On 10/9/15 9:10 AM, Ajasja Ljubetič wrote:
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?*
build_sequence builds the 3D coordinates from the internal coordinates given in the CHARMM topology file. These are per-residue-type and for an extended chain, so you'll always get an extended chain using that function. There are no functions in Modeller to exactly set backbone dihedral angles, sorry. You could query the current values (see e.g. http://salilab.org/modeller/9.15/manual/node353.html) and then rotate the model about the central bond to get the desired value, or you could add dihedral restraints and then optimize the model - but both approaches are probably no better than your current solution.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage