This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

Jmol/Quaternions

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

proteopedia link proteopedia link

@@ Line 20: / Line 20: @@
 <text>show axes</text></jmolButton></jmol>
+When a new structure is loaded, the axes point left, up, and out of the screen. The Jmol command "reset" puts the coordinate system back into that initial orientation.
+<jmol><jmolButton><script>reset</script>
+<text>reset to initial orientation</text></jmolButton></jmol>
+The Jmol command "q = quaternion()" assigns the current orientation to q. How is an orientation different from a rotation? An orientation is the rotation necessary to get the coordinate system from the "reset" orientation to the current orientation. The quaternion q0 for the initial orientation corresponds to no rotation, i.e. {0 0 1 0}. To get back to an orientation q after rotating, use "moveto 0 quaternion q".
 ==Combining two rotations==
 ==Interpolating between orientations==
 ==Interpreting a rotation==

Revision as of 19:19, 24 July 2019

Examples

spinqualitylabelsall models

Caption for this structure

Show:Asymmetric Unit Biological Assembly

Drag the structure with the mouse to rotate

Export Animated Image

http://proteopedia.org/wiki/images/7/76/Wobble.spt jmol script to move molecule around a given orientation in a precession movement.

1 Preliminaries
2 Combining two rotations
3 Interpolating between orientations
4 Interpreting a rotation

Preliminaries

A quaternion is an mathematical object (like a matrix or a complex number) with four parameters x y z w. It is useful to express orientations and rotations, and to do calculations (combining, interpolating, dissecting) on them.

Jmol shows structures (e.g. atom positions) on a display and allows the view to be rotated and individual atomic positions to be manipulated. The atoms have Cartesian coordinates x, y, z, and when you rotate the model, the coordinate system is rotated (same coordinates x, y, z, but axes of coordinate system point in different directions).

When a new structure is loaded, the axes point left, up, and out of the screen. The Jmol command "reset" puts the coordinate system back into that initial orientation.

The Jmol command "q = quaternion()" assigns the current orientation to q. How is an orientation different from a rotation? An orientation is the rotation necessary to get the coordinate system from the "reset" orientation to the current orientation. The quaternion q0 for the initial orientation corresponds to no rotation, i.e. {0 0 1 0}. To get back to an orientation q after rotating, use "moveto 0 quaternion q".