User:Karsten Theis/Animation course: Difference between revisions

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Karsten Theis (talk | contribs)
Editor, Macro, Print3D
4,602 edits
No edit summary
Karsten Theis (talk | contribs)
Editor, Macro, Print3D
4,602 edits
No edit summary
Line 1: Line 1:
<StructureSection load='' size='340' side='right' caption='' scene='52/520489/Ligand_pocket/2'>
<StructureSection load='' size='340' side='right' caption='' scene='52/520489/Ligand_pocket/2'>


==Learn how to animate with Jmol==
==Animate a scene with Jmol==
 
===Load the scene and choose a look===
<scene name='52/520489/Ligand_pocket/2'>mu opioid receptor</scene>
<scene name='52/520489/Ligand_pocket/2'>mu opioid receptor</scene>


Line 12: Line 14:
<jmol><jmolLink><script>console; show moveto</script><text>orientation</text></jmolLink> </jmol>
<jmol><jmolLink><script>console; show moveto</script><text>orientation</text></jmolLink> </jmol>


<jmol><jmolLink><script>select BF0;spacefill only;spacefill 0.4;wireframe 0.15</script><text>ball andstick</text></jmolLink> </jmol>
<jmol><jmolLink><script>select BF0;spacefill only;spacefill 0.4;wireframe 0.15</script><text>ball and stick</text></jmolLink> </jmol>


<jmol><jmolLink><script>select BF0;spacefill only;</script><text>ball andstick</text></jmolLink> </jmol>
<jmol><jmolLink><script>select BF0;spacefill only;</script><text>spacefill</text></jmolLink> </jmol>


<jmol>
<jmol>
  <jmolLink>
  <jmolLink>
   <script> slab on; depth 40; var a = [80,70,60,55,53,52]; for(var i IN a) {slab @i; delay 0.4;}; script "http://proteopedia.org/wiki/images/7/76/Wobble.spt"
   <script> slab on; depth 40; var a = [80,70,65,63,62]; for(var i IN a) {slab @i; delay 0.4;};  
   </script>
   </script>
   <text>Shave away and wobble</text>
   <text>Shave away</text>
</jmolLink>
</jmol>
 
<jmol>
<jmolLink>
  <script> slab off;
  </script>
  <text>Everything</text>
  </jmolLink>
  </jmolLink>
</jmol>
</jmol>
Line 32: Line 42:
<jmol><jmolLink><script>select protein; color structure</script><text>helix</text></jmolLink> </jmol>
<jmol><jmolLink><script>select protein; color structure</script><text>helix</text></jmolLink> </jmol>


===Save some orientations===
<jmol><jmolLink><script>x1 = script("show moveto")[11][0]</script><text>view 1</text></jmolLink> </jmol>
<jmol><jmolLink><script>x2 = script("show moveto")[11][0]</script><text>view 2</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>
x = script("show moveto")[11][0]
speed = "moveto 4.0"
script inline @{speed + x}
===Transition between orientations===
Select a transition speed: <jmol><jmolLink><script>speed = "moveto 1.0"</script><text>1 sec</text></jmolLink> <jmol><jmolLink><script>speed = "moveto 2.0"</script><text>2 sec</text></jmolLink> <jmol><jmolLink><script>speed = "moveto 4.0"</script><text>4 sec</text></jmolLink> <jmol><jmolLink><script>speed = "moveto 10.0"</script><text>10 sec</text></jmolLink> </jmol>
Go to different views: 
<jmol><jmolLink><script>script inline @{speed + x1}</script><text>V1</text></jmolLink> <jmol><jmolLink><script>script inline @{speed + x2}</script><text>V2</text></jmolLink> <jmol><jmolLink><script>script inline @{speed + x3}</script><text>V3</text></jmolLink> <jmol><jmolLink><script>script inline @{speed + x4}</script><text>V4</text></jmolLink> 




<script type="text/javascript">
jmolBr()
Jmol.setButtonCss(null,"style='width:120px'")
jmolButton("color cpk")
jmolButton("color group")
jmolButton("color amino")
jmolButton("color structure")
jmolBr()
jmolButton("trace only")
jmolButton("cartoon only")
jmolButton("backbone only")
jmolButton("spacefill only;spacefill 23%;wireframe 0.15","ball&stick")
jmolBr()
Jmol.setButtonCss(null,"style='width:60px'")
jmolButton("Model")
Jmol.setButtonCss(null,"style='width:50px'")
jmolButton("model; if (!isDssp) { save structure s1; isDssp = true; calculate structure DSSP;cartoons only;color structure}", "DSSP")
Jmol.setButtonCss(null,"style='width:50px'")
jmolButton("model; if (isDssp) { restore structure s1; isDssp = false; cartoons only;color structure}", "Auth")
Jmol.setButtonCss(null,"style='width:160px'")
jmolButton("Ramachandran relative")
jmolButton("Quaternion difference")
jmolBr()
Jmol.setButtonCss(null,"style='width:100px'")
jmolButton("console")
Jmol.jmolCommandInput(jmolApplet0)
</script>


==Collection of molecules==
==Collection of molecules==
Retrieved from "https://proteopedia.org/User:Karsten_Theis/Animation_course"