Dmitry Osolodkin wrote: > First of all, if I use optimisation of my structure (exactly as described in > Manual section 1.8.7.), do I need to minimise this system, for example, in > Sybyl to get better model? Or the model which I get is good enough for using > it without any further optimisation such as energy minimisation or molecular > dynamics?

You shouldn't need to do any further optimization - Modeller has already done CG minimization and MD simulated annealing for you. In fact, running an ordinary MD simulation of a Modeller model will often end up making the model worse, as you're throwing away the homology-derived restraints.

> Second, Modeller can build number of models by one script. For what can it be > useful? And is there any difference between obtained models? What's the > reason for such a difference?

Each model is built from a different randomized starting model, so they'll all differ slightly. You should build multiple models to allow for the possibility that the optimizer gets stuck in a local minimum.

> Third, is modelling of homomeric protein using the heteromeric template > authentical? All subunits of heteromer have the same folding as my homomer > and are homologous to my protein. Or can I build a model of one subunit of my > protein using the best template subunit and then build a pentamer using the > symmetry operations (rotation about C5 axis)? Is there such feature in > Modeller?

If you build one subunit, you'll be ignoring interactions between subunits, so your model will likely be incorrect. You can build a model of the whole system and use Modeller's symmetry restraints to ensure that each subunit has similar structure. Modeller has no facility to build new coordinates using symmetry operations.

Ben Webb, Modeller Caretaker