Jmol/Interactivity
From Proteopedia
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To show ligand(s), click on the sun symbol in the parentheses (<jmol> | To show ligand(s), click on the sun symbol in the parentheses (<jmol> | ||
<jmolLink> | <jmolLink> | ||
| - | <script> select ligand; selectionHalos ON; delay 0.5;selectionHalos OFF;</script> | + | <script> select ligand or ATP; selectionHalos ON; delay 0.5;selectionHalos OFF;</script> |
<text>☼</text> | <text>☼</text> | ||
</jmolLink> | </jmolLink> | ||
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As a shortcut, you can use a template that inserts the code for you by entering: | As a shortcut, you can use a template that inserts the code for you by entering: | ||
<nowiki> | <nowiki> | ||
| - | {{subst:blink|ligand}} | + | {{subst:blink|ligand or ATP}}</nowiki> |
| - | </nowiki> | + | |
Once you type this (or paste it) into the editor and save it, the code above will be inserted. | Once you type this (or paste it) into the editor and save it, the code above will be inserted. | ||
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<jmol> | <jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
| - | <scriptWhenUnChecked>hide ligand or hidden</scriptWhenUnChecked> | + | <scriptWhenUnChecked>hide ligand or ATP or hidden</scriptWhenUnChecked> |
| - | <scriptWhenchecked>hide hidden and not ligand</scriptWhenchecked> | + | <scriptWhenchecked>hide hidden and not (ligand or ATP)</scriptWhenchecked> |
<checked>true</checked> | <checked>true</checked> | ||
| - | <text> | + | <text>ATP and metals</text> |
</jmolCheckbox> | </jmolCheckbox> | ||
</jmol> | </jmol> | ||
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<jmol> | <jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
| - | <scriptWhenUnChecked>hide ligand or hidden | + | <scriptWhenUnChecked>hide ligand or ATP or hidden |
</scriptWhenUnChecked> | </scriptWhenUnChecked> | ||
| - | <scriptWhenchecked>hide hidden and not ligand | + | <scriptWhenchecked>hide hidden and not (ligand or ATP) |
</scriptWhenchecked> | </scriptWhenchecked> | ||
<checked>true</checked> | <checked>true</checked> | ||
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Again, you can use a template to type less: | Again, you can use a template to type less: | ||
<nowiki> | <nowiki> | ||
| - | {{subst:Hide button| | + | {{subst:Hide button|ATP and metals|(ligand or ATP)}}</nowiki> |
| - | </nowiki> | + | |
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</nowiki> | </nowiki> | ||
| + | Again, you can use a template to type less: | ||
| + | <nowiki> | ||
| + | {{subst:Triple radio button | ||
| + | |Residue 35|select sidechain; spacefill off; select sidechain and 35 ; spacefill on | ||
| + | |Residue 52|select sidechain; spacefill off; select sidechain and 52 ; spacefill on | ||
| + | |No side chains|select sidechain; spacefill off}}</nowiki> | ||
| + | |||
| + | |||
| + | {{subst:Triple radio button | ||
| + | |Residue 35|select sidechain; spacefill off; select sidechain and 35 ; spacefill on | ||
| + | |Residue 52|select sidechain; spacefill off; select sidechain and 52 ; spacefill on | ||
| + | |No side chains|select sidechain; spacefill off}} | ||
</StructureSection> | </StructureSection> | ||
Revision as of 01:00, 10 September 2020
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Advantages
The commands issued by these interactive elements are in effect immediately, i.e. without delay. You could accomplish the same effect by saving a separate 3D scene, but this will always have a loading delay. The effect is that "playing" with interactive elements is much more immediate than switching between green links.
Caveats
The commands will be issued to the Jmol window irrespective of what is shown there. If you click on a green link elsewhere and then try the buttons etc, the effect is unpredictable. You can try this here by using the interactive elements before clicking on the button that loads the lysozyme structure. If you do that, the commands associated with the interactive elements will act on the UvrB structure instead.
