Marta Rossini wrote: > I am using Modeller to model a structure in which there is a portion > - not present in the template - that I want to force to be an > alpha-helix. If I introduce the secondray structure restraints in the > entire corresponding region of sequence, I obtain a straightened > helix. In the sequence, however, there is a Proline in correspondence > of which I want to induce a little distortion of the helix. If I > force the secondary structure only before and after the proline, by > excluding it, I obtain some very strange angles of an helix with > respect to the other, that is a too pronounced bending. Is there in > Modeller a way to induce a "controlled" distortion (that in my case > corresponds to control the angle between the CO and NH groups of the > proline!)?

There is no 'kinked alpha-helix' restraint as such, but if you have an idea of what the angle is, you can just add in an angle restraint. See http://salilab.org/modeller/9v3/manual/node27.html for an example (that examples uses features.distance, but it's straightforward to use features.angle instead, which of course takes three atoms rather than two). Note that the mean and standard deviation of such a restraint should be given in radians - follow the link on that page through to http://salilab.org/modeller/9v3/manual/node97.html

Ben Webb, Modeller Caretaker