thanks for your help, it is difficult for me to imagine the effect of this operation, but I have read a few places that this should be the effect, but I might be wrong. Anyway, what I want is using two consecutive C-alphas as "flexible hinges" rotating the peptide plane between this two C-alphas around the imaginary bond between them leaving the coordinates of the rest of the molecule unchanged. How would I accomplish this?
best, Jakob

2010/6/28 Robert Campbell <>
Dear Jakob,

On Mon, 28 Jun 2010 15:32:59 +0200 Jakob Nielsen <>

> I would like to modify a protein pdb file with a "crankshaft" flip, which
> is the anti-correlated double change: psi(i-1) += delta and phi(i) -= delta.
> Such a change should leave the protein coordinates unchanged effecting only
> atoms in residues i-1 and i. However implementation in pymol (see below)
> changes the coordinates of _all_ residues from i-1 to the C-terminal. Can
> you help me? Can I somehow do the two changes simultanious?...
> set_dihedral 21/n, 21/ca, 21/c, 22/n,  148.435 #was 168.4
> set_dihedral 21/c, 22/n, 22/ca, 22/c, -83.704  #was -103.7

I don't see how this change can leave the other coordinates unchanged.  Even
if the psi(i-1) and phi(i) bonds are exactly parallel (meaning that the
angles CA-C-N and C-N-CA are exactly the same, which they are not
necessarily), rotation of the psi(i-1) bond will move the N(i) and
CA(i) atoms, so therefore while a rotation in the opposite direction of the
phi(i) bond will tend to keep the rest of the change travelling in the
direction it was before those two counter-rotations, the backbone itself will
be shifted.  One textbook I consulted lists the angles at the C(i-1) and N(i)
atoms as 116 and 122, respectively, so the psi(i-1) and phi(i) bonds are not
even theoretically going to be parallel.  In practice, with "real"
structures, they certainly are not usually going to be parallel.


Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Botterell Hall Rm 644
Department of Biochemistry, Queen's University,
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497

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