[gmx-developers] Fitting molecule along Z axis

Marc F. Lensink lensink at bigre.ulb.ac.be
Thu May 15 15:05:55 CEST 2008

On Thu, May 15, 2008 at 02:29:24PM +0200, Jonathan Khao wrote:
> Hello,
> We are trying to fit an helix along the Z axis.
> Are there any libraries that already  exist to detect the axis of the 
> helix and to rotate the entire system ?
> Thanks

i wrote a program that calculates the helix.  i suppose you can adapt
those routines to your own purposes.  it returns:
  initial point
  final point
  axis vector
  vector length
  rms deviation
  cos angle with z-axis

note that i make use of an external library, so you have to take that
into account.  but its use is free for academia.

contact me off-list, because i cannot simply put the program on the


Marc F. Lensink
Centre for Structural Biology and Bioinformatics          CSBB
Université Libre de Bruxelles           marc.lensink at ulb.ac.be
Boulevard du Triomphe - CP 263, B-1050 Brussels, Belgium
tel: +32 2 650 5411  secr: +32 2 650 2013  fax: +32 2 650 5425

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