On Mon, Mar 22, 2004 at 02:05:15PM +0100, Matthias wrote: > I took several runs on Modeller and gaint 2 models.Further I otpimized > these models by loop modelling and this final loop models present a very > low, regarding to the other, OBJECTIVCE FUNCTION. But, my question: > is this objective function relates only to the loop models or is it a > value for the global model?

The Modeller energy is always that of the currently selected restraints, so the energy of two models will only be directly comparable if the restraint set is the same. To be sure, you can call ENERGY again on the two models, using the same restraint set on both.

> Further: does anybody know if there should be great differences in > performin a modeller job in one or two top scripts.. it seems to work > better when splitted, why?

I'm not sure what you mean by "work better" in this context. Separate Modeller runs will generally be slower than one single combined run, as you have to do all the setup and cleanup of TOP, program arrays, etc. multiple times in the former case.

Ben Webb, Modeller Caretaker