On 5/17/10 7:57 PM, Michael Accardi wrote:
On May 16th I had asked how to form a pentamer, but I have settled for tackling the dimer situation first. As you suggested, I have included the chain break (/) character in my alignment. I have also tried using both automodel and the mymodel subclass inputs I obtained from http://salilab.org/modeller/9v8/manual/node28.html. Unfortunately, my resulting dimer does not look good. The automodel commands (#3; see below) produce a better model but with that said, one subunit appears to be normal where as the second subunit appears to have no structure whatsoever.
Right, because your alignment contains only a single chain template. The example I sent you contains a dimer modeled from a dimer template. Since your second chain isn't aligned to a template, you'll get garbage. Both sequences (template and model) need to be dimers.
If you only have a monomer template, you can still build a dimer model (just use two copies of the monomer as two templates, one aligned with your model 'A' chain and the other with the model 'B' chain). But note that since Modeller has no information about the interaction between the two subunits, that interaction will probably be poorly modeled.
The scripts you propose in 2) and 3) should actually behave identically - and either is fine.
Ben Webb, Modeller Caretaker
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