On 4/9/12 8:00 PM, Ashish Runthala wrote: > MODELLER based on your constructed alignment file > parsing the reliable template residues mapped against the target > ones, constructs and fixes the average alpha carbon backbone
Actually all atoms that have the same name in target and template will be simply copied into the model in this case. Usually this means all backbone atoms, not just alpha carbons.
> On increased sampling, > MODELLER tries best to satisfy the Lennard Jones and all the > energetic equations composing its DOPE energy function.
In fact the optimization tries to minimize the molecular PDF, which includes contributions from soft sphere (not Lennard Jones). DOPE is a separate, atomistic pairwise statistical potential. It is not used in comparative modeling.
Ben Webb, Modeller Caretaker