Dear Appu, Any of these input files would work; the most appropriate would be one containing free R flags. As in the extensive bulletin-board discussions recently, there is no "sigma level" that is the "correct" one to use. I like Dale Trunrod's suggestion: delete something in the model (perhaps a water molecule) that you know is there, then use the peak height at that position as a reference for "this is what density looks like for something that is definitely there". Another useful approach is to look at all contour levels; if at some level after your SA-omit map you see density that is clear (not connecting randomly to everything all around) and that matches the kind of shape you might expect to find there, then this density is probably a good description of what is actually there. All the best, Tom T ________________________________ From: [email protected] [[email protected]] on behalf of Appu kumar [[email protected]] Sent: Monday, December 17, 2012 10:17 PM To: [email protected] Subject: [phenixbb] composite simulated annealing omit map. Dear members, please guide me which mtz. file i should use to make composite SA omit map. Out of two mtz file which one should i consider, Initial mtz file which is an output of scalepacktomtz programme or the recent mtz file which is an output of phenix/refmac after refinement. What is the sigma level at which these map should be made.? Thanks in advance Appu