Hi Ajasja,
Have you tried the modeller function "restraints.add(secondary_structure...)"? If you don't really need to set exact values, but rather just need to generate a nice helical conformation, that may be good enough for you.
The example on this page http://www.salilab.org/modeller/wiki/Make%20alpha%20helix will not give you a "perfect" or ideal helix, but the minimization step should give you something reasonably stable to start from.
Good luck! -J'n
On Fri, Oct 9, 2015 at 11:10 AM, Ajasja Ljubetič ajasja.ljubetic@gmail.com wrote: > 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