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Hi, You could try to lower the threshold used to contour the maps for these side-chains (middle mouse "button" if you have a 3 button mouse with a wheel in the middle). Quite often such side chains have lowish electron density that does not appear at (say) 1.0 or 1.5 sigma (in the 2mFo-DFc maps), but that appears at (say) 0.7 sigma. If you delete such side-chain atoms you'll probably end up with negative difference density appearing in the difference Fourier after the next round of refinement. So these residues must be checked individually, much work I know... "To delete or not to delete, that is the question". Fred. Uma Ratu wrote: > Hello, > > I run my model in Coot to do "Temp Fact Variance Analysis". > There are red bars from the B-factor Variance graphy. > I click each red bar to exam the residues in Coot. Many of these > residues do not have the electronic density on their side chains, > especially Lys residues. > > Here is my questions: > > 1. The lack of electronic density is the cause of these red-bars? > 2. How do I fix them? delete the side chains? > > The diffraction data is 2A, and data completness is 98.8%. > > Thank you for comments > > Ros >