Bob diamond wrote the first? Model building/ refinement program using this approach. The trouble was that small deviations in angles resulted in large positional errors farther down the chain and methods correcting the local Map features replaced it..
But the algorithms to go from angles to coordinates must be embedded in other software such as COOT? Ask Paul ??? Good luck Eleanor On Fri, 4 Apr 2025 at 15:45, Gerard Bricogne < 0000ead34ec923cf-dmarc-requ...@jiscmail.ac.uk> wrote: > 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 > > > > ######################################################################## > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
