[modeller_usage] Some theoretical questions

[Dmitry Osolodkin <>]

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.