Dear all, I need help with finding water in my protein structure using Coot.
I tried to find water with peaks above 1.6 sigma for both the 2Fo-Fc and mFo-DFc maps. The result were 253 water molecules found for 2Fo-Fc map and 563 water molecules found for mFo-DFc map. My question is.... 1) Why is it the number of water molecules are different? 2) Which map should we use to correctly place the water molecules? 3) What is the sigma cut-off for finding water? 4) How can I validate these water molecules? Fyi, my crystal structure have 382 amino acid and 2 molecules per asymmetric unit.
