On 02/21/2011 11:08 AM, albert wrote:
I am using loop refinement protocol based on known PDB file method for loop refinement. What surprised me is that: the occupancy for each atom in the refined structure is more than 1.
It's impossible to tell what your problem is without seeing your input files.
However, Modeller does not use the occupancy field. If one is present in your input PDB, it'll leave whatever value is there. If it has to add atoms, those atoms will be given an occupancy of 1.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage