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Re: [modeller_usage] inducing kink in a helix

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

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
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage