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Mainchain can be generated using a set of C\alphas as guide-points (such as those from Baton-building) along the line of Esnouf 1 or Jones and coworkers 2. Briefly, 6-residue fragments of are generated from a list of high-quality 3 structures. The C\alpha atoms of these fragments are matched against overlapping sets of the guide-point C\alphas. The resulting matches are merged to provide positions for the mainchain (and C\beta) atoms. This procedure works well for helices and strands, but less well 4 for less common structural features.
This function is also available from the scripting interface:
(db-mainchain imol chain-id resno-start resno-end direction)
where direction is either "backwards" or "forwards".
Recall that the chain-id needs to be quoted, i.e.
use "A" not A. Note that chain-id is
"" when the C\alphas have been built with Baton Mode in
Coot.
[1] R. M. Esnouf “Polyalanine Reconstruction from C\alpha Positions Using the Program CALPHA Can Aid Initial Phasing of Data by Molecular Replacement Procedures” Acta Cryst. , D53, 666-672 (1997).
[2] T.A. Jones & S. Thirup “Using known substructures in protein model building and crystallography” EMBO J. 5, 819–822 (1986).
[3] and high resolution
[4] i.e. there are severely misplaced atoms