Hi Uma, Altering sigma affects the strength of geometry restraints throughout the model - bonds, angles, etc. Choosing a very low sigma will cause geometry to be more tightly restrained towards "ideal" values, which is why you observe improvements in Coot validation. Note that strengthening the geometry weight causes the observations (data) to be less influential in refinement. The "risk" of this is that your model may no longer appropriately/optimally describe your data. You can assess this locally by manual inspection of the electron density, and globally by considering overall refinement statistics (as reported at the bottom of the Refmac5 log file). Ideally, you want your model to both describe the data and have reasonable geometry.
Regards Rob On 26 Apr 2012, at 21:26, Uma Ratu wrote: > 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 > >
