User:Karsten Theis/Animation course

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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.
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Choose a background
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1. Choose a background
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<jmol><jmolLink><script>background black</script><text>background black</text></jmolLink> </jmol>
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<jmol>
 +
<jmolRadioGroup>
 +
<item>
 +
<script>background black</script>
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<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>
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<text>white</text>
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<checked>true</checked>
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<jmol><jmolLink><script>background white</script><text>background white</text></jmolLink> </jmol>
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</item>
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<jmol><jmolLink><script>background image "http://proteopedia.org/wiki/images/6/60/Grid.png"</script><text>background grid</text></jmolLink> </jmol>
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</jmolRadioGroup>
 +
</jmol>
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<jmol><jmolLink><script>console; show moveto</script><text>orientation</text></jmolLink> </jmol>
 
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How do you want the opioid to look like?
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2. How, if it all, do you want to show the protein?
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<jmol><jmolLink><script>select BF0;center selected; spacefill only;spacefill 0.4;wireframe 0.15</script><text>ball and stick</text></jmolLink> </jmol>
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<jmol>
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<jmolRadioGroup>
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<item>
 +
<script>select protein; color group;</script>
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<text>rainbow</text>
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</item>
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<item>
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<script>select protein; color structure;</script>
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<text>by structure</text>
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</item>
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<item>
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<script>select protein; color magenta;</script>
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<text>magenta</text>
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</item>
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<item>
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<script>select protein; color magenta transparent 0.1;</script>
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<text>transparent</text>
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</item>
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<item>
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<script>select protein; color chain;</script>
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<text>boring</text>
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<checked>true</checked>
 +
</item>
 +
</jmolRadioGroup>
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</jmol>
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<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>
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<jmolLink>
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<jmolRadioGroup>
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<script> slab on; depth 40; var a = [80,70,65,63,62]; for(var i IN a) {slab @i; delay 0.4;};
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<item>
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</script>
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<script>select BF0;spacefill only;spacefill 0.4;wireframe 0.15</script>
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<text>Shave away</text>
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<text>ball-and-stick</text>
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</jmolLink>
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</item>
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<item>
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<script>select BF0;spacefill off;wireframe 0.3</script>
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<text>grid</text>
 +
</item>
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<item>
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<script>select BF0;spacefill only;</script>
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<text>spacefill</text>
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<checked>true</checked>
 +
</item>
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</jmolRadioGroup>
</jmol>
</jmol>
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 +
4. Other choices
<jmol>
<jmol>
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<jmolLink>
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<jmolCheckbox>
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<script> slab off;
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<scriptWhenChecked>slab on; depth 40; var a = [80,70,65,63,62]; for(var i IN a) {slab @i; delay 0.4;};</scriptWhenChecked>
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</script>
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<scriptWhenUnchecked>slab off;</scriptWhenUnchecked>
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<text>Everything</text>
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<checked>false</checked>
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</jmolLink>
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<text>slab?</text>
 +
</jmolCheckbox>
</jmol>
</jmol>
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Decide how and whether to show the protein
 
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<jmol><jmolLink><script>select protein; cartoon only; color group</script><text>rainbow cartoon</text></jmolLink> </jmol>
 
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<jmol><jmolLink><script>select protein; cartoon only; color magenta</script><text>magenta cartoon</text></jmolLink> </jmol>
 
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<jmol><jmolLink><script>select protein; cartoon only; color structure</script><text>helix-emphasize cartoon</text></jmolLink> </jmol>
 
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<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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Revision as of 18:23, 13 September 2019

Drag the structure with the mouse to rotate

References

Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis

Retrieved from "http://52.214.119.220/wiki/index.php/User:Karsten_Theis/Animation_course"
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