[phenixbb] reliability of the peptide from Coot

Nathaniel Echols nechols at lbl.gov
Tue May 1 18:17:37 PDT 2012

On Tue, May 1, 2012 at 5:44 PM, Dialing Pretty <hdc123hdc123 at yahoo.com> wrote:
> By Coot we can build a peptide according to 2Fo-Fc and Fo-Fc. For the most
> part of the peptide especially in the middle of the peptide, the reliability
> constructed should be very high. But at each end of the peptide, there are
> 1-2 residues constructed based on 2Fo-Fc contoured at lower sigma (even
> 0.8).
> Will you please explain hot to analysis the reliability of the terminal
> reisudes constructed at each end of the peptide?

In theory you can use the correlation coefficient of these residues to
density, along with the 2Fo-FC level, and the presence or absence of
Fo-Fc density.  Personally, I would be very suspicious of
single-conformation residues which fall entirely outside of 2Fo-FC
density contoured at 1 sigma, or which have a CC below 0.8.  Certainly
it would be wise to avoid making any biological interpretations of
residues like this without additional supporting evidence.

But this is one of those questions that's very difficult to answer
non-interactively.  Please, please ask a friendly local
crystallographer (or even better, more than one) to inspect your maps
with you and confirm the reliability of the model.  There are plenty
of good crystallographers where you work (I can suggest a couple of
names if you don't know any), and you are certain to get a clearer
answer faster by
talking to them than by asking the phenixbb, especially when we don't
have your maps in front of us.


More information about the phenixbb mailing list