On 5/2/15 7:09 AM, CARLOS ARTURO CARVAJAL ARIAS wrote: > Hello. I would like to know the parameters of the default optimization > and refinement protocol?. I mean, for a.library_schedule is > autosched.normal and a.repeat_optimization=1, but for > a.max_var_iterations, a.md_level, a.max_molpdf, what parameters are > used?

You can just print them from a simple Python script - or you can look at the Python code itself. For example,

>>> e = environ() >>> a = automodel(e, ...) >>> print a.max_var_iterations, a.md_level, a.max_molpdf 200 <function very_fast at 0x7f41fb5c1f50> 10000000.0

> When the template has high sequence identity with the target, what > would be the recommended level of optimization and refinement?

The default parameters should be fine.

Ben Webb, Modeller Caretaker