Re: [modeller_usage] GA341 assessment

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

Lella Sana wrote:
> how could I carry out GA341 assessment on a model not produced by 
> MODELLER but by an ab initio method?
> I'm using MODELLER 9v2.

The example given at http://salilab.org/modeller/9v4/manual/node188.html 
should work for any PDB file - not just one produced by Modeller. But, 
as described in the manual, the sequence identity is a parameter used in 
the GA341 score, so you need to provide that. For models that are not 
homology-derived, you'll have to make a reasonable guess at some 
"equivalent sequence identity" or use a different assessment method, 
such as DOPE.

	Ben Webb, Modeller Caretaker
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