Jean-Paul Becker wrote: > I constructed a model of a protein using a template which contains > only the Calpha trace. > Due to a question of a reviewer of the article i submitted for publication, i > am seeking for precisions on how the Calpha trace is rebuilt to atomic > resolution and then made into the model. > I guess these steps are performed by the functions: > model.generate_topology() and/or Restraints.make(), > but i do not understand how modeller generates all the essential > restraints to build the model when almost all the atoms of the template > are missing except the Calpha. > Does these restraints come from a library ? > In this case, how is this library built ? > I did not mange to find many details concerning this point > in the manual, so i would really appreciate if anyone could > give me some explanations.
You will not find a lot of information on the specifics of the model building procedure in the manual, because that would be duplicating the information in the Modeller papers, which you should look at for the details. But in summary: the model is not made any differently for all-heavy-atom templates or for CA-only templates - exactly the same procedure is followed: i.e. restraints are constructed on the model and then the objective function is optimized.
For all intents and purposes you can imagine the initial model state to be random atom positions - the final structure is determined entirely by the set of restraints. These restraints include stereochemistry (from CHARMM) and soft sphere repulsion (which suffice to construct a random coil model), information from libraries (e.g. phi/psi preferences as a function of residue type, which are mined from known PDB structures) and homology information (e.g. CA-CA and N-O distances and sidechain dihedrals from your template). When your template contains only CA atoms, you simply lose some of this homology information, such as the N-O distances and the sidechain dihedrals.
Ben Webb, Modeller Caretaker