1 1 0 0
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| − | 5 16 1 0 0 0
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| − | 6 17 1 0 0 0
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| − | 6 18 1 0 0 0
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| − | M END
| |
| − | </inlineContents>
| |
| − | </jmolApplet>
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| − | </jmol>
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| − | </td>
| |
| − | <td>
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| − | <jmol>
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| − | <jmolApplet>
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| − | <size>150</size>
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| − | <color>green</color>
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| − | <inlineContents>|chair.mol
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| − | |Conformational analysis
| |
| − | |0
| |
| − | | 18 18 0 0 0 1 V2000
| |
| − | | 1.6881 2.1572 -3.0193 C 0 0 0 0 0
| |
| − | | 2.1484 3.6217 -2.9797 C 0 0 0 0 0
| |
| − | | 2.9361 3.9126 -1.6942 C 0 0 0 0 0
| |
| − | | 2.0927 3.5769 -0.4557 C 0 0 0 0 0
| |
| − | | 1.6329 2.1120 -0.4898 C 0 0 0 0 0
| |
| − | | 0.8532 1.8102 -1.7778 C 0 0 0 0 0
| |
| − | | 2.5807 1.4887 -3.0652 H 0 0 0 0 0
| |
| − | | 1.0897 1.9711 -3.9430 H 0 0 0 0 0
| |
| − | | 1.2578 4.2927 -3.0282 H 0 0 0 0 0
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| − | | 2.7791 3.8474 -3.8727 H 0 0 0 0 0
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| − | | 3.8725 3.3053 -1.6844 H 0 0 0 0 0
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| − | | 3.2413 4.9861 -1.6685 H 0 0 0 0 0
| |
| − | | 1.2005 4.2467 -0.4224 H 0 0 0 0 0
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| − | | 2.6835 3.7700 0.4714 H 0 0 0 0 0
| |
| − | | 0.9957 1.8928 0.4002 H 0 0 0 0 0
| |
| − | | 2.5240 1.4426 -0.4294 H 0 0 0 0 0
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| − | | 0.5642 0.7322 -1.8031 H 0 0 0 0 0
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| − | | -0.0919 2.4039 -1.7878 H 0 0 0 0 0
| |
| − | | 1 2 1 0 0 0
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| − | | 1 6 1 1 0 0
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| − | | 1 7 1 0 0 0
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| − | | 1 8 1 6 0 0
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| − | | 2 3 1 1 0 0
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| − | | 2 9 1 0 0 0
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| − | | 2 10 1 6 0 0
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| − | | 3 4 1 1 0 0
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| − | | 3 11 1 0 0 0
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| − | | 3 12 1 0 0 0
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| − | | 4 5 1 0 0 0
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| − | | 4 13 1 0 0 0
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| − | | 4 14 1 1 0 0
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| − | | 5 6 1 6 0 0
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| − | | 5 15 1 1 0 0
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| − | | 5 16 1 0 0 0
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| − | | 6 17 1 0 0 0
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| − | | 6 18 1 0 0 0
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| − | |M END
| |
| − | </inlineContents>
| |
| − | </jmolApplet>
| |
| − | </jmol>
| |
| − | </td>
| |
| − | </tr></table>
| |
| − | None of them work. This seems due to a defective parsing of newlines by the extension.
| |
| | | | |
| − | Let's test the same with inline PDB data:
| |
| − | <table width="100%"><tr>
| |
| − | <td>
| |
| − | <jmol>
| |
| − | <jmolApplet>
| |
| − | <size>150</size>
| |
| − | <inlineContents>
| |
| − | REMARK Butane
| |
| − | HETATM 1 C UNK 0 -0.769 0.000 0.000 C
| |
| − | HETATM 2 C UNK 0 0.769 0.000 0.000 C
| |
| − | HETATM 3 C UNK 0 -1.383 -0.728 1.203 C
| |
| − | HETATM 4 C UNK 0 1.382 -0.741 1.196 C
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| − | HETATM 5 H UNK 0 -1.127 1.059 0.007 H
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| − | HETATM 6 H UNK 0 -1.142 -0.461 -0.945 H
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| − | HETATM 7 H UNK 0 -1.001 -0.311 2.163 H
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| − | HETATM 8 H UNK 0 1.128 -0.488 -0.940 H
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| − | HETATM 9 H UNK 0 1.143 1.051 -0.017 H
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| − | HETATM 10 H UNK 0 -2.493 -0.625 1.206 H
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| − | HETATM 11 H UNK 0 -1.156 -1.818 1.183 H
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| − | HETATM 12 H UNK 0 2.492 -0.792 1.105 H
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| − | HETATM 13 H UNK 0 1.155 -0.230 2.158 H
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| − | HETATM 14 H UNK 0 1.000 -1.787 1.259 H
| |
| − | END
| |
| − | </inlineContents>
| |
| − | </jmolApplet>
| |
| − | </jmol>
| |
| − | </td>
| |
| − | <td>
| |
| − | <jmol>
| |
| − | <jmolApplet>
| |
| − | <size>150</size>
| |
| − | <inlineContents>
| |
| − | |REMARK Butane
| |
| − | |HETATM 1 C UNK 0 -0.769 0.000 0.000 C
| |
| − | |HETATM 2 C UNK 0 0.769 0.000 0.000 C
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| − | |HETATM 3 C UNK 0 -1.383 -0.728 1.203 C
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| − | |HETATM 4 C UNK 0 1.382 -0.741 1.196 C
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| − | |HETATM 5 H UNK 0 -1.127 1.059 0.007 H
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| − | |HETATM 6 H UNK 0 -1.142 -0.461 -0.945 H
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| − | |HETATM 7 H UNK 0 -1.001 -0.311 2.163 H
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| − | |HETATM 8 H UNK 0 1.128 -0.488 -0.940 H
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| − | |HETATM 9 H UNK 0 1.143 1.051 -0.017 H
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| − | |HETATM 10 H UNK 0 -2.493 -0.625 1.206 H
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| − | |HETATM 11 H UNK 0 -1.156 -1.818 1.183 H
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| − | |HETATM 12 H UNK 0 2.492 -0.792 1.105 H
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| − | |HETATM 13 H UNK 0 1.155 -0.230 2.158 H
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| − | |HETATM 14 H UNK 0 1.000 -1.787 1.259 H
| |
| − | |END
| |
| − | </inlineContents>
| |
| − | </jmolApplet>
| |
| − | </jmol>
| |
| − | </td>
| |
| − | </tr></table>
| |
| − | The right applet works. The difference with MOL format is likely because MOL requires the lines in a certain order, while PDB relies on the starting keyword.
| |
| − | I think that the extension is inserting extra newlines and quotes, that spoil the MOL parser but not the PDB parser. The newlines are ignored by Jmol.js, or replaced by pipes. Manually added pipes restore a proper start of line for the PDB parser.
| |
| − | --[[User:AngelHerraez|AngelHerraez]] 22:11, 30 November 2008 (CET)
| |
| | | | |
| | | | |
| − | Finally, if we insert the MOL data without any newlines and with pipes:
| |
| − | <jmol>
| |
| − | <jmolApplet>
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| − | <size>150</size>
| |
| − | <color>green</color>
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| − | <inlineContents>chair.mol|Conformational analysis|0| 18 18 0 0 0 1 V2000 | 1.6881 2.1572 -3.0193 C 0 0 0 0 0 | 2.1484 3.6217 -2.9797 C 0 0 0 0 0 | 2.9361 3.9126 -1.6942 C 0 0 0 0 0 | 2.0927 3.5769 -0.4557 C 0 0 0 0 0 | 1.6329 2.1120 -0.4898 C 0 0 0 0 0 | 0.8532 1.8102 -1.7778 C 0 0 0 0 0 | 2.5807 1.4887 -3.0652 H 0 0 0 0 0 | 1.0897 1.9711 -3.9430 H 0 0 0 0 0 | 1.2578 4.2927 -3.0282 H 0 0 0 0 0 | 2.7791 3.8474 -3.8727 H 0 0 0 0 0 | 3.8725 3.3053 -1.6844 H 0 0 0 0 0 | 3.2413 4.9861 -1.6685 H 0 0 0 0 0 | 1.2005 4.2467 -0.4224 H 0 0 0 0 0 | 2.6835 3.7700 0.4714 H 0 0 0 0 0 | 0.9957 1.8928 0.4002 H 0 0 0 0 0 | 2.5240 1.4426 -0.4294 H 0 0 0 0 0 | 0.5642 0.7322 -1.8031 H 0 0 0 0 0 | -0.0919 2.4039 -1.7878 H 0 0 0 0 0 | 1 2 1 0 0 0 | 1 6 1 1 0 0 | 1 7 1 0 0 0 | 1 8 1 6 0 0 | 2 3 1 1 0 0 | 2 9 1 0 0 0 | 2 10 1 6 0 0 | 3 4 1 1 0 0 | 3 11 1 0 0 0 | 3 12 1 0 0 0 | 4 5 1 0 0 0 | 4 13 1 0 0 0 | 4 14 1 1 0 0 | 5 6 1 6 0 0 | 5 15 1 1 0 0 | 5 16 1 0 0 0 | 6 17 1 0 0 0 | 6 18 1 0 0 0 |M END
| |
| − | </inlineContents>
| |
| − | </jmolApplet>
| |
| − | </jmol>
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| − | things work, so IT IS the newlines.
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| | | | |
| − | === Get the model from a different server ===
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| − | (Uses <code>urlContents</code>).
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| | | | |
| − | I'm not sure if the use of the signed applet is allowed in the configuration of the Jmol MediaWiki Extension for the Jmol Wiki (I rather think it is not).
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| − | But this example is working with the unsigned applet even if I set <code><signed>true</signed></code> or <code><signed>false</signed></code>.
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| | | | |
| − | Supposedly the unsigned applet should not load a model coming from a different web domain, as per Java security rules... What's going on?
| |
| | | | |
| − | <table width="100%">
| |
| − | <tr align="center">
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| − | <td>Using <code><signed>true</signed></code>:<br>
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| − | <jmol><jmolApplet>
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| − | <signed>true</signed>
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| − | <name>1CRN</name><color>[xFFAAAA]</color><size>300</size>
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| − | <urlContents>http://biomodel.uah.es/model3j/glc_bd_p.pdb</urlContents>
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| − | </jmolApplet></jmol>
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| − | </td>
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| − | <td>Using <code><signed>false</signed></code>:<br>
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| − | <jmol><jmolApplet>
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| − | <signed>false</signed>
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| − | <name>1CRN</name><color>[xFFFFAA]</color><size>300</size>
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| − | <urlContents>http://biomodel.uah.es/model3j/glc_bd_p.pdb</urlContents>
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| − | </jmolApplet></jmol>
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| − | </td>
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| − | </tr></table>
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| | | | |
| − | == Using a pop-up window ==
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| − | An image used for illustration and a caption for requesting the Jmol model:
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| | | | |
| − | {|name="userboxes" id="userboxes" style="margin-left: 1em; margin-bottom: 0.5em; width: 170px; border: {{{bordercolor|#99B3FF}}} solid 1px; background-color: {{{backgroundcolor|#FFFFFF}}}; {{{extra-css|}}}" align="right"
| + | |
| − | |-
| + | |
| − | |<center>[[Image:Ethane s.gif]]</center>
| + | |
| − | |-
| + | |
| − | | <center>'''Staggered ethane''' <br />
| + | |
| − | <jmol><jmolAppletLink><title>Show in 3D using Jmol (popup window)</title><color>gray</color>
| + | |
| − | <uploadedFileContents>ethane_s.pdb</uploadedFileContents></jmolAppletLink>
| + | |
| − | </jmol>
| + | |
| − | </center>
| + | |
| − | |-
| + | |
| − | |}
| + | |
| | + | |
| | + | |
| | + | |
| | + | |
| | + | |
| | + | |
| | + | |
| | + | . |
