On 5/31/12 11:06 AM, M wrote:
Thank you very much. One last question: how are the atoms (residues) chosen for individual CG step? For example if residue span range is 10, does it mean that only first residues are optimized?
I don't know what you mean by "first residues" here. The schedule isn't for picking which atoms are optimized (that is the job of the selection - see automodel's select_atoms method - which by default is all atoms). The schedule picks which *restraints* are optimized. If the span range is 10, that means all atom-atom restraints that act on atoms in residues at most 10 apart in sequence are optimized.
Ben Webb, Modeller Caretaker
--
http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage