User:Karsten Theis/Animation course: Difference between revisions

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Karsten Theis (talk | contribs)
Editor, Macro, Print3D
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Karsten Theis (talk | contribs)
Editor, Macro, Print3D
4,602 edits
No edit summary
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==Morph a helix==
==Morph a helix==


Here is the SARS-2 <scene name='82/824516/Spike/2'>spike protein</scene>.
Here is the SARS-2 <scene name='82/824516/Spike/3'>spike protein</scene>.
 
(
<jmol><jmolLink><script>delete not *:A; connect (912-985) (not 912-985) DELETE; model 1; select 912-985; cartoon on; select (912-985) and 1.1; set picking dragselected; set allowrotateselected; temp0 = {(912-985) and 1.1}.xyz.all</script><text>click to prepare</text></jmolLink></jmol>
<jmol><jmolLink><script>delete not *:A; model 1; seelct protein; backbone only; select :X; cartoon on; select :X; set picking dragselected; set allowrotateselected; temp0 = {:X}.xyz.all</script><text>click to prepare</text></jmolLink></jmol>


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:  
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:  
<jmol><jmolLink><script>temp1 = {(912-985) and 1.1}.xyz.all</script><text>store state 1</text></jmolLink></jmol>
<jmol><jmolLink><script>temp1 = {:X}.xyz.all</script><text>store state 1</text></jmolLink></jmol>


<jmol><jmolLink><script>temp2 = {(912-985) and 1.1}.xyz.all</script><text>store state 2</text></jmolLink></jmol>
<jmol><jmolLink><script>temp2 = {:X}.xyz.all</script><text>store state 2</text></jmolLink></jmol>


<jmol><jmolLink><script>temp3 = {(912-985) and 1.1}.xyz.all</script><text>store state 3</text></jmolLink></jmol>
<jmol><jmolLink><script>temp3 = {:X}.xyz.all</script><text>store state 3</text></jmolLink></jmol>


<jmol><jmolLink><script>temp4 = {(912-985) and 1.1}.xyz.all</script><text>store state 4</text></jmolLink></jmol>
<jmol><jmolLink><script>temp4 = {:X}.xyz.all</script><text>store state 4</text></jmolLink></jmol>


===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):
<jmol><jmolLink><script>ROTATE COMPARE {(912-985) and 1.1} @{temp0} -2</script><text>retrieve state 0</text></jmolLink></jmol>
<jmol><jmolLink><script>ROTATE COMPARE {:X} @{temp0} -2</script><text>retrieve state 0</text></jmolLink></jmol>


<jmol><jmolLink><script>ROTATE COMPARE {(912-985) and 1.1} @{temp1} -2</script><text>retrieve state 1</text></jmolLink></jmol>
<jmol><jmolLink><script>ROTATE COMPARE {:X} @{temp1} -2</script><text>retrieve state 1</text></jmolLink></jmol>


<jmol><jmolLink><script>ROTATE COMPARE {(912-985) and 1.1} @{temp2} -2</script><text>retrieve state 2</text></jmolLink></jmol>
<jmol><jmolLink><script>ROTATE COMPARE {:X} @{temp2} -2</script><text>retrieve state 2</text></jmolLink></jmol>


<jmol><jmolLink><script>ROTATE COMPARE {(912-985) and 1.1} @{temp3} -2</script><text>retrieve state 3</text></jmolLink></jmol>
<jmol><jmolLink><script>ROTATE COMPARE {:X} @{temp3} -2</script><text>retrieve state 3</text></jmolLink></jmol>


<jmol><jmolLink><script>ROTATE COMPARE {(912-985) and 1.1} @{temp4} -2</script><text>retrieve state 4</text></jmolLink></jmol>
<jmol><jmolLink><script>ROTATE COMPARE {:X} @{temp4} -2</script><text>retrieve state 4</text></jmolLink></jmol>


To animate, click below
To animate, click below
Line 373: Line 373:
<jmol><jmolLink><script>set picking none</script><text>turn of ligand dragging</text></jmolLink></jmol>
<jmol><jmolLink><script>set picking none</script><text>turn of ligand dragging</text></jmolLink></jmol>


<jmol><jmolLink><script>ROTATE COMPARE {912-985} @{temp3} -2; ROTATE COMPARE {912-985} @{temp2} -2; ROTATE COMPARE {912-985} @{temp1} -2; ROTATE COMPARE {912-985} @{temp0} -2;</script><text>bind</text></jmolLink></jmol>
<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>


<jmol><jmolLink><script>ROTATE COMPARE {912-985} @{temp1} -2; ROTATE COMPARE {912-985} @{temp2} -2; ROTATE COMPARE {912-985} @{temp3} -2; ROTATE COMPARE {912-985} @{temp4} -2;</script><text>dissociate</text></jmolLink></jmol>
<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>


<jmol><jmolLink><script>ROTATE COMPARE {912-985} @{temp3} -2; ROTATE HELIX COMPARE {912-985} @{temp2} -2; ROTATE HELIX COMPARE {912-985} @{temp1} -2; ROTATE HELIX COMPARE {912-985} @{temp0} -2;</script><text>bind helical path</text></jmolLink></jmol>
<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>


Show the saved states in a console:
Show the saved states in a console:
<jmol><jmolLink><script>console; show temp0; show temp1; show temp2; show temp3; show temp4; </script><text>show states</text></jmolLink></jmol>
<jmol><jmolLink><script>console; show temp0; show temp1; show temp2; show temp3; show temp4; </script><text>show states</text></jmolLink></jmol>


To get to state 1, the command "ROTATE COMPARE {912-985} @{temp1} -2" is used, etc.
To get to state 1, the command "ROTATE COMPARE {:X} @{temp1} -2" is used, etc.




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