Dear colleagues, I recently started working with Modeller8v0, so I have some questions about the authenticity of the models which I get. 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? 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? 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?
Hope for help, Dmitry Osolodkin.