Hi, Alex: > Which sigma do you mean?
The one for automatic weight, not for Jelly-body refinement. I did not turn the "Jelly-body refinement" on. Thanks Ros On Thu, Apr 26, 2012 at 4:08 PM, aaleshin <aales...@burnham.org> wrote: > Hi Uma, > Which sigma do you mean? The one for Jelly-body refinement? > J-B sigma=0.01 means very small fraction of the gradient will be used in > each step. It is used usually with very low resolution (less then 3A) > > Alex > > On Apr 26, 2012, at 11:38 AM, Uma Ratu wrote: > > > > > Dear All: > > > > I use Refmac5 to refine my structure model. > > > > When I set the sigma value to 0.3 (as recommended from tutorial), the > resulted model has many red-bars by coot validation (geometry, rotamer, > especially, Temp Facotr). > > > > I then lower the sigma value to 0.1, the resulted model is much improved > by coot validation. > > > > I then lower the sigma value to 0.01, the resulted model is almost > perfect, by coot validation and Molprobity. > > > > My question is: what is the risk for very low value sigma value? > > > > Thank you for your advice > > > > Ros > >
