On 7/19/19 9:34 AM, oivalf_nix--- via modeller_usage wrote: > I am trying to model a protein that has a C-terminal region without > template match. However, the secondary structure prediction strongly > suggests that part of this terminal region forms a beta-strand > (residues 125 to 128). I am trying to generate an antiparallel beta > sheet from this terminal segment, bonding with a pre-existing beta > strand (residues 79-82). However, the generated model does not answer > this command, being equal to the model generated without the > command. > > Could you point out what I am doing wrong?
Define your custom restraints by overriding the special_restraints() method, not special_patches().
Note also that Modeller's beta restraints are just additional terms in the scoring function, and it tries to satisfy all terms. So if you have conflicting information (e.g. an aligned template, steric clashes, etc.) you won't get a "perfect" sheet.
Ben Webb, Modeller Caretaker