Jmol/Interactivity: Difference between revisions

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Editor, Macro, Print3D
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Karsten Theis (talk | contribs)
Editor, Macro, Print3D
4,602 edits
No edit summary
 
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===Button===
===Button===
This button loads a different molecule and scene, and makes sure waters and hidden and zshade is turned off:
This button loads a different molecule and scene, and makes sure waters are hidden and zshade is turned off:


<jmol>
<jmol>
Line 24: Line 24:
</jmol>
</jmol>
</nowiki>
</nowiki>
As a shortcut, you can use a template that inserts the code for you by entering:
<nowiki>
{{subst:Scene button|Lysozyme|37/376372/Overall/3|hide water; set zshade off}}</nowiki>
The string behind the first vertical line (the first parameter) is the button label, the string behind the second vertical line (the second parameter) is the scene like given by the SAT, and the string behind the third vertical line (the third parameter is the list of commands called right after the scene is loaded. Once you type this (or paste it) into the editor and save it, the code above will be inserted. You can learn more about templates at [https://www.mediawiki.org/wiki/Help:Templates].


===Link===
===Link===
Line 45: Line 51:
</nowiki>
</nowiki>


As a shortcut, you can use a template that inserts the code for you by entering:
As a shortcut for making a part of the structure "blink", you can use a template that inserts the code for you by entering:
  <nowiki>
  <nowiki>
{{subst:blink|ligand or ATP}}</nowiki>
{{subst:blink|ligand or ATP}}</nowiki>
Once you type this (or paste it) into the editor and save it, the code above will be inserted.


===Check box===
===Check box===
Line 78: Line 83:
Again, you can use a template to type less:
Again, you can use a template to type less:
  <nowiki>
  <nowiki>
{{subst:Hide button|ATP and metals|(ligand or ATP)}}</nowiki>
{{subst:Hide button|ligand or ATP|(ligand or ATP)}}</nowiki>
 


<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>display displayed or ATP</scriptWhenChecked>
    <scriptWhenUnchecked>hide ATP or hidden</scriptWhenUnchecked>
    <checked>true</checked>
    <text> ATP molecule </text>
  </jmolCheckbox>
</jmol>


===Radio button===
===Radio button===


Please load <scene name='37/376372/Product_complex/6'>this scene</scene> before trying out the radiobuttons.
This set of buttons selects one side chain to be shown (or none).
This set of buttons selects one side chain to be shown (or none).
<jmol>
<jmol>
Line 134: Line 150:
|Residue 52|select sidechain; spacefill off; select sidechain and 52; spacefill on
|Residue 52|select sidechain; spacefill off; select sidechain and 52; spacefill on
|No side chains|select sidechain; spacefill off}}</nowiki>
|No side chains|select sidechain; spacefill off}}</nowiki>
Before you use the template above, please remove the line breaks so that the entire command is on a single line, otherwise it does not work.
===Buttons to store and retrieve orientation===
This pair of buttons allows to save an orientation by pressing the first button, and return to the same orienation by pressing the second. Multiple pairs of these buttons allow to choreograph an animation and play it by pushing the buttons. The orientations are not saved beyond a session, though.
<jmol><jmolButton><script>view1 = script("show moveto")[11][0]</script><text>store view 1</text></jmolButton> </jmol> <jmol><jmolButton><script>script inline @{"moveto 1.0" + view1}</script><text>retrieve view 1</text></jmolButton></jmol>
<nowiki>
<jmol>
  <jmolButton>
    <script>view1 = script("show moveto")[11][0]</script>
    <text>store view 1</text>
  </jmolButton>
</jmol> <jmol>
  <jmolButton>
    <script>script inline @{"moveto 1.0" + view1}</script>
    <text>retrieve view 1</text>
  </jmolButton>
</jmol></nowiki>
Again, you can use a template to type less:
<nowiki>
{{subst:Store view buttons}}</nowiki>
For more than one view, just add another pair of buttons and change view1 to view2. For a more elaborate example how to use buttons to dock a ligand, see [[User:Karsten Theis/Animation course]].
==Button to choose a fixed orientation and view==
Here is the <scene name='84/849728/Uvrb/1'>structure of UvrB</scene>. To zoom into different areas, use the two buttons below. The orientation and view are set manually and retrieved with the command "show moveto".


<jmol>
<jmol>
   <jmolRadioGroup>
   <jmolButton>
     <item>
     <script>moveto 1.0 { -905 -235 355 100.12} 535.03 0.0 0.0 {42.099225806451614 43.53887096774192 61.17029032258063} 68.42333343999844 {0 0 0} 0 0 0 3.0 0.0 0.0;</script>
      <script>select sidechain; spacefill off; select sidechain and 35; spacefill on</script>
    <text>🔎ATP binding</text>
      <text>Residue 35</text>
  </jmolButton>
    </item>
</jmol>
    <item>
 
      <script>select sidechain; spacefill off; select sidechain and 52; spacefill on</script>
<jmol>
      <text>Residue 52</text>
  <jmolButton>
    </item>
    <script>moveto 1.0 { -953 -276 126 132.73} 305.9 0.0 0.0 {61.51899999999999 9.498000000000001 60.450250000000004} 66.2379949723743 {0 0 0} 0 0 0 3.0 0.0 0.0;</script>
    <item>
    <text>🔎DNA padlock</text>
      <script>select sidechain; spacefill off</script>
  </jmolButton>
      <text>No side chains</text>
      <checked>true</checked>
    </item>
  </jmolRadioGroup>
</jmol>
</jmol>
<nowiki>
<jmol>
  <jmolButton>
    <script>moveto 1.0 { -953 -276 126 132.73} 305.9 0.0 0.0
{61.51899999999999 9.498000000000001 60.450250000000004}
66.2379949723743 {0 0 0} 0 0 0 3.0 0.0 0.0;</script>
    <text>🔎DNA padlock</text>
  </jmolButton>
</jmol></nowiki>
Again, you can use a template to type less:
<nowiki>
{{subst:Lookat button|ATP binding|1.0 { -905 -235 355 100.12}
535.03 0.0 0.0 {42.099225806451614 43.53887096774192 61.17029032258063}
68.42333343999844 {0 0 0} 0 0 0 3.0 0.0 0.0;}}</nowiki>


</StructureSection>
</StructureSection>
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