Michael Paterson wrote: > I have been generating models using the dopehr_loopmodel route, having > decided it would be more efficient to only generate loop models for the > lowest energy comparative model I switched to generating structures > using the automodel class and then defining the loop regions by > visualizing the lowest energy structure and plugging the values in to > the 'Loop refinement of an existing model' example script provided with > Modeller 9v1. The resulting loop models do not generate models of > nearly the same quality - as judged by Ramachandran plots - than the > automatically generated loop models. Is there a convenient way to > extract the loop sequence information that loop model uses to generate > it's models.
Sure - the automatic loop modeling classes all select all residues around gaps in your alignment for loop refinement. See http://salilab.org/modeller/9v1/manual/node378.html
This may be easier to see visually - try loading up one of the *.IL* files produced by this procedure. This contains the initial unoptimized loop, which simply consists of all of the loop atoms placed on a line between the two loop anchors. Since this is obviously unphysical, it should be easy to spot in any PDB viewer.
Ben Webb, Modeller Caretaker