Re: [modeller_usage] SET DEVIATION

[Modeller Caretaker <modeller-care@ucsf.edu>]

Adam C Marko wrote:
> I am using modeller 8v1 and trying to build a set of models that all 
> differ from one another.  I cannot figure out the equivalent command in 
> 8v1 to the command:
> 'SET DEVIATION = 4.0  # Amount of randomization between models' in 6v2.

Just specify 'deviation' when you create an automodel object (see 
http://salilab.org/modeller/manual/node37.html), e.g.
a = automodel(env, alnfile  = 'alignment.ali',
              knowns   = '5fd1', sequence = '1fdx',
              deviation=4.0)

or you can set it after you create the object, e.g.
a = automodel(env, alnfile  = 'alignment.ali',
              knowns   = '5fd1', sequence = '1fdx')
a.deviation = 4.0

Note also that TOP scripts from 6v2 will also work unchanged, provided 
that the name of the script ends in ".top".

	Ben Webb, Modeller Caretaker
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