Hi Anselm,
So the [T] data is the total rotation around an imaginary axis, while
the component values ([TX] [TY] [TZ]) are how much you rotate around
the system Cartesian axis. Just like how in Cartesian space you can
move in a positive direction in some axes and a negative one in
others, the same applies to rotations. So you could e.g. rotate in a
counterclockwise fashion around one axis but still have the overall
rotation be clockwise. Does that make sense?
-Dan
On Tue, Jan 7, 2025 at 12:22 PM Dr. Anselm Horn via AMBER
<amber.ambermd.org> wrote:
>
> Dear experts,
>
> I've a quick question regarding the rotation matrix output from "rotate"
> (in cpptraj) after a rmsd fit via, more specifically the Name[T] value:
>
> Is Name[T] the total rotation angle, i.e. the angle between the
> coordinate vectors of the original and the rotated position?
>
> I'm asking, because all Name[T] values are positive in my analysis,
> while the three individual components have varying signs.
>
> # Cpptraj analysis:
> # Obtain the rotation matrix for each trajectory structure
> # Four rotation angles are written to file:
> # Rot[TX], Rot[TY], Rot[TZ], and Rot[T].
> rmsd TTT savematrices savevectors combined
> rotate calcfrom TTT[RM] name Rot out rotation-table.dat
> #
>
> Best regards,
>
> Anselm
>
> Bioinformatik | NHR.FAU
> Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
> Germany
>
>
>
>
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Received on Tue Jan 07 2025 - 13:00:03 PST
