Subject: [modeller_usage] inducing kink in a helix
From: Marta Rossini <>
Date: Tue, 1 Apr 2008 15:18:12 +0000
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!)?
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