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
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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.