User:Karsten Theis/Animation course: Difference between revisions

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Karsten Theis (talk | contribs)
Editor, Macro, Print3D
4,602 edits
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Karsten Theis (talk | contribs)
Editor, Macro, Print3D
4,602 edits
No edit summary
Line 6: Line 6:
Open <jmol><jmolLink><script>script "http://proteopedia.org/scripts/52/520489/Ligand_pocket/2.spt"; x1 = script("show moveto")[11][0]; rotate y 90; x2 = script("show moveto")[11][0]; rotate x -90;x3 = script("show moveto")[11][0]; rotate y -90;x4 = script("show moveto")[11][0]; speed = "moveto 2.0"; script inline @{speed + x1}</script><text>mu opioid receptor</text></jmolLink></jmol> and use your skills learned from the [[viewing guide]] to explore the scene.
Open <jmol><jmolLink><script>script "http://proteopedia.org/scripts/52/520489/Ligand_pocket/2.spt"; x1 = script("show moveto")[11][0]; rotate y 90; x2 = script("show moveto")[11][0]; rotate x -90;x3 = script("show moveto")[11][0]; rotate y -90;x4 = script("show moveto")[11][0]; speed = "moveto 2.0"; script inline @{speed + x1}</script><text>mu opioid receptor</text></jmolLink></jmol> and use your skills learned from the [[viewing guide]] to explore the scene.


Choose a background
1. Choose a background
<jmol><jmolLink><script>background black</script><text>background black</text></jmolLink> </jmol>
<jmol>
  <jmolRadioGroup>
    <item>
      <script>background black</script>
      <text>black</text>
    </item>
    <item>
      <script>background image "http://proteopedia.org/wiki/images/6/60/Grid.png"</script>
      <text>grid</text>
    </item>
    <item>
      <script>background lightgray</script>
      <text>gray</text>
    </item>
    <item>
      <script>background white</script>
      <text>white</text>
      <checked>true</checked>


<jmol><jmolLink><script>background white</script><text>background white</text></jmolLink> </jmol>
    </item>


<jmol><jmolLink><script>background image "http://proteopedia.org/wiki/images/6/60/Grid.png"</script><text>background grid</text></jmolLink> </jmol>
  </jmolRadioGroup>
</jmol>


<jmol><jmolLink><script>console; show moveto</script><text>orientation</text></jmolLink> </jmol>


How do you want the opioid to look like?
2. How, if it all, do you want to show the protein?


<jmol><jmolLink><script>select BF0;center selected; spacefill only;spacefill 0.4;wireframe 0.15</script><text>ball and stick</text></jmolLink> </jmol>
<jmol>
  <jmolRadioGroup>
    <item>
      <script>select protein; color group;</script>
      <text>rainbow</text>
    </item>
    <item>
      <script>select protein; color structure;</script>
      <text>by structure</text>
    </item>
    <item>
      <script>select protein; color magenta;</script>
      <text>magenta</text>
    </item>
    <item>
      <script>select protein; color magenta transparent 0.1;</script>
      <text>transparent</text>
    </item>
    <item>
      <script>select protein; color chain;</script>
      <text>boring</text>
      <checked>true</checked>
    </item>
  </jmolRadioGroup>
</jmol>


<jmol><jmolLink><script>select BF0;center selected; spacefill only;</script><text>spacefill</text></jmolLink> </jmol>


3. How do you want the opioid to look like?
<jmol>
<jmol>
<jmolLink>
  <jmolRadioGroup>
  <script> slab on; depth 40; var a = [80,70,65,63,62]; for(var i IN a) {slab @i; delay 0.4;};  
    <item>
  </script>
      <script>select BF0;spacefill only;spacefill 0.4;wireframe 0.15</script>
  <text>Shave away</text>
      <text>ball-and-stick</text>
</jmolLink>
    </item>
    <item>
      <script>select BF0;spacefill off;wireframe 0.3</script>
      <text>grid</text>
    </item>
    <item>
      <script>select BF0;spacefill only;</script>
      <text>spacefill</text>
      <checked>true</checked>
    </item>
  </jmolRadioGroup>
</jmol>
</jmol>
4. Other choices


<jmol>
<jmol>
<jmolLink>
  <jmolCheckbox>
  <script> slab off;  
    <scriptWhenChecked>slab on; depth 40; var a = [80,70,65,63,62]; for(var i IN a) {slab @i; delay 0.4;};</scriptWhenChecked>
  </script>
    <scriptWhenUnchecked>slab off;</scriptWhenUnchecked>
  <text>Everything</text>
    <checked>false</checked>  
</jmolLink>
    <text>slab?</text>
  </jmolCheckbox>
</jmol>
</jmol>
Decide how and whether to show the protein
<jmol><jmolLink><script>select protein; cartoon only; color group</script><text>rainbow cartoon</text></jmolLink> </jmol>
<jmol><jmolLink><script>select protein; cartoon only; color magenta</script><text>magenta cartoon</text></jmolLink> </jmol>
<jmol><jmolLink><script>select protein; cartoon only; color structure</script><text>helix-emphasize cartoon</text></jmolLink> </jmol>
<jmol><jmolLink><script>select protein; cartoon off; </script><text>no protein</text></jmolLink> </jmol>


===Save some orientations===
===Save some orientations===
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<jmol><jmolLink><script>x3 = script("show moveto")[11][0]</script><text>view 3</text></jmolLink> </jmol>
<jmol><jmolLink><script>x3 = script("show moveto")[11][0]</script><text>view 3</text></jmolLink> </jmol>
<jmol><jmolLink><script>x4 = script("show moveto")[11][0]</script><text>view 4</text></jmolLink> </jmol>
<jmol><jmolLink><script>x4 = script("show moveto")[11][0]</script><text>view 4</text></jmolLink> </jmol>




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