Raik Gruenberg wrote: > already a while ago I have noticed that modeller tends to produce what I > would call spaghetti proteins (containing knots and other fancy > structures) when it is supplied with multiple templates that are far > from the target (35 % or less) and also quite diverse among each other. > > However, Modeller 9 seems to suffer more from this effect than the > previous versions
Just to resolve this for the benefit of the modeller_usage list: a bug in Modeller 9v1 caused the original template structures to be used in the generation of its initial model. This is different from the Modeller 8 behavior, in which the templates were first modified by alignment.check() (which does all pairwise superpositions). The Modeller 8 behavior has been restored in the new Modeller release, 9v2.
Ben Webb, Modeller Caretaker