Alex Brown wrote: > I would presume that automodel uses model.optimize when optimizing a > model, with a default of a single pass, automodel.repeat_optimization > having a default value of 1.

Actually it does one pass through the schedule (see http://salilab.org/modeller/8v2/manual/node147.html) which in turn does several optimize calls. These are generally conjugate gradient optimizations.

> However, according to the manual, the > optimization_method parameter of model.optimize has default value of > 999, whereas it should have a value of either 1 or 3. What default > optimization method does automodel use, can it be changed, and what does > the model.optimize default of 999 mean ?

The default value of 999 instructs Modeller to read the optimization method from the previously-defined optimization schedule instead. You can tweak the schedule a little with automodel.max_var_iterations and automodel.repeat_optimization (see http://salilab.org/modeller/8v2/manual/node36.html) or you can replace it entirely by setting library_schedule (see http://salilab.org/modeller/8v2/manual/node37.html).

After the schedule-controlled CG optimization, the model is refined by MD simulated annealing, which can be controlled with the automodel.md_level variable. The procedure is outlined in the Modeller papers.

Ben Webb, Modeller Caretaker