Re: [modeller_usage] Directly setting backbone dihedral angles (build an alpha helix)

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
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