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:[email protected]] Im Auftrag von Amlan Roychowdhury Gesendet: Montag, 10. März 2014 09:09 An: [email protected] 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.
