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
<> 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