Re: [modeller_usage] default optimization and refinement protocol

[Modeller Caretaker <>]

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
--
             http://www.salilab.org/modeller/
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