User:Karsten Theis/Animation course

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Current revision (13:39, 10 February 2025) (edit) (undo)
 
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<StructureSection load='' size='340' side='right' caption='' scene=''>
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<StructureSection load='' size='340' side='right' caption='' scene='52/520489/Ligand_pocket/2'>
==Animate a scene with Jmol==
==Animate a scene with Jmol==
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===Recall ligand position===
===Recall ligand position===
Clicking on the links below will restore the ligand position (scene0 is the original position in the binding pocket):
Clicking on the links below will restore the ligand position (scene0 is the original position in the binding pocket):
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<jmol><jmolLink><script>ROTATE COMPARE {BF0} @{temp0} -2</script><text>retrieve state 0</text></jmolLink></jmol>
<jmol><jmolLink><script>ROTATE COMPARE {BF0} @{temp0} -2</script><text>retrieve state 0</text></jmolLink></jmol>
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To animate, click below
To animate, click below
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<jmol><jmolLink><script>set picking none</script><text>turn of ligand dragging</text></jmolLink></jmol>
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<jmol><jmolLink><script>set picking none</script><text>turn off ligand dragging</text></jmolLink></jmol>
<jmol><jmolLink><script>ROTATE COMPARE {BF0} @{temp3} -2; ROTATE COMPARE {BF0} @{temp2} -2; ROTATE COMPARE {BF0} @{temp1} -2; ROTATE COMPARE {BF0} @{temp0} -2;</script><text>bind</text></jmolLink></jmol>
<jmol><jmolLink><script>ROTATE COMPARE {BF0} @{temp3} -2; ROTATE COMPARE {BF0} @{temp2} -2; ROTATE COMPARE {BF0} @{temp1} -2; ROTATE COMPARE {BF0} @{temp0} -2;</script><text>bind</text></jmolLink></jmol>
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<jmol><jmolLink><script>moveto 1.0 { 802 6 -597 24.36} 5.1 45.3 23.42 {-1.40835 0.07379999999999987 -0.28485000000000005} 9.158727403987475 {0 0 0} 0 0 0 3.0 0.0 0.0; </script><text>zoom out</text></jmolLink> </jmol>
<jmol><jmolLink><script>moveto 1.0 { 802 6 -597 24.36} 5.1 45.3 23.42 {-1.40835 0.07379999999999987 -0.28485000000000005} 9.158727403987475 {0 0 0} 0 0 0 3.0 0.0 0.0; </script><text>zoom out</text></jmolLink> </jmol>
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==Morph a helix==
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Here is the SARS-2 <scene name='82/824516/Spike/5'>spike protein</scene>.
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(<jmol><jmolLink><script>delete chain="B"; delete chain="C"; model 1; select protein; backbone only; select chain="X"; cartoon on; select 912, 982; spacefill 5.0; select 1.2; color red; model 0; select chain="X"; set picking dragselected; set allowrotateselected; temp0 = {chain="X"}.xyz.all</script><text>click to prepare</text></jmolLink></jmol>)
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Click and drag on the ligand to move it. Alt-click and drag on the ligand to rotate it. Click and drag away from the ligand to adjust the view. To store each consecutive ligand position, consecutively click on the links below:
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<jmol><jmolLink><script>temp1 = {:X}.xyz.all</script><text>store state 1</text></jmolLink></jmol>
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<jmol><jmolLink><script>temp2 = {:X}.xyz.all</script><text>store state 2</text></jmolLink></jmol>
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<jmol><jmolLink><script>temp3 = {:X}.xyz.all</script><text>store state 3</text></jmolLink></jmol>
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<jmol><jmolLink><script>temp4 = {:X}.xyz.all</script><text>store state 4</text></jmolLink></jmol>
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===Recall ligand position===
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Clicking on the links below will restore the ligand position (scene0 is the original position in the binding pocket):
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<jmol><jmolLink><script>ROTATE COMPARE {:X} @{temp0} -2</script><text>retrieve state 0</text></jmolLink></jmol>
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<jmol><jmolLink><script>ROTATE COMPARE {:X} @{temp1} -2</script><text>retrieve state 1</text></jmolLink></jmol>
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<jmol><jmolLink><script>ROTATE COMPARE {:X} @{temp2} -2</script><text>retrieve state 2</text></jmolLink></jmol>
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<jmol><jmolLink><script>ROTATE COMPARE {:X} @{temp3} -2</script><text>retrieve state 3</text></jmolLink></jmol>
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<jmol><jmolLink><script>ROTATE COMPARE {:X} @{temp4} -2</script><text>retrieve state 4</text></jmolLink></jmol>
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To animate, click below
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<jmol><jmolLink><script>set picking none</script><text>turn of ligand dragging</text></jmolLink></jmol>
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<jmol><jmolLink><script>ROTATE COMPARE {:X} @{temp3} -2; ROTATE COMPARE {:X} @{temp2} -2; ROTATE COMPARE {:X} @{temp1} -2; ROTATE COMPARE {:X} @{temp0} -2;</script><text>bind</text></jmolLink></jmol>
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<jmol><jmolLink><script>ROTATE COMPARE {:X} @{temp1} -2; ROTATE COMPARE {:X} @{temp2} -2; ROTATE COMPARE {:X} @{temp3} -2; ROTATE COMPARE {:X} @{temp4} -2;</script><text>dissociate</text></jmolLink></jmol>
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<jmol><jmolLink><script>ROTATE COMPARE {:X} @{temp3} -2; ROTATE HELIX COMPARE {:X} @{temp2} -2; ROTATE HELIX COMPARE {:X} @{temp1} -2; ROTATE HELIX COMPARE {:X} @{temp0} -2;</script><text>bind helical path</text></jmolLink></jmol>
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Show the saved states in a console:
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<jmol><jmolLink><script>console; show temp0; show temp1; show temp2; show temp3; show temp4; </script><text>show states</text></jmolLink></jmol>
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To get to state 1, the command "ROTATE COMPARE {:X} @{temp1} -2" is used, etc.

Current revision

Drag the structure with the mouse to rotate

References

Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis

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