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Dear Sir May i know how to refine the group occupancy for a ligand??? Thanx in advance On Mon, Mar 10, 2014 at 2:11 PM, <[log in to unmask]> wrote: > Dear Amlan, > > > > The sigma of an Fo-Fc map map depends on the residual noise in your map. In > a well-refined structure, the sigma will be low, so at 3 sigma it will show > very weak features. > > My guess is that your ligand is present in partial occupancy and that you > will find it in your 2Fo-Fc map when you scroll down your contour level. If > you see convincing Fo-Fc density without a ligand being fitted, the presence > of the ligand must be real and you can fit it. However, I would refine a > group occupancy for your ligand. > > > > Best, > > Herman > > > > > > Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Amlan > Roychowdhury > Gesendet: Montag, 10. März 2014 09:09 > An: [log in to unmask] > Betreff: [ccp4bb] regarding Fo-Fc map in coot > > > > Dear All, > > Some times during model building in coot we have found that at the position > of ligand molecules and water, there is a good Fo-Fc map (above 3 sigma), > devoid of any 2Fo-Fc map. > > 1.What does it physically mean and why the 2Fo-Fc map was not generated > properly? > > > > 2. Can we fit ligand molecule there? > > Thanks in advance. > > Best Wishes > > Amlan. > > > > -- > Amlan Roychowdhury. > Senior Research Fellow. > Protein Crystallography Lab. > Dept. of Biotechnology, > IIT Kharagpur. > Kharagpur 721302 > West Bengal. > India.