Dear Charles,
This is related to an old classical technique in computational
chemistry, called the Z-matrix, for switching from Cartesian to
internal coordinates and back: see
https://en.wikipedia.org/wiki/Z-matrix_(chemistry)
A problem with using this for macromolecules is that it is
numerically unstable, as one ends up with (say) C-terminal coordinates
whose computation has involved the consecutive multiplication of many
hundreds of matrices, together with an accumulation of the effects of
idealisation in bond lengths (as reported by Chris Richardson) away
from their observed values. It is probably to avoid this accumulation
of errors that Rosetta also keeps the coordinates of C-alpha atoms as
a reference against which to re-register local structure generation
from torsion angles.
The state of the art in this field has probably evolved a lot
compared with my distant (30-year old) memories of it. It will be
interesting to hear what programs you end up finding and evaluating.
With best wishes,
Gerard.
--
On Fri, Apr 04, 2025 at 10:27:31AM +0000, Carter, Charlie wrote:
> Does anyone know if there is a program that will take a sequence file
> associated with phi and psi angles and produce a 3D coordinate set in pdb
> format?
>
> I know this can be done in the sense that Byron Rubin’s bender did the same
> thing in analog fashion.
>
> Many thanks
>
> Charlie Carter
>
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