Dale Thank you for the case study. I will certainly remember it when I next see:
> "I don't see density for these atoms therefore they must be > disordered." You do mention though, that when you were able to assign the sequence to the beta sheets, that the loop regions became clear. I consider the case (which a majority of cases seem to be), where the author has built and sequence assigned 95% of the ASU, but is unable to model a loop region. One possibility is that the loop is truly disordered (95% of the ASU is built and is presumably right), the other possibility is that there's an inherent error in the existing structure that is affecting the interpretation of the loop region. The errors are probably extremely subtle and distributed throughout the model (think of the improvements DEN refinement gave for the rerefinement of p97). I guess in either case, because of the dependency of the map on the existing set of phases it's difficult to determine whether it's truly disordered or not. > > P.S.: The author should not look at an 2fofc-map but a > sigma-A-weighted map to reduce model bias. Tim, I assume a sigmaA weighted 2Fo-Fc map (which I believe is the default for most crystallographic refinement packages). F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
