Dear all,
I would like to build a perfect helix as an initial structure for some further manipulations.
(Without a good initial structure the homology modelling part I apply later does not converge).
Right now I'm using
mdl.build_sequence(d.entire_sequence)
to build the sequence, then I save it to a PDB, load it in VMD, set the backbone angles there (to get an alpha helix) save it to another PDB and load at back into modeller.
So I guess my basic question is: Is it possible to set backbone dihedral angles to a specific value? Or is there any other way to use mdl.build_sequence to get an alpha helix?
Thank you & best regards,
Ajasja Ljubetič
National Institute of Chemistry
Slovenia