Dear Jonathan,
In these cases, I usually see positive difference density nearby, indicating an
alternative position for one of the sulfurs, i.e. the disulfide bridge was
partly broken. I am too lazy to fit these, but if you want to do a perfect job,
you might want to fit an alternative conforma
Hi Jonathan,
this may also be a result of too strong SS bond restraints or/and
inaccurate SS bond restraints parameters or/and disorder (in some fraction
of unit cells there is no SS bond). More on the topic:
"Disulfide bond restraints" here:
http://phenix-online.org/newsletter/CCN_2015_01.pdf#pa
When you refine structures with disulphide bridges you often get negative
difference density for the sulphurs, presumably due to the well-known radiation
damage effects. The negative difference density often won't disappear with
usual B-factor refinement. However, it seems to go away if you refi
Dear colleagues,
> Does ncs bias R-free? And if so, can it be avoided by special selection of
the free set?
It occurs to me that we tend to forget that the objective of structure
determination is not the model with the lowest model bias, but the model which
is closest to the true structure
