From: Axel Kohlmeyer (
Date: Thu Apr 11 2013 - 00:41:14 CDT

On Wed, Apr 10, 2013 at 9:47 AM, Mohan maruthi sena
<> wrote:
> Hi all,
> I want to place a peptide fragment between two points, say
> A(x1,y1,z1) and B(x2,y2,z2). I know that we can use transoffset and move
> command to place a peptide near one point (say A) through one of its ends.
> But my question is how can we place the another end of the peptide fragment
> to the point B (so that it looks like the peptide fragment is connected
> through these two points A and B).

with a little vector math. after moving the fragment so the atom that
you want to be at point A is there, pick the atom that you want to be
collinear with the AB vector and construct a rotation/transformation
matrix that would rotate it into the AB vector and apply it to the
entire fragment.


> Thank you,
> Mohan

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.