Samuel Genheden (a03samge) wrote: > My question regards the theory behind and how Modeller creates the > models. The case is that I have been using the Missing residue-script > from the Modeller wiki-page to fill in a gap of 14 missing residues. But > how does Modeller build the gap when it does not have any template > structure as in my case?
For such regions, the initial atomic positions are constructed using internal coordinates; Modeller knows what the ideal bond lengths and angles are for all of the standard residue types. Modeller cannot know the orientation of each residue, however, so it simply builds an extended chain (look at the .ini file). It then optimizes the structure using a combination of the CHARMM forcefield (e.g. to minimize steric contacts) and its own library of statistical protein preferences (e.g. Ramachandran plot for phi/psi, and chi1-4 distributions).
Ben Webb, Modeller Caretaker