Thank you Afonine, Hans, Kumar, Deliang, Mark, Jose, Tim, Eleanor and Ed for
sharing your thoughts.
Here is a summary of the responses I received-
1. One should try to model residues based on 2Fo-Fc maps contoured at 1.0 sigma
level. Structures of mobile regions/loops can sometimes be modeled based on
maps carved at 0.5-0.6 sigma, but in such cases extreme care must be taken to
avoid modeling based on noise signals and not to omit genuine signals visible
in the region.
2. 2Fo-Fc maps contoured below 0.5 sigma and Fo-Fc maps contoured below 1.5
sigma are full of noise signals and hence need to be carefully analyzed. It is
advisable to avoid modeling anything based solely on signals seen below the
above-mentioned sigma cut offs. Fo-Fc maps sometimes improve significantly
after refining the initial model a couple of times.
3. There seems to be disagreement over modeling residues that one can not see
in maps and leaving out residues that one can see in maps.
Thanks a lot for your responses.
AM
