From: John Stone (
Date: Tue Jan 26 2021 - 00:18:09 CST

I'm afraid more information would be needed here and/or some
careful reading of the orient script. I don't remember what
technique it uses to compute the vectors it returns, but likely
this is endemic to the mathematical approach it uses, or changing
of the "handedness" of the inputs being processed with selections
that have time varying coordinates or the like. You may be
able to provide another direction vector as a reference and do a
flip yourself to force these vectors to face consistently in one
particular hemisphere.

Best regards,
  John Stone

On Mon, Jan 11, 2021 at 06:56:27PM -0300, Raul Araya wrote:
> Dear VMD users
> I'm using orient and tcl to compute the angle between the principal axes
> of two protein domains. However, I'm running into some issue I cannot
> solve. Sometimes the X or Y projection of the vectors flip (change sign)
> and thus the computed angle also changes. How can this flipping be
> prevented or solved?
> Thanks
> --------------------------------------------
> Raul R Araya-Secchi
> Postdoctoral researcher
> X-ray and Neutron Science,
> The Structural Biophysics Group,
> Universitetsparken 5,
> 2100 CPH, DK.
> [1]
> References
> Visible links
> 1.

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349