User:Karsten Theis/Animation course

From Proteopedia

(Difference between revisions)

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 [[Image:Chemical-structures-of-naloxone-naltrexone-6-naltrexol-and-nalbuphine.png|400px]]
-<jmol><jmolLink><script> load $naloxone; moveto /* time, axisAngle */ 1.0 { -72 91 993 174.51} /* zoom, translation */  132.25 0.0 0.0  /* center, rotationRadius */ {-1.3978000000000002 -0.06235000000000013 -0.06555} 7.508651193263373 /* navigation center, translation, depth */ {0 0 0} 0 0 0 /* cameraDepth, cameraX, cameraY */  3.0 0.0 0.0; hide _H; set zshade on;set zshadepower 2</script><text>naloxone</text></jmolLink> </jmol>
+<jmol><jmolLink><script> set refreshing false; load $naloxone; moveto /* time, axisAngle */ 1.0 { -72 91 993 174.51} /* zoom, translation */  132.25 0.0 0.0  /* center, rotationRadius */ {-1.3978000000000002 -0.06235000000000013 -0.06555} 7.508651193263373 /* navigation center, translation, depth */ {0 0 0} 0 0 0 /* cameraDepth, cameraX, cameraY */  3.0 0.0 0.0; hide _H; set zshade on;set zshadepower 2; set refreshing true</script><text>naloxone</text></jmolLink> </jmol>
-<jmol><jmolLink><script> load $naltrexone; moveto 1.0 { -40 88 995 173.71} 100.0 0.0 0.0 {-1.4783000000000002 -0.18854999999999977 -0.1490499999999999} 7.558499070154403 {0 0 0} 0 0 0 3.0 0.0 0.0; hide _H; set zshade on;set zshadepower 2</script><text>naltrexone</text></jmolLink> </jmol>
+<jmol><jmolLink><script> set refreshing false; load $naltrexone; moveto 1.0 { -40 88 995 173.71} 100.0 0.0 0.0 {-1.4783000000000002 -0.18854999999999977 -0.1490499999999999} 7.558499070154403 {0 0 0} 0 0 0 3.0 0.0 0.0; hide _H; set zshade on;set zshadepower 2; set refreshing true</script><text>naltrexone</text></jmolLink> </jmol>
 [[Image:Opioids.jpg|400px]]

Revision as of 22:06, 13 September 2019

spinqualitylabelsall models

Show:Asymmetric Unit Biological Assembly

Drag the structure with the mouse to rotate

Export Animated Image

1 Animate a scene with Jmol
2 Dock a ligand
- 2.1 Recall ligand position
3 Collection of molecules

Animate a scene with Jmol

Load the scene and choose a look

Open and try different representations and colors.

1. Choose a background:

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

3. How do you want the opioid to look like?

4. Other choices:

Save some orientations

Using your skills from the viewing guide, explore the scene (zoom, rotate, drag, label, measure etc). Every time you find an orientation (rotation, translation, zoom), click a different one of these links. You can restore the orientation by clicking on the link in the next section.

Transition between orientations

Go to different views:

Animate between the four views:

Select a transition speed:

The following animation brings you to view 1, then 2, 3, and 4

Show the underlying commands

Dock a ligand

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: