The PNAS paper you refer to talks about a "loss of definition" of exposed carboxyl O atoms, i.e. an increase in B factor, but presumably if this is modelled properly then it shouldn't leave a big hole in the difference map. After all, the paper is not claiming that C-O bonds are broken, only that there is "increased mobility" (or just as likely, induced static disorder). I'm wondering if this is related to too-tight B-factor restraints. I never use the default settings and always use more relaxed ones: in particular I set the weights of B factor restraints across angles to zero, IMO the across-bond restraints are more than sufficient. There has been a historical obsession with getting B factors as low as possible (too-tight restraints will certainly achieve this if that is your goal!), but isn't the true goal of refinement to obtain the model which best explains the data?
Cheers -- Ian On 4 April 2012 16:31, Roger Rowlett <rrowl...@colgate.edu> wrote: > PNAS 2000, 97, 623
