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Re: [modeller_usage] structure refinement and loop optimization protocol

On 6/16/10 7:45 AM, Thomas Evangelidis wrote:
...

From your experience what values
should be assigned to the following parameters:

# Normal VTFM model optimization:
a.library_schedule = autosched.normal
a.max_var_iterations = 200 # 200 by default
# Very thorough MD model optimization:
a.md_level = refine.slow
a.repeat_optimization = 1
a.loop.md_level       = refine.slow # Loop model refinement level
In my experience the defaults are generally fine here - there's little substitute for simply building more models to get a better sampling. 

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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