I have been using HADDOCK for calculating a protein-protein complex. The results appear good (restraint energy violations (+ ~8) and this echoed in other parameters as well.
When the resulting structures are displayed in PyMOL or Chimera etc., the secondary structure elements such as sheets are not well defined in cartoon display. The secondary structure elements are well defined in the starting structure.
May one include intramolecular restraints such as hydrogen bonds inorder to maintain strand registry?
Any advice would be useful.
First of all, I’d advise you, if you did not yet, to try reassign those secondary structure elements with DSSP. PyMol at least is using its own algorithm to favor aesthetics over accuracy (in overall it is really good but you never know…).
If those structured regions are at the interface, you can indeed tell HADDOCK to define dihedral restraints for 1) all backbone, 2) only alpha-helices or 3) only alpha-helices and beta-sheets. This can be done in the Guru interface, in the
Energy constants for hydrogen bond restraints sub-section of the
Restraints energy constants section.
Hope this will help,